Kitasatospora_NPDC089509 - 75 region(s)

Identified secondary metabolite regions using strictness 'relaxed'

NPDC089509.ctg-0001 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 1.1	NRPS,T2PKS,oligosaccharide	16,389	165,180	High	landomycin A	PKS:Type II+saccharide:hybrid/tailoring
Region 1.2	lanthipeptide-class-i	245,392	271,232
Region 1.3	NRPS-like,terpene,T1PKS	354,219	439,679	High	guanipiperazine A/guanipiperazine B	NRPS:Type I
Region 1.4	lassopeptide	475,242	497,922	Medium	anantin C	ribosomal:RiPP
Region 1.5	terpene	528,730	550,928	High	geosmin	terpene:Sesquiterpene
Region 1.6	lanthipeptide-class-iv	558,010	580,556	High	class IV lanthipeptide/SflA	ribosomal:RiPP
Region 1.7	terpene,NAPAA	628,505	685,253	Low	γ-poly-L-2,4-diaminobutyric acid	NRPS:Type I
Region 1.8	terpene	708,018	748,599
Region 1.9	PKS-like,NRPS,T1PKS	857,054	926,387
Region 1.10	T1PKS	935,863	972,029	Low	abyssomicin M/abyssomicin N/abyssomicin O/abyssomicin P/abyssomicin Q/abyssomicin R/abyssomicin S/abyssomicin T/abyssomicin U/abyssomicin V/abyssomicin W/abyssomicin X	PKS

NPDC089509.ctg-0002 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 2.1	NRPS	66,936	125,457	Medium	arylomycin	NRPS:Type I
Region 2.2	terpene	202,604	223,626
Region 2.3	NRPS	225,823	275,572	Low	feglymycin	NRPS:Type I
Region 2.4	RRE-containing	341,690	362,763
Region 2.5	terpene	423,521	446,046
Region 2.6	T1PKS,NRPS-like	525,119	680,144	High	candicidin	NRPS:Type I+PKS
Region 2.7	NRPS,butyrolactone,NRPS-like	702,722	743,055	High	antipain	NRPS:Type I

NPDC089509.ctg-0003 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 3.1	NRPS,terpene	1	62,472	High	raimonol	terpene
Region 3.2	NRPS-like	69,037	112,147
Region 3.3	NRPS-like	129,025	172,651
Region 3.4	T2PKS	221,162	293,644	Low	mutaxanthene A/mutaxanthene B/mutaxanthene D	PKS
Region 3.5	lipolanthine,lanthipeptide-class-iii,T1PKS	442,208	493,148	Low	kyamicin	ribosomal:RiPP
Region 3.6	phenazine	586,558	607,049	Low	endophenazine A/endophenazine B	other:phenazine
Region 3.7	lanthipeptide-class-ii	626,959	650,369

NPDC089509.ctg-0004 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 4.1	terpene-precursor	37,870	58,919
Region 4.2	butyrolactone	130,246	141,310

NPDC089509.ctg-0005 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 5.1	lanthipeptide-class-iv	337,935	360,784	Low	labyrinthopeptin A2/labyrinthopeptin A1/labyrinthopeptin A3	ribosomal:RiPP:Lanthipeptide
Region 5.2	T1PKS,NRPS-like,NRPS	390,209	455,862

NPDC089509.ctg-0006 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 6.1	NAPAA	1	28,516	High	ε-Poly-L-lysine	NRPS:Type I
Region 6.2	T1PKS,NRPS-like	137,170	184,752
Region 6.3	lanthipeptide-class-iii	261,877	284,540
Region 6.4	T1PKS,NRPS-like	387,229	435,045	Low	cinnabaramide A	NRPS:Type I+PKS:Type I

NPDC089509.ctg-0007 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 7.1	NI-siderophore	101,729	134,433	Low	peucechelin	NRPS:Type I
Region 7.2	NRP-metallophore,NRPS	248,386	302,659	High	griseobactin	NRPS:Type I
Region 7.3	NRPS-like	327,146	370,433
Region 7.4	NRPS	448,631	479,357	Low	Q6402A	NRPS:Type I

NPDC089509.ctg-0008 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 8.1	RiPP-like	146,010	156,897

NPDC089509.ctg-0009 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 9.1	transAT-PKS,NRPS-like,NRPS	200,936	305,203	Low	phthoxazolin	NRPS:Type I+PKS

NPDC089509.ctg-0010 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 10.1	hydrogen-cyanide	219,985	233,002

NPDC089509.ctg-0011 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 11.1	RiPP-like,terpene	120,816	147,205

NPDC089509.ctg-0012 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 12.1	aminopolycarboxylic-acid	44,890	58,259	High	Ethylenediaminesuccinic acid hydroxyarginine	other:other
Region 12.2	lanthipeptide-class-i	106,951	131,482
Region 12.3	terpene,T1PKS,NRPS-like	139,910	212,739

NPDC089509.ctg-0013 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 13.1	lanthipeptide-class-i	1	15,057
Region 13.2	lanthipeptide-class-ii	101,584	124,856

NPDC089509.ctg-0014 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 14.1	terpene,NAPAA	1	39,466	High	ε-Poly-L-lysine	NRPS:Type I
Region 14.2	lanthipeptide-class-v	124,771	166,841
Region 14.3	lanthipeptide-class-i	167,910	192,393

NPDC089509.ctg-0015 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 15.1	lanthipeptide-class-i	160,888	185,663

NPDC089509.ctg-0016 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 16.1	terpene-precursor	141,786	163,959

NPDC089509.ctg-0017 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 17.1	PKS-like	1	23,745
Region 17.2	NRPS-like	79,709	121,532

NPDC089509.ctg-0020 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 20.1	methanobactin	70,276	92,729
Region 20.2	NRPS	118,143	173,171	Medium	ishigamide	NRPS:Type I+PKS

NPDC089509.ctg-0022 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 22.1	terpene	94,206	121,042	Medium	hopene	terpene
Region 22.2	terpene	131,314	152,261

NPDC089509.ctg-0023 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 23.1	HR-T2PKS,NRPS,thioamide-NRP	31,850	110,069	High	ishigamide	NRPS:Type I+PKS

NPDC089509.ctg-0024 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 24.1	NRPS	68,188	127,216

NPDC089509.ctg-0026 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 26.1	NI-siderophore	38,003	71,690

NPDC089509.ctg-0027 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 27.1	NRPS	85,486	129,748

NPDC089509.ctg-0028 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 28.1	ectoine	24,168	34,542	Low	kosinostatin	NRPS:Type I+PKS:Type II+saccharide:hybrid/tailoring
Region 28.2	terpene	116,685	136,446

NPDC089509.ctg-0029 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 29.1	T3PKS	1	22,455	High	naringenin	PKS:Type III

NPDC089509.ctg-0031 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 31.1	azole-containing-RiPP	54,144	78,031

NPDC089509.ctg-0033 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 33.1	terpene-precursor	70,179	91,285

NPDC089509.ctg-0034 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 34.1	terpene	6,996	29,398

NPDC089509.ctg-0037 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 37.1	NRPS	12,051	81,362

NPDC089509.ctg-0038 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 38.1	NRPS-like,T1PKS	35,222	75,533	Low	reveromycin A	PKS

NPDC089509.ctg-0043 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 43.1	NRPS,PKS-like	1	54,306

NPDC089509.ctg-0045 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 45.1	T2PKS	1	40,778

NPDC089509.ctg-0050 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 50.1	NRPS-like	1	18,833

NPDC089509.ctg-0052 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 52.1	terpene	1	10,928	Low	viguiepinol	PKS

NPDC089509.ctg-0056 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 56.1	NRPS-like	1	3,522

NPDC089509.ctg-0057 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 57.1	T2PKS	1	3,218	Low	spore pigment	PKS

NPDC089509.ctg-0059 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 59.1	NRPS	1	2,401

No secondary metabolite regions were found in these records:: NPDC089509.ctg-0018 (Kitasatospora spp); NPDC089509.ctg-0019 (Kitasatospora spp); NPDC089509.ctg-0021 (Kitasatospora spp); NPDC089509.ctg-0025 (Kitasatospora spp); NPDC089509.ctg-0030 (Kitasatospora spp); NPDC089509.ctg-0032 (Kitasatospora spp); NPDC089509.ctg-0035 (Kitasatospora spp); NPDC089509.ctg-0036 (Kitasatospora spp); NPDC089509.ctg-0039 (Kitasatospora spp); NPDC089509.ctg-0040 (Kitasatospora spp); NPDC089509.ctg-0041 (Kitasatospora spp); NPDC089509.ctg-0042 (Kitasatospora spp); NPDC089509.ctg-0044 (Kitasatospora spp); NPDC089509.ctg-0046 (Kitasatospora spp); NPDC089509.ctg-0047 (Kitasatospora spp); NPDC089509.ctg-0048 (Kitasatospora spp); NPDC089509.ctg-0049 (Kitasatospora spp); NPDC089509.ctg-0051 (Kitasatospora spp); NPDC089509.ctg-0053 (Kitasatospora spp); NPDC089509.ctg-0054 (Kitasatospora spp); NPDC089509.ctg-0055 (Kitasatospora spp); NPDC089509.ctg-0058 (Kitasatospora spp); NPDC089509.ctg-0060 (Kitasatospora spp); NPDC089509.ctg-0061 (Kitasatospora spp); NPDC089509.ctg-0062 (Kitasatospora spp); NPDC089509.ctg-0063 (Kitasatospora spp); NPDC089509.ctg-0064 (Kitasatospora spp); NPDC089509.ctg-0065 (Kitasatospora spp); NPDC089509.ctg-0066 (Kitasatospora spp)

Compact view

NPDC089509.ctg-0001 - Region 1 - NRPS,T2PKS,oligosaccharide

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Location: 16,389 - 165,180 nt. (total: 148,792 nt) Show pHMM detection rules used

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T2PKS: (t2ks and t2clf)
oligosaccharide: (repeatable(3, [DUF1205, Glyco_transf_28, Glycos_transf_1, Glycos_transf_2, MGT]) and minscore(MGT, 150))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

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Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

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Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

CDS_00020: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_00039: pyridine nucleotide-disulfide oxidoreductase

smcogs: SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

CDS_00056: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_00062: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_00075: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_00080: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_00082: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_00083: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_00089: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

CDS_00101: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

CDS_00106: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

Transferases: acetyltransferase aminotransferase glycosyltransferase transferase

CDS_00033: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

CDS_00085: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_00087: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_00093: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_00094: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs: SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

CDS_00097: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs: SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

CDS_00099: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

Hydrolases: hydrolase

CDS_00018: alpha/beta hydrolase domain-containing protein

smcogs: SMCOG1066: alpha/beta hydrolase domain-containing protein

CDS_00029: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: cyclase dehydratase

CDS_00076: Polyketide synthesis cyclase

smcogs: SMCOG1225: Polyketide synthesis cyclase

CDS_00081: cyclase/dehydrase

smcogs: SMCOG1128: cyclase/dehydrase

CDS_00095: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_00096: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_00098: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase

CDS_00030: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_00031: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_00077: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_00078: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_00102: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: permease

CDS_00064: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000231.5	1.16	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0000278.3	1.03	PKS	urdamycin	Streptomyces fradiae
BGC0000234.5	0.95	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0001128.4	0.87	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.87	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001723.5	0.82	PKS	oviedomycin	Streptomyces antibioticus
BGC0002047.2	0.69	PKS	brasiliquinone A, brasiliquinone B	Nocardia brasiliensis
BGC0002276.2	0.64	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0002070.3	0.61	PKS	SEK90, pentangumycin	Saccharothrix espanaensis DSM 44229
BGC0000201.5	0.58	PKS, saccharide	auricin	Streptomyces aureofaciens

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000231.5	0.83	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0000278.3	0.80	PKS	urdamycin	Streptomyces fradiae
BGC0001723.5	0.77	PKS	oviedomycin	Streptomyces antibioticus
BGC0000234.5	0.77	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.72	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.72	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.70	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.09 out of 29.72

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.52 out of 19.26

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.79 out of 25.31

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.95 out of 23.79

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.06 out of 24.78

Confidence: medium

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 31.45 out of 36.53

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.99 out of 20.47

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.08 out of 25.31

Confidence: medium

Additional weak hits (33):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.43 out of 30.25

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.37 out of 31.73

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.17 out of 36.54

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.85 out of 36.54

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.68 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.03 out of 29.38

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.62 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.21 out of 29.38

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.17 out of 36.54

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.78 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.31 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.28 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.40 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.21 out of 30.25

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.39 out of 26.85

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.79 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.45 out of 27.78

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.15 out of 21.55

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.40 out of 29.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.93 out of 27.78

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.25 out of 30.25

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.98 out of 28.19

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.11 out of 32.93

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.29 out of 36.53

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 12.85 out of 18.57

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.38 out of 25.88

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.14 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.57 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.15 out of 33.14

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.60 out of 29.65

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.69 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.63 out of 29.65

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.15 out of 30.98

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

Type II PKS

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 16388 - 165180:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Leu - D-Ala - D-Leu - D-Ala - Leu) + (D-Orn - Thr - D-X - Val - D-Leu)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 16388 - 95185:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Leu - D-Ala - D-Leu - D-Ala - Leu) + (D-Orn - Thr - D-X - Val - D-Leu)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_00030: Leu - Ala - Leu - Ala - Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (41..435): Leu

nrpys: Leu

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DALLIGSIVK
Nearest Stachelhaus code(s):: Leu or 3OH-Leu DALLIGAVVK (71% 8Å match); Leu DALLIGAVVK (71% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1093..1497): Ala

nrpys: Ala

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
Single AA prediction:: ala (Ala)

Stachelhaus prediction details:

Stachelhaus sequence:: DVFSVALVYK
Nearest Stachelhaus code(s):: Ala DVFSVALVYK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2652..3045): Leu

nrpys: Leu

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: val (Val)

Stachelhaus prediction details:

Stachelhaus sequence:: DAYFWGVTFK
Nearest Stachelhaus code(s):: Leu DAYFWGVTFK (94% 8Å match); Val DAYFWGVTFK (91% 8Å match); Ile DAYFWGVTFK (85% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4179..4579): Ala

nrpys: Ala

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
Single AA prediction:: ala (Ala)

Stachelhaus prediction details:

Stachelhaus sequence:: DVFSLAVVYK
Nearest Stachelhaus code(s):: Ala DVFSLAVVYK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (5704..6089): Leu

nrpys: Leu

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DALLIGSVVK
Nearest Stachelhaus code(s):: Leu or 3OH-Leu DALLIGAVVK (71% 8Å match); Leu DALLIGAVVK (71% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_00031: Orn - Thr - X - Val - Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (502..903): Orn

nrpys: Orn

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: asp,asn (Asp, Asn)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DTEDMGYVDK
Nearest Stachelhaus code(s):: Orn DTEDMGYVDK (85% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2016..2422): Thr

nrpys: Thr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: thr (Thr)
Single AA prediction:: thr (Thr)

Stachelhaus prediction details:

Stachelhaus sequence:: DFWNVGMVHK
Nearest Stachelhaus code(s):: Thr DFWNVGMVHK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3078..3472): X

nrpys: Dhpg, Hpg

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: N/A
Small clusters prediction:: Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DTENLGVVDK
Nearest Stachelhaus code(s):: Orn DTEDMGYVDK (76% 8Å match); Ile DAQDLGVVDK (65% 8Å match); Asp DSWKLGVVDK (56% 8Å match)
Stachelhaus code match:: 70% (weak)

AMP-binding (4591..4970): Val

nrpys: Val

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: val (Val)

Stachelhaus prediction details:

Stachelhaus sequence:: DAFWWGGTFK
Nearest Stachelhaus code(s):: Val DAYWWGGTFK (91% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (5624..6001): Leu

nrpys: Leu

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DALLVGSVVK
Nearest Stachelhaus code(s):: Leu DALLVGAVVK (71% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_00102: Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (13..413): Leu

nrpys: Leu

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: leu (Leu)

Stachelhaus prediction details:

Stachelhaus sequence:: AAVFQGCPLK
Nearest Stachelhaus code(s):: Abu DAWFYGAPLK (26% 8Å match)
Stachelhaus code match:: 60% (weak)

Link to PARAS substrate predictor

Type II PKS gene cluster prediction details

Cluster section:: 92694 to 165180
Starter unit(s):: acetyl-CoA (Score: 0.0; E-value: 0)
Malonyl elongations:: 8|9 (Score: 729.2; E-value: 2.5e-222)
Product class(es):: angucycline
Product molecular weight(s):: acetyl-CoA_8: 1135 Da
acetyl-CoA_9: 1178 Da

CDS_00056: OXY (Score: 276.3; E-value: 1.2e-84)
CDS_00069: OXY (Score: 12.9; E-value: 0.0001)
CDS_00075: OXY (Score: 592.0; E-value: 2.1e-180)
CDS_00076: CYC C4-C17/C2-C19 (Score: 195.3; E-value: 2.2e-60)
CDS_00077: KS (Score: 788.7; E-value: 2.6e-240)
CDS_00078: CLF 8|9 (Score: 729.2; E-value: 2.5e-222)
CDS_00079: ACP (Score: 123.7; E-value: 5.3e-39)
CDS_00080: KR C9 (Score: 483.1; E-value: 4.5e-148)
CDS_00081: CYC C7-C12 (Score: 502.4; E-value: 8.6e-154)
CDS_00082: OXY (Score: 563.4; E-value: 1e-171)
CDS_00083: KR C15 (Score: 419.5; E-value: 9.9e-129)
CDS_00085: GT (Score: 413.5; E-value: 2.6e-126)
CDS_00087: GT (Score: 412.2; E-value: 6.8e-126)
CDS_00093: GT (Score: 387.2; E-value: 2.6e-118)
CDS_00099: GT (Score: 447.1; E-value: 1.7e-136)
CDS_00106: OXY (Score: 280.9; E-value: 5.1e-86)

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
CatR	H2O2-responsive repressor
DmdR1	Iron(II)-dependent repressor
IolR	Regulator of the inositol catabolism
LexA variant 2	Repressor of DNA damage response
NtrC	Nitrogen regulatory protein C
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0001 - Region 2 - lanthipeptide-class-i

Download region GenBank file

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Location: 245,392 - 271,232 nt. (total: 25,841 nt) Show pHMM detection rules used

lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Lanthipeptides

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_00183: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_00192: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

Lyases: cyclase dehydratase

CDS_00185: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_00187: Lanthionine synthetase C family protein

smcogs: SMCOG1140: Lanthionine synthetase C family protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002391.2	0.52	terpene	zealexin B3, zealexin C2	Zea mays
BGC0000207.5	0.49	PKS	chartreusin	Streptomyces chartreusis
BGC0001289.5	0.47	ribosomal	penisin	Paenibacillus ehimensis
BGC0000798.3	0.47	saccharide	dhurrin	Sorghum bicolor
BGC0001727.3	0.46	ribosomal	paenilan	Paenibacillus polymyxa E681
BGC0000542.3	0.46	ribosomal	paenicidin B	Paenibacillus terrae
BGC0002635.2	0.46	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0000541.5	0.46	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0000551.5	0.46	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0002721.2	0.45	saccharide	α-hydroxynitrile glucoside, β-hydroxynitrile glucoside, γ-hydroxynitrile glucoside	Hordeum vulgare subsp. vulgare

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002391.2	0.52	terpene	zealexin B3, zealexin C2	Zea mays
BGC0000207.5	0.49	PKS	chartreusin	Streptomyces chartreusis
BGC0001289.5	0.47	ribosomal	penisin	Paenibacillus ehimensis
BGC0000798.3	0.47	saccharide	dhurrin	Sorghum bicolor
BGC0001727.3	0.46	ribosomal	paenilan	Paenibacillus polymyxa E681
BGC0000542.3	0.46	ribosomal	paenicidin B	Paenibacillus terrae
BGC0002635.2	0.46	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0000541.5	0.46	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0000551.5	0.46	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0002721.2	0.45	saccharide	α-hydroxynitrile glucoside, β-hydroxynitrile glucoside, γ-hydroxynitrile glucoside	Hordeum vulgare subsp. vulgare

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for CDS_00191

CDS_00188

Leader:

MPEITALTDLDALIGDLDARITETTLPTPE

Core:

ASTAGCSGLCTVALCDTVLLCTGVYC

Core with dehydrations:

ADhaDhbAGCysDhaGLCysDhbVALCysDDhbVLLCysDhbGVYCys

antiSMASH-DB 4.0 matches for CDS_00188

65.4%

NZ_CP007574.1and 7 others:

NZ_CP007574.1 Lanthipeptides: DC74_RS44160_lanthipeptideNZ_CP026094.1 Lanthipeptides: SE95_RS40905_lanthipeptideNZ_CP026094.1 Lanthipeptides: SE95_RS40905_lanthipeptideNZ_CP104098.1 Lanthipeptides: N1H47_RS02655_lanthipeptideNZ_CP104098.1 Lanthipeptides: N1H47_RS02655_lanthipeptideNZ_CP119144.1 Lanthipeptides: P0D74_RS37975_lanthipeptideNZ_CP119144.1 Lanthipeptides: P0D74_RS37975_lanthipeptide

Lanthipeptides: DC74_RS44160_lanthipeptide

3

TAGCSGLCTVALCDTVLLCTGVYC

26

T GCSG+CTV +CDTVL C+GV C

1

TGGCSGVCTVIVCDTVLFCSGVVC

24

53.8%

NZ_CP015849.1:

Lanthipeptides: A8713_RS33905_lanthipeptide

1

ASTAGCSGLCTVALCDTVLLC

21

AST GCSGLCT+ +C TV++C

2

ASTVGCSGLCTIIVCATVVIC

22

46.2%

NZ_BMSK01000006.1:

Lanthipeptides: IE251_RS13810_lanthipeptide

3

TAGCSGLCTVALCDTVLLC

21

T GCSGLCT+ +C TV++C

4

TQGCSGLCTIVICATVVIC

22

with 4 more sequence matches

30.8%

NZ_CP076718.1:

Lassopeptides: GQ464_RS04180_lassopeptide

1

ASTAGCSGLCTVALCDTVLLCTGV

24

S GC C V D GV

2

QSAGGCDHPCGVNNIDNTFYSVGV

25

27.0%

NZ_CP021903.1and 6 others:

NZ_CP023409.1 Lanthipeptides: Bateq7PJ16_RS09270_lanthipeptideNZ_CP028218.1 Lanthipeptides: C7M30_RS01850_lanthipeptideNZ_CP035167.1 Lanthipeptides: EQJ08_RS08875_lanthipeptideNZ_CP089148.1 Lanthipeptides: LRO88_RS09410_lanthipeptideNZ_JAMYDW010000001.1 Lanthipeptides: NHM07_RS00470_lanthipeptideNZ_JAQOXM010000003.1 Lanthipeptides: PO770_RS15540_lanthipeptide

Lanthipeptides: CD007_RS08815_lanthipeptide

3

TAGCSG------LCTVALCDTVLL

20

T GCSG LC+ A+CD +++

5

TFGCSGGVASKALCSRAMCDGIVI

28

26.9%

NZ_SPFR01000005.1:

Lanthipeptides: FGQ83_RS17540_lanthipeptide

3

TAGCSGLCTVALCD

16

T GCS CT+ C

3

TKGCSQFCTIICCS

16

24.3%

NZ_JAJQVT010000008.1:

Lanthipeptides: PAF28_RS14660_lanthipeptide

3

TAGCSG------LCTVALCDTVLL

20

T GC+G LC+ A+CD +++

5

TFGCTGGVASKALCSRAMCDGIVI

28

CDS_00189

Leader:

MPEIAALTDLDALIGDLDARITETTLPTPE

Core:

ASTGGCSGLCTVLACDTVALCTGVLC

Core with dehydrations:

ADhaDhbGGCysDhaGLCysDhbVLACysDDhbVALCysDhbGVLCys

antiSMASH-DB 4.0 matches for CDS_00189

65.4%

NZ_CP007574.1and 7 others:

NZ_CP007574.1 Lanthipeptides: DC74_RS44160_lanthipeptideNZ_CP026094.1 Lanthipeptides: SE95_RS40905_lanthipeptideNZ_CP026094.1 Lanthipeptides: SE95_RS40905_lanthipeptideNZ_CP104098.1 Lanthipeptides: N1H47_RS02655_lanthipeptideNZ_CP104098.1 Lanthipeptides: N1H47_RS02655_lanthipeptideNZ_CP119144.1 Lanthipeptides: P0D74_RS37975_lanthipeptideNZ_CP119144.1 Lanthipeptides: P0D74_RS37975_lanthipeptide

Lanthipeptides: DC74_RS44160_lanthipeptide

3

TGGCSGLCTVLACDTVALCTGVLC

26

TGGCSG+CTV+ CDTV C+GV+C

1

TGGCSGVCTVIVCDTVLFCSGVVC

24

53.8%

NZ_CP015849.1:

Lanthipeptides: A8713_RS33905_lanthipeptide

1

ASTGGCSGLCTVLACDTVALC

21

AST GCSGLCT++ C TV +C

2

ASTVGCSGLCTIIVCATVVIC

22

46.2%

NZ_BMSK01000006.1:

Lanthipeptides: IE251_RS13810_lanthipeptide

3

TGGCSGLCTVLACDTVALC

21

T GCSGLCT++ C TV +C

4

TQGCSGLCTIVICATVVIC

22

with 7 more sequence matches

34.6%

NZ_CP076718.1:

Lassopeptides: GQ464_RS04180_lassopeptide

1

ASTGGCSGLCTVLACDTVALCTGV

24

S GGC C V D GV

2

QSAGGCDHPCGVNNIDNTFYSVGV

25

26.9%

NZ_CP015225.1and 3 others:

NZ_FMXH01000021.1 Lanthipeptides: BLT00_RS31975_lanthipeptideNZ_FNYG01000024.1 Lanthipeptides: BMZ15_RS31715_lanthipeptideNZ_FPIX01000022.1 Lanthipeptides: BT116_RS31075_lanthipeptide

Lanthipeptides: TK06_RS32800_lanthipeptide

9

LCTVLACDTVALCTGVLC

26

L T + C+T CT + C

1

LATTMECNTFGTCTNIGC

18

26.9%

NZ_CP035088.1and 1 other:

NZ_CP087200.1 Lanthipeptides: LOY66_RS24790_lanthipeptide

Lanthipeptides: EPZ47_RS30280_lanthipeptide

9

LCTVLACDTVALCTGVLC

26

L T + C+T CT + C

1

LVTTMECNTFGTCTAIEC

18

26.9%

NZ_CP072913.1:

Lanthipeptides: J9870_RS25175_lanthipeptide

9

LCTVLACDTVALCTGVLC

26

L T + C+T CT + C

1

LATTMECNTFGTCTAIEC

18

26.9%

NZ_SPFR01000005.1:

Lanthipeptides: FGQ83_RS17540_lanthipeptide

3

TGGCSGLCTVLACD

16

T GCS CT++ C

3

TKGCSQFCTIICCS

16

18.2%

NZ_CP019286.1:

Lanthipeptides: allorf_096660_096857_lanthipeptide

3

TGGCSG--LCTVLACDTVALCT

22

+ GC+G LCTV CD C

30

SNGCTGSCLCTVFDCDCEPSCN

51

15.4%

NZ_JAOQJV010000004.1:

Lanthipeptides: OCV65_RS05205_lanthipeptide

2

STGGCSGLCTVLAC

15

+G CSG T++ C

26

QSGNCSGFLTIICC

39

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47

Confidence: strong

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 25.13 out of 28.19

Confidence: strong

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.67 out of 28.19

Confidence: medium

Additional weak hits (11):

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.84 out of 21.55

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.16 out of 30.97

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.40 out of 18.57

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.21 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.14 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.25 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.62 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.44 out of 29.38

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 14.90 out of 20.97

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.42 out of 20.97

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lanthipeptides

RREFinder

TFBS Finder

Core peptide predictions

CDS_00188 - Class I

Cleavage pHMM score: -9.60

RODEO score: 19

Monoisotopic mass: 2431.1 Da

Molecular weight: 2432.9 Da

Number of bridges: 5

Additional modifications: OH

Alternative weights: (assuming N unmodified Ser/Thr residues); 2450.9 Da N = 1

CDS_00189 - Class I

Cleavage pHMM score: -9.60

RODEO score: 18

Monoisotopic mass: 2325.1 Da

Molecular weight: 2326.7 Da

Number of bridges: 5

Additional modifications: OH

Alternative weights: (assuming N unmodified Ser/Thr residues); 2344.7 Da N = 1

RRE predictions

: RRE type: Lanthipeptide_LanB_RRE; Location: 305 - 373; Score: 36.4

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems
ZuR variant 1	Zinc-responsive repressor

NPDC089509.ctg-0001 - Region 3 - NRPS-like,T1PKS,terpene

Download region GenBank file

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Location: 354,219 - 439,679 nt. (total: 85,461 nt) Show pHMM detection rules used

NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidase oxygenase

CDS_00280: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_00281: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_00290: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_00297: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

CDS_00299: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CDS_00300: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_00306: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_00307: FAD linked oxidase domain protein

smcogs: SMCOG1138: FAD linked oxidase domain protein

Transferases: aminotransferase

CDS_00298: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

CDS_00308: aminotransferase class V

smcogs: SMCOG1139: aminotransferase class V

Hydrolases: esterase

CDS_00291: thioesterase

smcogs: SMCOG1004: thioesterase

Lyases: cyclase

CDS_00279: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Ligases: ligase synthase

CDS_00282: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_00288: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_00289: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_00294: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_00295: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_00301: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_00303: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002582.3	2.16	NRPS	guanipiperazine A, guanipiperazine B	Streptomyces chrestomyceticus
BGC0001249.5	1.91	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002164.2	1.76	NRPS	peramine	Epichloe festucae
BGC0001250.4	1.68	NRPS	epichloenin A	Epichloe festucae
BGC0001251.4	1.68	NRPS	epichloenin A	Epichloe festucae
BGC0001132.4	1.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	1.67	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	1.66	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	1.65	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001261.3	1.63	NRPS	AM-toxin	Alternaria alternata

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002582.3	0.77	NRPS	guanipiperazine A, guanipiperazine B	Streptomyces chrestomyceticus
BGC0001276.3	0.76	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0000683.3	0.76	terpene	avermitilol	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002164.2	0.70	NRPS	peramine	Epichloe festucae
BGC0001250.4	0.68	NRPS	epichloenin A	Epichloe festucae
BGC0001251.4	0.68	NRPS	epichloenin A	Epichloe festucae
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0000041.3	0.68	PKS	oronofacic acid	Pseudomonas syringae
BGC0002286.3	0.68	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

No product predictions

Genes with terpene domains:

CDS_00279: T1TS

Domain 1 (4 - 327): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.10 out of 23.79

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

Additional weak hits (8):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.70 out of 26.33

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.84 out of 25.75

Confidence: weak

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.93 out of 24.78

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.61 out of 26.12

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.57 out of 30.98

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.57 out of 26.85

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

Terpene

TFBS Finder

Predicted core structure(s)

For candidate cluster 6, location 354218 - 439679:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X) + (X) + (mal) + (Arg) + (mal - Me-ccmal - mal) + (ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 354218 - 397323:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Arg) + (mal) + (X) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 9, location 363461 - 405312:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (mal - Me-ccmal - mal) + (Arg) + (mal) + (X) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 10, location 370843 - 439679:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X) + (X) + (mal) + (Arg) + (mal - Me-ccmal - mal) + (ccmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_00282: X

AMP-binding (33..432): X

nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DAIYSGFVVK
Nearest Stachelhaus code(s):: Leu DAWYLGNVVK (59% 8Å match); Leu or Ile DAIYLGVVLK (56% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_00285: X

AMP-binding (120..338): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVYNVGVLMK
Nearest Stachelhaus code(s):: Arg DVENVGVISK (35% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_00288: X

AMP-binding (38..428): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
Small clusters prediction:: pro (Pro)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DAKLLGVVLK
Nearest Stachelhaus code(s):: Glu DAKDLGVVDK (44% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_00294: mal

PKS_AT (532..828): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 70.8%; Propionyl-CoA: 54.2%; inactive: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 143.3
inactive: 85.1
Methoxymalonyl-CoA: 76.9
Methylmalonyl-CoA: 69.9
Ethylmalonyl-CoA: 54.9
Propionyl-CoA: 41.3
trans-1,2-CPDA: 32.9
fatty_acid: 28.1
Benzoyl-CoA: 25.5
Isobutyryl-CoA: 24.4
CHC-CoA: 23.6
Acetyl-CoA: 23.6
2-Methylbutyryl-CoA: 22.0
3-Methylbutyryl-CoA: 0.0

CDS_00295: Arg

Search NORINE for peptide: strict or relaxed

AMP-binding (31..433): Arg

nrpys: Arg

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVENVGAITK
Nearest Stachelhaus code(s):: Arg DVENVGAITK (76% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_00300: mal - mmal - mal

PKS_AT (588..877): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 214.4
inactive: 98.1
Methoxymalonyl-CoA: 59.9
Methylmalonyl-CoA: 57.2
Propionyl-CoA: 40.0
Ethylmalonyl-CoA: 35.4
Isobutyryl-CoA: 29.3
2-Methylbutyryl-CoA: 28.0
Acetyl-CoA: 24.8
Benzoyl-CoA: 22.5
fatty_acid: 19.6
CHC-CoA: 18.3
trans-1,2-CPDA: 12.6
3-Methylbutyryl-CoA: 0.0

PKS_AT (1607..1906): mmal

ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA, Malonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 79.2%; Methoxymalonyl-CoA: 79.2%; Malonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 166.0
Methoxymalonyl-CoA: 154.8
Ethylmalonyl-CoA: 152.0
Malonyl-CoA: 106.1
Propionyl-CoA: 103.9
trans-1,2-CPDA: 100.3
2-Methylbutyryl-CoA: 97.7
Isobutyryl-CoA: 71.7
CHC-CoA: 71.6
fatty_acid: 50.5
Benzoyl-CoA: 45.9
Acetyl-CoA: 45.6
3-Methylbutyryl-CoA: 32.1
inactive: 29.5

PKS_AT (3354..3629): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 164.3
inactive: 82.2
Methoxymalonyl-CoA: 55.8
Methylmalonyl-CoA: 49.1
Propionyl-CoA: 35.6
Isobutyryl-CoA: 23.9
fatty_acid: 19.2
Acetyl-CoA: 13.3
CHC-CoA: 9.3
2-Methylbutyryl-CoA: 9.2
Benzoyl-CoA: 8.7
trans-1,2-CPDA: 8.6
Ethylmalonyl-CoA: 7.2
3-Methylbutyryl-CoA: 0.0

CDS_00301: mal

PKS_AT (556..831): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 167.7
inactive: 76.3
Methoxymalonyl-CoA: 58.7
Methylmalonyl-CoA: 48.6
Propionyl-CoA: 30.0
Isobutyryl-CoA: 24.4
fatty_acid: 19.1
CHC-CoA: 14.6
Acetyl-CoA: 13.7
Benzoyl-CoA: 7.3
2-Methylbutyryl-CoA: 5.6
Ethylmalonyl-CoA: 2.7
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

CDS_00303: X

AMP-binding (62..496): X

nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: GGNVVASPAK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

Link to PARAS substrate predictor

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
CRP	Cyclic AMP receptor protein
IolR	Regulator of the inositol catabolism

NPDC089509.ctg-0001 - Region 4 - lassopeptide

Download region GenBank file

Download region SVG

Location: 475,242 - 497,922 nt. (total: 22,681 nt) Show pHMM detection rules used

lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Lasso peptides

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_00343: nucleotide sugar dehydrogenase

smcogs: SMCOG1152: nucleotide sugar dehydrogenase

Transferases: glycosyltransferase

CDS_00344: sugar transferase

smcogs: SMCOG1146: sugar transferase

Hydrolases: hydrolase

CDS_00352: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001552.3	0.72	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001506.5	0.69	ribosomal	anantin B1, anantin B2	Streptomyces sp. NRRL S-146
BGC0001507.3	0.65	ribosomal	anantin C	Streptomyces olindensis
BGC0001889.2	0.65	ribosomal	fusilassin	Thermobifida fusca YX
BGC0001493.5	0.63	ribosomal	achromosin	Streptomyces achromogenes subsp. achromogenes
BGC0001550.3	0.61	ribosomal	citrulassin D	Streptomyces katrae
BGC0001549.3	0.61	ribosomal	citrulassin B	Streptomyces aurantiacus JA 4570
BGC0002053.3	0.60	ribosomal	ulleungdin	Streptomyces sp.
BGC0001539.4	0.60	ribosomal	cattlecin	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001655.3	0.59	ribosomal	LP2006	Nocardiopsis alba DSM 43377

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001552.3	0.72	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001506.5	0.69	ribosomal	anantin B1, anantin B2	Streptomyces sp. NRRL S-146
BGC0001507.3	0.65	ribosomal	anantin C	Streptomyces olindensis
BGC0001889.2	0.65	ribosomal	fusilassin	Thermobifida fusca YX
BGC0001493.5	0.63	ribosomal	achromosin	Streptomyces achromogenes subsp. achromogenes
BGC0001550.3	0.61	ribosomal	citrulassin D	Streptomyces katrae
BGC0001549.3	0.61	ribosomal	citrulassin B	Streptomyces aurantiacus JA 4570
BGC0002053.3	0.60	ribosomal	ulleungdin	Streptomyces sp.
BGC0001539.4	0.60	ribosomal	cattlecin	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001655.3	0.59	ribosomal	LP2006	Nocardiopsis alba DSM 43377

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lasso peptide predictions

Lassopeptide(s) for CDS_00353

CDS_00353

Leader:

MTKNQKLPVRYTPPAAAKVGDFTKDTD

Full core:

GTIYTKKDATTFGFKKPR

Putative macrolactam:

GTIYTKKD

antiSMASH-DB 4.0 matches for CDS_00353

83.3%

NZ_QZFU01000023.1:

Lassopeptides: D5S18_RS34950_lassopeptide

1

GTIYTKKDATTFGFKK

16

GTI+TKKDATTFGFKK

1

GTIHTKKDATTFGFKK

16

77.8%

NZ_CP047146.1:

Lassopeptides: GR130_RS21510_lassopeptide

1

GTIYTKKDATTFGFKKPR

18

GTI+TKKDATT GFKK +

1

GTIHTKKDATTIGFKKSQ

18

77.8%

NZ_NDXL01000002.1:

Lassopeptides: B7024_RS41530_lassopeptide

1

GTIYTKKDATTFGFKKPR

18

GT+YT KDATT GFKKP+

1

GTVYTLKDATTLGFKKPK

18

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.78 out of 29.72

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.57 out of 27.04

Confidence: strong

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 27.04

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.90 out of 23.79

Confidence: medium

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12

Confidence: medium

Additional weak hits (7):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.21 out of 23.43

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.75 out of 27.78

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.10 out of 28.14

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.03 out of 30.22

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.27 out of 35.63

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.35 out of 27.18

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lasso peptides

RREFinder

TFBS Finder

Core peptide predictions

CDS_00353 - Class II: Cleavage pHMM score: -2.80; RODEO score: 20; Monoisotopic mass: 2040.1 Da; Molecular weight: 2041.3 Da; Number of bridges: 0

RRE predictions

: RRE type: Stand_Alone_Lasso_RRE; Location: 0 - 85; Score: 78.0

TFBS definitions

Regulator	Description
DasR	N-acetylglucosamine dependent repressor
IolR	Regulator of the inositol catabolism
NtrC	Nitrogen regulatory protein C
OsdR	Development and stress management regulator

NPDC089509.ctg-0001 - Region 5 - terpene

Download region GenBank file

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Location: 528,730 - 550,928 nt. (total: 22,199 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxidoreductase

CDS_00388: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

Transferases: formyltransferase

CDS_00394: methionyl-tRNA formyltransferase

smcogs: SMCOG1228: methionyl-tRNA formyltransferase

Hydrolases: hydrolase

CDS_00386: HAD-superfamily hydrolase, subfamily IA, variant

smcogs: SMCOG1115: HAD-superfamily hydrolase, subfamily IA, variant

Lyases: cyclase

CDS_00390: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001181.4	0.80	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0002425.3	0.33	ribosomal	stlassin	Streptomyces sp.
BGC0002755.2	0.31	NRPS	clovibactin	Eleftheria terrae P9846
BGC0001580.3	0.26	PKS	ebelactone	Kitasatospora aburaviensis
BGC0001919.4	0.26	NRPS, PKS	neoantimycin	Streptomyces orinoci
BGC0001875.4	0.24	PKS	nargenicin A1	Nocardia arthritidis AUSMDU00012717 Unclassified.
BGC0000029.5	0.23	PKS	BE-14106	Streptomyces sp. DSM 21069
BGC0002637.3	0.23	NRPS	rimomycin A, rimomycin B, rimomycin C	Streptomyces sp. WAC 06783
BGC0002024.3	0.23	PKS	nargenicin A1, nargenicin A1	Nocardia argentinensis
BGC0000162.5	0.21	PKS	tetrocarcin A	Micromonospora chalcea

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001181.4	0.80	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0002425.3	0.33	ribosomal	stlassin	Streptomyces sp.
BGC0002755.2	0.31	NRPS	clovibactin	Eleftheria terrae P9846
BGC0001580.3	0.26	PKS	ebelactone	Kitasatospora aburaviensis
BGC0001919.4	0.26	NRPS, PKS	neoantimycin	Streptomyces orinoci
BGC0001875.4	0.24	PKS	nargenicin A1	Nocardia arthritidis AUSMDU00012717 Unclassified.
BGC0000029.5	0.23	PKS	BE-14106	Streptomyces sp. DSM 21069
BGC0002637.3	0.23	NRPS	rimomycin A, rimomycin B, rimomycin C	Streptomyces sp. WAC 06783
BGC0002024.3	0.23	PKS	nargenicin A1, nargenicin A1	Nocardia argentinensis
BGC0000162.5	0.21	PKS	tetrocarcin A	Micromonospora chalcea

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
sesquiterpene		germacradienol	C15	C1-C10	OH

Genes with terpene domains:

CDS_00390: T1TS + T1TS

Domain 1 (2 - 326): Type 1 terpene synthase

Subtype: Geosmin synthase, N terminal domain

Reactions:: FPP → germacradienol

Domain 2 (372 - 701): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.87 out of 29.72

Confidence: medium

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 27.49 out of 30.12

Confidence: strong

Additional weak hits (3):

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.52 out of 29.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.55 out of 27.78

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.54 out of 29.65

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
FPP	Farnesyl diphosphate

TFBS definitions

Regulator	Description
NtrC	Nitrogen regulatory protein C
OsdR	Development and stress management regulator

NPDC089509.ctg-0001 - Region 6 - lanthipeptide-class-iv

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Location: 558,010 - 580,556 nt. (total: 22,547 nt) Show pHMM detection rules used

lanthipeptide-class-iv: (cds(LANC_like and Pkinase) and not micKC)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Lanthipeptides

TFBS Finder

Pfam domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxidoreductase

CDS_00414: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

Hydrolases: hydrolase

CDS_00415: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Lyases: decarboxylase

CDS_00425: Decarboxylase, pyridoxal-dependent

smcogs: SMCOG1180: Decarboxylase, pyridoxal-dependent

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002337.2	0.84	ribosomal	class IV lanthipeptide, SflA	Streptomyces sp. NRRL S-1022
BGC0000843.5	0.41	other (non-nrp beta-lactam)	alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate	Streptomyces clavuligerus ATCC 27064
BGC0001909.3	0.35	PKS	strobilurin A	Strobilurus tenacellus
BGC0000606.5	0.34	ribosomal	lactazole	Streptomyces lactacystinaeus
BGC0001151.5	0.32	other (non-nrp beta-lactam)	valclavam, (-)-2-(2-hydroxyethyl)clavam	Streptomyces antibioticus
BGC0001480.3	0.32	other (other)	tundrenone	Methylobacter tundripaludum 21/22
BGC0001556.5	0.31	NRPS, PKS	combamide	Streptomyces sp.
BGC0000175.5	0.31	PKS	cycloheximide	Streptomyces sp. YIM 56141
BGC0001850.4	0.30	other (shikimate-derived)	diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G	Streptomyces sp. F001
BGC0002081.3	0.29	PKS	streptoketide A, streptoketide B, streptoketide C, S2502, S2507, UWM5	Streptomyces sp. Tue6314

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002337.2	0.84	ribosomal	class IV lanthipeptide, SflA	Streptomyces sp. NRRL S-1022
BGC0000843.5	0.41	other (non-nrp beta-lactam)	alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate	Streptomyces clavuligerus ATCC 27064
BGC0001909.3	0.35	PKS	strobilurin A	Strobilurus tenacellus
BGC0000606.5	0.34	ribosomal	lactazole	Streptomyces lactacystinaeus
BGC0001151.5	0.32	other (non-nrp beta-lactam)	valclavam, (-)-2-(2-hydroxyethyl)clavam	Streptomyces antibioticus
BGC0001480.3	0.32	other (other)	tundrenone	Methylobacter tundripaludum 21/22
BGC0001556.5	0.31	NRPS, PKS	combamide	Streptomyces sp.
BGC0000175.5	0.31	PKS	cycloheximide	Streptomyces sp. YIM 56141
BGC0001850.4	0.30	other (shikimate-derived)	diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G	Streptomyces sp. F001
BGC0002081.3	0.29	PKS	streptoketide A, streptoketide B, streptoketide C, S2502, S2507, UWM5	Streptomyces sp. Tue6314

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptides - No core peptides found.

Transcription Factor Binding Sites

Binding sites found:

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 20.76 out of 21.84

Confidence: strong

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.93 out of 23.79

Confidence: medium

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.66 out of 30.12

Confidence: medium

Additional weak hits (6):

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.87 out of 20.01

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.02 out of 24.78

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.65 out of 24.78

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.59 out of 26.85

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Lanthipeptides

TFBS Finder

Core peptide predictions

No core peptides found.

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism
MexT	Global virulence regulator
OsdR	Development and stress management regulator

NPDC089509.ctg-0001 - Region 7 - NAPAA,terpene

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Location: 628,505 - 685,253 nt. (total: 56,749 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)
NAPAA: (AMP-binding and TIGR02353)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: aminotransferase glycosyltransferase methyltransferase

CDS_00482: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_00485: glycosyltransferase

smcogs: SMCOG1102: glycosyltransferase

CDS_00488: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Lyases: cyclase

CDS_00481: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

CDS_00513: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Ligases: ligase

CDS_00489: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000658.3	1.24	terpene	2-methylisoborneol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3	1.03	terpene	2-methylisoborneol	Saccharopolyspora erythraea NRRL 2338
BGC0000683.3	0.45	terpene	avermitilol	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002535.2	0.44	NRPS	γ-poly-L-2,4-diaminobutyric acid	Streptomyces celluloflavus
BGC0000657.5	0.44	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0002174.2	0.43	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0000852.5	0.36	other (other)	ectoine	Sporosarcina pasteurii
BGC0000858.3	0.34	other (other)	ectoine	Methylobacter marinus
BGC0000855.3	0.34	other (other)	ectoine	Methylomicrobium kenyense
BGC0000859.3	0.34	other (other)	ectoine	Methylomicrobium alcaliphilum

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000658.3	0.85	terpene	2-methylisoborneol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3	0.79	terpene	2-methylisoborneol	Saccharopolyspora erythraea NRRL 2338
BGC0000683.3	0.75	terpene	avermitilol	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002174.2	0.74	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0002535.2	0.64	NRPS	γ-poly-L-2,4-diaminobutyric acid	Streptomyces celluloflavus
BGC0001135.5	0.62	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.61	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001166.5	0.60	NRPS	HC-toxin	Alternaria jesenskae
BGC0001641.4	0.60	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.60	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Terpene cluster 1 (628,504 - 649,962):

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
monoterpene		2-methylisoborneol	C11	C1-C6	OH
monoterpene		2-methylenebornane	C11	C1-C6	none

Genes with terpene domains:

CDS_00481: T1TS

Domain 1 (146 - 479): Type 1 terpene synthase

Subtype: 2-Methylisoborneol synthase type

Reactions:: 2-MeGPP → 2-methylisoborneol; 2-MeGPP → 2-methylenebornane

Terpene cluster 2 (664,179 - 685,253):

Product predictions:

No product predictions

Genes with terpene domains:

CDS_00513: T1TS

Domain 1 (10 - 333): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47

Confidence: strong

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.95 out of 23.79

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.52 out of 23.79

Confidence: medium

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26

Confidence: medium

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.31 out of 18.57

Confidence: medium

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 24.24 out of 29.65

Confidence: medium

Additional weak hits (21):

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.36 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.52 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.91 out of 27.78

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.52 out of 20.97

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.39 out of 26.06

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.68 out of 30.22

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.15 out of 30.97

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.42 out of 31.73

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.46 out of 27.55

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.16 out of 31.73

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.36 out of 28.14

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.13 out of 36.54

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.97 out of 30.98

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.37 out of 28.19

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.50 out of 32.93

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.39 out of 33.14

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.77 out of 32.93

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.06 out of 24.78

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

Terpene

TFBS Finder

Predicted core structure(s)

For candidate cluster 14, location 628504 - 685253:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 16, location 632851 - 666898:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_00489: X

AMP-binding (37..430): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DFECLSVVSK
Nearest Stachelhaus code(s):: Ile or Val DFLCLGVVIK (53% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

Glossary

Acronym	Full name
2-MeGPP	2-methylgeranyl diphosphate

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
IolR	Regulator of the inositol catabolism
LexA variant 1	Repressor of DNA damage response
RpoN	Regulator of nitrogen assimilation and virulence
ToxT	Regulator of MSHA biosynthesis
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0001 - Region 8 - terpene

Download region GenBank file

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Location: 708,018 - 748,599 nt. (total: 40,582 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Pfam domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_00547: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Hydrolases: hydrolase

CDS_00591: HAD-superfamily hydrolase, subfamily IA, variant

smcogs: SMCOG1115: HAD-superfamily hydrolase, subfamily IA, variant

Lyases: cyclase

CDS_00556: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

CDS_00580: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Ligases: synthetase

CDS_00581: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001911.3	0.44	terpene	raimonol	Streptomyces anulatus
BGC0001633.3	0.44	other (other)	ketomemicin B3, ketomemicin B4	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000630.3	0.43	terpene	(2R,3S,3'S)-2-hydroxyastaxanthin	Paracoccus haeundaensis
BGC0000639.3	0.43	terpene	carotenoid	Enterobacteriaceae bacterium DC260
BGC0000641.3	0.43	terpene	carotenoid	Enterobacteriaceae bacterium DC416
BGC0000642.3	0.43	terpene	carotenoid	Enterobacteriaceae bacterium DC413
BGC0000638.3	0.43	terpene	carotenoid	Pantoea ananatis
BGC0000635.3	0.42	terpene	carotenoid	Paracoccus sp. N81106
BGC0001187.4	0.41	NRPS, PKS	xenolozoyenone	Glarea lozoyensis
BGC0001456.3	0.40	terpene	isorenieratene	Streptomyces argillaceus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001911.3	0.44	terpene	raimonol	Streptomyces anulatus
BGC0001633.3	0.44	other (other)	ketomemicin B3, ketomemicin B4	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000630.3	0.43	terpene	(2R,3S,3'S)-2-hydroxyastaxanthin	Paracoccus haeundaensis
BGC0000639.3	0.43	terpene	carotenoid	Enterobacteriaceae bacterium DC260
BGC0000641.3	0.43	terpene	carotenoid	Enterobacteriaceae bacterium DC416
BGC0000642.3	0.43	terpene	carotenoid	Enterobacteriaceae bacterium DC413
BGC0000638.3	0.43	terpene	carotenoid	Pantoea ananatis
BGC0000635.3	0.42	terpene	carotenoid	Paracoccus sp. N81106
BGC0001187.4	0.41	NRPS, PKS	xenolozoyenone	Glarea lozoyensis
BGC0001456.3	0.40	terpene	isorenieratene	Streptomyces argillaceus

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Product name	Chain length	Initial cyclisations	Functional groups
sesquiterpene precursor	FPP	C15	acyclic	PP
diterpene precursor	GGPP	C20	acyclic	PP
sesterterpene precursor	GFPP	C25	acyclic	PP
triterpene precursor	HPP	C30	acyclic	PP

Genes with terpene domains:

CDS_00556: T1TS

Domain 1 (3 - 314): Type 1 terpene synthase

Subtype: unknown

CDS_00580: T1TS

Domain 1 (11 - 320): Type 1 terpene synthase

Subtype: unknown

CDS_00581: PT_FPPS_like

Domain 1 (2 - 251): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

Reactions:: IPP, DMAPP → FPP; IPP, DMAPP → GGPP; IPP, DMAPP → GFPP; IPP, DMAPP → HPP

Transcription Factor Binding Sites

Binding sites found:

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

Additional weak hits (11):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.82 out of 39.62

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.71 out of 29.25

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.20 out of 30.22

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.19 out of 30.25

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.76 out of 36.54

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.08 out of 30.22

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.64 out of 35.63

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.19 out of 26.85

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.85 out of 28.19

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
GFPP	Geranylfarnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
HPP	Hexaprenyl diphosphate
IPP	Isopentenyl diphosphate
PP	Diphosphate

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator

NPDC089509.ctg-0001 - Region 9 - NRPS,PKS-like,T1PKS

Download region GenBank file

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Location: 857,054 - 926,387 nt. (total: 69,334 nt) Show pHMM detection rules used

PKS-like: (t2pks2 or ksIII)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

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Gene overview

Tailoring

MIBiG comparison

ClusterBlast

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TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_00691: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_00725: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_00728: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase aminotransferase methyltransferase

CDS_00687: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_00698: aminotransferase

smcogs: SMCOG1019: aminotransferase

CDS_00708: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_00717: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Lyases: hydratase

CDS_00690: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase

CDS_00695: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CDS_00696: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_00702: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CDS_00719: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.87	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002458.3	0.62	NRPS	alazopeptin	Streptacidiphilus griseoplanus
BGC0001833.4	0.62	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0000307.4	0.61	NRPS	AbT1	Aureobasidium pullulans
BGC0001758.4	0.59	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.57	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002276.2	0.56	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0001928.2	0.56	other (other)	(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid	Streptomyces sp. MA37
BGC0001295.5	0.52	other (other)	cremeomycin	Streptomyces cremeus
BGC0002621.2	0.50	other (other)	angustmycin A, angustmycin B, angustmycin C, aristeromycin, arabinofuranosyladenine	Streptomyces angustmyceticus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.65	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.64	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0000307.4	0.64	NRPS	AbT1	Aureobasidium pullulans
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.62	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002276.2	0.62	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0002458.3	0.57	NRPS	alazopeptin	Streptacidiphilus griseoplanus
BGC0001363.5	0.50	NRPS, PKS	ralsolamycin	Ralstonia solanacearum GMI1000
BGC0000894.4	0.50	other (other)	citrinin	Monascus aurantiacus
BGC0001928.2	0.50	other (other)	(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid	Streptomyces sp. MA37

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.29 out of 23.79

Confidence: medium

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.52 out of 29.51

Confidence: medium

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.40 out of 22.40

Confidence: strong

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52

Confidence: medium

Additional weak hits (20):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.51 out of 27.78

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.16 out of 28.14

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.04 out of 30.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.57 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.35 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.07 out of 30.25

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.92 out of 26.85

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.06 out of 28.14

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.16 out of 28.14

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.53 out of 21.84

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.15 out of 21.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.99 out of 27.78

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.49 out of 29.25

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.66 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.37 out of 26.06

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.28 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.77 out of 33.14

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 19, location 857053 - 926387:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X - mal - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 20, location 857053 - 898094:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X - mal - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 21, location 873172 - 926387:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X - mal - X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_00696: X

AMP-binding (73..474): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: AHSCVAGAQK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

CDS_00717: X - mal - X

AMP-binding (176..623): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: -LFWIAGTAK
Nearest Stachelhaus code(s):: Ala or Val DVFWIGGTFK (29% 8Å match); Val DAFWIGGTFK (26% 8Å match)
Stachelhaus code match:: 60% (weak)

PKS_AT (1902..2191): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 66.7%; inactive: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 141.4
Methylmalonyl-CoA: 78.7
Methoxymalonyl-CoA: 71.7
inactive: 69.0
Propionyl-CoA: 53.4
Isobutyryl-CoA: 53.0
CHC-CoA: 42.7
Ethylmalonyl-CoA: 42.5
fatty_acid: 26.6
Benzoyl-CoA: 18.6
2-Methylbutyryl-CoA: 16.6
trans-1,2-CPDA: 16.5
Acetyl-CoA: 4.7
3-Methylbutyryl-CoA: 0.0

AMP-binding (3834..4221): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVQHVGHGVK
Nearest Stachelhaus code(s):: Pro DVQFVAHVVK (71% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
DosR	Hypoxia stress response regulator
HypR	L-hydroxyproline utilization repressor
IolR	Regulator of the inositol catabolism

NPDC089509.ctg-0001 - Region 10 - T1PKS

Download region GenBank file

Download region SVG

Location: 935,863 - 972,029 nt. (total: 36,167 nt) Show pHMM detection rules used

Region on contig edge.

T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase

CDS_00748: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

CDS_00755: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_00758: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_00761: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase

CDS_00759: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_00760: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.73	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001257.3	0.63	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0001273.3	0.63	PKS	asperlactone	Aspergillus ochraceus
BGC0002154.2	0.63	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001258.3	0.63	PKS	1,3,6,8-tetrahydroxynaphthalene	Glarea lozoyensis
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001244.3	0.63	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0002175.3	0.63	PKS	YWA1	Aspergillus oryzae RIB40
BGC0000107.3	0.63	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0001275.3	0.63	PKS	6-methylsalicyclic acid	Glarea lozoyensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.73	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001257.3	0.63	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0001273.3	0.63	PKS	asperlactone	Aspergillus ochraceus
BGC0002154.2	0.63	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001258.3	0.63	PKS	1,3,6,8-tetrahydroxynaphthalene	Glarea lozoyensis
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001244.3	0.63	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0002175.3	0.63	PKS	YWA1	Aspergillus oryzae RIB40
BGC0000107.3	0.63	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0001275.3	0.63	PKS	6-methylsalicyclic acid	Glarea lozoyensis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 21.45 out of 25.31

Confidence: medium

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46

Confidence: medium

Additional weak hits (25):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.74 out of 26.33

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.02 out of 27.78

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.96 out of 30.25

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.68 out of 39.62

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.06 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.05 out of 32.74

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.45 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.62 out of 32.74

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.37 out of 29.25

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.46 out of 31.73

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.28 out of 20.97

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.80 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.18 out of 26.06

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.61 out of 30.97

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.27 out of 30.25

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 15.87 out of 30.97

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 13.51 out of 21.55

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 14.47 out of 33.14

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.95 out of 33.14

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.67 out of 29.65

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 11.45 out of 26.06

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.58 out of 29.25

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.50 out of 29.65

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.58 out of 30.11

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 22, location 935862 - 972029:

Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:: (ohmal) + (Me-ccmal - pk) + (mal)
Non-colinear ordering:: CDS_00761 + CDS_00760 + CDS_00759

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_00759: mal

PKS_AT (581..890): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 75.0%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 177.1
inactive: 89.9
Methoxymalonyl-CoA: 72.6
Methylmalonyl-CoA: 59.0
Propionyl-CoA: 50.9
Isobutyryl-CoA: 31.2
Acetyl-CoA: 22.7
2-Methylbutyryl-CoA: 20.5
fatty_acid: 18.4
Ethylmalonyl-CoA: 17.4
CHC-CoA: 15.4
3-Methylbutyryl-CoA: 8.0
trans-1,2-CPDA: 7.4
Benzoyl-CoA: -1.1

CDS_00760: mmal - pk

PKS_AT (586..884): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 100.0%; Methoxymalonyl-CoA: 95.8%; Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 219.2
Ethylmalonyl-CoA: 210.6
Methoxymalonyl-CoA: 182.4
2-Methylbutyryl-CoA: 142.0
trans-1,2-CPDA: 127.7
Propionyl-CoA: 118.7
Malonyl-CoA: 115.2
CHC-CoA: 95.9
Isobutyryl-CoA: 88.2
Benzoyl-CoA: 71.5
Acetyl-CoA: 58.2
3-Methylbutyryl-CoA: 43.8
fatty_acid: 38.2
inactive: 36.7

PKS_AT (2367..2665): pk

ATSignature: Methoxymalonyl-CoA

Top 3 matches:: Methoxymalonyl-CoA: 75.0%; Malonyl-CoA: 70.8%; Methylmalonyl-CoA: 70.8%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 169.1
Ethylmalonyl-CoA: 164.3
Methoxymalonyl-CoA: 158.4
2-Methylbutyryl-CoA: 110.8
Isobutyryl-CoA: 98.5
Propionyl-CoA: 98.0
CHC-CoA: 96.7
Malonyl-CoA: 96.6
trans-1,2-CPDA: 89.2
Benzoyl-CoA: 71.2
Acetyl-CoA: 41.7
inactive: 37.0
fatty_acid: 30.3
3-Methylbutyryl-CoA: 26.3

CDS_00761: mal

PKS_AT (0..192): mal

ATSignature: (unknown)

No matches above 50%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 89.9
inactive: 51.3
Methoxymalonyl-CoA: 30.8
Methylmalonyl-CoA: 20.5
Propionyl-CoA: 4.3
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CatR	H2O2-responsive repressor
RpoN	Regulator of nitrogen assimilation and virulence

NPDC089509.ctg-0002 - Region 1 - NRPS

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Location: 66,936 - 125,457 nt. (total: 58,522 nt) Show pHMM detection rules used

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

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Gene overview

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TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: aminotransferase glycosyltransferase

CDS_00803: aminotransferase

smcogs: SMCOG1019: aminotransferase

CDS_00805: glycosyl transferase group 1

smcogs: SMCOG1045: glycosyl transferase group 1

Hydrolases: dehalogenase

CDS_00804: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Ligases: ligase

CDS_00800: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter

CDS_00810: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000342.4	0.73	NRPS	enniatin	Fusarium equiseti
BGC0001135.5	0.70	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.70	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0001128.4	0.69	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.68	NRPS	AbT1	Aureobasidium pullulans
BGC0002286.3	0.68	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000342.4	0.73	NRPS	enniatin	Fusarium equiseti
BGC0001135.5	0.70	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.70	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0001128.4	0.69	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.68	NRPS	AbT1	Aureobasidium pullulans
BGC0002286.3	0.68	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.38 out of 29.72

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 17.88 out of 23.79

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.98 out of 23.79

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.35 out of 23.79

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.15 out of 23.79

Confidence: medium

Additional weak hits (11):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.82 out of 26.33

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.80 out of 30.22

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.84 out of 30.22

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.12 out of 29.65

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 18.76 out of 27.04

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.11 out of 26.85

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.35 out of 29.65

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.35 out of 24.78

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 21.84

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.96 out of 27.18

Confidence: weak

Module view

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Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 66935 - 125457:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X - Ser - NMe-Gly - Asn - D-Ser)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_00800: X - Ser - Gly - Asn - Ser

Search NORINE for peptide: strict or relaxed

AMP-binding (465..884): X

nrpys: Val, Leu, Ile, Abu, Ival

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: N/A
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: VDSIITFGDK
Nearest Stachelhaus code(s):: bAla VDTVISLGDK (53% 8Å match)
Stachelhaus code match:: 60% (weak)

AMP-binding (1547..1949): Ser

nrpys: Ser

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: ser (Ser)
Single AA prediction:: ser (Ser)

Stachelhaus prediction details:

Stachelhaus sequence:: DVWHLSLVDK
Nearest Stachelhaus code(s):: Ser DVWHLSLVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2605..2994): Gly

nrpys: Gly

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
Single AA prediction:: gly (Gly)

Stachelhaus prediction details:

Stachelhaus sequence:: DILQLGLIWK
Nearest Stachelhaus code(s):: Gly DILQLGLIWK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4048..4452): Asn

nrpys: Asn

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: asp,asn (Asp, Asn)
Single AA prediction:: asn (Asn)

Stachelhaus prediction details:

Stachelhaus sequence:: DLVKLGHVHK
Nearest Stachelhaus code(s):: Asn DLTKLGEVGK (74% 8Å match)
Stachelhaus code match:: 70% (weak)

AMP-binding (5107..5506): Ser

nrpys: Ser

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: ser (Ser)
Single AA prediction:: ser (Ser)

Stachelhaus prediction details:

Stachelhaus sequence:: DVWHFSLVEK
Nearest Stachelhaus code(s):: Ser DVWHFSLVDK (91% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
IolR	Regulator of the inositol catabolism
NtrC	Nitrogen regulatory protein C
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0002 - Region 2 - terpene

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Location: 202,604 - 223,626 nt. (total: 21,023 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

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Gene overview

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MIBiG comparison

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SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase

CDS_00891: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_00895: pyridine nucleotide-disulfide oxidoreductase

smcogs: SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000623.3	0.42	ribosomal	plantaricin W α, plantaricin W β	Lactobacillus plantarum
BGC0000513.3	0.42	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000551.5	0.42	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000554.4	0.41	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998
BGC0000496.5	0.41	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000590.5	0.41	ribosomal	microcin N	Escherichia coli
BGC0000519.4	0.41	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000504.5	0.40	ribosomal	cytolysin ClyLl, cytolysin ClyLs	Plasmid pAD1
BGC0001638.4	0.40	ribosomal	klebsazolicin	Klebsiella pneumoniae subsp. ozaenae
BGC0001525.3	0.40	other (other)	bartoloside B, bartoloside C, bartoloside D	Synechocystis salina LEGE 06155

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000623.3	0.42	ribosomal	plantaricin W α, plantaricin W β	Lactobacillus plantarum
BGC0000513.3	0.42	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000551.5	0.42	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000554.4	0.41	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998
BGC0000496.5	0.41	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000590.5	0.41	ribosomal	microcin N	Escherichia coli
BGC0000519.4	0.41	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000504.5	0.40	ribosomal	cytolysin ClyLl, cytolysin ClyLs	Plasmid pAD1
BGC0001638.4	0.40	ribosomal	klebsazolicin	Klebsiella pneumoniae subsp. ozaenae
BGC0001525.3	0.40	other (other)	bartoloside B, bartoloside C, bartoloside D	Synechocystis salina LEGE 06155

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

No product predictions

Genes with terpene domains:

No domains found

Transcription Factor Binding Sites

Binding sites found:

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 28.31 out of 30.12

Confidence: strong

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47

Confidence: medium

Additional weak hits (7):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.68 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.32 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.79 out of 30.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.82 out of 26.06

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.97 out of 29.38

Confidence: weak

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.55 out of 29.51

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.36 out of 35.63

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
OsdR	Development and stress management regulator
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0002 - Region 3 - NRPS

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Location: 225,823 - 275,572 nt. (total: 49,750 nt) Show pHMM detection rules used

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_00925: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_00926: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

CDS_00931: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase

CDS_00907: aminotransferase

smcogs: SMCOG1019: aminotransferase

Hydrolases: hydrolase

CDS_00927: metallo-beta-lactamase family protein

smcogs: SMCOG1170: metallo-beta-lactamase family protein

Ligases: ligase

CDS_00910: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.71	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0000342.4	0.68	NRPS	enniatin	Fusarium equiseti
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001833.4	0.68	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001135.5	0.68	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.68	NRPS	HC-toxin	Alternaria jesenskae
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.67	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.71	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0000342.4	0.68	NRPS	enniatin	Fusarium equiseti
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001833.4	0.68	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001135.5	0.68	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.68	NRPS	HC-toxin	Alternaria jesenskae
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.67	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.92 out of 26.85

Confidence: medium

Additional weak hits (25):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.07 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.58 out of 30.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.80 out of 27.78

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.92 out of 27.55

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.61 out of 30.25

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.29 out of 29.65

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.48 out of 29.65

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.74 out of 26.85

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.08 out of 26.85

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.11 out of 26.85

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.55 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.12 out of 29.65

Confidence: weak

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52

Confidence: weak

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.38 out of 29.51

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.48 out of 29.65

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.11 out of 26.85

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.98 out of 26.85

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.01 out of 39.62

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.37 out of 29.65

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.40 out of 24.78

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.48 out of 29.65

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.60 out of 29.65

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.82 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.29 out of 28.19

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 3, location 225822 - 275572:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Leu - Hpg)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_00910: X - Leu - Hpg

Search NORINE for peptide: strict or relaxed

AMP-binding (101..498): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVSDIGSVIK
Nearest Stachelhaus code(s):: Lys DAEDIGSVIK (68% 8Å match); Lys or Arg DVEDIGSVAK (53% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1623..2010): Leu

nrpys: Leu

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: val (Val)

Stachelhaus prediction details:

Stachelhaus sequence:: DAYFWGVTFK
Nearest Stachelhaus code(s):: Leu DAYFWGVTFK (76% 8Å match); Val DAYFWGVTFK (74% 8Å match); Ile DAYFWGVTFK (71% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2660..3058): Hpg

nrpys: Hpg

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
Single AA prediction:: hpg (Hpg)

Stachelhaus prediction details:

Stachelhaus sequence:: DAYHLGLLCK
Nearest Stachelhaus code(s):: Hpg DAYHLGLLCK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0002 - Region 4 - RRE-containing

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Location: 341,690 - 362,763 nt. (total: 21,074 nt) Show pHMM detection rules used

RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Hydrolases: hydrolase

CDS_00992: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

CDS_01004: hydrolase

smcogs: SMCOG1179: hydrolase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000585.5	0.47	ribosomal	microcin C7	Escherichia coli
BGC0000583.5	0.38	ribosomal	grisemycin	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3	0.36	other (other)	4-hydroxy-3-nitrosobenzamide	Streptomyces murayamaensis
BGC0001513.3	0.34	PKS	anthrabenzoxocinone	Actinobacteria bacterium
BGC0002436.2	0.33	other (other)	coformycin	Streptomyces citricolor
BGC0000582.4	0.33	ribosomal	cypemycin	Streptomyces sp. OH-4156
BGC0000662.5	0.33	terpene	grixazone A	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001137.5	0.32	other (other)	marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D	Marinactinospora thermotolerans
BGC0002462.3	0.31	saccharide	coformycin	Streptomyces kaniharaensis
BGC0000821.5	0.31	other (other)	rebeccamycin	Lechevalieria aerocolonigenes

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000585.5	0.47	ribosomal	microcin C7	Escherichia coli
BGC0000583.5	0.38	ribosomal	grisemycin	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3	0.36	other (other)	4-hydroxy-3-nitrosobenzamide	Streptomyces murayamaensis
BGC0001513.3	0.34	PKS	anthrabenzoxocinone	Actinobacteria bacterium
BGC0002436.2	0.33	other (other)	coformycin	Streptomyces citricolor
BGC0000582.4	0.33	ribosomal	cypemycin	Streptomyces sp. OH-4156
BGC0000662.5	0.33	terpene	grixazone A	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001137.5	0.32	other (other)	marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D	Marinactinospora thermotolerans
BGC0002462.3	0.31	saccharide	coformycin	Streptomyces kaniharaensis
BGC0000821.5	0.31	other (other)	rebeccamycin	Lechevalieria aerocolonigenes

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.48 out of 24.78

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 20.47

Confidence: medium

Additional weak hits (17):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.77 out of 29.38

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.54 out of 26.85

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.40 out of 26.06

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.77 out of 35.63

Confidence: weak

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.71 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.17 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.33 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.15 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.38 out of 27.78

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.19 out of 31.73

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.05 out of 21.55

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.20 out of 29.65

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.60 out of 24.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.45 out of 26.06

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.20 out of 33.14

Confidence: weak

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.61 out of 25.31

Confidence: weak

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

RREFinder

TFBS Finder

RRE predictions

: RRE type: Pantocin_Microcin_RRE; Location: 0 - 89; Score: 63.9

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
LexA variant 2	Repressor of DNA damage response
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0002 - Region 5 - terpene

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Location: 423,521 - 446,046 nt. (total: 22,526 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxygenase

CDS_01080: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: aminotransferase methyltransferase

CDS_01073: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_01074: aminotransferase

smcogs: SMCOG1019: aminotransferase

Lyases: dehydratase

CDS_01085: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000660.5	0.58	terpene	albaflavenone	Streptomyces coelicolor A3(2)
BGC0002458.3	0.50	NRPS	alazopeptin	Streptacidiphilus griseoplanus
BGC0000675.5	0.49	terpene	(+)-T-muurolol	Streptomyces clavuligerus ATCC 27064
BGC0000677.5	0.45	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002449.2	0.45	other (other)	sarasinoside	uncultured bacterium
BGC0002392.2	0.42	terpene	10-Oxodepressin	Oryza sativa Japonica Group
BGC0001911.3	0.41	terpene	raimonol	Streptomyces anulatus
BGC0000678.5	0.39	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000916.5	0.39	other (other)	molybdenum cofactor	Staphylococcus carnosus
BGC0000777.3	0.38	saccharide	lipopolysaccharide	Escherichia coli

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000660.5	0.58	terpene	albaflavenone	Streptomyces coelicolor A3(2)
BGC0002458.3	0.50	NRPS	alazopeptin	Streptacidiphilus griseoplanus
BGC0000675.5	0.49	terpene	(+)-T-muurolol	Streptomyces clavuligerus ATCC 27064
BGC0000677.5	0.45	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002449.2	0.45	other (other)	sarasinoside	uncultured bacterium
BGC0002392.2	0.42	terpene	10-Oxodepressin	Oryza sativa Japonica Group
BGC0001911.3	0.41	terpene	raimonol	Streptomyces anulatus
BGC0000678.5	0.39	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000916.5	0.39	other (other)	molybdenum cofactor	Staphylococcus carnosus
BGC0000777.3	0.38	saccharide	lipopolysaccharide	Escherichia coli

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

No product predictions

Genes with terpene domains:

CDS_01080: T1TS

Domain 1 (463 - 834): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26

Confidence: medium

Additional weak hits (8):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.48 out of 27.78

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.87 out of 30.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.37 out of 29.38

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.65 out of 27.55

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.32 out of 29.38

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.49 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.95 out of 29.65

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein

NPDC089509.ctg-0002 - Region 6 - NRPS-like,T1PKS

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Location: 525,119 - 680,144 nt. (total: 155,026 nt) Show pHMM detection rules used

T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxygenase

CDS_01203: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_01208: monooxygenase FAD-binding

smcogs: SMCOG1246: monooxygenase FAD-binding

Transferases: aminotransferase glycosyltransferase

CDS_01204: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs: SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

CDS_01205: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

Hydrolases: esterase

CDS_01201: thioesterase

smcogs: SMCOG1004: thioesterase

Lyases: dehydratase

CDS_01183: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Isomerases: isomerase

CDS_01200: isochorismate synthase

smcogs: SMCOG1018: isochorismate synthase

Ligases: synthase

CDS_01168: argininosuccinate synthase

smcogs: SMCOG1291: argininosuccinate synthase

CDS_01185: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_01186: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_01187: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_01188: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_01189: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_01199: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.71	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.70	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.70	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.70	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001257.3	0.60	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0002154.2	0.60	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0002175.3	0.60	PKS	YWA1	Aspergillus oryzae RIB40
BGC0001258.3	0.59	PKS	1,3,6,8-tetrahydroxynaphthalene	Glarea lozoyensis
BGC0000107.3	0.59	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0001284.4	0.57	PKS	alternariol	Parastagonospora nodorum SN15

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.74	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.74	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.74	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.74	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0000034.5	0.67	NRPS, PKS	candicidin	Streptomyces sp. FR-008
BGC0000041.3	0.67	PKS	oronofacic acid	Pseudomonas syringae
BGC0001257.3	0.64	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0002154.2	0.64	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0002175.3	0.63	PKS	YWA1	Aspergillus oryzae RIB40

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47

Confidence: medium

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.75 out of 23.05

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 17.88 out of 23.79

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.72 out of 20.47

Confidence: medium

Additional weak hits (24):

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 14.99 out of 31.73

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.63 out of 25.75

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.58 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.83 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.07 out of 32.74

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 13.68 out of 21.55

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.14 out of 21.55

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.19 out of 28.19

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.71 out of 20.01

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.44 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.87 out of 27.78

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.68 out of 29.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.92 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.61 out of 30.25

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.97 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.43 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.86 out of 30.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.14 out of 27.78

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.35 out of 27.04

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.45 out of 24.78

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 6, location 525118 - 680144:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (ccmal - ccmal - pk - ohmal - ohmal - ohmal) + (ccmal - ccmal) + (ccmal - ohmal - ccmal) + (ohmal - Me-redmal - Me-ccmal) + (ccmal - ccmal - ccmal - ccmal - ccmal - ccmal) + (X - mal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_01185: mal - mal - pk - mal - mal - mal

PKS_AT (572..864): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 70.8%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 197.6
inactive: 78.1
Methoxymalonyl-CoA: 60.0
Methylmalonyl-CoA: 52.4
Acetyl-CoA: 24.2
Isobutyryl-CoA: 23.6
Benzoyl-CoA: 19.4
Ethylmalonyl-CoA: 18.7
Propionyl-CoA: 14.3
fatty_acid: 9.3
CHC-CoA: 7.4
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

PKS_AT (2319..2613): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 70.8%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 196.5
inactive: 79.8
Methoxymalonyl-CoA: 60.0
Methylmalonyl-CoA: 47.8
Propionyl-CoA: 34.0
Acetyl-CoA: 21.9
Isobutyryl-CoA: 16.5
Benzoyl-CoA: 15.5
fatty_acid: 12.5
2-Methylbutyryl-CoA: 11.0
CHC-CoA: 8.4
Ethylmalonyl-CoA: 7.6
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (3846..4144): pk

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 100.0%; Malonyl-CoA: 91.7%; Methoxymalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:

Ethylmalonyl-CoA: 211.6
Methylmalonyl-CoA: 209.9
Methoxymalonyl-CoA: 173.4
2-Methylbutyryl-CoA: 139.0
trans-1,2-CPDA: 131.8
Propionyl-CoA: 110.6
CHC-CoA: 108.2
Malonyl-CoA: 101.4
Isobutyryl-CoA: 89.0
Benzoyl-CoA: 64.0
fatty_acid: 56.3
Acetyl-CoA: 47.7
inactive: 28.8
3-Methylbutyryl-CoA: 23.1

PKS_AT (5392..5687): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 70.8%; Propionyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 207.5
inactive: 109.6
Methoxymalonyl-CoA: 72.9
Methylmalonyl-CoA: 65.4
Propionyl-CoA: 38.7
Acetyl-CoA: 36.2
Isobutyryl-CoA: 33.7
Ethylmalonyl-CoA: 23.5
fatty_acid: 19.2
Benzoyl-CoA: 17.7
2-Methylbutyryl-CoA: 14.0
CHC-CoA: 8.2
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: -2.4

PKS_AT (6881..7169): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 100.0%; inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 220.3
inactive: 97.6
Methoxymalonyl-CoA: 57.0
Methylmalonyl-CoA: 49.0
Propionyl-CoA: 25.6
Acetyl-CoA: 18.7
Benzoyl-CoA: 16.0
Isobutyryl-CoA: 15.4
fatty_acid: 14.4
2-Methylbutyryl-CoA: 13.0
Ethylmalonyl-CoA: 10.1
CHC-CoA: 7.2
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (8389..8673): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 75.0%; Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 230.2
inactive: 106.3
Methoxymalonyl-CoA: 66.4
Methylmalonyl-CoA: 54.3
Propionyl-CoA: 47.3
Isobutyryl-CoA: 31.3
Ethylmalonyl-CoA: 21.3
2-Methylbutyryl-CoA: 19.4
Benzoyl-CoA: 18.2
Acetyl-CoA: 15.8
fatty_acid: 11.2
CHC-CoA: 7.2
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

CDS_01186: mal - mal

PKS_AT (543..814): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 223.2
inactive: 106.4
Methoxymalonyl-CoA: 61.3
Methylmalonyl-CoA: 49.4
Propionyl-CoA: 27.6
Isobutyryl-CoA: 22.4
Acetyl-CoA: 18.0
Benzoyl-CoA: 12.1
fatty_acid: 8.9
2-Methylbutyryl-CoA: 7.3
Ethylmalonyl-CoA: 2.6
trans-1,2-CPDA: 0.0
CHC-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (2162..2437): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 221.4
inactive: 100.8
Methoxymalonyl-CoA: 67.1
Methylmalonyl-CoA: 59.9
Propionyl-CoA: 34.0
Isobutyryl-CoA: 26.5
Benzoyl-CoA: 19.2
Acetyl-CoA: 18.4
2-Methylbutyryl-CoA: 18.1
Ethylmalonyl-CoA: 17.0
fatty_acid: 15.4
CHC-CoA: 11.3
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

CDS_01187: mal - mal - mal

PKS_AT (550..818): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 227.6
inactive: 103.2
Methoxymalonyl-CoA: 69.2
Methylmalonyl-CoA: 62.4
Propionyl-CoA: 32.3
Acetyl-CoA: 20.1
Isobutyryl-CoA: 19.9
Ethylmalonyl-CoA: 18.7
Benzoyl-CoA: 17.9
2-Methylbutyryl-CoA: 13.5
fatty_acid: 12.6
CHC-CoA: 11.9
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (2222..2507): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 79.2%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 228.1
inactive: 99.4
Methoxymalonyl-CoA: 60.7
Methylmalonyl-CoA: 54.5
Propionyl-CoA: 30.5
Ethylmalonyl-CoA: 19.5
Acetyl-CoA: 18.5
Isobutyryl-CoA: 18.3
Benzoyl-CoA: 17.7
CHC-CoA: 16.4
fatty_acid: 14.1
trans-1,2-CPDA: 9.0
2-Methylbutyryl-CoA: 8.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (3724..4009): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 229.0
inactive: 102.3
Methoxymalonyl-CoA: 59.5
Methylmalonyl-CoA: 55.9
Propionyl-CoA: 30.9
Acetyl-CoA: 21.4
Isobutyryl-CoA: 18.9
Benzoyl-CoA: 15.8
fatty_acid: 13.8
2-Methylbutyryl-CoA: 11.2
Ethylmalonyl-CoA: 10.7
CHC-CoA: 9.1
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

CDS_01188: mal - mmal - mmal

PKS_AT (562..850): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 230.4
inactive: 103.8
Methoxymalonyl-CoA: 61.3
Methylmalonyl-CoA: 55.2
Propionyl-CoA: 33.7
Acetyl-CoA: 19.9
Isobutyryl-CoA: 19.6
Benzoyl-CoA: 16.0
fatty_acid: 13.7
CHC-CoA: 11.0
2-Methylbutyryl-CoA: 11.0
Ethylmalonyl-CoA: 10.2
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (2109..2406): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 100.0%; Methoxymalonyl-CoA: 91.7%; Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 223.2
Ethylmalonyl-CoA: 216.5
Methoxymalonyl-CoA: 186.2
2-Methylbutyryl-CoA: 162.4
trans-1,2-CPDA: 134.8
Propionyl-CoA: 115.6
CHC-CoA: 101.3
Malonyl-CoA: 101.1
Benzoyl-CoA: 68.4
Isobutyryl-CoA: 68.3
Acetyl-CoA: 56.2
3-Methylbutyryl-CoA: 41.8
fatty_acid: 33.6
inactive: 28.4

PKS_AT (4182..4479): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 95.8%; Malonyl-CoA: 87.5%; Methoxymalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 203.0
Ethylmalonyl-CoA: 197.0
Methoxymalonyl-CoA: 171.0
2-Methylbutyryl-CoA: 158.5
trans-1,2-CPDA: 133.0
Propionyl-CoA: 109.2
Malonyl-CoA: 99.8
CHC-CoA: 86.5
Isobutyryl-CoA: 70.6
Benzoyl-CoA: 63.1
Acetyl-CoA: 45.4
3-Methylbutyryl-CoA: 43.4
fatty_acid: 29.8
inactive: 28.3

CDS_01189: mal - mal - mal - mal - mal - mal

PKS_AT (565..846): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 229.6
inactive: 105.5
Methoxymalonyl-CoA: 60.1
Methylmalonyl-CoA: 56.4
Propionyl-CoA: 31.8
Isobutyryl-CoA: 19.4
Acetyl-CoA: 17.8
Benzoyl-CoA: 16.9
Ethylmalonyl-CoA: 14.3
CHC-CoA: 12.4
fatty_acid: 10.5
2-Methylbutyryl-CoA: 9.8
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (2215..2496): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 79.2%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 230.4
inactive: 101.7
Methoxymalonyl-CoA: 64.1
Methylmalonyl-CoA: 61.7
Propionyl-CoA: 36.8
2-Methylbutyryl-CoA: 18.8
Benzoyl-CoA: 16.7
Ethylmalonyl-CoA: 15.7
Acetyl-CoA: 15.1
Isobutyryl-CoA: 14.1
trans-1,2-CPDA: 11.8
CHC-CoA: 11.6
fatty_acid: 9.1
3-Methylbutyryl-CoA: 0.0

PKS_AT (3861..4148): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 79.2%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 235.9
inactive: 104.7
Methoxymalonyl-CoA: 63.7
Methylmalonyl-CoA: 58.4
Propionyl-CoA: 28.5
Isobutyryl-CoA: 25.4
Acetyl-CoA: 22.3
Benzoyl-CoA: 18.7
Ethylmalonyl-CoA: 17.1
2-Methylbutyryl-CoA: 14.1
CHC-CoA: 13.8
fatty_acid: 12.0
trans-1,2-CPDA: 5.9
3-Methylbutyryl-CoA: 0.0

PKS_AT (5551..5835): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 228.8
inactive: 109.5
Methoxymalonyl-CoA: 63.5
Methylmalonyl-CoA: 61.6
Propionyl-CoA: 39.5
Isobutyryl-CoA: 29.6
2-Methylbutyryl-CoA: 22.5
Acetyl-CoA: 20.2
Benzoyl-CoA: 15.6
Ethylmalonyl-CoA: 14.8
fatty_acid: 13.2
CHC-CoA: 10.9
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (7269..7553): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 233.7
inactive: 105.9
Methoxymalonyl-CoA: 62.8
Methylmalonyl-CoA: 61.1
Propionyl-CoA: 36.4
Isobutyryl-CoA: 22.2
Ethylmalonyl-CoA: 21.5
2-Methylbutyryl-CoA: 18.6
Benzoyl-CoA: 17.7
Acetyl-CoA: 17.5
CHC-CoA: 14.2
fatty_acid: 13.0
trans-1,2-CPDA: 7.3
3-Methylbutyryl-CoA: 0.0

PKS_AT (8921..9206): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 79.2%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 228.2
inactive: 104.3
Methoxymalonyl-CoA: 60.4
Methylmalonyl-CoA: 59.5
Propionyl-CoA: 34.4
Isobutyryl-CoA: 25.0
Benzoyl-CoA: 20.6
Acetyl-CoA: 20.5
2-Methylbutyryl-CoA: 18.4
Ethylmalonyl-CoA: 15.4
fatty_acid: 11.9
CHC-CoA: 11.2
trans-1,2-CPDA: 6.2
3-Methylbutyryl-CoA: 0.0

CDS_01199: X - mal

AMP-binding (28..438): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: LFQFRAVTGK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

PKS_AT (1203..1488): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 167.3
inactive: 70.6
Methoxymalonyl-CoA: 57.7
Methylmalonyl-CoA: 40.0
Propionyl-CoA: 22.6
Isobutyryl-CoA: 16.9
Acetyl-CoA: 15.1
Ethylmalonyl-CoA: 13.1
Benzoyl-CoA: 10.4
CHC-CoA: 9.1
fatty_acid: 7.3
2-Methylbutyryl-CoA: 2.3
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0002 - Region 7 - NRPS,NRPS-like,butyrolactone

Download region GenBank file

Download region SVG

Location: 702,722 - 743,055 nt. (total: 40,334 nt) Show pHMM detection rules used

Region on contig edge.

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
butyrolactone: AfsA
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_01249: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase acetyltransferase

CDS_01248: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

CDS_01266: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1060: 4'-phosphopantetheinyl transferase

Hydrolases: deacetylase

CDS_01262: polysaccharide deacetylase

smcogs: SMCOG1235: polysaccharide deacetylase

Lyases: dehydratase

CDS_01256: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase

CDS_01252: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_01253: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_01254: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_01255: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000849.4	1.99	other (butyrolactone)	SCB1, SCB2, SCB3	Streptomyces coelicolor A3(2)
BGC0000848.5	1.96	other (other)	A-factor	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5	1.48	other (other)	γ-butyrolactone	Streptomyces acidiscabies
BGC0001249.5	1.26	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001261.3	1.14	NRPS	AM-toxin	Alternaria alternata
BGC0000342.4	1.10	NRPS	enniatin	Fusarium equiseti
BGC0001135.5	1.09	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	1.09	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002051.2	1.09	NRPS	antipain	Streptomyces sp.
BGC0001128.4	1.05	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000849.4	0.78	other (butyrolactone)	SCB1, SCB2, SCB3	Streptomyces coelicolor A3(2)
BGC0000848.5	0.78	other (other)	A-factor	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001261.3	0.70	NRPS	AM-toxin	Alternaria alternata
BGC0000850.5	0.70	other (other)	γ-butyrolactone	Streptomyces acidiscabies
BGC0002051.2	0.70	NRPS	antipain	Streptomyces sp.
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0001135.5	0.69	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.69	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.68	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.24 out of 26.85

Confidence: medium

Additional weak hits (20):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.68 out of 30.22

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.77 out of 30.25

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.23 out of 21.55

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.06 out of 24.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.43 out of 26.06

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.11 out of 18.57

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.92 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.82 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.77 out of 26.06

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.11 out of 18.57

Confidence: weak

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.61 out of 25.31

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.25 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.22 out of 29.38

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.14 out of 32.93

Confidence: weak

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.19 out of 25.75

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.19 out of 24.78

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.67 out of 29.65

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.61 out of 29.25

Confidence: weak

Module view

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Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 7, location 702721 - 743055:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Arg) + (Phe) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 9, location 705965 - 743055:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Arg) + (Phe) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 10, location 707803 - 743055:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Arg) + (Phe) + (X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_01253: Arg

Search NORINE for peptide: strict or relaxed

AMP-binding (458..848): Arg

nrpys: Arg

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVENVGAVTK
Nearest Stachelhaus code(s):: Arg DVENVGAVTK (85% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_01254: Phe

Search NORINE for peptide: strict or relaxed

AMP-binding (20..410): Phe

nrpys: Phe

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DPLVTGAVAK
Nearest Stachelhaus code(s):: Phe DPLVVGAVVK (85% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_01255: X

AMP-binding (12..402): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: val (Val)

Stachelhaus prediction details:

Stachelhaus sequence:: DAFFAGVTFK
Nearest Stachelhaus code(s):: Ile DAFFLGVTFK (71% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
RutR	Regulator of the pyrimidine and purine metabolism

NPDC089509.ctg-0003 - Region 1 - NRPS,terpene

Download region GenBank file

Download region SVG

Location: 1 - 62,472 nt. (total: 62,472 nt) Show pHMM detection rules used

Region on contig edge.

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_01275: Dioxygenase TauD/TfdA

smcogs: SMCOG1046: Dioxygenase TauD/TfdA

CDS_01277: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_01295: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_01298: Oxidation

MITE: MITE0000108Oxidation (identity: 66.90%)
smcogs: SMCOG1034: cytochrome P450

CDS_01302: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase

CDS_01271: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: esterase hydrolase

CDS_01278: thioesterase

smcogs: SMCOG1004: thioesterase

CDS_01301: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: cyclase lyase

CDS_01299: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

CDS_01307: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthetase

CDS_01274: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_01279: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_01280: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_01281: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_01296: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001911.3	0.95	terpene	raimonol	Streptomyces anulatus
BGC0001910.4	0.82	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0000677.5	0.47	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0001128.4	0.46	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.46	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001132.4	0.46	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0000660.5	0.45	terpene	albaflavenone	Streptomyces coelicolor A3(2)
BGC0001135.5	0.45	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.45	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.45	NRPS	icosalide A, icosalide B	Burkholderia gladioli

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001911.3	0.80	terpene	raimonol	Streptomyces anulatus
BGC0001128.4	0.76	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.76	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001132.4	0.76	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001135.5	0.76	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.75	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001910.4	0.75	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002075.3	0.73	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Detailed terpene predictions

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
diterpene			C20	C6-C11 + C10-C15	none

Genes with terpene domains:

CDS_01296: PT_FPPS_like

Domain 1 (51 - 358): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

Reactions:: IPP, DMAPP → FPP; IPP, DMAPP → GGPP; IPP, DMAPP → GFPP; IPP, DMAPP → HPP

CDS_01297: T2TS

Domain 1 (23 - 536): Type 2 terpene synthase

Subtype: Diterpene synthase

Reactions:: GGPP → diterpene_C6-C11/C10-C15_PP

CDS_01299: T1TS

Domain 1 (4 - 325): Type 1 terpene synthase

Subtype: Labdatriene synthase type

Reactions:: diterpene_C6-C11/C10-C15_PP → diterpene_C6-C11/C10-C15

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (11):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.85 out of 26.06

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.75 out of 29.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.20 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.89 out of 30.25

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.03 out of 25.88

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.07 out of 27.78

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.35 out of 27.55

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.26 out of 32.74

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.27 out of 35.63

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.24 out of 24.78

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 24.00 out of 35.63

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

Terpene

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 62472:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X - X) + (Thr - X) + (Val - Ser - Leu)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 0 - 52401:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X - X) + (Thr - X) + (Val - Ser - Leu)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_01274: Val - Ser - Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (474..861): Val

nrpys: Val

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: val (Val)

Stachelhaus prediction details:

Stachelhaus sequence:: DAYWTGGTFK
Nearest Stachelhaus code(s):: Val DAYWWGGTFK (85% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1516..1917): Ser

nrpys: Ser

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: ser (Ser)
Single AA prediction:: ser (Ser)

Stachelhaus prediction details:

Stachelhaus sequence:: DVWHFSLVDK
Nearest Stachelhaus code(s):: Ser DVWHFSLVDK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2589..2978): Leu

nrpys: Leu

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DAYFAGLTAK
Nearest Stachelhaus code(s):: Leu DAWLAGLTAK (62% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_01279: X

AMP-binding (13..392): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: glu,gln (Glu, Gln)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DAQDFGLVDK
Nearest Stachelhaus code(s):: Ile DAQDLGVVDK (79% 8Å match); OH-Orn DAQEGGLVDK (68% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_01280: Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (462..868): Thr

nrpys: Thr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: thr (Thr)
Single AA prediction:: thr (Thr)

Stachelhaus prediction details:

Stachelhaus sequence:: DWWCMGLVHK
Nearest Stachelhaus code(s):: Thr DFWSFGLVHK (74% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_01281: X - X

AMP-binding (9..378): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVENIGAITK
Nearest Stachelhaus code(s):: Arg DVENVGAITK (62% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (989..1386): X

nrpys: Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DALQFAGGLK
Nearest Stachelhaus code(s):: Trp DAWAFAGVAK (47% 8Å match); Val DAWMFAAILK (41% 8Å match)
Stachelhaus code match:: 60% (weak)

Link to PARAS substrate predictor

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
GFPP	Geranylfarnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
HPP	Hexaprenyl diphosphate
IPP	Isopentenyl diphosphate

TFBS definitions

Regulator	Description

NPDC089509.ctg-0003 - Region 2 - NRPS-like

Download region GenBank file

Download region SVG

Location: 69,037 - 112,147 nt. (total: 43,111 nt) Show pHMM detection rules used

NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_01324: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_01326: monooxygenase FAD-binding

smcogs: SMCOG1246: monooxygenase FAD-binding

CDS_01332: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: aminotransferase

CDS_01315: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs: SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: hydrolase

CDS_01322: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase

CDS_01331: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001268.4	0.60	NRPS, PKS	fusarin C	Fusarium fujikuroi
BGC0002164.2	0.58	NRPS	peramine	Epichloe festucae
BGC0001641.4	0.57	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.57	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001128.4	0.57	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.57	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001758.4	0.57	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.57	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.57	NRPS	AbT1	Aureobasidium pullulans
BGC0001833.4	0.57	NRPS	icosalide A, icosalide B	Burkholderia gladioli

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001268.4	0.60	NRPS, PKS	fusarin C	Fusarium fujikuroi
BGC0002164.2	0.58	NRPS	peramine	Epichloe festucae
BGC0001641.4	0.57	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.57	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001128.4	0.57	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.57	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001758.4	0.57	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.57	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.57	NRPS	AbT1	Aureobasidium pullulans
BGC0001833.4	0.57	NRPS	icosalide A, icosalide B	Burkholderia gladioli

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.60 out of 19.26

Confidence: medium

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.05 out of 27.55

Confidence: medium

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.44 out of 27.18

Confidence: medium

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.59 out of 25.88

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.13 out of 20.47

Confidence: medium

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05

Confidence: medium

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46

Confidence: medium

Additional weak hits (12):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.49 out of 30.22

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.07 out of 36.54

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.07 out of 36.54

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.83 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.50 out of 26.06

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.07 out of 21.84

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.04 out of 28.19

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.61 out of 24.78

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.48 out of 28.19

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS substrates

TFBS Finder

NRPS/PKS substrate predictions

CDS_01327: X

AMP-binding (65..268): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: TLFSLASVDK
Nearest Stachelhaus code(s):: Ala DVFSLAVVYK (32% 8Å match); Pro DLFYLALVCK (29% 8Å match)
Stachelhaus code match:: 60% (weak)

CDS_01328: X

AMP-binding (484..726): X

nrpys: Val, Leu, Ile, Abu, Ival

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: N/A
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: -YLFFGAVDK
Nearest Stachelhaus code(s):: Arg DALFFGLVDK (44% 8Å match); His DYWHFGAVDK (38% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_01331: Val

Search NORINE for peptide: strict or relaxed

AMP-binding (3..414): Val

nrpys: Val

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: val (Val)

Stachelhaus prediction details:

Stachelhaus sequence:: DALWLGCVFK
Nearest Stachelhaus code(s):: Val DALWLGGVFK (56% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
CRP	Cyclic AMP receptor protein
GnfM	Regulator of nitrogen-fixation genes
NrdR	Represses ribonucleotide reductase encoding genes
PsrA	Oleic acid responsive regulator
RpoN	Regulator of nitrogen assimilation and virulence
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0003 - Region 3 - NRPS-like

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Location: 129,025 - 172,651 nt. (total: 43,627 nt) Show pHMM detection rules used

NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Hydrolases: dehalogenase

CDS_01370: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Ligases: ligase

CDS_01379: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001295.5	0.42	other (other)	cremeomycin	Streptomyces cremeus
BGC0000595.3	0.42	ribosomal	SCO-2138	Streptomyces coelicolor A3(2)
BGC0001895.4	0.42	PKS	huanglongmycin A, huanglongmycin B, huanglongmycin C	Streptomyces sp. CB09001
BGC0000860.3	0.41	other (other)	ectoine	Methylarcula marina
BGC0001627.4	0.40	NRPS	isonitrile lipopeptides	Mycobacterium tuberculosis H37Rv
BGC0002621.2	0.39	other (other)	angustmycin A, angustmycin B, angustmycin C, aristeromycin, arabinofuranosyladenine	Streptomyces angustmyceticus
BGC0001542.3	0.37	PKS	cercosporin	Cercospora zeina
BGC0000876.5	0.37	other (other)	neopolyoxin C	Streptomyces tendae
BGC0002037.3	0.37	NRPS	azetidomonamide A, azetidomonamide B	Pseudomonas aeruginosa PAO1
BGC0002293.2	0.37	NRPS	ohmyungsamycin A, ohmyungsamycin B	Streptomyces sp.

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001295.5	0.42	other (other)	cremeomycin	Streptomyces cremeus
BGC0000595.3	0.42	ribosomal	SCO-2138	Streptomyces coelicolor A3(2)
BGC0001895.4	0.42	PKS	huanglongmycin A, huanglongmycin B, huanglongmycin C	Streptomyces sp. CB09001
BGC0000860.3	0.41	other (other)	ectoine	Methylarcula marina
BGC0001627.4	0.40	NRPS	isonitrile lipopeptides	Mycobacterium tuberculosis H37Rv
BGC0002621.2	0.39	other (other)	angustmycin A, angustmycin B, angustmycin C, aristeromycin, arabinofuranosyladenine	Streptomyces angustmyceticus
BGC0001542.3	0.37	PKS	cercosporin	Cercospora zeina
BGC0000876.5	0.37	other (other)	neopolyoxin C	Streptomyces tendae
BGC0002037.3	0.37	NRPS	azetidomonamide A, azetidomonamide B	Pseudomonas aeruginosa PAO1
BGC0002293.2	0.37	NRPS	ohmyungsamycin A, ohmyungsamycin B	Streptomyces sp.

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 29.91 out of 35.63

Confidence: medium

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12

Confidence: medium

Additional weak hits (14):

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.58 out of 29.38

Confidence: weak

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.74 out of 29.72

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.97 out of 30.22

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.90 out of 20.01

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.37 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.57 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.41 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.79 out of 27.78

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.45 out of 30.25

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.98 out of 32.74

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.11 out of 31.73

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.53 out of 35.63

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.98 out of 24.78

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 5, location 129024 - 172651:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_01379: X

AMP-binding (99..533): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: MMGVWVGTVK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
NrtR	NAD synthesis repressor
OsdR	Development and stress management regulator

NPDC089509.ctg-0003 - Region 4 - T2PKS

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Location: 221,162 - 293,644 nt. (total: 72,483 nt) Show pHMM detection rules used

T2PKS: (t2ks and t2clf)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

CDS_01456: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_01457: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

CDS_01462: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_01463: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_01465: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_01467: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_01469: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_01471: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_01482: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

Transferases: acylase methyltransferase

CDS_01455: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

CDS_01461: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

CDS_01466: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Lyases: cyclase

CDS_01458: cyclase/dehydrase

smcogs: SMCOG1128: cyclase/dehydrase

CDS_01459: cyclase/dehydrase

smcogs: SMCOG1128: cyclase/dehydrase

Ligases: ligase synthase

CDS_01460: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_01474: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_01475: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_01481: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CDS_01496: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transport

CDS_01499: MMPL domain-containing transport protein

smcogs: SMCOG1035: MMPL domain-containing transport protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000231.5	0.65	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0000234.5	0.65	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0001244.3	0.63	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001276.3	0.63	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001275.3	0.63	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.62	PKS	asperlactone	Aspergillus ochraceus
BGC0002276.2	0.60	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0002175.3	0.60	PKS	YWA1	Aspergillus oryzae RIB40
BGC0002154.2	0.60	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0000037.4	0.59	PKS	cichorine	Aspergillus nidulans FGSC A4

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000231.5	0.65	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0000234.5	0.65	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0001244.3	0.63	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001276.3	0.63	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001275.3	0.63	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.62	PKS	asperlactone	Aspergillus ochraceus
BGC0002276.2	0.60	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0002175.3	0.60	PKS	YWA1	Aspergillus oryzae RIB40
BGC0002154.2	0.60	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0000037.4	0.59	PKS	cichorine	Aspergillus nidulans FGSC A4

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.79 out of 25.31

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.71 out of 20.47

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.57 out of 20.97

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.14 out of 27.04

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.17 out of 25.31

Confidence: medium

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.12 out of 26.85

Confidence: medium

Additional weak hits (23):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.67 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.11 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.00 out of 26.06

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.33 out of 30.97

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.70 out of 26.33

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.79 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.64 out of 32.74

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 25.75

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.67 out of 26.33

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 19.26

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.56 out of 32.74

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.97 out of 29.38

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.33 out of 30.97

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.57 out of 20.97

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.09 out of 30.22

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.13 out of 32.93

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.13 out of 28.14

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.29 out of 29.25

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.06 out of 29.25

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.21 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.01 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.52 out of 29.65

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.89 out of 29.65

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS substrates

Type II PKS

TFBS Finder

NRPS/PKS substrate predictions

CDS_01460: X

AMP-binding (14..416): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: KFMYAGGPLK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

CDS_01466: mal

PKS_AT (15..295): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 66.7%; inactive: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 63.3
Methylmalonyl-CoA: 45.7
Methoxymalonyl-CoA: 36.3
Propionyl-CoA: 21.4
inactive: 18.3
fatty_acid: 17.0
Acetyl-CoA: 16.0
Ethylmalonyl-CoA: 15.6
2-Methylbutyryl-CoA: 13.9
trans-1,2-CPDA: 11.8
CHC-CoA: 9.5
Benzoyl-CoA: 8.7
Isobutyryl-CoA: 7.6
3-Methylbutyryl-CoA: 0.0

CDS_01496: X

AMP-binding (33..429): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: GVRFALSGIK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

Link to PARAS substrate predictor

Type II PKS gene cluster prediction details

Cluster section:: 221161 to 293644
Starter unit(s):: malonamyl-CoA (Score: 462.0; E-value: 1.42e-157)
propionyl-CoA (Score: 302.0; E-value: 6.35e-105)
Malonyl elongations:: 8|9 (Score: 633.7; E-value: 2.5e-193)
Product class(es):: anthracycline
aureolic acid
tetracycline
Product molecular weight(s):: malonamyl-CoA_8: 442 Da
malonamyl-CoA_9: 484 Da
propionyl-CoA_8: 413 Da
propionyl-CoA_9: 455 Da

CDS_01455: MET C10 (Score: 359.7; E-value: 2.9e-110)
CDS_01456: OXY (Score: 464.3; E-value: 1.1e-141)
CDS_01457: KR (Score: 59.2; E-value: 1.1e-18)
CDS_01458: CYC C7-C12 (Score: 238.7; E-value: 1.7e-73)
CDS_01459: CYC C7-C12 (Score: 450.6; E-value: 5.1e-138)
CDS_01460: LIG (Score: 548.7; E-value: 2.5e-167); LIG ELQ83297.1_Oxytetracycline_malonamyl-CoA (Score: 462.0; E-value: 1.42e-157)
CDS_01461: MET (Score: 226.0; E-value: 1.6e-69)
CDS_01462: OXY (Score: 235.7; E-value: 2.6e-72)
CDS_01463: KR (Score: 148.4; E-value: 6.9e-46)
CDS_01464: CYC C5-C14/C3-C16 (Score: 430.8; E-value: 4.1e-132)
CDS_01465: OXY (Score: 391.1; E-value: 1.8e-119)
CDS_01466: AT (Score: 378.8; E-value: 5.3e-116); AT BAB72049.1_Aklavinone_propionyl-CoA (Score: 302.0; E-value: 6.35e-105)
CDS_01467: OXY (Score: 206.1; E-value: 2.4e-63)
CDS_01469: KR C9 (Score: 443.6; E-value: 4.8e-136)
CDS_01470: CYC C1-C18|C2-C19 (Score: 193.6; E-value: 3.1e-60)
CDS_01473: ACP (Score: 105.4; E-value: 2.6e-33)
CDS_01474: CLF 8|9 (Score: 633.7; E-value: 2.5e-193)
CDS_01475: KS (Score: 758.1; E-value: 5.2e-231)
CDS_01480: ACP (Score: 33.4; E-value: 8.1e-11)

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
CatR	H2O2-responsive repressor
CcpA	Catabolite control protein A
DasR	N-acetylglucosamine dependent repressor
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0003 - Region 5 - T1PKS,lanthipeptide-class-iii,lipolanthine

Download region GenBank file

Download region SVG

Location: 442,208 - 493,148 nt. (total: 50,941 nt) Show pHMM detection rules used

lipolanthine: (micKC and Flavoprotein)
lanthipeptide-class-iii: (micKC and not PKS_KS)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Lanthipeptides

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidase

CDS_01656: pyruvate oxidase/decarboxylase

smcogs: SMCOG1055: pyruvate oxidase/decarboxylase

CDS_01671: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_01672: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase

CDS_01669: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase

CDS_01690: metallo-beta-lactamase family protein

smcogs: SMCOG1170: metallo-beta-lactamase family protein

Ligases: ligase synthase

CDS_01664: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_01665: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_01667: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002174.2	0.87	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0001135.5	0.87	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001758.4	0.82	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001132.4	0.81	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.81	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001641.4	0.81	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001160.5	0.81	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002286.3	0.81	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.81	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3	0.81	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.74	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.74	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001244.3	0.73	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001254.3	0.64	PKS	ACT-Toxin II	Alternaria alternata
BGC0001160.5	0.64	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001164.3	0.63	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001276.3	0.63	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002174.2	0.63	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0001135.5	0.63	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for CDS_01660

CDS_01661

Leader:

MTESVLDLQELETSEEETALMAAS

CDS_01663

Leader:

MTESVLDLQELETSEEETALMAAS

Shared core:

ASSWNC

Core with dehydrations:

ADhaDhaWNCys

antiSMASH-DB 4.0 matches for CDS_01661

100.0%

NZ_CP053109.1and 1 other:

NZ_CP053109.1 Lanthipeptides: HJD23_RS43020_lanthipeptide

Lanthipeptides: HJD23_RS43025_lanthipeptide

1

ASSWNC

6

ASSWNC

1

ASSWNC

6

CDS_01662

Leader:

MTESVLDLQELETSEEETALMAAS

Core:

VSSWSC

Core with dehydrations:

VDhaDhaWDhaCys

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.94 out of 23.79

Confidence: medium

Additional weak hits (23):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.47 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.18 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 30.25

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.28 out of 31.73

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.13 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.92 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.41 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.45 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.42 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.67 out of 31.73

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.61 out of 39.62

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.65 out of 31.73

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.35 out of 18.57

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.06 out of 20.97

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.84 out of 21.55

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.72 out of 29.25

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.57 out of 20.97

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.24 out of 28.19

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 30.98

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.08 out of 28.19

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

Lanthipeptides

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Core peptide predictions

CDS_01661 - Class III

Cleavage pHMM score: 9.70

RODEO score: 0

Monoisotopic mass: 584.2 Da

Molecular weight: 584.7 Da

Number of bridges: 0

Additional modifications: AviCys

Alternative weights: (assuming N unmodified Ser/Thr residues); 602.7 Da N = 1

CDS_01662 - Class III

Cleavage pHMM score: 9.70

RODEO score: 0

Monoisotopic mass: 567.3 Da

Molecular weight: 567.7 Da

Number of bridges: 0

Additional modifications: AviCys

Alternative weights: (assuming N unmodified Ser/Thr residues); 585.7 Da N = 1; 603.7 Da N = 2

CDS_01663 - Class III

Cleavage pHMM score: 9.70

RODEO score: 0

Monoisotopic mass: 584.2 Da

Molecular weight: 584.7 Da

Number of bridges: 0

Additional modifications: AviCys

Alternative weights: (assuming N unmodified Ser/Thr residues); 602.7 Da N = 1

Predicted core structure(s)

For candidate cluster 7, location 442207 - 493148:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (pk)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 9, location 447433 - 493148:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (pk)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_01664: X

AMP-binding (16..372): X

nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: QYSDCGGNVK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

CDS_01667: AHBA

CAL_domain (56..499): AHBA

minowa: AHBA

Prediction, score:

AHBA: 14.6
NH2: 11.6
fatty_acid: 5.3
shikimic_acid: 0.4
Acetyl-CoA: -2.5

CDS_01669: pk

PKS_AT (662..956): pk

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 87.5%; Methoxymalonyl-CoA: 75.0%; Ethylmalonyl-CoA: 70.8%

minowa: Ethylmalonyl-CoA

Prediction, score:

Ethylmalonyl-CoA: 143.5
Methylmalonyl-CoA: 141.6
Methoxymalonyl-CoA: 116.1
Malonyl-CoA: 98.0
2-Methylbutyryl-CoA: 97.1
Propionyl-CoA: 79.6
trans-1,2-CPDA: 59.7
Isobutyryl-CoA: 58.4
fatty_acid: 57.9
Acetyl-CoA: 52.2
3-Methylbutyryl-CoA: 38.0
Benzoyl-CoA: 36.7
CHC-CoA: 32.3
inactive: 26.1

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism

NPDC089509.ctg-0003 - Region 6 - phenazine

Download region GenBank file

Download region SVG

Location: 586,558 - 607,049 nt. (total: 20,492 nt) Show pHMM detection rules used

phenazine: phzB

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: acetyltransferase methyltransferase

CDS_01789: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

CDS_01793: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: hydrolase

CDS_01783: isochorismatase

smcogs: SMCOG1027: isochorismatase

CDS_01787: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: lyase

CDS_01791: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Isomerases: isomerase

CDS_01784: isochorismate synthase

smcogs: SMCOG1018: isochorismate synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002439.3	0.50	other (other)	diastaphenazine, izumiphenazine C	Streptomyces diastaticus
BGC0001868.4	0.48	other (phenazine)	iodinin	Xenorhabdus szentirmaii DSM 16338
BGC0002561.3	0.48	other (other)	phenazine SA, phenazine SB, phenazine SC	Streptomyces sp.
BGC0000885.3	0.46	other (other)	4-hydroxy-3-nitrosobenzamide	Streptomyces murayamaensis
BGC0000936.5	0.46	other (other)	pyocyanine	Pseudomonas aeruginosa PAO1
BGC0000846.5	0.45	other (other)	tabtoxin	Pseudomonas syringae
BGC0001302.5	0.44	other (other)	lomofungin	Streptomyces lomondensis
BGC0001869.4	0.44	NRPS, other (phenazine)	griseoluteic acid, demethoxygriseoluteic acid, phenaszentine A, phenaszentine C, phenaszenketide C, phenaszenketide D	Xenorhabdus szentirmaii DSM 16338
BGC0000343.5	0.43	NRPS	enterobactin	Pseudomonas sp. J465
BGC0001374.5	0.43	other (other)	thienodolin	Streptomyces albogriseolus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002439.3	0.50	other (other)	diastaphenazine, izumiphenazine C	Streptomyces diastaticus
BGC0001868.4	0.48	other (phenazine)	iodinin	Xenorhabdus szentirmaii DSM 16338
BGC0002561.3	0.48	other (other)	phenazine SA, phenazine SB, phenazine SC	Streptomyces sp.
BGC0000885.3	0.46	other (other)	4-hydroxy-3-nitrosobenzamide	Streptomyces murayamaensis
BGC0000936.5	0.46	other (other)	pyocyanine	Pseudomonas aeruginosa PAO1
BGC0000846.5	0.45	other (other)	tabtoxin	Pseudomonas syringae
BGC0001302.5	0.44	other (other)	lomofungin	Streptomyces lomondensis
BGC0001869.4	0.44	NRPS, other (phenazine)	griseoluteic acid, demethoxygriseoluteic acid, phenaszentine A, phenaszentine C, phenaszenketide C, phenaszenketide D	Xenorhabdus szentirmaii DSM 16338
BGC0000343.5	0.43	NRPS	enterobactin	Pseudomonas sp. J465
BGC0001374.5	0.43	other (other)	thienodolin	Streptomyces albogriseolus

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (12):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.70 out of 29.38

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.48 out of 29.25

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.07 out of 25.88

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.63 out of 26.85

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.01 out of 21.55

Confidence: weak

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.45 out of 29.51

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.70 out of 28.19

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.77 out of 24.78

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 35.63

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.62 out of 29.65

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description

NPDC089509.ctg-0003 - Region 7 - lanthipeptide-class-ii

Download region GenBank file

Download region SVG

Location: 626,959 - 650,369 nt. (total: 23,411 nt) Show pHMM detection rules used

lanthipeptide-class-ii: cds(LANC_like and DUF4135)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Lanthipeptides

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_01832: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

CDS_01833: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: cyclase

CDS_01825: lanthionine synthetase C family protein

smcogs: SMCOG1070: lanthionine synthetase C family protein

Translocases: permease

CDS_01829: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000554.4	0.57	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998
BGC0002276.2	0.55	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0001210.5	0.53	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0000516.4	0.53	ribosomal	geobacillin II	Geobacillus thermodenitrificans
BGC0000527.5	0.52	ribosomal	mersacidin	Bacillus sp. HIL-Y85/54728
BGC0000517.4	0.52	ribosomal	haloduracin β, haloduracin α	Bacillus halodurans C-125
BGC0000500.5	0.50	ribosomal	carnolysin A1, carnolysin A2	Carnobacterium maltaromaticum
BGC0000525.5	0.50	ribosomal	lichenicidin VK21 A1, lichenicidin VK21 A2	Bacillus licheniformis
BGC0001407.5	0.48	ribosomal	bicereucin	Bacillus cereus SJ1
BGC0001928.2	0.48	other (other)	(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid	Streptomyces sp. MA37

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000554.4	0.57	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998
BGC0002276.2	0.55	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0001210.5	0.53	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0000516.4	0.53	ribosomal	geobacillin II	Geobacillus thermodenitrificans
BGC0000527.5	0.52	ribosomal	mersacidin	Bacillus sp. HIL-Y85/54728
BGC0000517.4	0.52	ribosomal	haloduracin β, haloduracin α	Bacillus halodurans C-125
BGC0000500.5	0.50	ribosomal	carnolysin A1, carnolysin A2	Carnobacterium maltaromaticum
BGC0000525.5	0.50	ribosomal	lichenicidin VK21 A1, lichenicidin VK21 A2	Bacillus licheniformis
BGC0001407.5	0.48	ribosomal	bicereucin	Bacillus cereus SJ1
BGC0001928.2	0.48	other (other)	(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid	Streptomyces sp. MA37

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for CDS_01825

CDS_01827

Leader:

MSDHEIVRAWKDPEADRSATGYPLGDPDLTAIFGG

Core:

EEMITWDGGCTTVWTVNVGCGSNSYAGLC

Core with dehydrations:

EEMIDhbWDGGCysDhbDhbVWDhbVNVGCysGDhaNDhaYAGLCys

antiSMASH-DB 4.0 matches for CDS_01827

31.0%

NZ_CP009933.1:

Lassopeptides: Csca_RS26925_lassopeptide

5

TWDGGCTTVWTVNVGCGSNSYAG

27

TW GG WT G S++G

2

TWQGGVDATWTDGSGNTWESHSG

24

31.0%

NZ_CP029710.1:

Lanthipeptides: allorf_5610752_5610895_lanthipeptide

1

EEMITWDGGCTTVW-TVNVGC

20

E TW GC W T + GC

8

EAWSTWSSGCHESWSTASTGC

28

27.6%

NZ_CP058259.1and 1 other:

NZ_MSQE01000005.1 Lanthipeptides: allorf_114261_114458_lanthipeptide

Lanthipeptides: allorf_2945427_2945657_lanthipeptide

2

EMITWDGGCTTVW-TVNVGC

20

+ TW GC W T + GC

1

RLSTWSSGCNVSWSTWSAGC

20

with 6 more sequence matches

27.6%

NZ_CP093340.1:

Lanthipeptides: MNO14_RS13850_lanthipeptide

9

GCTTVWTVNVGCGSN

23

GCT N GCGS+

9

GCTCSTASNTGCGSS

23

22.9%

NZ_CP075175.1:

Lanthipeptides: KIK04_RS00235_lanthipeptide

12

TVWTVNVGCGSNSYAGLC

29

+VW + GCG+ + AG C

3

SVWNCSGGCGNGNTAGTC

20

22.9%

NZ_CP075175.1:

Lanthipeptides: KIK04_RS00230_lanthipeptide

11

TTVWTVNVGCGSNSYAGLC

29

T+VW + GCG+ + A C

2

TSVWNCSRGCGNGNTANTC

20

20.7%

NZ_CP036524.1:

Lanthipeptides: LAJLEIBI_RS18025_lanthipeptide

5

TWDGGCTTVWTV

16

TW CTT +T+

1

TWSKACTTFFTI

12

20.7%

NZ_CP061033.1and 1 other:

NZ_CP061033.1 Lanthipeptides: allorf_2076770_2076883_lanthipeptide

Lanthipeptides: allorf_2076770_2076883_lanthipeptide

13

VWTVNVGCGSNSYA

26

+W + VGC ++S A

3

IWVLQVGCRTSSQA

16

17.8%

NZ_CAKXKJ010000002.1:

Lanthipeptides: allorf_129124_129330_lanthipeptide

2

EMITWDGGCTTVWTVNVGCG

21

E ++ DGGC+ T + CG

15

EALSCDGGCSGSDTCGITCG

34

MIBiG 4.0 matches for CDS_01827

24.1%

BGC0000580.3 (EGD17355.1):

Lasso peptide: xanthomonin II or xanthomonin I

1

EEMITWDGGCTTV

13

EEM GG TT+

7

EEM----GGITTL

15

20.7%

BGC0000581.6 (AAD28494.1):

Lasso peptide: microcin J25

8

GGCTTVWTVNVGCGS

22

GG V VG G+

1

GGAGHVPEYFVGIGT

15

allorf_632180_632317

Leader:

MQGPCSSPQVGRPARRREGRPAG

Core:

RGESACVRWVQCRRSGRAVWRR

Core with dehydrations:

RGEDhaACysVRWVQCysRRDhaGRAVWRR

antiSMASH-DB 4.0 matches for allorf_632180_632317

23.5%

NZ_KB913037.1:

Lanthipeptides: allorf_10324079_10324312_lanthipeptide

4

SACVRWVQCRRSGRAVWRR

22

S C + RRSG A+ R+

9

SGCRGAIGLRRSGHALLRQ

27

22.5%

NZ_CP035088.1and 1 other:

NZ_CP087200.1 Lanthipeptides: allorf_5646169_5646318_lanthipeptide

Lanthipeptides: allorf_5772610_5772759_lanthipeptide

8

RWVQCRRSGRAVWR

21

R+VQCRRS AV++

21

RFVQCRRSLGAVFQ

34

21.9%

NZ_CP013979.1:

Lanthipeptides: ATC03_RS20455_lanthipeptide

6

CVRWVQCRRSG

16

CVRWV+ RR+

19

CVRWVRARRAA

29

with 1 more sequence matches

18.8%

NZ_CP031746.1:

Lanthipeptides: allorf_1813979_1814164_lanthipeptide

5

ACVRWVQCRRSG

16

C RWV C G

6

GCARWVPCSLLG

17

allorf_634551_634694

Leader:

MCTGSLQPSSPTARPTGSSSAVRRDSVAGT

Core:

SASVGRRLSAAVCRVPA

Core with dehydrations:

DhaADhaVGRRLDhaAAVCysRVPA

antiSMASH-DB 4.0 matches for allorf_634551_634694

23.5%

NZ_CP095481.1:

Lanthipeptides: allorf_08453940_08454071_lanthipeptide

6

RRLSAAVCRVPA

17

RR A CRVPA

15

RRPGAHGCRVPA

26

allorf_636311_636523

Leader:

MADRERPVRGLPDSLGA

Core:

GEAEPRLVAVRARREASWAPAVGAAARLEDLTRPCLPGGEGAATRECRAGPGG

Core with dehydrations:

GEAEPRLVAVRARREADhaWAPAVGAAARLEDLDhbRPCysLPGGEGAADhbRECysRAGPGG

antiSMASH-DB 4.0 matches for allorf_636311_636523

22.6%

NZ_LT575476.1and 1 other:

NZ_LT575476.1 Lanthipeptides: BN6628_RS02295_lanthipeptide

Lanthipeptides: BN6628_RS02295_lanthipeptide

2

EAEPRLVAVRARREASWAPAVGAAARLEDLTRPCLPGGEGAATREC

47

E E L+A + W P + LT P A T+ C

3

ENELELLAGNEDVKGGWTPVATVVISVIGLTMNATPCPTSACTKSC

48

18.9%

NZ_JAGGRJ010000031.1:

Lanthipeptides: allorf_023920_024030_lanthipeptide

25

AARLEDLTR----PCLPGG

39

AA +EDL+R PC P G

1

AAAIEDLSRPVWNPCHPSG

19

18.9%

NZ_LJIW01000001.1:

Lanthipeptides: allorf_0961135_0961344_lanthipeptide

9

AVRARREASWAPAVGAAAR

27

+VR R++ W PAV AAR

27

SVRQSRQSRWCPAVEGAAR

45

MIBiG 4.0 matches for allorf_636311_636523

13.2%

BGC0002110.3 (QKV49893.1):

Lanthipeptide: birimositide

12

ARREASWAPAVGAAARLEDLTRPCLPG

38

S + A+G LT+ C P

2

TTNTFSLSNALGNNGGWCTLTKECQPN

28

allorf_636462_636545

Leader:

MARREWPGG

Core:

RSGAAGPGVTGLARCGRG

Core with dehydrations:

RDhaGAAGPGVDhbGLARCysGRG

antiSMASH-DB 4.0 matches for allorf_636462_636545

25.0%

NZ_CP072913.1:

Lanthipeptides: allorf_5794222_5794335_lanthipeptide

5

AGPGVTGLARCG

16

AGP +GL CG

7

AGPLASGLHYCG

18

MIBiG 4.0 matches for allorf_636462_636545

13.5%

BGC0001229.4 (SBI_06989):

Lanthipeptide: SBI-06990 A1 or SBI-06989 A2

7

PGVTGL

12

P VTGL

3

PAVTGL

8

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

Additional weak hits (4):

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.54 out of 26.12

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.91 out of 30.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.46 out of 27.78

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lanthipeptides

TFBS Finder

Core peptide predictions

CDS_01827 - Class II

Cleavage pHMM score: -1.90

RODEO score: 0

Monoisotopic mass: 2944.3 Da

Molecular weight: 2946.2 Da

Number of bridges: 3

Alternative weights: (assuming N unmodified Ser/Thr residues); 2964.3 Da N = 1; 2982.3 Da N = 2; 3000.3 Da N = 3

allorf_632180_632317 - Class II

Cleavage pHMM score: -6.90

RODEO score: 0

Monoisotopic mass: 2637.4 Da

Molecular weight: 2639.0 Da

Number of bridges: 2

allorf_634551_634694 - Class II

Cleavage pHMM score: -2.50

RODEO score: 0

Monoisotopic mass: 1646.9 Da

Molecular weight: 1647.9 Da

Number of bridges: 1

Additional modifications: Lac

Alternative weights: (assuming N unmodified Ser/Thr residues); 1665.9 Da N = 1; 1684.0 Da N = 2

allorf_636311_636523 - Class II

Cleavage pHMM score: -2.20

RODEO score: 0

Monoisotopic mass: 5326.7 Da

Molecular weight: 5329.9 Da

Number of bridges: 2

Alternative weights: (assuming N unmodified Ser/Thr residues); 5348.0 Da N = 1

allorf_636462_636545 - Class II

Cleavage pHMM score: -5.10

RODEO score: 0

Monoisotopic mass: 1605.8 Da

Molecular weight: 1606.8 Da

Number of bridges: 1

Alternative weights: (assuming N unmodified Ser/Thr residues); 1624.8 Da N = 1

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator

NPDC089509.ctg-0004 - Region 1 - terpene-precursor

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Location: 37,870 - 58,919 nt. (total: 21,050 nt) Show pHMM detection rules used

terpene-precursor: (PT_FPPS_like and not PT_HPP)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Lyases: dehydratase

CDS_01949: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthetase

CDS_01948: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000657.5	0.44	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0002151.2	0.43	ribosomal	alboverticillin	Streptomyces griseocarneus
BGC0002150.2	0.43	ribosomal	triculamin	Streptomyces triculaminicus
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0000551.5	0.42	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000623.3	0.42	ribosomal	plantaricin W α, plantaricin W β	Lactobacillus plantarum
BGC0000513.3	0.41	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000501.3	0.41	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0001555.4	0.41	ribosomal	colicin V	Escherichia coli chi7122
BGC0000519.4	0.41	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000657.5	0.44	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0002151.2	0.43	ribosomal	alboverticillin	Streptomyces griseocarneus
BGC0002150.2	0.43	ribosomal	triculamin	Streptomyces triculaminicus
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0000551.5	0.42	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000623.3	0.42	ribosomal	plantaricin W α, plantaricin W β	Lactobacillus plantarum
BGC0000513.3	0.41	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000501.3	0.41	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0001555.4	0.41	ribosomal	colicin V	Escherichia coli chi7122
BGC0000519.4	0.41	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Product name	Chain length	Initial cyclisations	Functional groups
sesquiterpene precursor	FPP	C15	acyclic	PP
diterpene precursor	GGPP	C20	acyclic	PP
sesterterpene precursor	GFPP	C25	acyclic	PP
triterpene precursor	HPP	C30	acyclic	PP

Genes with terpene domains:

CDS_01948: PT_FPPS_like

Domain 1 (60 - 348): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

Reactions:: IPP, DMAPP → FPP; IPP, DMAPP → GGPP; IPP, DMAPP → GFPP; IPP, DMAPP → HPP

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (9):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 26.33

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.98 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.18 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.70 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.35 out of 26.06

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.77 out of 32.74

Confidence: weak

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.48 out of 25.31

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.57 out of 26.85

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.06 out of 28.19

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
GFPP	Geranylfarnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
HPP	Hexaprenyl diphosphate
IPP	Isopentenyl diphosphate
PP	Diphosphate

TFBS definitions

Regulator	Description

NPDC089509.ctg-0004 - Region 2 - butyrolactone

Download region GenBank file

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Location: 130,246 - 141,310 nt. (total: 11,065 nt) Show pHMM detection rules used

butyrolactone: AfsA

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: transferase

CDS_02031: acetyl-CoA carboxylase, carboxyl transferase,

smcogs: SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000848.5	0.77	other (other)	A-factor	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4	0.68	other (butyrolactone)	SCB1, SCB2, SCB3	Streptomyces coelicolor A3(2)
BGC0000850.5	0.62	other (other)	γ-butyrolactone	Streptomyces acidiscabies
BGC0002578.2	0.43	other (other)	gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F	Streptomyces venezuelae ATCC 10712
BGC0000122.5	0.36	PKS	phenylnannolone A, phenylnannolone B, phenylnannolone C	Nannocystis pusilla
BGC0001458.4	0.31	other (aminocoumarin)	salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K	Salinispora tropica CNB-440
BGC0000914.5	0.31	other (other)	methylenomycin A	Streptomyces coelicolor A3(2)
BGC0002477.3	0.29	PKS	thioangucycline A, thioangucycline B	Streptomyces sp. CB00072
BGC0001771.4	0.28	NRPS	scleric acid	Streptomyces sclerotialus
BGC0000248.5	0.27	PKS	α naphtocyclinoic acid, fogacin	Streptomyces arenae DSM 40737

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000848.5	0.77	other (other)	A-factor	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4	0.68	other (butyrolactone)	SCB1, SCB2, SCB3	Streptomyces coelicolor A3(2)
BGC0000850.5	0.62	other (other)	γ-butyrolactone	Streptomyces acidiscabies
BGC0002578.2	0.43	other (other)	gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F	Streptomyces venezuelae ATCC 10712
BGC0000122.5	0.36	PKS	phenylnannolone A, phenylnannolone B, phenylnannolone C	Nannocystis pusilla
BGC0001458.4	0.31	other (aminocoumarin)	salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K	Salinispora tropica CNB-440
BGC0000914.5	0.31	other (other)	methylenomycin A	Streptomyces coelicolor A3(2)
BGC0002477.3	0.29	PKS	thioangucycline A, thioangucycline B	Streptomyces sp. CB00072
BGC0001771.4	0.28	NRPS	scleric acid	Streptomyces sclerotialus
BGC0000248.5	0.27	PKS	α naphtocyclinoic acid, fogacin	Streptomyces arenae DSM 40737

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.60 out of 19.26

Confidence: medium

Additional weak hits (3):

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.71 out of 25.31

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.35 out of 27.78

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 30.98

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein

NPDC089509.ctg-0005 - Region 1 - lanthipeptide-class-iv

Download region GenBank file

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Location: 337,935 - 360,784 nt. (total: 22,850 nt) Show pHMM detection rules used

lanthipeptide-class-iv: (cds(LANC_like and Pkinase) and not micKC)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Lanthipeptides

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_02728: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

Isomerases: mutase

CDS_02737: phosphoglycerate mutase

smcogs: SMCOG1101: phosphoglycerate mutase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000551.5	0.60	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000513.3	0.57	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000519.4	0.56	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000501.3	0.56	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0000496.5	0.56	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000563.4	0.53	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0001226.4	0.53	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0002698.2	0.51	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0002111.3	0.46	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000554.4	0.46	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000551.5	0.60	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000513.3	0.57	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000519.4	0.56	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000501.3	0.56	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0000496.5	0.56	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000563.4	0.53	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0001226.4	0.53	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0002698.2	0.51	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0002111.3	0.46	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000554.4	0.46	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptides - No core peptides found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.72 out of 20.47

Confidence: medium

Additional weak hits (4):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.40 out of 29.38

Confidence: weak

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.70 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.75 out of 27.78

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lanthipeptides

TFBS Finder

Core peptide predictions

No core peptides found.

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0005 - Region 2 - NRPS,NRPS-like,T1PKS

Download region GenBank file

Download region SVG

Location: 390,209 - 455,862 nt. (total: 65,654 nt) Show pHMM detection rules used

T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_02769: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02778: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_02798: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_02809: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02812: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

Transferases: acylase aminotransferase

CDS_02783: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_02796: aminotransferase class V

smcogs: SMCOG1139: aminotransferase class V

Hydrolases: esterase glucosidase

CDS_02768: Alpha-glucosidase

smcogs: SMCOG1257: Alpha-glucosidase

CDS_02770: putative esterase

smcogs: SMCOG1104: putative esterase

CDS_02782: thioesterase

smcogs: SMCOG1004: thioesterase

Lyases: dehydratase lyase

CDS_02780: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

CDS_02787: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

CDS_02791: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

CDS_02813: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Isomerases: racemase

CDS_02792: mandelate racemase/muconate lactonizing enzyme

smcogs: SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase

CDS_02784: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_02797: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002164.2	0.97	NRPS	peramine	Epichloe festucae
BGC0001132.4	0.97	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001261.3	0.97	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.96	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001128.4	0.96	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.96	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	0.92	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.91	NRPS	AbT1	Aureobasidium pullulans
BGC0001240.4	0.90	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001758.4	0.89	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001132.4	0.67	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.67	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.67	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.66	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.66	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002164.2	0.66	NRPS	peramine	Epichloe festucae
BGC0001276.3	0.66	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.66	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.66	PKS	6-methylsalicyclic acid	Glarea lozoyensis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.76 out of 26.85

Confidence: medium

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.03 out of 29.72

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.98 out of 26.85

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.67 out of 28.19

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.59 out of 27.04

Confidence: strong

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52

Confidence: medium

Additional weak hits (23):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.91 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.46 out of 27.78

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.57 out of 29.38

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.37 out of 30.25

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.69 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.58 out of 33.14

Confidence: weak

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.69 out of 30.97

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.39 out of 26.85

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.99 out of 30.97

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.27 out of 21.55

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.03 out of 26.85

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.00 out of 21.55

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.42 out of 29.65

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.43 out of 24.78

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.07 out of 21.84

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.57 out of 33.14

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.20 out of 30.98

Confidence: weak

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31

Confidence: weak

Module view

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Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 2, location 390208 - 455862:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Val) + (His) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 390208 - 435871:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Val) + (His) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 412766 - 455862:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Val) + (His) + (mal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_02783: mal

PKS_AT (545..828): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 70.8%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 138.9
Methoxymalonyl-CoA: 72.8
inactive: 60.9
Methylmalonyl-CoA: 53.8
Propionyl-CoA: 39.6
2-Methylbutyryl-CoA: 30.1
Ethylmalonyl-CoA: 29.7
CHC-CoA: 25.8
trans-1,2-CPDA: 16.4
Acetyl-CoA: 16.4
Isobutyryl-CoA: 14.8
fatty_acid: 12.6
Benzoyl-CoA: 9.7
3-Methylbutyryl-CoA: 0.0

CDS_02784: His

Search NORINE for peptide: strict or relaxed

AMP-binding (255..653): His

nrpys: His

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DSALIAEVWK
Nearest Stachelhaus code(s):: His DSALIAEVWK (85% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_02797: Val

Search NORINE for peptide: strict or relaxed

AMP-binding (15..397): Val

nrpys: Val

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DALWMGGVFK
Nearest Stachelhaus code(s):: Val DALWMGGVFK (53% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
DasR	N-acetylglucosamine dependent repressor
NtrC	Nitrogen regulatory protein C
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems
ZuR variant 1	Zinc-responsive repressor

NPDC089509.ctg-0006 - Region 1 - NAPAA

Download region GenBank file

Download region SVG

Location: 1 - 28,516 nt. (total: 28,516 nt) Show pHMM detection rules used

Region on contig edge.

NAPAA: (AMP-binding and TIGR02353)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: acyltransferase

CDS_02878: acyltransferase

smcogs: SMCOG1141: acyltransferase

Hydrolases: hydrolase

CDS_02876: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

CDS_02882: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase

CDS_02874: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002174.2	0.77	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0001135.5	0.61	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.61	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.60	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0000307.4	0.60	NRPS	AbT1	Aureobasidium pullulans
BGC0001261.3	0.60	NRPS	AM-toxin	Alternaria alternata
BGC0000342.4	0.60	NRPS	enniatin	Fusarium equiseti
BGC0001166.5	0.60	NRPS	HC-toxin	Alternaria jesenskae
BGC0001128.4	0.60	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001251.4	0.60	NRPS	epichloenin A	Epichloe festucae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002174.2	0.77	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0001135.5	0.61	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.61	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.60	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0000307.4	0.60	NRPS	AbT1	Aureobasidium pullulans
BGC0001261.3	0.60	NRPS	AM-toxin	Alternaria alternata
BGC0000342.4	0.60	NRPS	enniatin	Fusarium equiseti
BGC0001166.5	0.60	NRPS	HC-toxin	Alternaria jesenskae
BGC0001128.4	0.60	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001251.4	0.60	NRPS	epichloenin A	Epichloe festucae

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 25.32 out of 29.72

Confidence: medium

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52

Confidence: medium

Additional weak hits (12):

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.79 out of 28.14

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.22 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.36 out of 27.78

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.66 out of 30.25

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.21 out of 30.97

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.96 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.51 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.18 out of 27.78

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.53 out of 21.55

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.34 out of 28.19

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.39 out of 23.43

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 28516:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_02874: X

AMP-binding (42..422): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DAESIGTVVK
Nearest Stachelhaus code(s):: Lys DAEDIGTVVK (71% 8Å match); Gln or Tyr DAESVGTVVK (65% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
NtrC	Nitrogen regulatory protein C

NPDC089509.ctg-0006 - Region 2 - NRPS-like,T1PKS

Download region GenBank file

Download region SVG

Location: 137,170 - 184,752 nt. (total: 47,583 nt) Show pHMM detection rules used

T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_03008: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_03010: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CDS_03018: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_03027: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_03028: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: PPTase acyltransferase aminotransferase

CDS_02999: acyltransferase 3

smcogs: SMCOG1088: acyltransferase 3

CDS_03003: aminotransferase

smcogs: SMCOG1019: aminotransferase

CDS_03005: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: esterase phosphatase

CDS_03006: thioesterase

smcogs: SMCOG1004: thioesterase

CDS_03007: FkbH like protein

smcogs: SMCOG1256: FkbH like protein

Ligases: ligase synthase

CDS_03011: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_03012: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_03017: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001132.4	0.61	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001273.3	0.60	PKS	asperlactone	Aspergillus ochraceus
BGC0002286.3	0.60	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001276.3	0.60	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001128.4	0.60	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001275.3	0.60	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002154.2	0.60	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001257.3	0.59	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0001258.3	0.59	PKS	1,3,6,8-tetrahydroxynaphthalene	Glarea lozoyensis
BGC0002191.2	0.59	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001132.4	0.64	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0002286.3	0.64	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001276.3	0.63	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001128.4	0.63	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001275.3	0.63	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002154.2	0.63	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001257.3	0.63	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0001258.3	0.63	PKS	1,3,6,8-tetrahydroxynaphthalene	Glarea lozoyensis
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.93 out of 26.33

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47

Confidence: medium

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 24.72 out of 29.72

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.15 out of 27.04

Confidence: strong

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.73 out of 26.85

Confidence: medium

Additional weak hits (7):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.70 out of 26.33

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.02 out of 21.55

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.26 out of 27.18

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.91 out of 29.65

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.06 out of 20.01

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 2, location 137169 - 184752:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X) + (ccmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_03011: mal

PKS_AT (532..836): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 79.2%; inactive: 62.5%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 154.1
inactive: 93.4
Methoxymalonyl-CoA: 68.3
Methylmalonyl-CoA: 47.3
Propionyl-CoA: 37.3
Isobutyryl-CoA: 33.3
Acetyl-CoA: 21.2
CHC-CoA: 20.0
3-Methylbutyryl-CoA: 17.3
Ethylmalonyl-CoA: 15.3
fatty_acid: 14.4
2-Methylbutyryl-CoA: 13.9
Benzoyl-CoA: 12.7
trans-1,2-CPDA: 9.1

CDS_03012: X

AMP-binding (14..418): X

nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: AHTTRAASLK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

CDS_03017: X

AMP-binding (12..396): X

nrpys: Phe, Trp

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
Small clusters prediction:: Unpolar aromatic ring (Phe, Trp)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: NTLVVAYPCK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
DasR	N-acetylglucosamine dependent repressor
NtrC	Nitrogen regulatory protein C
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0006 - Region 3 - lanthipeptide-class-iii

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Location: 261,877 - 284,540 nt. (total: 22,664 nt) Show pHMM detection rules used

lanthipeptide-class-iii: (micKC and not PKS_KS)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

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Gene overview

Tailoring

MIBiG comparison

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Lanthipeptides

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Hydrolases: protease

CDS_03124: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002700.2	0.48	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0000553.3	0.48	ribosomal	SRO15-2212	Streptomyces filamentosus NRRL 15998
BGC0000496.5	0.47	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5	0.47	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000513.3	0.46	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000519.4	0.46	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000501.3	0.45	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0002111.3	0.45	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000518.3	0.43	ribosomal	informatipeptin	Streptomyces viridochromogenes DSM 40736
BGC0002128.3	0.43	other (other)	5-dimethylallylindole-3-acetonitrile	Streptomyces coelicolor A3(2)

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002700.2	0.48	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0000553.3	0.48	ribosomal	SRO15-2212	Streptomyces filamentosus NRRL 15998
BGC0000496.5	0.47	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5	0.47	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000513.3	0.46	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000519.4	0.46	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000501.3	0.45	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0002111.3	0.45	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000518.3	0.43	ribosomal	informatipeptin	Streptomyces viridochromogenes DSM 40736
BGC0002128.3	0.43	other (other)	5-dimethylallylindole-3-acetonitrile	Streptomyces coelicolor A3(2)

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for CDS_03120

CDS_03122

Leader:

MAENIENMEQNIEEPSGEESAEVEAHAANVLDLQALKVLQAASDGN

Core:

CFSIVSYVNSAETSAS

Core with dehydrations:

CysFDhaIVDhaYVNDhaAEDhbDhaADha

antiSMASH-DB 4.0 matches for CDS_03122

37.5%

NC_018499.1and 5 others:

NC_018499.1 Lanthipeptides: BCK_RS29530_lanthipeptideNC_018499.1 Lanthipeptides: BCK_RS29525_lanthipeptideNC_018499.1 Lanthipeptides: BCK_RS29530_lanthipeptideNC_018499.1 Lanthipeptides: BCK_RS29525_lanthipeptideNZ_JAOPQW010000026.1 Lanthipeptides: OCD10_RS25130_lanthipeptide

Lanthipeptides: allorf_14712_14813_lanthipeptide

1

CFSIVSYVNSAET

13

CFS+ + ++SA+T

1

CFSLSTNISSADT

13

15.8%

NC_018499.1and 10 others:

NC_018499.1 Lanthipeptides: BCK_RS29520_lanthipeptideNZ_CP036019.1 Lanthipeptides: EXW52_RS27155_lanthipeptideNZ_CP036019.1 Lanthipeptides: EXW52_RS27150_lanthipeptideNZ_CP036019.1 Lanthipeptides: EXW52_RS27145_lanthipeptideNZ_CP036019.1 Lanthipeptides: EXW52_RS27155_lanthipeptideNZ_CP036019.1 Lanthipeptides: EXW52_RS27150_lanthipeptideNZ_CP036019.1 Lanthipeptides: EXW52_RS27145_lanthipeptideNZ_JAOPQW010000026.1 Lanthipeptides: OCD10_RS25140_lanthipeptideNZ_MLKL01000042.1 Lanthipeptides: BKK45_RS28640_lanthipeptideNZ_MLKL01000042.1 Lanthipeptides: BKK45_RS28635_lanthipeptide

Lanthipeptides: BCK_RS29520_lanthipeptide

1

CFSIVSYVNSAETS

14

CFS+ + ++SA+T

1

CFSLSTNISSADTP

14

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.70 out of 29.51

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47

Confidence: medium

Additional weak hits (3):

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.49 out of 19.26

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.18 out of 25.75

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 14.73 out of 20.97

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lanthipeptides

TFBS Finder

Core peptide predictions

CDS_03122 - Class III

Cleavage pHMM score: 3.50

RODEO score: 0

Monoisotopic mass: 1555.7 Da

Molecular weight: 1556.7 Da

Number of bridges: 1

Alternative weights: (assuming N unmodified Ser/Thr residues); 1574.7 Da N = 1; 1592.7 Da N = 2; 1610.7 Da N = 3; 1628.7 Da N = 4; 1646.8 Da N = 5

TFBS definitions

Regulator	Description
DosR	Hypoxia stress response regulator
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0006 - Region 4 - NRPS-like,T1PKS

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Location: 387,229 - 435,045 nt. (total: 47,817 nt) Show pHMM detection rules used

T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase phosphate reductase

CDS_03223: N-acetyl-gamma-glutamyl-phosphate reductase

smcogs: SMCOG1219: N-acetyl-gamma-glutamyl-phosphate reductase

CDS_03236: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

CDS_03239: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_03245: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_03257: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

Transferases: aminotransferase formyltransferase

CDS_03224: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs: SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

CDS_03246: methionyl-tRNA formyltransferase

smcogs: SMCOG1228: methionyl-tRNA formyltransferase

Lyases: dehydratase lyase

CDS_03228: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

CDS_03250: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase

CDS_03242: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_03243: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_03244: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.79	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.75	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.73	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.71	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.71	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0000342.4	0.70	NRPS	enniatin	Fusarium equiseti
BGC0001825.4	0.69	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.69	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.68	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.72	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.70	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.69	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.68	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.68	NRPS	HC-toxin	Alternaria jesenskae
BGC0000342.4	0.68	NRPS	enniatin	Fusarium equiseti
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.68	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.67	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.21 out of 23.79

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.79 out of 25.31

Confidence: medium

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52

Confidence: medium

Additional weak hits (18):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.49 out of 26.85

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.88 out of 27.78

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.92 out of 26.33

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.71 out of 33.73

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.88 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.09 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.19 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.80 out of 28.14

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.03 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.46 out of 27.78

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.65 out of 33.14

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.35 out of 24.78

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.23 out of 29.65

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.52 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.48 out of 26.06

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.76 out of 28.19

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 4, location 387228 - 435045:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_03242: pk - mmal

PKS_AT (601..889): pk

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 66.7%; Methylmalonyl-CoA: 54.2%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 94.2
Methoxymalonyl-CoA: 78.6
Malonyl-CoA: 72.3
Ethylmalonyl-CoA: 69.1
Propionyl-CoA: 64.4
trans-1,2-CPDA: 49.7
Isobutyryl-CoA: 45.5
Benzoyl-CoA: 45.4
2-Methylbutyryl-CoA: 42.8
inactive: 42.5
CHC-CoA: 40.1
Acetyl-CoA: 36.4
3-Methylbutyryl-CoA: 20.7
fatty_acid: 20.0

PKS_AT (1028..1323): mmal

ATSignature: CE-Malonyl-CoA

Top 3 matches:: CE-Malonyl-CoA: 75.0%; Ethylmalonyl-CoA: 62.5%; Methylmalonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 99.6
Ethylmalonyl-CoA: 88.4
Methoxymalonyl-CoA: 85.9
Malonyl-CoA: 68.2
Propionyl-CoA: 52.9
2-Methylbutyryl-CoA: 52.0
Acetyl-CoA: 43.0
trans-1,2-CPDA: 41.1
CHC-CoA: 37.5
Isobutyryl-CoA: 33.0
Benzoyl-CoA: 28.9
fatty_acid: 21.2
3-Methylbutyryl-CoA: 17.7
inactive: 14.4

CDS_03243: X

AMP-binding (11..393): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DMMNVGAVFK
Nearest Stachelhaus code(s):: Hch DLMNVGGVFK (76% 8Å match)
Stachelhaus code match:: 80% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
CatR	H2O2-responsive repressor
IolR	Regulator of the inositol catabolism

NPDC089509.ctg-0007 - Region 1 - NI-siderophore

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Location: 101,729 - 134,433 nt. (total: 32,705 nt) Show pHMM detection rules used

NI-siderophore: IucA_IucC

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: aminotransferase

CDS_03420: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Hydrolases: dehalogenase phosphatase

CDS_03405: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

CDS_03418: inositol monophosphatase

smcogs: SMCOG1207: inositol monophosphatase

Lyases: decarboxylase

CDS_03417: diaminopimelate decarboxylase

smcogs: SMCOG1264: diaminopimelate decarboxylase

CDS_03419: Decarboxylase, pyridoxal-dependent

smcogs: SMCOG1180: Decarboxylase, pyridoxal-dependent

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000946.5	0.77	other (other)	vibrioferrin	Vibrio parahaemolyticus
BGC0002527.2	0.70	other (other)	vibrioferrin	Azotobacter vinelandii CA
BGC0001408.5	0.70	other (other)	xanthoferrin	Xanthomonas oryzae pv. oryzae KACC 10331
BGC0002633.2	0.58	other (other)	schizokinen	Leptolyngbya sp. PCC 7376
BGC0000947.5	0.57	other (other)	vibrioferrin	Vibrio alginolyticus
BGC0000939.5	0.55	other (other)	aerobactin	Grimontia hollisae
BGC0002682.2	0.55	other (other)	aerobactin	Vibrio mimicus
BGC0002683.2	0.54	NRPS	schizokinen	Nostoc sp. PCC 7120 = FACHB-418
BGC0001478.5	0.54	other (other)	desferrioxamine E	Streptomyces sp. ID38640
BGC0001572.3	0.53	other (other)	desferrioxamine E	Pantoea agglomerans

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000946.5	0.77	other (other)	vibrioferrin	Vibrio parahaemolyticus
BGC0002527.2	0.70	other (other)	vibrioferrin	Azotobacter vinelandii CA
BGC0001408.5	0.70	other (other)	xanthoferrin	Xanthomonas oryzae pv. oryzae KACC 10331
BGC0002633.2	0.58	other (other)	schizokinen	Leptolyngbya sp. PCC 7376
BGC0000947.5	0.57	other (other)	vibrioferrin	Vibrio alginolyticus
BGC0000939.5	0.55	other (other)	aerobactin	Grimontia hollisae
BGC0002682.2	0.55	other (other)	aerobactin	Vibrio mimicus
BGC0002683.2	0.54	NRPS	schizokinen	Nostoc sp. PCC 7120 = FACHB-418
BGC0001478.5	0.54	other (other)	desferrioxamine E	Streptomyces sp. ID38640
BGC0001572.3	0.53	other (other)	desferrioxamine E	Pantoea agglomerans

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26

Confidence: strong

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.20 out of 36.53

Confidence: medium

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.90 out of 36.53

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.67 out of 25.31

Confidence: medium

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.03 out of 36.53

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.67 out of 28.19

Confidence: medium

Additional weak hits (7):

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.24 out of 32.38

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.24 out of 36.53

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.94 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.22 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.29 out of 28.14

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.45 out of 29.65

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
CatR	H2O2-responsive repressor
DmdR1	Iron(II)-dependent repressor
ZuR variant 1	Zinc-responsive repressor

NPDC089509.ctg-0007 - Region 2 - NRP-metallophore,NRPS

Download region GenBank file

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Location: 248,386 - 302,659 nt. (total: 54,274 nt) Show pHMM detection rules used

NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_03549: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_03557: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

CDS_03558: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_03559: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CDS_03561: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acyltransferase

CDS_03542: polyketide synthase associated protein papA3

smcogs: SMCOG1209: polyketide synthase associated protein papA3

Hydrolases: esterase hydrolase

CDS_03535: enterobactin/ferric enterobactin esterase

smcogs: SMCOG1098: enterobactin/ferric enterobactin esterase

CDS_03536: metallo-beta-lactamase family protein

smcogs: SMCOG1170: metallo-beta-lactamase family protein

CDS_03543: amidohydrolase

smcogs: SMCOG1244: amidohydrolase

CDS_03546: isochorismatase

smcogs: SMCOG1027: isochorismatase

Isomerases: isomerase

CDS_03548: isochorismate synthase

smcogs: SMCOG1018: isochorismate synthase

Ligases: ligase

CDS_03544: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_03547: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001185.5	0.92	NRPS	bacillibactin	Bacillus velezensis FZB42
BGC0002075.3	0.85	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0000401.5	0.81	NRPS	paenibactin	Paenibacillus elgii B69
BGC0000343.5	0.78	NRPS	enterobactin	Pseudomonas sp. J465
BGC0001132.4	0.77	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.74	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.74	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001758.4	0.73	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.72	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001185.5	0.76	NRPS	bacillibactin	Bacillus velezensis FZB42
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0000401.5	0.72	NRPS	paenibactin	Paenibacillus elgii B69
BGC0000343.5	0.71	NRPS	enterobactin	Pseudomonas sp. J465
BGC0001132.4	0.71	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.70	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.70	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.70	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001758.4	0.69	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.69	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 32.19 out of 36.53

Confidence: strong

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 33.36 out of 36.53

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47

Confidence: strong

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.90 out of 36.53

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.46 out of 26.85

Confidence: medium

Additional weak hits (16):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.39 out of 30.22

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.75 out of 30.22

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.91 out of 26.85

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.30 out of 21.55

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.51 out of 30.22

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 26.33

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 26.33

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.03 out of 27.04

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.55 out of 29.65

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.54 out of 33.14

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.94 out of 29.65

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.34 out of 28.19

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.82 out of 24.78

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 17.91 out of 35.63

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 2, location 248385 - 302659:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X - Thr)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_03542: X - Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (483..881): X

nrpys: Lys, Arg

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DADDAGLVDK
Nearest Stachelhaus code(s):: Arg DADDVGLVDK (82% 8Å match); Lys DADDAGTVDK (68% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1557..1974): Thr

nrpys: Thr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: thr (Thr)
Single AA prediction:: thr (Thr)

Stachelhaus prediction details:

Stachelhaus sequence:: DFWNVGMVHK
Nearest Stachelhaus code(s):: Thr DFWNVGMVHK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_03544: X

AMP-binding (53..248): X

nrpys: Asp, Asn, Glu, Gln, Aad

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: PELNDGGRPK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

CDS_03547: diOH-Bz

Search NORINE for peptide: strict or relaxed

AMP-binding (55..469): diOH-Bz

nrpys: diOH-Bz

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
Small clusters prediction:: Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
Single AA prediction:: dhb (diOH-Bz)

Stachelhaus prediction details:

Stachelhaus sequence:: PLPGLGVVNK
Nearest Stachelhaus code(s):: diOH-Bz PLPGLGVVNK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
DmdR1	Iron(II)-dependent repressor
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0007 - Region 3 - NRPS-like

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Location: 327,146 - 370,433 nt. (total: 43,288 nt) Show pHMM detection rules used

NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: acetyltransferase

CDS_03598: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Ligases: ligase synthase

CDS_03609: 2-isopropylmalate synthase

smcogs: SMCOG1271: 2-isopropylmalate synthase

CDS_03622: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001168.5	0.67	NRPS	Livipeptin	Streptomyces lividans 1326
BGC0001135.5	0.61	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002164.2	0.61	NRPS	peramine	Epichloe festucae
BGC0002135.2	0.61	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.60	NRPS	AbT1	Aureobasidium pullulans
BGC0002276.2	0.60	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000357.5	0.60	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0001833.4	0.60	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002174.2	0.60	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0000342.4	0.60	NRPS	enniatin	Fusarium equiseti

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001168.5	0.67	NRPS	Livipeptin	Streptomyces lividans 1326
BGC0001135.5	0.61	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002164.2	0.61	NRPS	peramine	Epichloe festucae
BGC0002135.2	0.61	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.60	NRPS	AbT1	Aureobasidium pullulans
BGC0002276.2	0.60	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000357.5	0.60	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0001833.4	0.60	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002174.2	0.60	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0000342.4	0.60	NRPS	enniatin	Fusarium equiseti

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.64 out of 27.55

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.21 out of 23.79

Confidence: medium

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.89 out of 29.72

Confidence: medium

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84

Confidence: medium

Additional weak hits (13):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.58 out of 30.25

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.89 out of 21.55

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.88 out of 25.75

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.77 out of 27.55

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.22 out of 29.38

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.62 out of 27.78

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.95 out of 35.63

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.96 out of 28.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.93 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.44 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.57 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.59 out of 29.65

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 3, location 327145 - 370433:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Arg)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_03622: Arg

Search NORINE for peptide: strict or relaxed

AMP-binding (103..498): Arg

nrpys: Arg

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DTEDVGAVTK
Nearest Stachelhaus code(s):: Arg DTEDVGAVDK (47% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
GnfM	Regulator of nitrogen-fixation genes
IolR	Regulator of the inositol catabolism
MexT	Global virulence regulator
NtrC	Nitrogen regulatory protein C

NPDC089509.ctg-0007 - Region 4 - NRPS

Download region GenBank file

Download region SVG

Location: 448,631 - 479,357 nt. (total: 30,727 nt) Show pHMM detection rules used

Region on contig edge.

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: aminotransferase

CDS_03714: aminotransferase

smcogs: SMCOG1019: aminotransferase

Hydrolases: dehalogenase

CDS_03709: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Ligases: ligase

CDS_03706: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_03719: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001132.4	0.71	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0000426.5	0.71	NRPS	sevadicin	Paenibacillus larvae
BGC0001128.4	0.70	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.69	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.69	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001133.4	0.68	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001641.4	0.67	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001132.4	0.71	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0000426.5	0.71	NRPS	sevadicin	Paenibacillus larvae
BGC0001128.4	0.70	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.69	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.69	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001133.4	0.68	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001641.4	0.67	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (4):

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.32 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.36 out of 29.38

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.49 out of 27.78

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.91 out of 28.19

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 4, location 448630 - 479357:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X - D-Hpg) + (Gly)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_03706: X

AMP-binding (67..460): X

nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: -VREFTSVVK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

CDS_03719: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (464..869): Gly

nrpys: Gly

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
Single AA prediction:: gly (Gly)

Stachelhaus prediction details:

Stachelhaus sequence:: DILQLGLVWK
Nearest Stachelhaus code(s):: Gly DILQLGLVWK (85% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_03720: X - Hpg

Search NORINE for peptide: strict or relaxed

AMP-binding (126..522): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
Small clusters prediction:: Polar aromatic ring (Tyr, bOH-Tyr)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DAGMIGAVCK
Nearest Stachelhaus code(s):: Leu DAWCIGAVCK (68% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1184..1579): Hpg

nrpys: Hpg

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
Single AA prediction:: hpg (Hpg)

Stachelhaus prediction details:

Stachelhaus sequence:: DIYHLGLLCK
Nearest Stachelhaus code(s):: Hpg DIYHLGLLCK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description

NPDC089509.ctg-0008 - Region 1 - RiPP-like

Download region GenBank file

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Location: 146,010 - 156,897 nt. (total: 10,888 nt) Show pHMM detection rules used

RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

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Gene overview

Tailoring

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TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_03827: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002788.2	0.24	PKS	14-hydroxyisochainin	Streptomyces peucetius subsp. caesius ATCC 27952
BGC0000241.5	0.19	PKS, saccharide	lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E	Salinispora tropica CNB-440
BGC0001693.3	0.19	PKS	nenestatin	Micromonospora echinospora

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002788.2	0.24	PKS	14-hydroxyisochainin	Streptomyces peucetius subsp. caesius ATCC 27952
BGC0000241.5	0.19	PKS, saccharide	lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E	Salinispora tropica CNB-440
BGC0001693.3	0.19	PKS	nenestatin	Micromonospora echinospora

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (6):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.20 out of 27.78

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.58 out of 32.93

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.28 out of 28.14

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.63 out of 18.57

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.97 out of 27.04

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.75 out of 35.63

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description

NPDC089509.ctg-0009 - Region 1 - NRPS,NRPS-like,transAT-PKS

Download region GenBank file

Download region SVG

Location: 200,936 - 305,203 nt. (total: 104,268 nt) Show pHMM detection rules used

transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

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TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: acylase formyltransferase halogenase

CDS_04213: methionyl-tRNA formyltransferase

smcogs: SMCOG1228: methionyl-tRNA formyltransferase

CDS_04217: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_04221: flavin-dependent tyrosine-like hpg halogenase

halogenases: flavin-dependent tyrosine-like hpg halogenase
MITE: MITE0000028Halogenation (identity: 70.80%)
smcogs: SMCOG1119: halogenase

Hydrolases: glucanase

CDS_04207: Pullulanase, type I

smcogs: SMCOG1297: Pullulanase, type I

Ligases: ligase synthase

CDS_04212: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_04215: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_04218: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_04219: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	1.23	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001261.3	1.16	NRPS	AM-toxin	Alternaria alternata
BGC0000342.4	1.13	NRPS	enniatin	Fusarium equiseti
BGC0001135.5	1.10	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	1.09	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002135.2	1.08	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001128.4	1.05	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	1.05	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.99	NRPS	AbT1	Aureobasidium pullulans
BGC0001833.4	0.99	NRPS	icosalide A, icosalide B	Burkholderia gladioli

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002341.2	0.77	other (other)	3,5-dibromo-p-anisic acid	Planctomycetales bacterium 10988
BGC0002608.2	0.76	NRPS, PKS	ochratoxin A	Aspergillus steynii
BGC0000342.4	0.74	NRPS	enniatin	Fusarium equiseti
BGC0001261.3	0.74	NRPS	AM-toxin	Alternaria alternata
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002135.2	0.72	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.72	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.72	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.70	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.70	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.75 out of 23.79

Confidence: strong

Additional weak hits (29):

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.63 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.34 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.38 out of 32.74

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 26.85

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.41 out of 29.25

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.91 out of 32.74

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 14.88 out of 20.97

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.42 out of 26.12

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.23 out of 19.26

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.20 out of 26.12

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.23 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.81 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.27 out of 30.25

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.08 out of 21.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.79 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.57 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.63 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.12 out of 27.78

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.21 out of 30.97

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.50 out of 25.88

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.81 out of 36.54

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.27 out of 19.26

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.14 out of 26.12

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.06 out of 21.55

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.04 out of 21.55

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.98 out of 29.25

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.40 out of 33.14

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.76 out of 35.63

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.79 out of 26.85

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 200935 - 305203:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (ccmal - Me-ccmal) + (Gly) + (Me-ohmal - Gly - ccmal - mal) + (ohmal - mal - Thr) + (Thr - NMe-X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_04213: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (589..976): Gly

nrpys: Gly

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
Single AA prediction:: gly (Gly)

Stachelhaus prediction details:

Stachelhaus sequence:: DILQLGMIWK
Nearest Stachelhaus code(s):: Gly DILQLGMIWK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_04216: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (2224..2611): Gly

nrpys: Gly

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
Single AA prediction:: gly (Gly)

Stachelhaus prediction details:

Stachelhaus sequence:: DILQLGLIWK
Nearest Stachelhaus code(s):: Gly DILQLGLIWK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_04217: mal - mal

PKS_AT (14..297): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 31.7
Methylmalonyl-CoA: 27.9
Methoxymalonyl-CoA: 24.9
Benzoyl-CoA: 18.4
Isobutyryl-CoA: 17.2
inactive: 17.1
Propionyl-CoA: 15.9
fatty_acid: 11.4
2-Methylbutyryl-CoA: 6.3
trans-1,2-CPDA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (358..638): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 75.0%; inactive: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 108.1
Methylmalonyl-CoA: 44.0
Methoxymalonyl-CoA: 41.1
inactive: 38.5
Isobutyryl-CoA: 30.1
Propionyl-CoA: 27.0
2-Methylbutyryl-CoA: 22.8
fatty_acid: 20.0
CHC-CoA: 19.3
trans-1,2-CPDA: 0.0
Ethylmalonyl-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

CDS_04218: Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (3306..3713): Thr

nrpys: Thr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: N/A
Small clusters prediction:: thr (Thr)
Single AA prediction:: thr (Thr)

Stachelhaus prediction details:

Stachelhaus sequence:: DFWGVGMVVK
Nearest Stachelhaus code(s):: Thr DFWGVGMVHK (68% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_04219: Thr - X

Search NORINE for peptide: strict or relaxed

AMP-binding (514..921): Thr

nrpys: Thr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: thr (Thr)
Single AA prediction:: thr (Thr)

Stachelhaus prediction details:

Stachelhaus sequence:: DFWNVGMVHK
Nearest Stachelhaus code(s):: Thr DFWNVGMVHK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1642..2050): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DAQLAVGIAK
Nearest Stachelhaus code(s):: Tyr DAQTIVGIAK (59% 8Å match)
Stachelhaus code match:: 80% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0010 - Region 1 - hydrogen-cyanide

Download region GenBank file

Download region SVG

Location: 219,985 - 233,002 nt. (total: 13,018 nt) Show pHMM detection rules used

hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase reductase

CDS_04483: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

CDS_04486: alkyl hydroperoxide reductase subunit

smcogs: SMCOG1176: alkyl hydroperoxide reductase subunit

CDS_04488: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002345.2	0.63	other (other)	hydrogen cyanide	Pseudomonas fluorescens
BGC0001423.4	0.33	NRPS, PKS	myxochromide C	Myxococcus hansupus
BGC0001428.4	0.33	NRPS, PKS	myxochromide A	Myxococcus xanthus
BGC0001424.4	0.33	NRPS, PKS	myxochromide C	Myxococcus virescens
BGC0001427.4	0.33	NRPS, PKS	myxochromide A	Myxococcus xanthus
BGC0001421.4	0.33	NRPS, PKS	myxochromide B	Myxococcus sp.
BGC0001422.4	0.32	NRPS, PKS	myxochromide A	Myxococcus fulvus HW-1
BGC0001739.3	0.30	other (other)	phosphonoacetic Acid	Streptomyces sp. NRRL F-525
BGC0001108.5	0.28	NRPS, PKS	pederin, pseudopederin, pederone	Uncultured bacterium
BGC0002083.3	0.28	PKS	gladiofungin A, gladiofungin B	Burkholderia gladioli

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002345.2	0.63	other (other)	hydrogen cyanide	Pseudomonas fluorescens
BGC0001423.4	0.33	NRPS, PKS	myxochromide C	Myxococcus hansupus
BGC0001428.4	0.33	NRPS, PKS	myxochromide A	Myxococcus xanthus
BGC0001424.4	0.33	NRPS, PKS	myxochromide C	Myxococcus virescens
BGC0001427.4	0.33	NRPS, PKS	myxochromide A	Myxococcus xanthus
BGC0001421.4	0.33	NRPS, PKS	myxochromide B	Myxococcus sp.
BGC0001422.4	0.32	NRPS, PKS	myxochromide A	Myxococcus fulvus HW-1
BGC0001739.3	0.30	other (other)	phosphonoacetic Acid	Streptomyces sp. NRRL F-525
BGC0001108.5	0.28	NRPS, PKS	pederin, pseudopederin, pederone	Uncultured bacterium
BGC0002083.3	0.28	PKS	gladiofungin A, gladiofungin B	Burkholderia gladioli

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (9):

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.17 out of 36.54

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.05 out of 31.73

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.29 out of 18.57

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.06 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.62 out of 26.06

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.34 out of 33.14

Confidence: weak

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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TFBS Finder

TFBS definitions

Regulator	Description

NPDC089509.ctg-0011 - Region 1 - RiPP-like,terpene

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Location: 120,816 - 147,205 nt. (total: 26,390 nt) Show pHMM detection rules used

RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

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core biosynthetic genes

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TTA codons

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Gene details

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Gene overview

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Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxidoreductase oxygenase

CDS_04689: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

CDS_04690: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

Hydrolases: dehalogenase

CDS_04670: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Lyases: cyclase decarboxylase

CDS_04687: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

CDS_04691: diaminopimelate decarboxylase

smcogs: SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthetase

CDS_04686: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

CDS_04688: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000660.5	0.24	terpene	albaflavenone	Streptomyces coelicolor A3(2)
BGC0002397.2	0.24	terpene	astallatene	Arabidopsis thaliana
BGC0000658.3	0.23	terpene	2-methylisoborneol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0002043.3	0.21	ribosomal	cittilin A, cittilin B	Myxococcus xanthus DK 1622
BGC0002400.2	0.21	terpene	boleracene	Brassica oleracea var. oleracea
BGC0001911.3	0.21	terpene	raimonol	Streptomyces anulatus
BGC0000677.5	0.21	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0001910.4	0.21	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0002309.2	0.19	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002398.2	0.19	terpene	(-)-ent-quiannulatene	Arabidopsis thaliana

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000660.5	0.57	terpene	albaflavenone	Streptomyces coelicolor A3(2)
BGC0002397.2	0.57	terpene	astallatene	Arabidopsis thaliana
BGC0000658.3	0.57	terpene	2-methylisoborneol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0002043.3	0.54	ribosomal	cittilin A, cittilin B	Myxococcus xanthus DK 1622
BGC0002400.2	0.54	terpene	boleracene	Brassica oleracea var. oleracea
BGC0001911.3	0.53	terpene	raimonol	Streptomyces anulatus
BGC0000677.5	0.53	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0001910.4	0.53	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0002309.2	0.52	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002398.2	0.51	terpene	(-)-ent-quiannulatene	Arabidopsis thaliana

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
diterpene			C20	C6-C11 + C10-C15	none

Genes with terpene domains:

CDS_04686: PT_FPPS_like

Domain 1 (64 - 372): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

Reactions:: IPP, DMAPP → FPP; IPP, DMAPP → GGPP; IPP, DMAPP → GFPP; IPP, DMAPP → HPP

CDS_04687: T1TS

Domain 1 (15 - 313): Type 1 terpene synthase

Subtype: Labdatriene synthase type

Reactions:: diterpene_C6-C11/C10-C15_PP → diterpene_C6-C11/C10-C15

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.31 out of 23.79

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.67 out of 19.26

Confidence: medium

Additional weak hits (8):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.75 out of 30.22

Confidence: weak

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.43 out of 29.51

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.10 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.85 out of 29.38

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.33 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.67 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.02 out of 28.19

Confidence: weak

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Terpene

TFBS Finder

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
GFPP	Geranylfarnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
HPP	Hexaprenyl diphosphate
IPP	Isopentenyl diphosphate

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
IolR	Regulator of the inositol catabolism

NPDC089509.ctg-0012 - Region 1 - aminopolycarboxylic-acid

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Location: 44,890 - 58,259 nt. (total: 13,370 nt) Show pHMM detection rules used

aminopolycarboxylic-acid: (AesA and AesB and AesC)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

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TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Hydrolases: deaminase

CDS_04818: ornithine cyclodeaminase

smcogs: SMCOG1158: ornithine cyclodeaminase

Lyases: decarboxylase

CDS_04817: diaminopimelate decarboxylase

smcogs: SMCOG1264: diaminopimelate decarboxylase

Ligases: synthase

CDS_04816: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001587.5	0.83	other (other)	ethylenediaminesuccinic acid hydroxyarginine (EDHA)	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002568.2	0.78	other (other)	Ethylenediaminesuccinic acid hydroxyarginine	Streptomyces scabiei 87.22
BGC0002567.2	0.68	other (other)	EDHA	Streptomyces sp. MA5143a
BGC0000943.5	0.40	other (other)	staphyloferrin B	Staphylococcus aureus subsp. aureus NCTC 8325
BGC0000932.5	0.36	other (other)	tropodithietic acid, hydroxytropodithietic acid	Phaeobacter inhibens DSM 17395
BGC0002487.3	0.35	other (other)	staphylopine	Staphylococcus aureus subsp. aureus Mu50
BGC0002213.3	0.33	PKS	HEx-pks16 polyketide	Punctularia strigosozonata HHB-11173 SS5
BGC0001790.4	0.32	NRPS	sulfazecin	Pseudomonas acidophila
BGC0000188.5	0.32	other (other)	saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2	Cylindrospermopsis raciborskii T3
BGC0000721.4	0.29	saccharide	tobramycin	Streptoalloteichus tenebrarius

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001587.5	0.83	other (other)	ethylenediaminesuccinic acid hydroxyarginine (EDHA)	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002568.2	0.78	other (other)	Ethylenediaminesuccinic acid hydroxyarginine	Streptomyces scabiei 87.22
BGC0002567.2	0.68	other (other)	EDHA	Streptomyces sp. MA5143a
BGC0000943.5	0.40	other (other)	staphyloferrin B	Staphylococcus aureus subsp. aureus NCTC 8325
BGC0000932.5	0.36	other (other)	tropodithietic acid, hydroxytropodithietic acid	Phaeobacter inhibens DSM 17395
BGC0002487.3	0.35	other (other)	staphylopine	Staphylococcus aureus subsp. aureus Mu50
BGC0002213.3	0.33	PKS	HEx-pks16 polyketide	Punctularia strigosozonata HHB-11173 SS5
BGC0001790.4	0.32	NRPS	sulfazecin	Pseudomonas acidophila
BGC0000188.5	0.32	other (other)	saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2	Cylindrospermopsis raciborskii T3
BGC0000721.4	0.29	saccharide	tobramycin	Streptoalloteichus tenebrarius

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (3):

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.14 out of 36.53

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.12 out of 36.53

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.82 out of 36.53

Confidence: weak

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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TFBS Finder

TFBS definitions

Regulator	Description

NPDC089509.ctg-0012 - Region 2 - lanthipeptide-class-i

Download region GenBank file

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Location: 106,951 - 131,482 nt. (total: 24,532 nt) Show pHMM detection rules used

lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

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Gene overview

Tailoring

MIBiG comparison

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KnownClusterBlast

SubClusterBlast

Lanthipeptides

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Hydrolases: hydrolase

CDS_04868: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Lyases: cyclase dehydratase

CDS_04876: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

CDS_04877: Lanthionine synthetase C family protein

smcogs: SMCOG1140: Lanthionine synthetase C family protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.76	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0001289.5	0.59	ribosomal	penisin	Paenibacillus ehimensis
BGC0000542.3	0.56	ribosomal	paenicidin B	Paenibacillus terrae
BGC0000541.5	0.56	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0000515.4	0.52	ribosomal	geobacillin I	Geobacillus thermodenitrificans NG80-2
BGC0000544.4	0.50	ribosomal	planosporicin	Planomonospora alba
BGC0002635.2	0.49	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0000538.3	0.48	ribosomal	nisin Z	Lactococcus lactis
BGC0000560.5	0.47	ribosomal	subtilomycin	Bacillus subtilis
BGC0000543.5	0.47	ribosomal	pep5	Staphylococcus epidermidis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.76	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0001289.5	0.59	ribosomal	penisin	Paenibacillus ehimensis
BGC0000542.3	0.56	ribosomal	paenicidin B	Paenibacillus terrae
BGC0000541.5	0.56	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0000515.4	0.52	ribosomal	geobacillin I	Geobacillus thermodenitrificans NG80-2
BGC0000544.4	0.50	ribosomal	planosporicin	Planomonospora alba
BGC0002635.2	0.49	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0000538.3	0.48	ribosomal	nisin Z	Lactococcus lactis
BGC0000560.5	0.47	ribosomal	subtilomycin	Bacillus subtilis
BGC0000543.5	0.47	ribosomal	pep5	Staphylococcus epidermidis

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for CDS_04876

CDS_04875

Leader:

MNDILELDVLEINAPAQEETEAQ

Core:

NAAVAASWPYSCNSTRNSRCCD

Core with dehydrations:

NAAVAADhaWPYDhaCysNDhaDhbRNDhaRCysCysD

antiSMASH-DB 4.0 matches for CDS_04875

68.2%

NZ_CP025394.1:

Lanthipeptides: CFP65_RS41770_lanthipeptide

1

NAAVAASWPYSCNSTRNSRCC

21

+ A SWPYSC STRNSRCC

1

DGAANTSWPYSCTSTRNSRCC

21

25.0%

NZ_CP102509.1:

Lanthipeptides: JIW86_RS16015_lanthipeptide

10

YSCNSTRNSRCCD

22

YSC T S CCD

9

YSCKGTCASYCCD

21

14.0%

NZ_JAMTCR010000003.1:

Lanthipeptides: LV79_RS16640_lanthipeptide

2

AAVAASWPYS

11

AAVAA+WP S

39

AAVAANWPGS

48

with 1 more sequence matches

8.2%

NZ_BNBY01000021.1:

Lanthipeptides: allorf_108020_108247_lanthipeptide

1

NAAVAASWPYSCNS

14

+ V WP+ C +

10

DKRVFGEWPHGCGA

23

MIBiG 4.0 matches for CDS_04875

5.9%

BGC0002120.3 (NQE92413.1):

Lanthipeptide: nocathioamide A

11

SCNSTRNSRCC

21

+C++ + CC

39

ACHTLSSLPCC

49

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (2):

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.05 out of 20.97

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 15.59 out of 28.19

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lanthipeptides

RREFinder

TFBS Finder

Core peptide predictions

CDS_04875 - Class I

Cleavage pHMM score: -6.10

RODEO score: 20

Monoisotopic mass: 2285.0 Da

Molecular weight: 2286.5 Da

Number of bridges: 3

Alternative weights: (assuming N unmodified Ser/Thr residues); 2304.5 Da N = 1; 2322.5 Da N = 2

RRE predictions

: RRE type: Lanthipeptide_LanB_RRE; Location: 165 - 258; Score: 54.8

TFBS definitions

Regulator	Description

NPDC089509.ctg-0012 - Region 3 - NRPS-like,T1PKS,terpene

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Location: 139,910 - 212,739 nt. (total: 72,830 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase synthase

CDS_04908: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_04918: riboflavin biosynthesis protein RibD

smcogs: SMCOG1240: riboflavin biosynthesis protein RibD

CDS_04919: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_04939: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

CDS_04941: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase acyltransferase aminotransferase methyltransferase

CDS_04910: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_04934: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

CDS_04935: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_04938: acyltransferase 3

smcogs: SMCOG1088: acyltransferase 3

Hydrolases: dehalogenase hydrolase synthase

CDS_04906: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

CDS_04912: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

CDS_04918: riboflavin biosynthesis protein RibD

smcogs: SMCOG1240: riboflavin biosynthesis protein RibD

CDS_04932: alpha/beta hydrolase domain-containing protein

smcogs: SMCOG1066: alpha/beta hydrolase domain-containing protein

CDS_04942: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

CDS_04945: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Lyases: cyclase

CDS_04907: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

CDS_04915: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Ligases: synthase

CDS_04929: cobalamin synthesis protein/P47K family protein

smcogs: SMCOG1178: cobalamin synthesis protein/P47K family protein

CDS_04936: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_04937: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001746.3	1.36	terpene	pristinol	Streptomyces pristinaespiralis ATCC 25486
BGC0000683.3	1.33	terpene	avermitilol	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000041.3	0.67	PKS	oronofacic acid	Pseudomonas syringae
BGC0002191.2	0.62	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001273.3	0.61	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.61	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001276.3	0.61	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001257.3	0.60	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0001275.3	0.60	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002154.2	0.60	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001746.3	0.76	terpene	pristinol	Streptomyces pristinaespiralis ATCC 25486
BGC0000683.3	0.75	terpene	avermitilol	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000041.3	0.67	PKS	oronofacic acid	Pseudomonas syringae
BGC0002191.2	0.64	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.64	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001276.3	0.64	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001257.3	0.64	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0001275.3	0.64	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002154.2	0.64	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

No product predictions

Genes with terpene domains:

CDS_04907: T1TS

Domain 1 (2 - 316): Type 1 terpene synthase

Subtype: unknown

CDS_04915: T1TS

Domain 1 (10 - 306): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.46 out of 23.79

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.08 out of 23.79

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.09 out of 20.47

Confidence: medium

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.16 out of 26.33

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 17.94 out of 23.79

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.45 out of 28.19

Confidence: medium

Additional weak hits (18):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33

Confidence: weak

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.86 out of 29.38

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.44 out of 31.73

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.28 out of 19.26

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.39 out of 26.85

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.79 out of 30.97

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.26 out of 29.38

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.03 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 15.85 out of 28.19

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.78 out of 27.18

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.45 out of 33.14

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.52 out of 29.65

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.12 out of 24.78

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.26 out of 33.14

Confidence: weak

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.87 out of 29.65

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

Terpene

TFBS Finder

Predicted core structure(s)

For candidate cluster 3, location 139909 - 212739:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X - Me-ohmal) + (ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 159838 - 212739:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X - Me-ohmal) + (ccmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_04935: X - mmal

AMP-binding (12..417): X

nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: IGNFVAACFK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

PKS_AT (1161..1459): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 95.8%; Methoxymalonyl-CoA: 91.7%; Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 187.6
Ethylmalonyl-CoA: 170.2
Methoxymalonyl-CoA: 155.6
trans-1,2-CPDA: 100.8
2-Methylbutyryl-CoA: 97.6
Malonyl-CoA: 92.6
Propionyl-CoA: 90.8
CHC-CoA: 67.7
Isobutyryl-CoA: 49.3
Benzoyl-CoA: 45.3
inactive: 30.6
Acetyl-CoA: 27.0
fatty_acid: 25.0
3-Methylbutyryl-CoA: 15.9

CDS_04936: mal

PKS_AT (565..857): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 75.0%; inactive: 62.5%; Propionyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 147.7
inactive: 58.1
Methylmalonyl-CoA: 57.7
Methoxymalonyl-CoA: 56.0
Isobutyryl-CoA: 32.9
Propionyl-CoA: 23.1
Acetyl-CoA: 17.1
Ethylmalonyl-CoA: 14.7
Benzoyl-CoA: 13.7
trans-1,2-CPDA: 13.5
3-Methylbutyryl-CoA: 9.2
fatty_acid: 7.6
2-Methylbutyryl-CoA: 6.6
CHC-CoA: 5.9

Link to PARAS substrate predictor

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
CRP	Cyclic AMP receptor protein
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems
ZuR variant 1	Zinc-responsive repressor

NPDC089509.ctg-0013 - Region 1 - lanthipeptide-class-i

Download region GenBank file

Download region SVG

Location: 1 - 15,057 nt. (total: 15,057 nt) Show pHMM detection rules used

Region on contig edge.

lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Lanthipeptides

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Lyases: cyclase dehydratase

CDS_04971: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

CDS_04973: Lanthionine synthetase C family protein

smcogs: SMCOG1140: Lanthionine synthetase C family protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.76	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0002640.2	0.56	ribosomal	thalassomonasin A, thalassomonasin B	Thalassomonas actiniarum
BGC0001289.5	0.53	ribosomal	penisin	Paenibacillus ehimensis
BGC0000542.3	0.49	ribosomal	paenicidin B	Paenibacillus terrae
BGC0002635.2	0.49	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0000541.5	0.49	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0000544.4	0.48	ribosomal	planosporicin	Planomonospora alba
BGC0002316.2	0.48	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0000506.4	0.46	ribosomal	entianin	Bacillus subtilis subsp. spizizenii
BGC0000515.4	0.45	ribosomal	geobacillin I	Geobacillus thermodenitrificans NG80-2

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.76	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0002640.2	0.56	ribosomal	thalassomonasin A, thalassomonasin B	Thalassomonas actiniarum
BGC0001289.5	0.53	ribosomal	penisin	Paenibacillus ehimensis
BGC0000542.3	0.49	ribosomal	paenicidin B	Paenibacillus terrae
BGC0002635.2	0.49	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0000541.5	0.49	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0000544.4	0.48	ribosomal	planosporicin	Planomonospora alba
BGC0002316.2	0.48	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0000506.4	0.46	ribosomal	entianin	Bacillus subtilis subsp. spizizenii
BGC0000515.4	0.45	ribosomal	geobacillin I	Geobacillus thermodenitrificans NG80-2

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for CDS_04971

CDS_04972

Leader:

MCNTYILISNPLFPWEQTMQNTAFIEAAELHFDAFDLDLQETAQAGETAQVQ

Core:

HPSLATCFCTYSHCH

Core with dehydrations:

HPDhaLADhbCysFCysDhbYDhaHCysH

antiSMASH-DB 4.0 matches for CDS_04972

26.1%

NZ_BBXF01000001.1:

Lanthipeptides: AW274_RS42555_lanthipeptide

2

PSLATCFCTYS

12

PSL+ CF +S

9

PSLSLCFSNWS

19

25.9%

NZ_JAEQNB010000006.1:

Lanthipeptides: JJB07_RS18720_lanthipeptide

5

ATCFCTYSHCH

15

TCFCT S C

12

GTCFCTISGCS

22

23.1%

NZ_JAEQNB010000006.1:

Lanthipeptides: JJB07_RS18750_lanthipeptide

6

TCFCTYSHCH

15

TC CT S C

13

TCLCTISGCD

22

with 1 more sequence matches

18.5%

NZ_JAEQNB010000006.1:

Lanthipeptides: JJB07_RS18730_lanthipeptide

5

ATCFCTYSHCH

15

+CFCT + C

12

GSCFCTIASCS

22

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (9):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.70 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.55 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.99 out of 26.06

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 14.92 out of 20.97

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.33 out of 28.14

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.88 out of 36.54

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.18 out of 33.14

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.61 out of 20.01

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.79 out of 30.98

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lanthipeptides

RREFinder

TFBS Finder

Core peptide predictions

CDS_04972 - Class I

Cleavage pHMM score: 5.00

RODEO score: 14

Monoisotopic mass: 1633.7 Da

Molecular weight: 1634.8 Da

Number of bridges: 3

Alternative weights: (assuming N unmodified Ser/Thr residues); 1652.9 Da N = 1

RRE predictions

: RRE type: Lanthipeptide_LanB_RRE; Location: 176 - 270; Score: 67.2

TFBS definitions

Regulator	Description

NPDC089509.ctg-0013 - Region 2 - lanthipeptide-class-ii

Download region GenBank file

Download region SVG

Location: 101,584 - 124,856 nt. (total: 23,273 nt) Show pHMM detection rules used

lanthipeptide-class-ii: cds(LANC_like and DUF4135)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Lanthipeptides

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxygenase

CDS_05065: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Lyases: cyclase

CDS_05072: lanthionine synthetase C family protein

smcogs: SMCOG1070: lanthionine synthetase C family protein

Ligases: synthase

CDS_05077: polyprenol-monophosphomannose synthase ppm1

smcogs: SMCOG1123: polyprenol-monophosphomannose synthase ppm1

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000528.5	0.57	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000525.5	0.50	ribosomal	lichenicidin VK21 A1, lichenicidin VK21 A2	Bacillus licheniformis
BGC0002316.2	0.48	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0000503.5	0.48	ribosomal	cinnamycin	Streptomyces cinnamoneus
BGC0002127.3	0.47	PKS	flaviolin, 1,3,6,8-tetrahydroxynaphthalene	Streptomyces coelicolor A3(2)
BGC0002346.3	0.46	ribosomal	kyamicin	Saccharopolyspora sp.
BGC0000902.4	0.46	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0002703.2	0.45	ribosomal	archalan α	Halorussus salinus
BGC0001660.3	0.43	ribosomal	mathermycin	Marinactinospora thermotolerans
BGC0001986.3	0.42	other (other)	purincyclamide	Streptomyces chrestomyceticus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000528.5	0.57	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000525.5	0.50	ribosomal	lichenicidin VK21 A1, lichenicidin VK21 A2	Bacillus licheniformis
BGC0002316.2	0.48	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0000503.5	0.48	ribosomal	cinnamycin	Streptomyces cinnamoneus
BGC0002127.3	0.47	PKS	flaviolin, 1,3,6,8-tetrahydroxynaphthalene	Streptomyces coelicolor A3(2)
BGC0002346.3	0.46	ribosomal	kyamicin	Saccharopolyspora sp.
BGC0000902.4	0.46	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0002703.2	0.45	ribosomal	archalan α	Halorussus salinus
BGC0001660.3	0.43	ribosomal	mathermycin	Marinactinospora thermotolerans
BGC0001986.3	0.42	other (other)	purincyclamide	Streptomyces chrestomyceticus

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for CDS_05072

CDS_05071

Leader:

MQPTADQVRALKDEDFRITLGQGHSVHPAGELVDELYV

Core:

TAAVQNSTCDGWSSCGRVCSY

Core with dehydrations:

DhbAAVQNDhaDhbCysDGWDhaDhaCysGRVCysDhaY

antiSMASH-DB 4.0 matches for CDS_05071

95.2%

NZ_CP020567.1:

Lanthipeptides: B6264_RS23020_lanthipeptide

1

TAAVQNSTCDGWSSCGRVCSY

21

TAAV NSTCDGWSSCGRVCSY

1

TAAVLNSTCDGWSSCGRVCSY

21

42.9%

NZ_BMSK01000044.1and 2 others:

NZ_BNBI01000017.1 Lanthipeptides: IE316_RS30460_lanthipeptideNZ_CP050504.1 Lanthipeptides: HB370_RS00700_lanthipeptide

Lanthipeptides: IE251_RS40210_lanthipeptide

8

TCDGWSSCGRVCSY

21

TC+ +SSC R+CSY

5

TCESYSSCARMCSY

18

28.0%

NZ_CP035758.1:

Lanthipeptides: EPA93_RS12375_lanthipeptide

7

STCDGWSSCGRVCSY

21

+TCD ++C CSY

9

ATCDFNTTCAATCSY

23

with 3 more sequence matches

20.0%

NZ_LR027842.1:

Lanthipeptides: E0E39_RS01495_lanthipeptide

10

DGWSSCGRVCSY

21

GW+ CG VCS+

19

SGWTVCGLVCSH

30

17.5%

NZ_QKUF01000011.1:

Lanthipeptides: EI42_RS16965_lanthipeptide

8

TCDGWSSCGRVCS

20

TC G+S+C CS

19

TCSGYSTCSSTCS

31

17.1%

NZ_FNAD01000024.1:

Lanthipeptides: BLQ63_RS26050_lanthipeptide

11

GWSSCGRVCS

20

GW+ CG +CS

20

GWTVCGSLCS

29

MIBiG 4.0 matches for CDS_05071

19.0%

BGC0001155.5 (AGY49587.1):

Thiopeptide: GE2270

14

SCGRVCSY

21

SC VC +

1

SCNCVCGF

8

14.8%

BGC0002144.3 (RCCGEPOP_RS37510):

LAP: phazolicin

9

CDGWSSC

15

CD S C

6

CDSSSRC

12

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.96 out of 23.79

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.36 out of 25.31

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

Additional weak hits (6):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.87 out of 29.38

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.42 out of 32.93

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.09 out of 30.98

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.50 out of 26.85

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.07 out of 33.14

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lanthipeptides

TFBS Finder

Core peptide predictions

CDS_05071 - Class II

Cleavage pHMM score: -5.20

RODEO score: 0

Monoisotopic mass: 2101.9 Da

Molecular weight: 2103.2 Da

Number of bridges: 3

Additional modifications: OH

Alternative weights: (assuming N unmodified Ser/Thr residues); 2121.3 Da N = 1; 2139.3 Da N = 2; 2157.3 Da N = 3

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
CatR	H2O2-responsive repressor
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0014 - Region 1 - NAPAA,terpene

Download region GenBank file

Download region SVG

Location: 1 - 39,466 nt. (total: 39,466 nt) Show pHMM detection rules used

Region on contig edge.

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)
NAPAA: (AMP-binding and TIGR02353)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_05197: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_05227: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: methyltransferase

CDS_05201: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_05215: isoprenylcysteine carboxyl methyltransferase

smcogs: SMCOG1150: isoprenylcysteine carboxyl methyltransferase

Lyases: cyclase

CDS_05191: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Ligases: ligase

CDS_05214: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001181.4	0.48	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0002174.2	0.47	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0002135.2	0.27	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.27	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.26	NRPS	HC-toxin	Alternaria jesenskae
BGC0000307.4	0.26	NRPS	AbT1	Aureobasidium pullulans
BGC0001261.3	0.26	NRPS	AM-toxin	Alternaria alternata
BGC0001249.5	0.26	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001641.4	0.26	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.26	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001181.4	0.77	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0002174.2	0.77	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0002135.2	0.61	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.61	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.60	NRPS	HC-toxin	Alternaria jesenskae
BGC0000307.4	0.60	NRPS	AbT1	Aureobasidium pullulans
BGC0001261.3	0.60	NRPS	AM-toxin	Alternaria alternata
BGC0001249.5	0.60	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001641.4	0.59	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.59	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

No product predictions

Genes with terpene domains:

CDS_05191: T1TS

Domain 1 (8 - 313): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.22 out of 18.46

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47

Confidence: medium

Additional weak hits (19):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.81 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.42 out of 29.38

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.37 out of 30.22

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.71 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.89 out of 30.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.31 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.68 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.13 out of 29.38

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.86 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.67 out of 30.25

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.68 out of 29.65

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.48 out of 35.63

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.83 out of 29.65

Confidence: weak

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.79 out of 32.93

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.65 out of 27.18

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

Terpene

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 39466:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 5470 - 39466:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_05214: X

AMP-binding (40..413): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DAESIGTVVK
Nearest Stachelhaus code(s):: Lys DAEDIGTVVK (71% 8Å match); Gln or Tyr DAESVGTVVK (59% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
RpoN	Regulator of nitrogen assimilation and virulence
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0014 - Region 2 - lanthipeptide-class-v

Download region GenBank file

Download region SVG

Location: 124,771 - 166,841 nt. (total: 42,071 nt) Show pHMM detection rules used

lanthipeptide-class-v: (APH and HopA1)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Lanthipeptides

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxidoreductase oxygenase

CDS_05331: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_05352: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_05358: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_05360: pyridine nucleotide-disulfide oxidoreductase

smcogs: SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: acetyltransferase halogenase

CDS_05347: conventional flavin-dependent halogenase

halogenases: conventional flavin-dependent halogenase
smcogs: SMCOG1119: halogenase

CDS_05363: Chloramphenicol acetyltransferase

smcogs: SMCOG1156: Chloramphenicol acetyltransferase

Lyases: dehydratase

CDS_05332: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase

CDS_05328: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CDS_05330: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002341.2	0.77	other (other)	3,5-dibromo-p-anisic acid	Planctomycetales bacterium 10988
BGC0002608.2	0.76	NRPS, PKS	ochratoxin A	Aspergillus steynii
BGC0001128.4	0.55	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002631.2	0.54	ribosomal	Myxarylin	Pyxidicoccus fallax
BGC0001310.5	0.50	PKS	naringenin	Streptomyces clavuligerus ATCC 27064
BGC0000844.5	0.50	other (other)	clavulanic acid	Streptomyces clavuligerus
BGC0001948.3	0.49	other (other)	naseseazine C, C3-aryl pyrroloindolines	Streptomyces sp.
BGC0002260.3	0.46	terpene	trichobrasilenol, xylarenic acid B, brasilane A, brasilane F, brasilane E, brasilane D	Annulohypoxylon truncatum
BGC0001224.5	0.46	other (other)	reductasporine	uncultured bacterium
BGC0002303.3	0.46	ribosomal	pristinin A3	Streptomyces pristinaespiralis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002341.2	0.77	other (other)	3,5-dibromo-p-anisic acid	Planctomycetales bacterium 10988
BGC0002608.2	0.76	NRPS, PKS	ochratoxin A	Aspergillus steynii
BGC0001128.4	0.55	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002631.2	0.54	ribosomal	Myxarylin	Pyxidicoccus fallax
BGC0001310.5	0.50	PKS	naringenin	Streptomyces clavuligerus ATCC 27064
BGC0000844.5	0.50	other (other)	clavulanic acid	Streptomyces clavuligerus
BGC0001948.3	0.49	other (other)	naseseazine C, C3-aryl pyrroloindolines	Streptomyces sp.
BGC0002260.3	0.46	terpene	trichobrasilenol, xylarenic acid B, brasilane A, brasilane F, brasilane E, brasilane D	Annulohypoxylon truncatum
BGC0001224.5	0.46	other (other)	reductasporine	uncultured bacterium
BGC0002303.3	0.46	ribosomal	pristinin A3	Streptomyces pristinaespiralis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptides - No core peptides found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.71 out of 20.47

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.24 out of 23.79

Confidence: medium

Additional weak hits (18):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.44 out of 26.06

Confidence: weak

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.35 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.61 out of 28.14

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.30 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.69 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.05 out of 27.78

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.81 out of 18.57

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 15.94 out of 26.12

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.58 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.79 out of 30.25

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.98 out of 28.19

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.42 out of 20.01

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 15.94 out of 26.12

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.36 out of 32.74

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.09 out of 30.98

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.07 out of 28.19

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lanthipeptides

TFBS Finder

Core peptide predictions

No core peptides found.

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0014 - Region 3 - lanthipeptide-class-i

Download region GenBank file

Download region SVG

Location: 167,910 - 192,393 nt. (total: 24,484 nt) Show pHMM detection rules used

lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Lanthipeptides

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Lyases: cyclase dehydratase

CDS_05382: Lanthionine synthetase C family protein

smcogs: SMCOG1140: Lanthionine synthetase C family protein

CDS_05383: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.76	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0000541.5	0.46	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0000542.3	0.46	ribosomal	paenicidin B	Paenibacillus terrae
BGC0001289.5	0.46	ribosomal	penisin	Paenibacillus ehimensis
BGC0000560.5	0.41	ribosomal	subtilomycin	Bacillus subtilis
BGC0002635.2	0.41	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0000544.4	0.40	ribosomal	planosporicin	Planomonospora alba
BGC0000506.4	0.39	ribosomal	entianin	Bacillus subtilis subsp. spizizenii
BGC0000515.4	0.39	ribosomal	geobacillin I	Geobacillus thermodenitrificans NG80-2
BGC0001727.3	0.39	ribosomal	paenilan	Paenibacillus polymyxa E681

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.76	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0000541.5	0.46	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0000542.3	0.46	ribosomal	paenicidin B	Paenibacillus terrae
BGC0001289.5	0.46	ribosomal	penisin	Paenibacillus ehimensis
BGC0000560.5	0.41	ribosomal	subtilomycin	Bacillus subtilis
BGC0002635.2	0.41	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0000544.4	0.40	ribosomal	planosporicin	Planomonospora alba
BGC0000506.4	0.39	ribosomal	entianin	Bacillus subtilis subsp. spizizenii
BGC0000515.4	0.39	ribosomal	geobacillin I	Geobacillus thermodenitrificans NG80-2
BGC0001727.3	0.39	ribosomal	paenilan	Paenibacillus polymyxa E681

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptides - No core peptides found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.09 out of 20.47

Confidence: medium

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.71 out of 23.79

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

Additional weak hits (15):

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.14 out of 26.12

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.53 out of 21.55

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.29 out of 21.55

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.13 out of 26.06

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.03 out of 30.22

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.70 out of 27.78

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.91 out of 36.54

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.77 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.42 out of 33.14

Confidence: weak

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.50 out of 30.25

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.74 out of 28.14

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.73 out of 32.93

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lanthipeptides

RREFinder

TFBS Finder

Core peptide predictions

No core peptides found.

RRE predictions

: RRE type: Lanthipeptide_LanB_RRE; Location: 211 - 273; Score: 46.6

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0015 - Region 1 - lanthipeptide-class-i

Download region GenBank file

Download region SVG

Location: 160,888 - 185,663 nt. (total: 24,776 nt) Show pHMM detection rules used

lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Lanthipeptides

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: acetyltransferase

CDS_05584: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: esterase hydrolase

CDS_05589: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

CDS_05596: thioesterase superfamily protein

smcogs: SMCOG1144: thioesterase superfamily protein

Lyases: cyclase dehydratase

CDS_05592: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

CDS_05593: Lanthionine synthetase C family protein

smcogs: SMCOG1140: Lanthionine synthetase C family protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.75	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0002640.2	0.56	ribosomal	thalassomonasin A, thalassomonasin B	Thalassomonas actiniarum
BGC0001289.5	0.54	ribosomal	penisin	Paenibacillus ehimensis
BGC0000541.5	0.52	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0000542.3	0.52	ribosomal	paenicidin B	Paenibacillus terrae
BGC0002635.2	0.49	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0000544.4	0.48	ribosomal	planosporicin	Planomonospora alba
BGC0000543.5	0.48	ribosomal	pep5	Staphylococcus epidermidis
BGC0000560.5	0.47	ribosomal	subtilomycin	Bacillus subtilis
BGC0000538.3	0.47	ribosomal	nisin Z	Lactococcus lactis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.75	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0002640.2	0.56	ribosomal	thalassomonasin A, thalassomonasin B	Thalassomonas actiniarum
BGC0001289.5	0.54	ribosomal	penisin	Paenibacillus ehimensis
BGC0000541.5	0.52	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0000542.3	0.52	ribosomal	paenicidin B	Paenibacillus terrae
BGC0002635.2	0.49	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0000544.4	0.48	ribosomal	planosporicin	Planomonospora alba
BGC0000543.5	0.48	ribosomal	pep5	Staphylococcus epidermidis
BGC0000560.5	0.47	ribosomal	subtilomycin	Bacillus subtilis
BGC0000538.3	0.47	ribosomal	nisin Z	Lactococcus lactis

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for CDS_05592

CDS_05594

Leader:

MEQDFDLDVRVAVAPKVAATPD

Core:

GFASIGTTCWSCADSCNCPITVGFPTIC

Core with dehydrations:

GFADhaIGDhbDhbCysWDhaCysADDhaCysNCysPIDhbVGFPDhbICys

antiSMASH-DB 4.0 matches for CDS_05594

72.4%

NZ_CP071595.1:

Lanthipeptides: J3S04_RS01545_lanthipeptide

1

GFASIGTTCWSCAD-SCNCPITVGFPTIC

28

GFASIG+TCWSC + SC CPIT+G+PT+C

1

GFASIGSTCWSCNNASCGCPITIGYPTVC

29

28.6%

NZ_QKUF01000004.1:

Lanthipeptides: EI42_RS08635_lanthipeptide

4

SIGTTCWSCADSCNCP

19

S TTCWSC+ +C

3

SFVTTCWSCSRCTDCK

18

25.0%

NZ_CP061336.1:

Sactipeptides: allorf_4015774_4015902_sactipeptide

11

SCADSCNCPITVGFPTI

27

SC+D NC + V FP +

2

SCSDCLNCAVCVTFPGL

18

with 4 more sequence matches

21.4%

NZ_LMUE01000002.1:

Lanthipeptides: allorf_0100736_0100864_lanthipeptide

11

SCADSCNCP

19

+CAD C+CP

8

ACADICHCP

16

21.4%

NZ_LT907978.1:

Lanthipeptides: allorf_2780875_2780979_lanthipeptide

1

GFASIGTTC

9

G+A IG TC

9

GYADIGITC

17

18.8%

NZ_CP061007.1:

Lanthipeptides: IAG28_RS29035_lanthipeptide

1

GFASIGTTCW

10

G ++GTTCW

11

GPITVGTTCW

20

18.2%

NZ_SLWA01000002.1:

Lanthipeptides: EV142_RS24000_lanthipeptide

10

WSCADSCNC

18

WSC+DS C

5

WSCSDSTQC

13

MIBiG 4.0 matches for CDS_05594

14.3%

BGC0002111.3 (EVG22_32245):

Lanthipeptide: andalusicin A or andalusicin B

9

CWSCADSCNC

18

W+ S NC

14

AWASTISNNC

23

14.3%

BGC0002111.3 (multiple genes):

Lanthipeptide: andalusicin A or andalusicin B

10

WSCADSCNC

18

W+ S NC

15

WASTISNNC

23

11.8%

BGC0000535.4 (ADJ56352.1):

Lanthipeptide: nisin A

15

SCNCPITV

22

+C+C I V

25

TCHCSIHV

32

with 1 more sequence matches

10.3%

BGC0001229.4 (SBI_06990):

Lanthipeptide: SBI-06990 A1 or SBI-06989 A2

7

TTCWSCADSCN

17

T C +CN

29

TLSKECQPNCN

39

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 21.08 out of 23.43

Confidence: medium

Additional weak hits (12):

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.40 out of 29.38

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 19.26

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.78 out of 31.73

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.35 out of 18.57

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.76 out of 27.78

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.04 out of 21.55

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.84 out of 35.63

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.17 out of 29.65

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.18 out of 33.14

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.35 out of 33.14

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lanthipeptides

RREFinder

TFBS Finder

Core peptide predictions

CDS_05594 - Class I

Cleavage pHMM score: 0.00

RODEO score: 21

Monoisotopic mass: 2727.2 Da

Molecular weight: 2729.1 Da

Number of bridges: 5

Alternative weights: (assuming N unmodified Ser/Thr residues); 2747.1 Da N = 1; 2765.2 Da N = 2

RRE predictions

: RRE type: Lanthipeptide_LanB_RRE; Location: 194 - 281; Score: 55.1

TFBS definitions

Regulator	Description
BldD	Development and antibiotic global regulator

NPDC089509.ctg-0016 - Region 1 - terpene-precursor

Download region GenBank file

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Location: 141,786 - 163,959 nt. (total: 22,174 nt) Show pHMM detection rules used

terpene-precursor: (PT_FPPS_like and not PT_HPP)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: methyltransferase

CDS_05763: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

Hydrolases: hydrolase

CDS_05758: isochorismatase

smcogs: SMCOG1027: isochorismatase

Ligases: synthetase

CDS_05760: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

CDS_05761: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000677.5	0.46	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002309.2	0.42	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000817.4	0.42	other (other)	methylarcyriarubin	uncultured bacterium
BGC0001911.3	0.41	terpene	raimonol	Streptomyces anulatus
BGC0000665.5	0.40	other (other), terpene	xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C	Streptomyces sp. HKI0576
BGC0000642.3	0.40	terpene	carotenoid	Enterobacteriaceae bacterium DC413
BGC0001221.5	0.39	other (phenazine)	marinophenazine A, phenaziterpene A	Streptomyces sp. CNQ-509
BGC0001910.4	0.39	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0001456.3	0.39	terpene	isorenieratene	Streptomyces argillaceus
BGC0000664.5	0.38	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000677.5	0.46	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002309.2	0.42	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000817.4	0.42	other (other)	methylarcyriarubin	uncultured bacterium
BGC0001911.3	0.41	terpene	raimonol	Streptomyces anulatus
BGC0000665.5	0.40	other (other), terpene	xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C	Streptomyces sp. HKI0576
BGC0000642.3	0.40	terpene	carotenoid	Enterobacteriaceae bacterium DC413
BGC0001221.5	0.39	other (phenazine)	marinophenazine A, phenaziterpene A	Streptomyces sp. CNQ-509
BGC0001910.4	0.39	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0001456.3	0.39	terpene	isorenieratene	Streptomyces argillaceus
BGC0000664.5	0.38	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Product name	Chain length	Initial cyclisations	Functional groups
sesquiterpene precursor	FPP	C15	acyclic	PP
diterpene precursor	GGPP	C20	acyclic	PP
sesterterpene precursor	GFPP	C25	acyclic	PP
triterpene precursor	HPP	C30	acyclic	PP

Genes with terpene domains:

CDS_05760: PT_FPPS_like

Domain 1 (61 - 337): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

Reactions:: IPP, DMAPP → FPP; IPP, DMAPP → GGPP; IPP, DMAPP → GFPP; IPP, DMAPP → HPP

CDS_05761: PT_FPPS_like

Domain 1 (60 - 338): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

Reactions:: IPP, DMAPP → FPP; IPP, DMAPP → GGPP; IPP, DMAPP → GFPP; IPP, DMAPP → HPP

Transcription Factor Binding Sites

Binding sites found:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47

Confidence: medium

Additional weak hits (10):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.28 out of 26.33

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.97 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.58 out of 30.25

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.71 out of 21.55

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.54 out of 36.54

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.83 out of 26.06

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.94 out of 27.18

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
GFPP	Geranylfarnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
HPP	Hexaprenyl diphosphate
IPP	Isopentenyl diphosphate
PP	Diphosphate

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0017 - Region 1 - PKS-like

Download region GenBank file

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Location: 1 - 23,745 nt. (total: 23,745 nt) Show pHMM detection rules used

Region on contig edge.

PKS-like: (t2pks2 or ksIII)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Ligases: synthase

CDS_05798: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001485.4	0.36	other (other)	chuangxinmycin	Actinoplanes tsinanensis
BGC0001810.3	0.36	PKS	trehangelin	Polymorphospora rubra
BGC0001483.4	0.35	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8
BGC0002227.3	0.35	NRPS	AKML B, AKML D, AKML A, AKML C	Aspergillus luchuensis IFO 4308
BGC0000843.5	0.33	other (non-nrp beta-lactam)	alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate	Streptomyces clavuligerus ATCC 27064
BGC0000248.5	0.32	PKS	α naphtocyclinoic acid, fogacin	Streptomyces arenae DSM 40737
BGC0001521.3	0.32	NRPS	auriculamide	Herpetosiphon aurantiacus DSM 785
BGC0000214.5	0.30	PKS	cosmomycin B	Streptomyces olindensis
BGC0000217.5	0.30	PKS	daunorubicin	Streptomyces sp.
BGC0002361.3	0.30	PKS, saccharide	baikalomycin B, baikalomycin A, baikalomycin C	Streptomyces sp. IB201691-2A2

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001485.4	0.36	other (other)	chuangxinmycin	Actinoplanes tsinanensis
BGC0001810.3	0.36	PKS	trehangelin	Polymorphospora rubra
BGC0001483.4	0.35	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8
BGC0002227.3	0.35	NRPS	AKML B, AKML D, AKML A, AKML C	Aspergillus luchuensis IFO 4308
BGC0000843.5	0.33	other (non-nrp beta-lactam)	alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate	Streptomyces clavuligerus ATCC 27064
BGC0000248.5	0.32	PKS	α naphtocyclinoic acid, fogacin	Streptomyces arenae DSM 40737
BGC0001521.3	0.32	NRPS	auriculamide	Herpetosiphon aurantiacus DSM 785
BGC0000214.5	0.30	PKS	cosmomycin B	Streptomyces olindensis
BGC0000217.5	0.30	PKS	daunorubicin	Streptomyces sp.
BGC0002361.3	0.30	PKS, saccharide	baikalomycin B, baikalomycin A, baikalomycin C	Streptomyces sp. IB201691-2A2

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.31 out of 23.79

Confidence: medium

Additional weak hits (1):

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.87 out of 29.65

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism

NPDC089509.ctg-0017 - Region 2 - NRPS-like

Download region GenBank file

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Location: 79,709 - 121,532 nt. (total: 41,824 nt) Show pHMM detection rules used

NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: aminotransferase

CDS_05893: aminotransferase

smcogs: SMCOG1019: aminotransferase

Hydrolases: hydrolase

CDS_05896: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: dehydratase

CDS_05886: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase

CDS_05894: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_05895: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001641.4	0.61	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001273.3	0.61	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.61	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001128.4	0.61	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.61	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.61	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001276.3	0.61	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0000107.3	0.61	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0002175.3	0.61	PKS	YWA1	Aspergillus oryzae RIB40
BGC0002174.2	0.60	NRPS	ε-Poly-L-lysine	Epichloe festucae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001641.4	0.61	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001273.3	0.61	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.61	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001128.4	0.61	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.61	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.61	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001276.3	0.61	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0000107.3	0.61	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0002175.3	0.61	PKS	YWA1	Aspergillus oryzae RIB40
BGC0002174.2	0.60	NRPS	ε-Poly-L-lysine	Epichloe festucae

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.75 out of 23.79

Confidence: medium

Additional weak hits (4):

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.35 out of 30.97

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.32 out of 27.78

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 35.63

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 2, location 79708 - 121532:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Arg)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_05894: Arg

Search NORINE for peptide: strict or relaxed

AMP-binding (10..395): Arg

nrpys: Arg

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVEELGVITK
Nearest Stachelhaus code(s):: Arg DVEEIGAITK (56% 8Å match)
Stachelhaus code match:: 80% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism

NPDC089509.ctg-0020 - Region 1 - methanobactin

Download region GenBank file

Download region SVG

Location: 70,276 - 92,729 nt. (total: 22,454 nt) Show pHMM detection rules used

methanobactin: (DUF692 and MbnC)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxidoreductase

CDS_06387: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

Hydrolases: hydrolase

CDS_06407: hydrolase

smcogs: SMCOG1179: hydrolase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002150.2	0.43	ribosomal	triculamin	Streptomyces triculaminicus
BGC0002151.2	0.43	ribosomal	alboverticillin	Streptomyces griseocarneus
BGC0002442.3	0.42	ribosomal	toyoncin	Bacillus toyonensis
BGC0001210.5	0.42	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0001552.3	0.42	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000513.3	0.42	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0001229.4	0.42	ribosomal	SBI-06990 A1, SBI-06989 A2	Streptomyces bingchenggensis BCW-1
BGC0002116.3	0.42	ribosomal	darobactin A	Photorhabdus khanii HGB 1456
BGC0000571.3	0.41	ribosomal	burhizin	Paraburkholderia rhizoxinica HKI 454

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002150.2	0.43	ribosomal	triculamin	Streptomyces triculaminicus
BGC0002151.2	0.43	ribosomal	alboverticillin	Streptomyces griseocarneus
BGC0002442.3	0.42	ribosomal	toyoncin	Bacillus toyonensis
BGC0001210.5	0.42	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0001552.3	0.42	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000513.3	0.42	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0001229.4	0.42	ribosomal	SBI-06990 A1, SBI-06989 A2	Streptomyces bingchenggensis BCW-1
BGC0002116.3	0.42	ribosomal	darobactin A	Photorhabdus khanii HGB 1456
BGC0000571.3	0.41	ribosomal	burhizin	Paraburkholderia rhizoxinica HKI 454

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.07 out of 20.47

Confidence: medium

Additional weak hits (6):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.20 out of 30.22

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.39 out of 30.25

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.18 out of 27.55

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.12 out of 29.65

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.29 out of 28.14

Confidence: weak

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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TFBS Finder

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0020 - Region 2 - NRPS

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Location: 118,143 - 173,171 nt. (total: 55,029 nt) Show pHMM detection rules used

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

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NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

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Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase reductase

CDS_06440: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

CDS_06445: alkyl hydroperoxide reductase subunit

smcogs: SMCOG1176: alkyl hydroperoxide reductase subunit

CDS_06452: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase methyltransferase

CDS_06437: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

CDS_06446: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_06451: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

CDS_06471: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: deaminase hydrolase

CDS_06449: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

CDS_06467: ornithine cyclodeaminase

smcogs: SMCOG1158: ornithine cyclodeaminase

Ligases: ligase synthase

CDS_06454: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_06457: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_06458: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_06459: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

Translocases: transport

CDS_06466: MMPL domain-containing transport protein

smcogs: SMCOG1035: MMPL domain-containing transport protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001833.4	0.73	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.73	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2	0.71	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000426.5	0.71	NRPS	sevadicin	Paenibacillus larvae
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4	0.70	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.70	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001833.4	0.73	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.73	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2	0.71	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000426.5	0.71	NRPS	sevadicin	Paenibacillus larvae
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4	0.70	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.70	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26

Confidence: medium

Additional weak hits (8):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.61 out of 30.22

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.12 out of 23.43

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.80 out of 30.25

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.43 out of 24.78

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.62 out of 26.85

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.97 out of 26.06

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.26 out of 32.93

Confidence: weak

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.77 out of 32.38

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 2, location 118142 - 173171:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X - D-X) + (X - Gly)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_06457: X - Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (470..877): X

nrpys: Dpr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DIWEVTADDK
Nearest Stachelhaus code(s):: Dpr DIWEVTADDK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1539..1941): Gly

nrpys: Gly

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
Single AA prediction:: gly (Gly)

Stachelhaus prediction details:

Stachelhaus sequence:: DILQLGLIWK
Nearest Stachelhaus code(s):: Gly DILQLGLIWK (85% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_06458: X - X

AMP-binding (472..875): X

nrpys: Dpr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DIWEVTADDK
Nearest Stachelhaus code(s):: Dpr DIWEVTADDK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1537..1941): X

nrpys: Leu, Met

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
Small clusters prediction:: Unpolar aromatic ring (Phe, Trp)
Single AA prediction:: phe (Phe)

Stachelhaus prediction details:

Stachelhaus sequence:: DAWCIAAVCK
Nearest Stachelhaus code(s):: Leu or Met DAWCIAAVCK (74% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein

NPDC089509.ctg-0022 - Region 1 - terpene

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Location: 94,206 - 121,042 nt. (total: 26,837 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

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TFBS Finder

Pfam domains

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Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_06725: dehydrogenase

smcogs: SMCOG1181: dehydrogenase

CDS_06732: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

CDS_06742: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase transferase

CDS_06724: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs: SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

CDS_06738: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Ligases: synthase synthetase

CDS_06733: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

CDS_06737: 1-deoxy-D-xylulose-5-phosphate synthase

smcogs: SMCOG1110: 1-deoxy-D-xylulose-5-phosphate synthase

Translocases: permease

CDS_06720: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001248.3	0.74	terpene	clavaric acid	Hypholoma sublateritium
BGC0000663.5	0.70	terpene	hopene	Streptomyces coelicolor A3(2)
BGC0000647.3	0.57	terpene	carotenoid	Rhodobacter sphaeroides
BGC0002276.2	0.55	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000648.3	0.52	terpene	carotenoid	Myxococcus xanthus
BGC0000656.5	0.50	terpene	zeaxanthin	Xanthobacter autotrophicus Py2
BGC0001361.3	0.50	terpene	sodorifen	Serratia plymuthica 4Rx13
BGC0002283.2	0.50	terpene	sodorifen	Serratia plymuthica
BGC0001839.3	0.50	terpene	squalestatin S1	Aspergillus sp. Z5
BGC0000630.3	0.49	terpene	(2R,3S,3'S)-2-hydroxyastaxanthin	Paracoccus haeundaensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001248.3	0.74	terpene	clavaric acid	Hypholoma sublateritium
BGC0000663.5	0.70	terpene	hopene	Streptomyces coelicolor A3(2)
BGC0000647.3	0.57	terpene	carotenoid	Rhodobacter sphaeroides
BGC0002276.2	0.55	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000648.3	0.52	terpene	carotenoid	Myxococcus xanthus
BGC0000656.5	0.50	terpene	zeaxanthin	Xanthobacter autotrophicus Py2
BGC0001361.3	0.50	terpene	sodorifen	Serratia plymuthica 4Rx13
BGC0002283.2	0.50	terpene	sodorifen	Serratia plymuthica
BGC0001839.3	0.50	terpene	squalestatin S1	Aspergillus sp. Z5
BGC0000630.3	0.49	terpene	(2R,3S,3'S)-2-hydroxyastaxanthin	Paracoccus haeundaensis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
triterpene	hopanoid		C30	hopanoid skeleton	unknown
triterpene	polypodane		C30	polypodane skeleton	unknown

Genes with terpene domains:

CDS_06730: PT_phytoene_like

Domain 1 (19 - 318): Prenyltransferase; Phytoene synthase like

Subtype: unknown

Reactions:: FPP → squalene; FPP → PSPP; FPP → diapophytoene; GGPP → phytoene; PSPP → hydroxysqualene

CDS_06731: PT_phytoene_like

Domain 1 (2 - 279): Prenyltransferase; Phytoene synthase like

Subtype: unknown

Reactions:: FPP → squalene; FPP → PSPP; FPP → diapophytoene; GGPP → phytoene; PSPP → hydroxysqualene

CDS_06733: PT_FPPS_like

Domain 1 (65 - 355): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

Reactions:: IPP, DMAPP → FPP; IPP, DMAPP → GGPP; IPP, DMAPP → GFPP; IPP, DMAPP → HPP

CDS_06734: T2TS

Domain 1 (53 - 675): Type 2 terpene synthase

Subtype: Squalene substrate

Reactions:: squalene → hopanoid; squalene → polypodane

Transcription Factor Binding Sites

Binding sites found:

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12

Confidence: medium

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52

Confidence: strong

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

Additional weak hits (12):

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.07 out of 25.88

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 19.26

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.38 out of 30.25

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.74 out of 32.74

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.03 out of 29.38

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.20 out of 24.78

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.94 out of 29.65

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.45 out of 23.43

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.62 out of 29.65

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.53 out of 28.14

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.42 out of 39.62

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.87 out of 30.98

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
GFPP	Geranylfarnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
HPP	Hexaprenyl diphosphate
IPP	Isopentenyl diphosphate
PSPP	Presqualene diphosphate

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
OsdR	Development and stress management regulator

NPDC089509.ctg-0022 - Region 2 - terpene

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Location: 131,314 - 152,261 nt. (total: 20,948 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

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resistance

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

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Terpene

TFBS Finder

Pfam domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_06762: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

Hydrolases: hydrolase

CDS_06760: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: cyclase

CDS_06763: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Translocases: transporter

CDS_06767: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000683.3	0.77	terpene	avermitilol	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000674.5	0.44	terpene	(-)-δ-cadinene	Streptomyces clavuligerus ATCC 27064
BGC0002285.2	0.39	ribosomal	aborycin	Streptomyces sp. ZS0098
BGC0000678.5	0.38	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002535.2	0.36	NRPS	γ-poly-L-2,4-diaminobutyric acid	Streptomyces celluloflavus
BGC0000804.5	0.35	saccharide	acarviostatin I03, acarviostatin II03, acarviostatin III03, acarviostatin IV03	Streptomyces coelicoflavus ZG0656
BGC0001865.4	0.34	PKS	elsinochrome C	Parastagonospora nodorum SN15
BGC0000709.5	0.34	saccharide	neomycin	Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000711.5	0.33	saccharide	neomycin	Streptomyces fradiae
BGC0000495.5	0.33	ribosomal	actagardine	Actinoplanes garbadinensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000683.3	0.77	terpene	avermitilol	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000674.5	0.44	terpene	(-)-δ-cadinene	Streptomyces clavuligerus ATCC 27064
BGC0002285.2	0.39	ribosomal	aborycin	Streptomyces sp. ZS0098
BGC0000678.5	0.38	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002535.2	0.36	NRPS	γ-poly-L-2,4-diaminobutyric acid	Streptomyces celluloflavus
BGC0000804.5	0.35	saccharide	acarviostatin I03, acarviostatin II03, acarviostatin III03, acarviostatin IV03	Streptomyces coelicoflavus ZG0656
BGC0001865.4	0.34	PKS	elsinochrome C	Parastagonospora nodorum SN15
BGC0000709.5	0.34	saccharide	neomycin	Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000711.5	0.33	saccharide	neomycin	Streptomyces fradiae
BGC0000495.5	0.33	ribosomal	actagardine	Actinoplanes garbadinensis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

No product predictions

Genes with terpene domains:

CDS_06763: T1TS

Domain 1 (5 - 312): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (8):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.33 out of 21.55

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.37 out of 26.12

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.92 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.28 out of 26.06

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.45 out of 21.55

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.01 out of 30.25

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.24 out of 20.97

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.61 out of 29.65

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

No acronyms to display

TFBS definitions

Regulator	Description

NPDC089509.ctg-0023 - Region 1 - HR-T2PKS,NRPS,thioamide-NRP

Download region GenBank file

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Location: 31,850 - 110,069 nt. (total: 78,220 nt) Show pHMM detection rules used

HR-T2PKS: (hr-t2pks-ksa and (t2fas or APE_KS2 or ketoacyl-synt))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
thioamide-NRP: (ATP-grasp and AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC))

Legend:

core biosynthetic genes

additional biosynthetic genes

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other genes

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binding site

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Select a gene to view the details available for it

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Pfam domains

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NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_06827: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

CDS_06828: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_06841: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_06856: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase

CDS_06840: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: deaminase

CDS_06826: ornithine cyclodeaminase

smcogs: SMCOG1158: ornithine cyclodeaminase

Lyases: decarboxylase

CDS_06845: diaminopimelate decarboxylase

smcogs: SMCOG1264: diaminopimelate decarboxylase

CDS_06853: putative carboxymuconolactone decarboxylase

smcogs: SMCOG1298: putative carboxymuconolactone decarboxylase

Ligases: ligase synthase

CDS_06829: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_06830: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_06833: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_06834: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_06835: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

CDS_06847: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

Translocases: transport

CDS_06839: MMPL domain-containing transport protein

smcogs: SMCOG1035: MMPL domain-containing transport protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	1.31	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002075.3	1.28	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0002135.2	1.24	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001132.4	1.23	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	1.23	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	1.22	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002286.3	1.20	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001623.4	1.20	NRPS, PKS	ishigamide	Streptomyces sp. MSC090213JE08
BGC0001758.4	1.17	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	1.14	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001623.4	0.76	NRPS, PKS	ishigamide	Streptomyces sp. MSC090213JE08
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001128.4	0.73	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.73	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.73	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001758.4	0.72	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.71	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.19 out of 20.47

Confidence: strong

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.78 out of 20.97

Confidence: medium

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.15 out of 29.72

Confidence: medium

Additional weak hits (21):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.93 out of 29.38

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.19 out of 21.55

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.94 out of 27.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.78 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.69 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.57 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.08 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.74 out of 29.38

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.10 out of 20.97

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.64 out of 27.55

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.83 out of 33.14

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.81 out of 29.65

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.98 out of 24.78

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.24 out of 29.65

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.14 out of 18.57

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.44 out of 28.19

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.19 out of 35.63

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.32 out of 30.98

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 31849 - 110069:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Thr - Ile) + (D-X - X) + (Gly - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 31849 - 74350:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Thr - Ile) + (D-X - X) + (Gly - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 35214 - 110069:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Thr - Ile) + (D-X - X) + (Gly - X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_06833: Thr - Ile

Search NORINE for peptide: strict or relaxed

AMP-binding (507..907): Thr

nrpys: Thr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: thr (Thr)
Single AA prediction:: thr (Thr)

Stachelhaus prediction details:

Stachelhaus sequence:: DFWNVGMVHK
Nearest Stachelhaus code(s):: Thr DFWNVGMVHK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1601..2000): Ile

nrpys: Ile

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: val (Val)

Stachelhaus prediction details:

Stachelhaus sequence:: DAFFLGVTFK
Nearest Stachelhaus code(s):: Ile DAFFLGVTFK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_06834: X - X

AMP-binding (489..912): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVWEVTADDK
Nearest Stachelhaus code(s):: Ser DVWEMTADDK (97% 8Å match); Dpr DIWEVTADDK (85% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (2086..2496): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVWEVTADDK
Nearest Stachelhaus code(s):: Ser DVWEMTADDK (97% 8Å match); Dpr DIWEVTADDK (85% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_06836: Gly - X

Search NORINE for peptide: strict or relaxed

AMP-binding (492..893): Gly

nrpys: Gly

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
Single AA prediction:: gly (Gly)

Stachelhaus prediction details:

Stachelhaus sequence:: DILQLGVVWK
Nearest Stachelhaus code(s):: Gly DILQLGVVWK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1577..2001): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
Small clusters prediction:: Unpolar aromatic ring (Phe, Trp)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DAWIAGAVCK
Nearest Stachelhaus code(s):: Leu DAWILGAVAK (88% 8Å match)
Stachelhaus code match:: 80% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
NtrC	Nitrogen regulatory protein C
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0024 - Region 1 - NRPS

Download region GenBank file

Download region SVG

Location: 68,188 - 127,216 nt. (total: 59,029 nt) Show pHMM detection rules used

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_07008: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_07010: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CDS_07028: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: acetyltransferase acylase aminotransferase

CDS_06993: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

CDS_07006: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_07013: aminotransferase

smcogs: SMCOG1019: aminotransferase

Hydrolases: hydrolase

CDS_07011: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Ligases: ligase

CDS_07012: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07015: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_07016: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.75	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001833.4	0.73	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0000426.5	0.72	NRPS	sevadicin	Paenibacillus larvae
BGC0001132.4	0.72	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4	0.71	NRPS	enniatin	Fusarium equiseti
BGC0001758.4	0.70	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002135.2	0.70	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.75	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001833.4	0.73	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0000426.5	0.72	NRPS	sevadicin	Paenibacillus larvae
BGC0001132.4	0.72	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4	0.71	NRPS	enniatin	Fusarium equiseti
BGC0001758.4	0.70	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002135.2	0.70	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47

Confidence: medium

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.17 out of 23.43

Confidence: medium

Additional weak hits (12):

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.04 out of 21.84

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.15 out of 30.25

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.22 out of 31.73

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.26 out of 20.01

Confidence: weak

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.87 out of 20.01

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.09 out of 33.14

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.38 out of 23.43

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.57 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.95 out of 32.93

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 68187 - 127216:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (NH2 - Lys) + (D-X) + (Ser)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07006: mal

PKS_AT (110..419): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 70.8%; inactive: 58.3%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 87.7
Methoxymalonyl-CoA: 66.5
Methylmalonyl-CoA: 44.3
inactive: 37.9
Propionyl-CoA: 36.4
fatty_acid: 28.5
Isobutyryl-CoA: 24.0
CHC-CoA: 19.2
Acetyl-CoA: 17.4
2-Methylbutyryl-CoA: 15.9
3-Methylbutyryl-CoA: 13.7
Ethylmalonyl-CoA: 13.3
Benzoyl-CoA: 10.2
trans-1,2-CPDA: 7.1

CDS_07012: NH2 - Lys

Search NORINE for peptide: strict or relaxed

CAL_domain (47..508): NH2

minowa: NH2

Prediction, score:

NH2: 150.2
fatty_acid: 16.2
Acetyl-CoA: 5.3
AHBA: 3.9
shikimic_acid: -4.0

AMP-binding (1176..1584): Lys

nrpys: Lys

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DTEDIGSIVK
Nearest Stachelhaus code(s):: Lys DTEDIGSVVK (76% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_07015: X

AMP-binding (504..923): X

nrpys: Ahp

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVEEIGVVTK
Nearest Stachelhaus code(s):: Ahp DVENAGVVTK (50% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_07016: Ser

Search NORINE for peptide: strict or relaxed

AMP-binding (469..870): Ser

nrpys: Ser

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: ser (Ser)
Single AA prediction:: ser (Ser)

Stachelhaus prediction details:

Stachelhaus sequence:: DVWHFSLVDK
Nearest Stachelhaus code(s):: Ser DVWHFSLVDK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
BldD	Development and antibiotic global regulator
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0026 - Region 1 - NI-siderophore

Download region GenBank file

Download region SVG

Location: 38,003 - 71,690 nt. (total: 33,688 nt) Show pHMM detection rules used

NI-siderophore: IucA_IucC

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

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resistance

TTA codons

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxygenase

CDS_07218: lysine/ornithine N-monooxygenase

smcogs: SMCOG1080: lysine/ornithine N-monooxygenase

CDS_07231: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002692.2	0.64	other (other)	speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B	Kribbella speibonae
BGC0001572.3	0.61	other (other)	desferrioxamine E	Pantoea agglomerans
BGC0002469.2	0.59	other (other)	woodybactin A, woodybactin B, woodybactin C, woodybactin D	Shewanella woodyi ATCC 51908
BGC0001713.5	0.55	other (other)	ochrobactin	Ochrobactrum anthropi
BGC0000942.4	0.54	other (other)	petrobactin	Bacillus anthracis str. Ames
BGC0000295.5	0.54	NRPS	acinetoferrin	Acinetobacter haemolyticus
BGC0001478.5	0.54	other (other)	desferrioxamine E	Streptomyces sp. ID38640
BGC0001498.5	0.53	other (other)	aerobactin	Xenorhabdus szentirmaii DSM 16338
BGC0000941.3	0.53	other (other)	desferrioxamin B	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001531.5	0.52	other (other)	bisucaberin B	Tenacibaculum mesophilum

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002692.2	0.64	other (other)	speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B	Kribbella speibonae
BGC0001572.3	0.61	other (other)	desferrioxamine E	Pantoea agglomerans
BGC0002469.2	0.59	other (other)	woodybactin A, woodybactin B, woodybactin C, woodybactin D	Shewanella woodyi ATCC 51908
BGC0001713.5	0.55	other (other)	ochrobactin	Ochrobactrum anthropi
BGC0000942.4	0.54	other (other)	petrobactin	Bacillus anthracis str. Ames
BGC0000295.5	0.54	NRPS	acinetoferrin	Acinetobacter haemolyticus
BGC0001478.5	0.54	other (other)	desferrioxamine E	Streptomyces sp. ID38640
BGC0001498.5	0.53	other (other)	aerobactin	Xenorhabdus szentirmaii DSM 16338
BGC0000941.3	0.53	other (other)	desferrioxamin B	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001531.5	0.52	other (other)	bisucaberin B	Tenacibaculum mesophilum

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.47 out of 27.18

Confidence: strong

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.93 out of 24.78

Confidence: medium

Additional weak hits (10):

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.12 out of 32.74

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.11 out of 27.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.57 out of 27.78

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.16 out of 36.53

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.09 out of 29.65

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.77 out of 25.88

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.59 out of 29.65

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.32 out of 24.78

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.04 out of 27.18

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description
LexA variant 2	Repressor of DNA damage response
NrdR	Represses ribonucleotide reductase encoding genes

NPDC089509.ctg-0027 - Region 1 - NRPS

Download region GenBank file

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Location: 85,486 - 129,748 nt. (total: 44,263 nt) Show pHMM detection rules used

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

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NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_07373: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

CDS_07382: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CDS_07392: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_07403: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

CDS_07407: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: aminotransferase

CDS_07390: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Hydrolases: amidase dehalogenase

CDS_07374: amidase

smcogs: SMCOG1105: amidase

CDS_07401: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Lyases: decarboxylase dehydratase

CDS_07378: diaminopimelate decarboxylase

smcogs: SMCOG1264: diaminopimelate decarboxylase

CDS_07389: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000357.5	0.68	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0002164.2	0.63	NRPS	peramine	Epichloe festucae
BGC0001135.5	0.63	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.63	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.63	NRPS	AM-toxin	Alternaria alternata
BGC0000307.4	0.62	NRPS	AbT1	Aureobasidium pullulans
BGC0001240.4	0.62	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001249.5	0.62	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001166.5	0.62	NRPS	HC-toxin	Alternaria jesenskae
BGC0000342.4	0.62	NRPS	enniatin	Fusarium equiseti

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000357.5	0.68	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0002164.2	0.63	NRPS	peramine	Epichloe festucae
BGC0001135.5	0.63	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.63	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.63	NRPS	AM-toxin	Alternaria alternata
BGC0000307.4	0.62	NRPS	AbT1	Aureobasidium pullulans
BGC0001240.4	0.62	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001249.5	0.62	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001166.5	0.62	NRPS	HC-toxin	Alternaria jesenskae
BGC0000342.4	0.62	NRPS	enniatin	Fusarium equiseti

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47

Confidence: strong

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 19.09 out of 20.01

Confidence: strong

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.47 out of 23.79

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.68 out of 19.26

Confidence: medium

Additional weak hits (15):

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.66 out of 28.14

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.83 out of 27.78

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.07 out of 31.73

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.37 out of 29.65

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.11 out of 27.04

Confidence: weak

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.00 out of 32.38

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.64 out of 23.43

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.04 out of 23.43

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.92 out of 30.97

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.67 out of 30.97

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.73 out of 27.78

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.06 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.16 out of 29.65

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.06 out of 28.19

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.55 out of 20.01

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 85485 - 129748:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (D-Asp)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07389: Asp

Search NORINE for peptide: strict or relaxed

AMP-binding (22..425): Asp

nrpys: Asp

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: asp,asn (Asp, Asn)
Single AA prediction:: asp (Asp)

Stachelhaus prediction details:

Stachelhaus sequence:: DLTKLGHVGK
Nearest Stachelhaus code(s):: Asp DLTKVGHVGK (74% 8Å match); Asn DLTKLGEVGK (62% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
ArgR	Regulator of arginine biosynthesis genes
CRP	Cyclic AMP receptor protein
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0028 - Region 1 - ectoine

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Location: 24,168 - 34,542 nt. (total: 10,375 nt) Show pHMM detection rules used

ectoine: ectoine_synt

Legend:

core biosynthetic genes

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resistance

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Select a gene to view the details available for it

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Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_07449: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

Ligases: ligase

CDS_07444: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001778.5	0.52	other (other)	showdomycin	Streptomyces showdoensis
BGC0000858.3	0.49	other (other)	ectoine	Methylobacter marinus
BGC0002097.3	0.45	NRPS, PKS, saccharide	kosinostatin	Micromonospora sp. 28ISP2-46
BGC0000343.5	0.45	NRPS	enterobactin	Pseudomonas sp. J465
BGC0001073.5	0.44	NRPS, PKS	kosinostatin	Micromonospora sp. TP-A0468
BGC0001168.5	0.42	NRPS	Livipeptin	Streptomyces lividans 1326
BGC0001463.4	0.41	other (other)	2,3,4,5-tetrabromopyrrole	Pseudoalteromonas piscicida
BGC0001464.3	0.41	other (other)	tetrabromopyrrole	Pseudoalteromonas sp. PS5
BGC0001517.3	0.40	NRPS	asperphenamate	Aspergillus terreus NIH2624
BGC0001895.4	0.40	PKS	huanglongmycin A, huanglongmycin B, huanglongmycin C	Streptomyces sp. CB09001

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001778.5	0.52	other (other)	showdomycin	Streptomyces showdoensis
BGC0000858.3	0.49	other (other)	ectoine	Methylobacter marinus
BGC0002097.3	0.45	NRPS, PKS, saccharide	kosinostatin	Micromonospora sp. 28ISP2-46
BGC0000343.5	0.45	NRPS	enterobactin	Pseudomonas sp. J465
BGC0001073.5	0.44	NRPS, PKS	kosinostatin	Micromonospora sp. TP-A0468
BGC0001168.5	0.42	NRPS	Livipeptin	Streptomyces lividans 1326
BGC0001463.4	0.41	other (other)	2,3,4,5-tetrabromopyrrole	Pseudoalteromonas piscicida
BGC0001464.3	0.41	other (other)	tetrabromopyrrole	Pseudoalteromonas sp. PS5
BGC0001517.3	0.40	NRPS	asperphenamate	Aspergillus terreus NIH2624
BGC0001895.4	0.40	PKS	huanglongmycin A, huanglongmycin B, huanglongmycin C	Streptomyces sp. CB09001

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

NPDC089509.ctg-0028 - Region 2 - terpene

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Location: 116,685 - 136,446 nt. (total: 19,762 nt) Show pHMM detection rules used

Region on contig edge.

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

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Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_07525: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_07537: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase

CDS_07528: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: hydrolase protease

CDS_07522: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

CDS_07524: HAD-superfamily hydrolase, subfamily IA, variant

smcogs: SMCOG1115: HAD-superfamily hydrolase, subfamily IA, variant

Lyases: cyclase

CDS_07533: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001746.3	0.76	terpene	pristinol	Streptomyces pristinaespiralis ATCC 25486
BGC0002276.2	0.52	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0001310.5	0.50	PKS	naringenin	Streptomyces clavuligerus ATCC 27064
BGC0001224.5	0.44	other (other)	reductasporine	uncultured bacterium
BGC0000902.4	0.41	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0001336.5	0.41	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0002482.2	0.40	other (other)	tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M	Symphyonema bifilamentata 97.28
BGC0000903.3	0.40	other (other)	fluorometabolite	Streptomyces cattleya
BGC0001605.3	0.40	terpene	gibberellin	Sinorhizobium fredii NGR234
BGC0002347.3	0.39	other (other)	cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D	Actinoalloteichus caeruleus WH1-2216-6

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001746.3	0.76	terpene	pristinol	Streptomyces pristinaespiralis ATCC 25486
BGC0002276.2	0.52	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0001310.5	0.50	PKS	naringenin	Streptomyces clavuligerus ATCC 27064
BGC0001224.5	0.44	other (other)	reductasporine	uncultured bacterium
BGC0000902.4	0.41	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0001336.5	0.41	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0002482.2	0.40	other (other)	tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M	Symphyonema bifilamentata 97.28
BGC0000903.3	0.40	other (other)	fluorometabolite	Streptomyces cattleya
BGC0001605.3	0.40	terpene	gibberellin	Sinorhizobium fredii NGR234
BGC0002347.3	0.39	other (other)	cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D	Actinoalloteichus caeruleus WH1-2216-6

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

No product predictions

Genes with terpene domains:

CDS_07533: T1TS

Domain 1 (2 - 327): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (8):

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.31 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.50 out of 28.14

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 18.77 out of 33.73

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.14 out of 32.93

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.75 out of 21.55

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.53 out of 21.55

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.76 out of 28.19

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.62 out of 27.04

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

No acronyms to display

TFBS definitions

Regulator	Description

NPDC089509.ctg-0029 - Region 1 - T3PKS

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Location: 1 - 22,455 nt. (total: 22,455 nt) Show pHMM detection rules used

Region on contig edge.

T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

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TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxygenase

CDS_07547: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: methyltransferase

CDS_07560: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: deformylase

CDS_07559: peptide deformylase

smcogs: SMCOG1275: peptide deformylase

Ligases: synthase

CDS_07546: chalcone and stilbene synthase domain protein

smcogs: SMCOG1024: chalcone and stilbene synthase domain protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001310.5	0.82	PKS	naringenin	Streptomyces clavuligerus ATCC 27064
BGC0002127.3	0.71	PKS	flaviolin, 1,3,6,8-tetrahydroxynaphthalene	Streptomyces coelicolor A3(2)
BGC0000902.4	0.67	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0000285.5	0.61	PKS, saccharide	flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin	Saccharopolyspora erythraea
BGC0002084.4	0.57	ribosomal	biarylitide YYH	Planomonospora sp. ID82291
BGC0002099.3	0.57	ribosomal	biarylitide YFH	Planomonospora sp. ID107089
BGC0000844.5	0.50	other (other)	clavulanic acid	Streptomyces clavuligerus
BGC0001948.3	0.49	other (other)	naseseazine C, C3-aryl pyrroloindolines	Streptomyces sp.
BGC0000280.5	0.48	PKS	2,4-diacetylphloroglucinol	Pseudomonas fluorescens
BGC0000281.3	0.47	PKS	2,4-diacetylphloroglucinol	Pseudomonas fluorescens

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001310.5	0.82	PKS	naringenin	Streptomyces clavuligerus ATCC 27064
BGC0002127.3	0.71	PKS	flaviolin, 1,3,6,8-tetrahydroxynaphthalene	Streptomyces coelicolor A3(2)
BGC0000902.4	0.67	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0000285.5	0.61	PKS, saccharide	flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin	Saccharopolyspora erythraea
BGC0002084.4	0.57	ribosomal	biarylitide YYH	Planomonospora sp. ID82291
BGC0002099.3	0.57	ribosomal	biarylitide YFH	Planomonospora sp. ID107089
BGC0000844.5	0.50	other (other)	clavulanic acid	Streptomyces clavuligerus
BGC0001948.3	0.49	other (other)	naseseazine C, C3-aryl pyrroloindolines	Streptomyces sp.
BGC0000280.5	0.48	PKS	2,4-diacetylphloroglucinol	Pseudomonas fluorescens
BGC0000281.3	0.47	PKS	2,4-diacetylphloroglucinol	Pseudomonas fluorescens

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.64 out of 27.55

Confidence: medium

Additional weak hits (2):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.70 out of 26.33

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
GnfM	Regulator of nitrogen-fixation genes

NPDC089509.ctg-0031 - Region 1 - azole-containing-RiPP

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Location: 54,144 - 78,031 nt. (total: 23,888 nt) Show pHMM detection rules used

azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)

Legend:

core biosynthetic genes

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TFBS Finder

Azole RiPPs

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_07834: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000565.5	0.53	ribosomal	goadsporin	Streptomyces sp. TP-A0584
BGC0002698.2	0.52	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0001555.4	0.52	ribosomal	colicin V	Escherichia coli chi7122
BGC0002005.2	0.51	ribosomal	RaxX	Xanthomonas oryzae pv. oryzae
BGC0000590.5	0.50	ribosomal	microcin N	Escherichia coli
BGC0002699.2	0.49	ribosomal	nostolysamide A, nostolysamide B	Nostoc punctiforme PCC 73102
BGC0002551.2	0.49	other (other), ribosomal, terpene	muscoride A, muscoride B	Nostoc sp. UHCC-0398
BGC0000588.5	0.49	ribosomal	microcin L	Escherichia coli
BGC0002485.2	0.48	other (other), ribosomal	muscoride A, muscoride B	Desmonostoc sp. PCC 7906
BGC0000483.5	0.48	ribosomal	aeruginosamide B, aeruginosamide C	Microcystis aeruginosa PCC 9432

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000565.5	0.53	ribosomal	goadsporin	Streptomyces sp. TP-A0584
BGC0002698.2	0.52	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0001555.4	0.52	ribosomal	colicin V	Escherichia coli chi7122
BGC0002005.2	0.51	ribosomal	RaxX	Xanthomonas oryzae pv. oryzae
BGC0000590.5	0.50	ribosomal	microcin N	Escherichia coli
BGC0002699.2	0.49	ribosomal	nostolysamide A, nostolysamide B	Nostoc punctiforme PCC 73102
BGC0002551.2	0.49	other (other), ribosomal, terpene	muscoride A, muscoride B	Nostoc sp. UHCC-0398
BGC0000588.5	0.49	ribosomal	microcin L	Escherichia coli
BGC0002485.2	0.48	other (other), ribosomal	muscoride A, muscoride B	Desmonostoc sp. PCC 7906
BGC0000483.5	0.48	ribosomal	aeruginosamide B, aeruginosamide C	Microcystis aeruginosa PCC 9432

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (2):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.23 out of 31.73

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.48 out of 33.14

Confidence: weak

(Thi)azol(in)e containing peptide predictions

No core peptides found.

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

RREFinder

TFBS Finder

Azole RiPPs

RRE predictions

: RRE type: NHLP_CD_RRE; Location: 1 - 93; Score: 48.7; RRE type: Cyanobactin_D_RRE; Location: 4 - 77; Score: 42.9; RRE type: Goadsporin_CD_RRE; Location: 5 - 97; Score: 36.0

TFBS definitions

Regulator	Description

Core peptide predictions

No core peptides found.

NPDC089509.ctg-0033 - Region 1 - terpene-precursor

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Location: 70,179 - 91,285 nt. (total: 21,107 nt) Show pHMM detection rules used

terpene-precursor: (PT_FPPS_like and not PT_HPP)

Legend:

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TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase

CDS_08043: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

CDS_08049: pyridine nucleotide-disulfide oxidoreductase

smcogs: SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

CDS_08050: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

Transferases: phosphorylase

CDS_08047: thiamine-phosphate pyrophosphorylase

smcogs: SMCOG1280: thiamine-phosphate pyrophosphorylase

Ligases: synthetase

CDS_08046: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002345.2	0.43	other (other)	hydrogen cyanide	Pseudomonas fluorescens
BGC0000677.5	0.43	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0001483.4	0.42	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8
BGC0000664.5	0.41	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3	0.41	terpene	isorenieratene	Streptomyces argillaceus
BGC0000648.3	0.40	terpene	carotenoid	Myxococcus xanthus
BGC0000649.3	0.40	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3	0.40	terpene	carotenoid	Streptomyces avermitilis
BGC0002561.3	0.40	other (other)	phenazine SA, phenazine SB, phenazine SC	Streptomyces sp.
BGC0001227.3	0.40	terpene	isorenieratene	Streptomyces collinus Tu 365

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002345.2	0.43	other (other)	hydrogen cyanide	Pseudomonas fluorescens
BGC0000677.5	0.43	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0001483.4	0.42	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8
BGC0000664.5	0.41	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3	0.41	terpene	isorenieratene	Streptomyces argillaceus
BGC0000648.3	0.40	terpene	carotenoid	Myxococcus xanthus
BGC0000649.3	0.40	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3	0.40	terpene	carotenoid	Streptomyces avermitilis
BGC0002561.3	0.40	other (other)	phenazine SA, phenazine SB, phenazine SC	Streptomyces sp.
BGC0001227.3	0.40	terpene	isorenieratene	Streptomyces collinus Tu 365

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Product name	Chain length	Initial cyclisations	Functional groups
sesquiterpene precursor	FPP	C15	acyclic	PP
diterpene precursor	GGPP	C20	acyclic	PP
sesterterpene precursor	GFPP	C25	acyclic	PP
triterpene precursor	HPP	C30	acyclic	PP

Genes with terpene domains:

CDS_08046: PT_FPPS_like

Domain 1 (50 - 367): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

Reactions:: IPP, DMAPP → FPP; IPP, DMAPP → GGPP; IPP, DMAPP → GFPP; IPP, DMAPP → HPP

Transcription Factor Binding Sites

Binding sites found:

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31

Confidence: medium

Additional weak hits (13):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.15 out of 30.25

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.63 out of 27.78

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.69 out of 31.73

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.63 out of 27.78

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.57 out of 24.78

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.49 out of 32.93

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.37 out of 36.53

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.54 out of 36.53

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.08 out of 36.53

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 20.07 out of 22.40

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
GFPP	Geranylfarnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
HPP	Hexaprenyl diphosphate
IPP	Isopentenyl diphosphate
PP	Diphosphate

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
CatR	H2O2-responsive repressor

NPDC089509.ctg-0034 - Region 1 - terpene

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Location: 6,996 - 29,398 nt. (total: 22,403 nt) Show pHMM detection rules used

Region on contig edge.

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

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KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Lyases: cyclase

CDS_08083: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001181.4	0.81	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0001572.3	0.37	other (other)	desferrioxamine E	Pantoea agglomerans
BGC0001959.4	0.34	other (other)	taylorflavin A, taylorflavin B	Streptomyces hiroshimensis
BGC0001336.5	0.34	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0001972.4	0.33	other (other)	toxoflavin, fervenulin	Streptomyces hiroshimensis
BGC0002669.2	0.32	ribosomal	TVA-YJ-2	Streptomyces sp. NRRL S-87
BGC0002194.3	0.32	PKS	epipyrone A	Epicoccum nigrum
BGC0002058.3	0.31	NRPS, PKS	mutanocyclin	Streptococcus mutans B04Sm5
BGC0000277.5	0.31	PKS	urdamycin	Streptomyces fradiae
BGC0002287.2	0.31	NRPS	mutanocyclin, leuvalin, tyrvalin	Streptococcus mutans

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001181.4	0.81	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0001572.3	0.37	other (other)	desferrioxamine E	Pantoea agglomerans
BGC0001959.4	0.34	other (other)	taylorflavin A, taylorflavin B	Streptomyces hiroshimensis
BGC0001336.5	0.34	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0001972.4	0.33	other (other)	toxoflavin, fervenulin	Streptomyces hiroshimensis
BGC0002669.2	0.32	ribosomal	TVA-YJ-2	Streptomyces sp. NRRL S-87
BGC0002194.3	0.32	PKS	epipyrone A	Epicoccum nigrum
BGC0002058.3	0.31	NRPS, PKS	mutanocyclin	Streptococcus mutans B04Sm5
BGC0000277.5	0.31	PKS	urdamycin	Streptomyces fradiae
BGC0002287.2	0.31	NRPS	mutanocyclin, leuvalin, tyrvalin	Streptococcus mutans

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
sesquiterpene		germacradienol	C15	C1-C10	OH
sesquiterpene		geosmin	C12	C1-C10	OH

Genes with terpene domains:

CDS_08083: T1TS + T1TS

Domain 1 (2 - 326): Type 1 terpene synthase

Subtype: Geosmin synthase, N terminal domain

Reactions:: FPP → germacradienol

Domain 2 (374 - 742): Type 1 terpene synthase

Subtype: Geosmin synthase, C terminal domain

Reactions:: germacradienol → geosmin

Transcription Factor Binding Sites

Binding sites found:

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.77 out of 29.72

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.27 out of 27.04

Confidence: medium

Additional weak hits (1):

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.60 out of 26.85

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
FPP	Farnesyl diphosphate

TFBS definitions

Regulator	Description
DasR	N-acetylglucosamine dependent repressor
NtrC	Nitrogen regulatory protein C

NPDC089509.ctg-0037 - Region 1 - NRPS

Download region GenBank file

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Location: 12,051 - 81,362 nt. (total: 69,312 nt) Show pHMM detection rules used

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

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resistance

TTA codons

binding site

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Gene details

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Gene overview

Tailoring

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TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase

CDS_08334: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_08335: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: methyltransferase

CDS_08314: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: hydrolase

CDS_08319: alpha/beta hydrolase domain-containing protein

smcogs: SMCOG1066: alpha/beta hydrolase domain-containing protein

Isomerases: racemase

CDS_08333: mandelate racemase/muconate lactonizing enzyme

smcogs: SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase

CDS_08325: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_08326: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001758.4	0.76	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002071.2	0.76	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.74	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.74	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.74	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.73	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001641.4	0.72	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001758.4	0.76	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002071.2	0.76	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.74	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.74	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.74	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.73	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001641.4	0.72	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12

Confidence: medium

Additional weak hits (15):

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.56 out of 32.93

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.03 out of 30.22

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.19 out of 36.54

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.04 out of 20.97

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.16 out of 29.38

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.68 out of 26.85

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.83 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.18 out of 27.78

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.82 out of 22.40

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.39 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.14 out of 28.19

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 12050 - 81362:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Ser - X - X - Gly - X) + (Pro - Pro - Ser - Tyr)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_08325: Ser - X - X - Gly - X

Search NORINE for peptide: strict or relaxed

AMP-binding (466..865): Ser

nrpys: Ser

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: ser (Ser)
Single AA prediction:: ser (Ser)

Stachelhaus prediction details:

Stachelhaus sequence:: DVWHLSLVDK
Nearest Stachelhaus code(s):: Ser DVWHLSLVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1523..1922): X

nrpys: CysA

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: asp,asn (Asp, Asn)
Single AA prediction:: asn (Asn)

Stachelhaus prediction details:

Stachelhaus sequence:: DATKMGHVGK
Nearest Stachelhaus code(s):: CysA DATKMGHVGK (88% 8Å match); Asp DATKMGHVGK (79% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2596..2995): X

nrpys: CysA

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: asp,asn (Asp, Asn)
Single AA prediction:: asn (Asn)

Stachelhaus prediction details:

Stachelhaus sequence:: DATKMGHVGK
Nearest Stachelhaus code(s):: CysA DATKMGHVGK (88% 8Å match); Asp DATKMGHVGK (79% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3669..4058): Gly

nrpys: Gly

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
Single AA prediction:: gly (Gly)

Stachelhaus prediction details:

Stachelhaus sequence:: DILQLGLIWK
Nearest Stachelhaus code(s):: Gly DILQLGLIWK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4715..5117): X

nrpys: meSer

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVFESGGVAK
Nearest Stachelhaus code(s):: meSer DVFESGGVAK (82% 8Å match); Lys DVFESGGVAK (79% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_08326: Pro - Pro - Ser - Tyr

Search NORINE for peptide: strict or relaxed

AMP-binding (465..860): Pro

nrpys: Pro

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
Small clusters prediction:: pro (Pro)
Single AA prediction:: pro (Pro)

Stachelhaus prediction details:

Stachelhaus sequence:: DVQYIAHVAK
Nearest Stachelhaus code(s):: Pro DVQYIAHVVK (88% 8Å match); 4Me-Pro DVQFIAHVAK (71% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1515..1910): Pro

nrpys: Pro

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
Small clusters prediction:: pro (Pro)
Single AA prediction:: pro (Pro)

Stachelhaus prediction details:

Stachelhaus sequence:: DVQYIAHVVK
Nearest Stachelhaus code(s):: Pro DVQYIAHVVK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2571..2970): Ser

nrpys: Ser

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: ser (Ser)
Single AA prediction:: ser (Ser)

Stachelhaus prediction details:

Stachelhaus sequence:: DVWHLSLVDK
Nearest Stachelhaus code(s):: Ser DVWHLSLVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3633..4033): Tyr

nrpys: Tyr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
Small clusters prediction:: Polar aromatic ring (Tyr, bOH-Tyr)
Single AA prediction:: tyr (Tyr)

Stachelhaus prediction details:

Stachelhaus sequence:: DASFVGAVCK
Nearest Stachelhaus code(s):: Tyr DASTVAAVCK (79% 8Å match)
Stachelhaus code match:: 80% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
OsdR	Development and stress management regulator

NPDC089509.ctg-0038 - Region 1 - NRPS-like,T1PKS

Download region GenBank file

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Location: 35,222 - 75,533 nt. (total: 40,312 nt) Show pHMM detection rules used

Region on contig edge.

NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_08366: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_08375: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_08376: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

CDS_08377: dehydrogenase

smcogs: SMCOG1072: dehydrogenase

CDS_08379: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_08384: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_08385: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: acylase

CDS_08378: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: ligase synthase

CDS_08382: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CDS_08383: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001641.4	0.59	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000107.3	0.59	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0002175.3	0.59	PKS	YWA1	Aspergillus oryzae RIB40
BGC0001758.4	0.58	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.57	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001284.4	0.57	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001254.3	0.56	PKS	ACT-Toxin II	Alternaria alternata
BGC0001164.3	0.55	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.55	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001276.3	0.54	PKS	6-methylsalicyclic acid	Aspergillus terreus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001641.4	0.63	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000107.3	0.63	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0002175.3	0.63	PKS	YWA1	Aspergillus oryzae RIB40
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.62	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001254.3	0.62	PKS	ACT-Toxin II	Alternaria alternata
BGC0001164.3	0.61	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.61	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001276.3	0.61	PKS	6-methylsalicyclic acid	Aspergillus terreus

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.69 out of 30.11

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.85 out of 26.85

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.96 out of 23.79

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.13 out of 20.47

Confidence: medium

Additional weak hits (6):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.87 out of 30.22

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11

Confidence: weak

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.74 out of 25.31

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.54 out of 35.63

Confidence: weak

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.74 out of 29.72

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 35221 - 75533:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X - Me-mal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_08378: X - mmal

AMP-binding (26..416): X

nrpys: Val, Leu, Ile, Abu, Ival

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: LFLFRG-GTK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

PKS_AT (1171..1462): mmal

ATSignature: Malonyl-CoA, Methylmalonyl-CoA

Top 3 matches:: Malonyl-CoA: 83.3%; Methylmalonyl-CoA: 83.3%; Methoxymalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 161.5
Ethylmalonyl-CoA: 160.0
Methoxymalonyl-CoA: 141.9
trans-1,2-CPDA: 100.0
Propionyl-CoA: 96.4
Malonyl-CoA: 92.3
2-Methylbutyryl-CoA: 92.1
CHC-CoA: 75.0
Isobutyryl-CoA: 64.0
fatty_acid: 41.0
Benzoyl-CoA: 36.4
inactive: 28.8
3-Methylbutyryl-CoA: 25.7
Acetyl-CoA: 23.4

CDS_08383: X

AMP-binding (33..505): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DMFAAGGLKK
Nearest Stachelhaus code(s):: Val DGFFAGGVFK (35% 8Å match); Cys DMFNFGVLWK (32% 8Å match)
Stachelhaus code match:: 60% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CelR	Cellobiose uptake repressor
IolR	Regulator of the inositol catabolism
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0043 - Region 1 - NRPS,PKS-like

Download region GenBank file

Download region SVG

Location: 1 - 54,306 nt. (total: 54,306 nt) Show pHMM detection rules used

Region on contig edge.

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
PKS-like: (t2pks2 or ksIII)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_08658: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

Transferases: acyltransferase aminotransferase

CDS_08638: aminotransferase

smcogs: SMCOG1019: aminotransferase

CDS_08640: polyketide synthase associated protein papA3

smcogs: SMCOG1209: polyketide synthase associated protein papA3

Lyases: decarboxylase

CDS_08649: diaminopimelate decarboxylase

smcogs: SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase

CDS_08639: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_08642: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_08644: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_08650: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_08651: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CDS_08657: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CDS_08659: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.92	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.86	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0000342.4	0.85	NRPS	enniatin	Fusarium equiseti
BGC0001833.4	0.81	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001261.3	0.81	NRPS	AM-toxin	Alternaria alternata
BGC0001166.5	0.78	NRPS	HC-toxin	Alternaria jesenskae
BGC0001758.4	0.78	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001132.4	0.78	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.77	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.77	NRPS	AbT1	Aureobasidium pullulans

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.78	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.76	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0000342.4	0.76	NRPS	enniatin	Fusarium equiseti
BGC0001833.4	0.74	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001758.4	0.73	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001166.5	0.72	NRPS	HC-toxin	Alternaria jesenskae
BGC0001128.4	0.72	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.72	NRPS	AbT1	Aureobasidium pullulans
BGC0001261.3	0.72	NRPS	AM-toxin	Alternaria alternata
BGC0001240.4	0.71	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.51 out of 27.04

Confidence: medium

Additional weak hits (9):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.97 out of 30.25

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.16 out of 19.26

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 13.63 out of 21.55

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.00 out of 27.55

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.38 out of 28.19

Confidence: weak

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.24 out of 32.38

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.83 out of 25.75

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 14.58 out of 33.14

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 54306:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Acetyl-CoA - Gly) + (X) + (NMe-Thr) + (X - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 0 - 48728:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Acetyl-CoA - Gly) + (X) + (NMe-Thr) + (X - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 15146 - 54306:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Acetyl-CoA - Gly) + (X) + (NMe-Thr)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_08639: X - X

AMP-binding (469..877): X

nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DPHSLGSFCK
Nearest Stachelhaus code(s):: Lys DAESIGSVCK (35% 8Å match)
Stachelhaus code match:: 60% (weak)

AMP-binding (1546..1942): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVEEAGVCTK
Nearest Stachelhaus code(s):: Ahp DVENAGVVTK (47% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_08640: Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (511..907): Thr

nrpys: Thr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: thr (Thr)
Single AA prediction:: thr (Thr)

Stachelhaus prediction details:

Stachelhaus sequence:: DFWSVGMVHK
Nearest Stachelhaus code(s):: Thr DFWSVGMVHK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_08642: X

AMP-binding (486..893): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Polar, uncharged (aliphatic with -SH) (Cys)
Small clusters prediction:: Polar, uncharged (aliphatic with -SH) (Cys)
Single AA prediction:: Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:

Stachelhaus sequence:: DMYNFGLVHK
Nearest Stachelhaus code(s):: Lys DMYNFGLIHK (82% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_08644: Acetyl-CoA - Gly

Search NORINE for peptide: strict or relaxed

CAL_domain (40..487): Acetyl-CoA

minowa: Acetyl-CoA

Prediction, score:

Acetyl-CoA: 46.0
fatty_acid: 25.6
NH2: 21.8
AHBA: 15.1
shikimic_acid: 2.9

AMP-binding (1176..1568): Gly

nrpys: Gly

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
Single AA prediction:: gly (Gly)

Stachelhaus prediction details:

Stachelhaus sequence:: DILQLGVVWK
Nearest Stachelhaus code(s):: Gly DILQLGVVWK (82% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_08650: Asp

Search NORINE for peptide: strict or relaxed

AMP-binding (30..427): Asp

nrpys: Asp

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DYYPTTMRVK
Nearest Stachelhaus code(s):: Asp DYYPTTMRVK (79% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
DasR	N-acetylglucosamine dependent repressor

NPDC089509.ctg-0045 - Region 1 - T2PKS

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Location: 1 - 40,778 nt. (total: 40,778 nt) Show pHMM detection rules used

Region on contig edge.

T2PKS: (t2ks and t2clf)

Legend:

core biosynthetic genes

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TFBS Finder

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxygenase

CDS_08719: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Hydrolases: amidase hydrolase

CDS_08731: amidase

smcogs: SMCOG1105: amidase

CDS_08733: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Lyases: cyclase

CDS_08713: Polyketide synthesis cyclase

smcogs: SMCOG1225: Polyketide synthesis cyclase

Ligases: synthase

CDS_08714: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_08715: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000231.5	0.67	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0000234.5	0.66	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0001723.5	0.59	PKS	oviedomycin	Streptomyces antibioticus
BGC0000275.4	0.57	PKS	tetracenomycin C	Streptomyces glaucescens
BGC0001513.3	0.56	PKS	anthrabenzoxocinone	Actinobacteria bacterium
BGC0000271.5	0.55	PKS	spore pigment	Streptomyces avermitilis
BGC0001197.5	0.55	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0002000.4	0.54	PKS	setomimycin	Streptomyces aurantiacus JA 4570
BGC0001366.5	0.54	PKS	BE-24566B, zunyimycin A	Streptomyces sp. FJS31-2
BGC0000272.3	0.54	PKS	spore pigment	Streptomyces collinus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000231.5	0.67	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0000234.5	0.66	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0001723.5	0.59	PKS	oviedomycin	Streptomyces antibioticus
BGC0000275.4	0.57	PKS	tetracenomycin C	Streptomyces glaucescens
BGC0001513.3	0.56	PKS	anthrabenzoxocinone	Actinobacteria bacterium
BGC0000271.5	0.55	PKS	spore pigment	Streptomyces avermitilis
BGC0001197.5	0.55	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0002000.4	0.54	PKS	setomimycin	Streptomyces aurantiacus JA 4570
BGC0001366.5	0.54	PKS	BE-24566B, zunyimycin A	Streptomyces sp. FJS31-2
BGC0000272.3	0.54	PKS	spore pigment	Streptomyces collinus

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52

Confidence: medium

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.00 out of 20.47

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.37 out of 20.97

Confidence: medium

Additional weak hits (18):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.76 out of 26.33

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.96 out of 21.55

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.01 out of 27.55

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.69 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.41 out of 26.06

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.38 out of 27.78

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.16 out of 30.22

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.44 out of 36.53

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.89 out of 29.38

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.30 out of 32.93

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.46 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.04 out of 26.06

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.38 out of 32.93

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.60 out of 26.06

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.47 out of 28.19

Confidence: weak

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31

Confidence: weak

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31

Confidence: weak

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Detailed domain annotation

Selected features only

Show module domains

Type II PKS

TFBS Finder

Type II PKS gene cluster prediction details

Cluster section:: 0 to 40778
Starter unit(s):: acetyl-CoA (Score: 0.0; E-value: 0)
Malonyl elongations:: 8|9 (Score: 693.1; E-value: 2.3e-211)
Product class(es):: angucycline
anthracycline
aureolic acid
tetracenomycin
tetracycline
Product molecular weight(s):: acetyl-CoA_8: 379 Da
acetyl-CoA_9: 421 Da

CDS_08714: KS (Score: 788.5; E-value: 3.1e-240)
CDS_08715: CLF 8|9 (Score: 693.1; E-value: 2.3e-211)
CDS_08716: ACP (Score: 98.9; E-value: 3e-31)

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
CcpA	Catabolite control protein A
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0050 - Region 1 - NRPS-like

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Location: 1 - 18,833 nt. (total: 18,833 nt) Show pHMM detection rules used

Region on contig edge.

NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

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resistance

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Gene overview

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NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Ligases: ligase

CDS_08896: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.71	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002164.2	0.65	NRPS	peramine	Epichloe festucae
BGC0001261.3	0.64	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.63	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.62	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.62	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4	0.62	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0000307.4	0.62	NRPS	AbT1	Aureobasidium pullulans
BGC0002135.2	0.61	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.71	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002164.2	0.65	NRPS	peramine	Epichloe festucae
BGC0001261.3	0.64	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.63	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.62	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.62	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4	0.62	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0000307.4	0.62	NRPS	AbT1	Aureobasidium pullulans
BGC0002135.2	0.61	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16

Confidence: strong

Additional weak hits (2):

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 24.40 out of 33.73

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.19 out of 29.25

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 18833:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_08896: X

AMP-binding (19..414): X

nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DSECYGGVTK
Nearest Stachelhaus code(s):: OH-Orn DGEGSGGVTK (41% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
CatR	H2O2-responsive repressor
OsdR	Development and stress management regulator

NPDC089509.ctg-0052 - Region 1 - terpene

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Location: 1 - 10,928 nt. (total: 10,928 nt) Show pHMM detection rules used

Region on contig edge.

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

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Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxygenase

CDS_08911: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

Lyases: cyclase

CDS_08912: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Ligases: synthetase

CDS_08905: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000660.5	0.58	terpene	albaflavenone	Streptomyces coelicolor A3(2)
BGC0002610.3	0.56	terpene	stellatic acid	Aspergillus stellatus
BGC0000673.3	0.54	terpene	pimara-8(14),15-diene	Aspergillus nidulans FGSC A4
BGC0000286.3	0.52	PKS	viguiepinol	Streptomyces sp. KO-3988
BGC0002309.2	0.52	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000677.5	0.51	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002043.3	0.49	ribosomal	cittilin A, cittilin B	Myxococcus xanthus DK 1622
BGC0001911.3	0.47	terpene	raimonol	Streptomyces anulatus
BGC0000675.5	0.46	terpene	(+)-T-muurolol	Streptomyces clavuligerus ATCC 27064
BGC0001910.4	0.45	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000660.5	0.58	terpene	albaflavenone	Streptomyces coelicolor A3(2)
BGC0002610.3	0.56	terpene	stellatic acid	Aspergillus stellatus
BGC0000673.3	0.54	terpene	pimara-8(14),15-diene	Aspergillus nidulans FGSC A4
BGC0000286.3	0.52	PKS	viguiepinol	Streptomyces sp. KO-3988
BGC0002309.2	0.52	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000677.5	0.51	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002043.3	0.49	ribosomal	cittilin A, cittilin B	Myxococcus xanthus DK 1622
BGC0001911.3	0.47	terpene	raimonol	Streptomyces anulatus
BGC0000675.5	0.46	terpene	(+)-T-muurolol	Streptomyces clavuligerus ATCC 27064
BGC0001910.4	0.45	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Product name	Chain length	Initial cyclisations	Functional groups
sesquiterpene precursor	FPP	C15	acyclic	PP
diterpene precursor	GGPP	C20	acyclic	PP
sesterterpene precursor	GFPP	C25	acyclic	PP
triterpene precursor	HPP	C30	acyclic	PP

Genes with terpene domains:

CDS_08905: PT_FPPS_like

Domain 1 (39 - 347): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

Reactions:: IPP, DMAPP → FPP; IPP, DMAPP → GGPP; IPP, DMAPP → GFPP; IPP, DMAPP → HPP

CDS_08910: TS_Pyr4

Domain 1 (3 - 205): Pyr4 type terpene synthase

Subtype: unknown

CDS_08912: T1TS

Domain 1 (8 - 322): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47

Confidence: medium

Additional weak hits (4):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.57 out of 30.25

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.31 out of 26.06

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
GFPP	Geranylfarnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
HPP	Hexaprenyl diphosphate
IPP	Isopentenyl diphosphate
PP	Diphosphate

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0056 - Region 1 - NRPS-like

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Location: 1 - 3,522 nt. (total: 3,522 nt) Show pHMM detection rules used

Region on contig edge.

NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Ligases: ligase

CDS_08921: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.63	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.63	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.63	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.63	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.63	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.62	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002277.2	0.62	NRPS	atromentin	Suillus grevillei
BGC0002075.3	0.62	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0002135.2	0.62	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.63	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.63	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.63	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.63	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.63	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.62	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002277.2	0.62	NRPS	atromentin	Suillus grevillei
BGC0002075.3	0.62	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0002135.2	0.62	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004

Similar known clusters

No significant matches found.

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Module view

Legend

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

Predicted core structure(s)

For candidate cluster 1, location 0 - 3522:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_08921: X

AMP-binding (85..490): X

nrpys: OH-Asn, Asn

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: asp,asn (Asp, Asn)
Single AA prediction:: asn (Asn)

Stachelhaus prediction details:

Stachelhaus sequence:: DLTKVGEVGK
Nearest Stachelhaus code(s):: OH-Asn DLTKVGEVGK (85% 8Å match); Asn DLTKVGEVGK (85% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

NPDC089509.ctg-0057 - Region 1 - T2PKS

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Location: 1 - 3,218 nt. (total: 3,218 nt) Show pHMM detection rules used

Region on contig edge.

T2PKS: (t2ks and t2clf)

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core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

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Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

NRPS/PKS domains

Gene/CDS overview

Filter:

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Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Lyases: cyclase

CDS_08925: cyclase/dehydrase

smcogs: SMCOG1128: cyclase/dehydrase

CDS_08926: Polyketide synthesis cyclase

smcogs: SMCOG1225: Polyketide synthesis cyclase

Ligases: synthase

CDS_08922: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_08923: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000272.3	0.81	PKS	spore pigment	Streptomyces collinus
BGC0000271.5	0.71	PKS	spore pigment	Streptomyces avermitilis
BGC0000215.5	0.67	PKS	curamycin	Streptomyces cyaneus
BGC0000231.5	0.61	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0001197.5	0.60	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0000275.4	0.55	PKS	tetracenomycin C	Streptomyces glaucescens
BGC0001513.3	0.53	PKS	anthrabenzoxocinone	Actinobacteria bacterium
BGC0000234.5	0.53	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0000221.5	0.53	PKS	erdacin	uncultured soil bacterium V167
BGC0001366.5	0.53	PKS	BE-24566B, zunyimycin A	Streptomyces sp. FJS31-2

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000272.3	0.81	PKS	spore pigment	Streptomyces collinus
BGC0000271.5	0.71	PKS	spore pigment	Streptomyces avermitilis
BGC0000215.5	0.67	PKS	curamycin	Streptomyces cyaneus
BGC0000231.5	0.61	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0001197.5	0.60	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0000275.4	0.55	PKS	tetracenomycin C	Streptomyces glaucescens
BGC0001513.3	0.53	PKS	anthrabenzoxocinone	Actinobacteria bacterium
BGC0000234.5	0.53	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0000221.5	0.53	PKS	erdacin	uncultured soil bacterium V167
BGC0001366.5	0.53	PKS	BE-24566B, zunyimycin A	Streptomyces sp. FJS31-2

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47

Confidence: medium

Detailed Pfam domain annotation

Selected features only

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Detailed domain annotation

Selected features only

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Type II PKS

TFBS Finder

Type II PKS gene cluster prediction details

Cluster section:: 0 to 3218
Starter unit(s):: acetyl-CoA (Score: 0.0; E-value: 0)

CDS_08922: KS (Score: 494.1; E-value: 6.9e-151)
CDS_08923: CLF (Score: 544.0; E-value: 4.5e-166)
CDS_08924: ACP (Score: 57.7; E-value: 2.1e-18)
CDS_08925: CYC C9-C14 (Score: 253.5; E-value: 1.3e-78)
CDS_08926: CYC C4-C21/C2-C23|C2-C19 (Score: 149.9; E-value: 4.9e-47)

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

NPDC089509.ctg-0059 - Region 1 - NRPS

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Location: 1 - 2,401 nt. (total: 2,401 nt) Show pHMM detection rules used

Region on contig edge.

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

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resistance

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Gene overview

Tailoring

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NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Ligases: ligase

ctg59_1: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.74	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001135.5	0.67	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002164.2	0.67	NRPS	peramine	Epichloe festucae
BGC0000900.5	0.67	other (other)	ferrichrome	Aspergillus oryzae
BGC0001261.3	0.67	NRPS	AM-toxin	Alternaria alternata
BGC0001132.4	0.66	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.65	NRPS	AbT1	Aureobasidium pullulans
BGC0002135.2	0.64	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.74	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001135.5	0.67	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002164.2	0.67	NRPS	peramine	Epichloe festucae
BGC0000900.5	0.67	other (other)	ferrichrome	Aspergillus oryzae
BGC0001261.3	0.67	NRPS	AM-toxin	Alternaria alternata
BGC0001132.4	0.66	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.65	NRPS	AbT1	Aureobasidium pullulans
BGC0002135.2	0.64	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004

Similar known clusters

No significant matches found.

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Module view

Legend

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

Predicted core structure(s)

For candidate cluster 1, location 0 - 2401:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Val)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

ctg59_1: Val

Search NORINE for peptide: strict or relaxed

AMP-binding (132..535): Val

nrpys: Val

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: val (Val)

Stachelhaus prediction details:

Stachelhaus sequence:: DAYWMGGVFK
Nearest Stachelhaus code(s):: Val DAYWWGGVFK (82% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor