Kitasatospora_NPDC024463 - 77 region(s)

Identified secondary metabolite regions using strictness 'relaxed'

NPDC024463.ctg-0001 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 1.1	RRE-containing	609,985	631,109

NPDC024463.ctg-0002 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 2.1	ranthipeptide,T1PKS,azoxy-crosslink	96,962	170,556
Region 2.2	T1PKS	368,707	412,876
Region 2.3	oligosaccharide,PKS-like	470,056	535,824	Medium	antibiotic HKI 10311129/antibiotic A2121-1/cervimycin D/cervimycin C/cervimycin A	PKS+saccharide:hybrid/tailoring
Region 2.4	terpene-precursor	615,700	636,917

NPDC024463.ctg-0003 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 3.1	terpene	219,692	242,016	High	geosmin	terpene:Sesquiterpene
Region 3.2	transAT-PKS,NRPS	250,431	326,391	Low	oxazolomycin	NRPS:Type I+PKS
Region 3.3	NAPAA	405,592	439,638
Region 3.4	terpene-precursor	474,074	495,189
Region 3.5	crocagin	619,863	646,182
Region 3.6	lanthipeptide-class-iv	647,360	669,579

NPDC024463.ctg-0004 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 4.1	T3PKS,azole-containing-RiPP	235,211	276,701	Low	glycinocin A	NRPS:Type I
Region 4.2	lanthipeptide-class-i	280,835	305,654
Region 4.3	RiPP-like	387,157	399,073
Region 4.4	NRPS	399,534	492,916
Region 4.5	NAPAA,guanidinotides,terpene	499,527	563,785

NPDC024463.ctg-0005 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 5.1	terpene	33,703	54,653
Region 5.2	NRPS-like,terpene	117,425	167,871
Region 5.3	terpene	360,720	385,804	High	raimonol	terpene
Region 5.4	T3PKS,T1PKS	436,924	493,964	High	2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone/2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol	PKS:Type III

NPDC024463.ctg-0006 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 6.1	lanthipeptide-class-ii	32,632	55,955
Region 6.2	T1PKS	97,555	142,390
Region 6.3	NRPS-like	152,805	196,038	Low	lipstatin	NRPS:Type I
Region 6.4	NRPS,transAT-PKS-like	199,704	248,473	Low	acidobactin A/acidobactin B	NRPS:Type I+PKS
Region 6.5	NRPS,indole	265,674	313,155
Region 6.6	NI-siderophore	361,610	394,428	Low	peucechelin	NRPS:Type I
Region 6.7	lanthipeptide-class-ii	428,227	451,316

NPDC024463.ctg-0007 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 7.1	NRPS	29,200	108,149
Region 7.2	terpene	208,680	229,657
Region 7.3	lanthipeptide-class-i,T1PKS	417,609	469,042	High	tetrafibricin	PKS+other:other

NPDC024463.ctg-0008 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 8.1	T1PKS	1	54,397	High	halstoctacosanolide A	PKS
Region 8.2	RiPP-like	99,062	109,862
Region 8.3	T3PKS,amglyccycl	113,860	156,040
Region 8.4	T2PKS	183,361	255,885	High	spore pigment	PKS
Region 8.5	terpene	279,426	300,646	Medium	2-methylisoborneol	terpene:Monoterpene

NPDC024463.ctg-0009 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 9.1	lassopeptide	139,597	162,158	Low	fusilassin	ribosomal:RiPP:Lasso peptide
Region 9.2	T1PKS	310,025	338,671

NPDC024463.ctg-0010 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 10.1	T1PKS	1	66,232	Medium	griseochelin	PKS
Region 10.2	NRPS,T1PKS	92,959	178,117	Low	clipibicyclene/azabicyclene B/azabicyclene C/azabicyclene D	NRPS:Type I+PKS
Region 10.3	NRPS-like,T1PKS	225,662	271,895

NPDC024463.ctg-0011 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 11.1	terpene	129,929	150,360

NPDC024463.ctg-0013 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 13.1	melanin	170,897	181,307	Low	melanin	other:other

NPDC024463.ctg-0015 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 15.1	terpene	1	14,965
Region 15.2	PKS-like,T1PKS,terpene	135,936	192,956	Medium	pentalenolactone	terpene
Region 15.3	NRPS	193,139	241,310	Low	phthoxazolin	NRPS:Type I+PKS

NPDC024463.ctg-0016 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 16.1	azole-containing-RiPP	163,854	187,854

NPDC024463.ctg-0017 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 17.1	NRPS-like,NRPS	1	32,834	Low	stenothricin	NRPS:Type I
Region 17.2	terpene-precursor	171,059	192,207

NPDC024463.ctg-0018 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 18.1	terpene	3,970	25,133
Region 18.2	hydrogen-cyanide	123,994	137,028

NPDC024463.ctg-0019 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 19.1	T1PKS	1	40,052	High	tetrafibricin	PKS+other:other

NPDC024463.ctg-0020 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 20.1	NI-siderophore	66,011	99,550

NPDC024463.ctg-0021 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 21.1	azole-containing-RiPP,RRE-containing	12,053	38,516
Region 21.2	T1PKS	49,963	106,801

NPDC024463.ctg-0022 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 22.1	transAT-PKS,linaridin,NRPS	87,057	127,952

NPDC024463.ctg-0023 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 23.1	NAPAA	29,368	63,291	High	ε-Poly-L-lysine	NRPS:Type I

NPDC024463.ctg-0024 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 24.1	lanthipeptide-class-iii	51,347	73,941

NPDC024463.ctg-0025 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 25.1	transAT-PKS,NRPS	1	32,714

NPDC024463.ctg-0026 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 26.1	azole-containing-RiPP	75,151	104,853	Medium	lactazole	ribosomal:RiPP:Thiopeptide

NPDC024463.ctg-0027 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 27.1	lanthipeptide-class-iv	21,397	43,994

NPDC024463.ctg-0028 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 28.1	NRPS,arylpolyene,T2PKS	1	89,682	Low	allocyclinone A/allocyclinone B/allocyclinone C/allocyclinone D	PKS

NPDC024463.ctg-0030 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 30.1	terpene	19,054	40,148

NPDC024463.ctg-0031 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 31.1	terpene	27,127	48,074
Region 31.2	terpene	49,576	76,280	High	hopene	terpene

NPDC024463.ctg-0032 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 32.1	NRPS,phosphonate	1	35,436

NPDC024463.ctg-0034 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 34.1	terpene	1	11,351

NPDC024463.ctg-0035 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 35.1	T1PKS	1	40,276	Low	funisamine	PKS

NPDC024463.ctg-0036 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 36.1	T1PKS,NRPS	1	46,297	Low	chlorothricin/deschlorothricin	PKS:Type I+saccharide:oligosaccharide

NPDC024463.ctg-0037 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 37.1	T1PKS,NRPS-like	1	46,176	Low	ECO-02301	PKS

NPDC024463.ctg-0038 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 38.1	azole-containing-RiPP	12,036	45,533

NPDC024463.ctg-0040 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 40.1	T1PKS	1	41,493

NPDC024463.ctg-0041 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 41.1	PKS-like,butyrolactone	3,702	31,898

NPDC024463.ctg-0044 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 44.1	NRPS	1	19,973

NPDC024463.ctg-0045 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 45.1	T1PKS	1	16,836	Low	desulfoclethramycin/clethramycin	other:other

NPDC024463.ctg-0048 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 48.1	NRPS-like	1	8,799

NPDC024463.ctg-0050 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 50.1	NRPS-like	1	8,324

NPDC024463.ctg-0062 (Kitasatospora spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 62.1	T1PKS	1	1,988

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 1.1	RRE-containing	609,985	631,109
Region 2.1	ranthipeptide,T1PKS,azoxy-crosslink	96,962	170,556
Region 2.2	T1PKS	368,707	412,876
Region 2.3	oligosaccharide,PKS-like	470,056	535,824	Medium	antibiotic HKI 10311129/antibiotic A2121-1/cervimycin D/cervimycin C/cervimycin A	PKS+saccharide:hybrid/tailoring
Region 2.4	terpene-precursor	615,700	636,917
Region 3.1	terpene	219,692	242,016	High	geosmin	terpene:Sesquiterpene
Region 3.2	transAT-PKS,NRPS	250,431	326,391	Low	oxazolomycin	NRPS:Type I+PKS
Region 3.3	NAPAA	405,592	439,638
Region 3.4	terpene-precursor	474,074	495,189
Region 3.5	crocagin	619,863	646,182
Region 3.6	lanthipeptide-class-iv	647,360	669,579
Region 4.1	T3PKS,azole-containing-RiPP	235,211	276,701	Low	glycinocin A	NRPS:Type I
Region 4.2	lanthipeptide-class-i	280,835	305,654
Region 4.3	RiPP-like	387,157	399,073
Region 4.4	NRPS	399,534	492,916
Region 4.5	NAPAA,guanidinotides,terpene	499,527	563,785
Region 5.1	terpene	33,703	54,653
Region 5.2	NRPS-like,terpene	117,425	167,871
Region 5.3	terpene	360,720	385,804	High	raimonol	terpene
Region 5.4	T3PKS,T1PKS	436,924	493,964	High	2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone/2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol	PKS:Type III
Region 6.1	lanthipeptide-class-ii	32,632	55,955
Region 6.2	T1PKS	97,555	142,390
Region 6.3	NRPS-like	152,805	196,038	Low	lipstatin	NRPS:Type I
Region 6.4	NRPS,transAT-PKS-like	199,704	248,473	Low	acidobactin A/acidobactin B	NRPS:Type I+PKS
Region 6.5	NRPS,indole	265,674	313,155
Region 6.6	NI-siderophore	361,610	394,428	Low	peucechelin	NRPS:Type I
Region 6.7	lanthipeptide-class-ii	428,227	451,316
Region 7.1	NRPS	29,200	108,149
Region 7.2	terpene	208,680	229,657
Region 7.3	lanthipeptide-class-i,T1PKS	417,609	469,042	High	tetrafibricin	PKS+other:other
Region 8.1	T1PKS	1	54,397	High	halstoctacosanolide A	PKS
Region 8.2	RiPP-like	99,062	109,862
Region 8.3	T3PKS,amglyccycl	113,860	156,040
Region 8.4	T2PKS	183,361	255,885	High	spore pigment	PKS
Region 8.5	terpene	279,426	300,646	Medium	2-methylisoborneol	terpene:Monoterpene
Region 9.1	lassopeptide	139,597	162,158	Low	fusilassin	ribosomal:RiPP:Lasso peptide
Region 9.2	T1PKS	310,025	338,671
Region 10.1	T1PKS	1	66,232	Medium	griseochelin	PKS
Region 10.2	NRPS,T1PKS	92,959	178,117	Low	clipibicyclene/azabicyclene B/azabicyclene C/azabicyclene D	NRPS:Type I+PKS
Region 10.3	NRPS-like,T1PKS	225,662	271,895
Region 11.1	terpene	129,929	150,360
Region 13.1	melanin	170,897	181,307	Low	melanin	other:other
Region 15.1	terpene	1	14,965
Region 15.2	PKS-like,T1PKS,terpene	135,936	192,956	Medium	pentalenolactone	terpene
Region 15.3	NRPS	193,139	241,310	Low	phthoxazolin	NRPS:Type I+PKS
Region 16.1	azole-containing-RiPP	163,854	187,854
Region 17.1	NRPS-like,NRPS	1	32,834	Low	stenothricin	NRPS:Type I
Region 17.2	terpene-precursor	171,059	192,207
Region 18.1	terpene	3,970	25,133
Region 18.2	hydrogen-cyanide	123,994	137,028
Region 19.1	T1PKS	1	40,052	High	tetrafibricin	PKS+other:other
Region 20.1	NI-siderophore	66,011	99,550
Region 21.1	azole-containing-RiPP,RRE-containing	12,053	38,516
Region 21.2	T1PKS	49,963	106,801
Region 22.1	transAT-PKS,linaridin,NRPS	87,057	127,952
Region 23.1	NAPAA	29,368	63,291	High	ε-Poly-L-lysine	NRPS:Type I
Region 24.1	lanthipeptide-class-iii	51,347	73,941
Region 25.1	transAT-PKS,NRPS	1	32,714
Region 26.1	azole-containing-RiPP	75,151	104,853	Medium	lactazole	ribosomal:RiPP:Thiopeptide
Region 27.1	lanthipeptide-class-iv	21,397	43,994
Region 28.1	NRPS,arylpolyene,T2PKS	1	89,682	Low	allocyclinone A/allocyclinone B/allocyclinone C/allocyclinone D	PKS
Region 30.1	terpene	19,054	40,148
Region 31.1	terpene	27,127	48,074
Region 31.2	terpene	49,576	76,280	High	hopene	terpene
Region 32.1	NRPS,phosphonate	1	35,436
Region 34.1	terpene	1	11,351
Region 35.1	T1PKS	1	40,276	Low	funisamine	PKS
Region 36.1	T1PKS,NRPS	1	46,297	Low	chlorothricin/deschlorothricin	PKS:Type I+saccharide:oligosaccharide
Region 37.1	T1PKS,NRPS-like	1	46,176	Low	ECO-02301	PKS
Region 38.1	azole-containing-RiPP	12,036	45,533
Region 40.1	T1PKS	1	41,493
Region 41.1	PKS-like,butyrolactone	3,702	31,898
Region 44.1	NRPS	1	19,973
Region 45.1	T1PKS	1	16,836	Low	desulfoclethramycin/clethramycin	other:other
Region 48.1	NRPS-like	1	8,799
Region 50.1	NRPS-like	1	8,324
Region 62.1	T1PKS	1	1,988

No secondary metabolite regions were found in these records:: NPDC024463.ctg-0012 (Kitasatospora spp); NPDC024463.ctg-0014 (Kitasatospora spp); NPDC024463.ctg-0029 (Kitasatospora spp); NPDC024463.ctg-0033 (Kitasatospora spp); NPDC024463.ctg-0039 (Kitasatospora spp); NPDC024463.ctg-0042 (Kitasatospora spp); NPDC024463.ctg-0043 (Kitasatospora spp); NPDC024463.ctg-0046 (Kitasatospora spp); NPDC024463.ctg-0047 (Kitasatospora spp); NPDC024463.ctg-0049 (Kitasatospora spp); NPDC024463.ctg-0051 (Kitasatospora spp); NPDC024463.ctg-0052 (Kitasatospora spp); NPDC024463.ctg-0053 (Kitasatospora spp); NPDC024463.ctg-0054 (Kitasatospora spp); NPDC024463.ctg-0055 (Kitasatospora spp); NPDC024463.ctg-0056 (Kitasatospora spp); NPDC024463.ctg-0057 (Kitasatospora spp); NPDC024463.ctg-0058 (Kitasatospora spp); NPDC024463.ctg-0059 (Kitasatospora spp); NPDC024463.ctg-0060 (Kitasatospora spp); NPDC024463.ctg-0061 (Kitasatospora spp); NPDC024463.ctg-0063 (Kitasatospora spp); NPDC024463.ctg-0064 (Kitasatospora spp); NPDC024463.ctg-0065 (Kitasatospora spp); NPDC024463.ctg-0066 (Kitasatospora spp); NPDC024463.ctg-0067 (Kitasatospora spp); NPDC024463.ctg-0068 (Kitasatospora spp); NPDC024463.ctg-0069 (Kitasatospora spp); NPDC024463.ctg-0070 (Kitasatospora spp); NPDC024463.ctg-0071 (Kitasatospora spp)

Compact view

NPDC024463.ctg-0001 - Region 1 - RRE-containing

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Location: 609,985 - 631,109 nt. (total: 21,125 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])

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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

TIGRFAM domains

Gene/CDS overview

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

Tailoring functions

Transferases: acetyltransferase

CDS_00553: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Lyases: dehydratase

CDS_00564: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000916.5	0.35	other (other)	molybdenum cofactor	Staphylococcus carnosus
BGC0001060.5	0.23	PKS	dynemicin A	Micromonospora chersina
BGC0001111.5	0.20	NRPS, PKS	rhizopodin	Stigmatella aurantiaca Sg a15
BGC0001751.3	0.20	NRPS, PKS	pyxipyrrolone A, pyxipyrrolone B	Pyxidicoccus sp. MCy9557
BGC0000974.5	0.20	NRPS, PKS	crocacin	Chondromyces crocatus
BGC0002039.3	0.19	other (other)	coformycin, formycin A	Nocardia interforma ATCC 21072
BGC0000380.5	0.19	NRPS, PKS	Leupyrrin A1, Leupyrrin A2, Leupyrrin B1, Leupyrrin B2, Leupyrrin C, Leupyrrin D	Sorangium cellulosum

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000916.5	0.35	other (other)	molybdenum cofactor	Staphylococcus carnosus
BGC0001060.5	0.23	PKS	dynemicin A	Micromonospora chersina
BGC0001111.5	0.20	NRPS, PKS	rhizopodin	Stigmatella aurantiaca Sg a15
BGC0001751.3	0.20	NRPS, PKS	pyxipyrrolone A, pyxipyrrolone B	Pyxidicoccus sp. MCy9557
BGC0000974.5	0.20	NRPS, PKS	crocacin	Chondromyces crocatus
BGC0002039.3	0.19	other (other)	coformycin, formycin A	Nocardia interforma ATCC 21072
BGC0000380.5	0.19	NRPS, PKS	Leupyrrin A1, Leupyrrin A2, Leupyrrin B1, Leupyrrin B2, Leupyrrin C, Leupyrrin D	Sorangium cellulosum

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:

AbrC3

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

Confidence: strong

Additional weak hits (6):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.75 out of 30.25

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.95 out of 28.19

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.51 out of 32.93

Confidence: weak

HypR

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

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.09 out of 32.93

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75

Confidence: weak

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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RREFinder

TFBS Finder

RRE predictions

: RRE type: Pantocin_Microcin_RRE; Location: 0 - 88; Score: 28.0

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator

NPDC024463.ctg-0002 - Region 1 - T1PKS,azoxy-crosslink,ranthipeptide

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Location: 96,962 - 170,556 nt. (total: 73,595 nt) Show pHMM detection rules used

ranthipeptide: (TIGR03973 or SCIFF or (cds(PF04055 and (TIGR04085 or SPASM)) and 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]) and not (TIGR01716 or subtilosin or TIGR02111 or TIGR03966 or TIGR04103 or (YcaO or TIGR03604))))
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
azoxy-crosslink: (azdH and LPG_synthase_C and azdO and vlmB)

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 oxidoreductase oxygenase

CDS_00827: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_00834: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_00838: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

CDS_00839: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_00843: flavin reductase domain protein FMN-binding

smcogs: SMCOG1160: flavin reductase domain protein FMN-binding

CDS_00853: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_00864: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_00866: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

Transferases: aminotransferase transferase

CDS_00799: glucose-1-phosphate adenylyl/thymidylyltransferase

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

CDS_00814: DegT/DnrJ/EryC1/StrS aminotransferase

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

CDS_00840: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

CDS_00859: acetyl-CoA carboxylase, carboxyl transferase,

smcogs: SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Hydrolases: esterase hydrolase

CDS_00828: thioesterase superfamily protein

smcogs: SMCOG1144: thioesterase superfamily protein

CDS_00833: thioesterase

smcogs: SMCOG1004: thioesterase

CDS_00862: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: decarboxylase dehydratase

CDS_00815: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_00818: Decarboxylase, pyridoxal-dependent

smcogs: SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: ligase synthase

CDS_00835: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_00836: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_00845: 3-oxoacyl-(acyl carrier protein) synthase III

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

CDS_00847: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Translocases: permease

CDS_00848: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.92	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001275.3	0.67	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.66	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.66	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0002191.2	0.59	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001164.3	0.59	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.59	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001284.4	0.58	PKS	alternariol	Parastagonospora nodorum SN15
BGC0000107.3	0.57	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0001257.3	0.57	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.76	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001275.3	0.67	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.66	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.66	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001164.3	0.64	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.64	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0000107.3	0.64	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0001257.3	0.64	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
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
BGC0002175.3	0.63	PKS	YWA1	Aspergillus oryzae RIB40

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46

Confidence: strong

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57

Confidence: strong

VqsM

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

Confidence: strong

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.98 out of 27.04

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.75 out of 23.79

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.61 out of 24.78

Confidence: medium

Additional weak hits (28):

HipB

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

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33

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

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.47 out of 30.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.85 out of 27.78

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.94 out of 30.25

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.58 out of 18.57

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.61 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.30 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.28 out of 26.06

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 22.07 out of 30.97

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.01 out of 27.78

Confidence: weak

MogR

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

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.94 out of 27.55

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.73 out of 30.25

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.05 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.90 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.19 out of 29.65

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.54 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.06 out of 28.19

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 30.98

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.04 out of 29.65

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.49 out of 27.04

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.75 out of 29.65

Confidence: weak

ZuR variant 1

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

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.08 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.15 out of 29.65

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.07 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

RREFinder

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 96961 - 170556:

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

Polymer prediction:: (ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 115077 - 160798:

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

Polymer prediction:: (ccmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_00835: X

AMP-binding (13..428): 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:: GIIFAGISVK
Nearest Stachelhaus code(s):: Ant GIILFGVGVK (26% 8Å match)
Stachelhaus code match:: 60% (weak)

CDS_00836: mal

PKS_AT (542..837): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 83.3%; 2-Rhyd-Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 186.7
inactive: 112.1
Methylmalonyl-CoA: 69.7
Methoxymalonyl-CoA: 66.8
Propionyl-CoA: 49.0
Isobutyryl-CoA: 34.3
Ethylmalonyl-CoA: 30.0
Benzoyl-CoA: 27.7
2-Methylbutyryl-CoA: 22.4
CHC-CoA: 22.3
Acetyl-CoA: 16.4
fatty_acid: 12.2
trans-1,2-CPDA: 10.9
3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

RRE predictions

: RRE type: Stand_Alone_Lasso_RRE; Location: 28 - 84; Score: 46.4; RRE type: PqqD_RRE; Location: 9 - 83; Score: 41.8

TFBS definitions

Regulator	Description
DasR	N-acetylglucosamine dependent repressor
IolR	Regulator of the inositol catabolism
LexA variant 2	Repressor of DNA damage response
RpoN	Regulator of nitrogen assimilation and virulence
ToxT	Regulator of MSHA biosynthesis
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0002 - Region 2 - T1PKS

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Location: 368,707 - 412,876 nt. (total: 44,170 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))

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: phosphate reductase

CDS_01071: N-acetyl-gamma-glutamyl-phosphate reductase

smcogs: SMCOG1219: N-acetyl-gamma-glutamyl-phosphate reductase

Transferases: acylase

CDS_01079: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase

CDS_01095: metallo-beta-lactamase family protein

smcogs: SMCOG1170: metallo-beta-lactamase family protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.64	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001275.3	0.63	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0002191.2	0.60	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0000107.3	0.60	PKS	naphthopyrone	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
BGC0001257.3	0.60	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0002192.3	0.59	PKS	FR901512	fungal sp. No.14919

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.64	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001275.3	0.63	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0002191.2	0.60	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0000107.3	0.60	PKS	naphthopyrone	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
BGC0001257.3	0.60	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0002192.3	0.59	PKS	FR901512	fungal sp. No.14919

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46

Confidence: strong

CRP

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

Confidence: medium

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.68 out of 19.52

Confidence: medium

Additional weak hits (23):

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.93 out of 39.62

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.66 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.14 out of 31.73

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.37 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.56 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.94 out of 26.06

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.55 out of 25.88

Confidence: weak

ANR

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

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.40 out of 29.38

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.67 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.28 out of 30.25

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.58 out of 28.14

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.72 out of 30.97

Confidence: weak

ANR

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

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.63 out of 29.38

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.85 out of 36.54

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.17 out of 26.12

Confidence: weak

ANR

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

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.69 out of 36.54

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.29 out of 33.14

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.60 out of 33.14

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.67 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 5, location 368706 - 412876:

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

Polymer prediction:: (Me-mal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_01079: mmal

PKS_AT (553..865): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 83.3%; Malonyl-CoA: 66.7%; Ethylmalonyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 125.1
Methoxymalonyl-CoA: 109.6
Malonyl-CoA: 84.8
Ethylmalonyl-CoA: 79.6
Isobutyryl-CoA: 72.1
Benzoyl-CoA: 48.1
Propionyl-CoA: 40.9
2-Methylbutyryl-CoA: 39.6
Acetyl-CoA: 30.3
3-Methylbutyryl-CoA: 27.5
CHC-CoA: 27.0
inactive: 24.3
fatty_acid: 21.8
trans-1,2-CPDA: 16.5

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
CRP	Cyclic AMP receptor protein
RpoN	Regulator of nitrogen assimilation and virulence

NPDC024463.ctg-0002 - Region 3 - PKS-like,oligosaccharide

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Location: 470,056 - 535,824 nt. (total: 65,769 nt) Show pHMM detection rules used

oligosaccharide: (repeatable(3, [DUF1205, Glyco_transf_28, Glycos_transf_1, Glycos_transf_2, MGT]) and minscore(MGT, 150))
PKS-like: (t2pks2 or ksIII)

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

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_01148: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_01149: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_01150: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_01155: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_01159: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_01164: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

CDS_01167: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_01169: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

CDS_01176: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

Transferases: aminotransferase glycosyltransferase halogenase methyltransferase transferase

CDS_01153: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_01157: flavin-dependent pyrrole halogenase

halogenases: flavin-dependent pyrrole halogenase
smcogs: SMCOG1119: halogenase

CDS_01160: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_01161: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_01162: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_01165: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_01168: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_01171: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_01174: glucose-1-phosphate adenylyl/thymidylyltransferase

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

CDS_01177: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

CDS_01178: DegT/DnrJ/EryC1/StrS aminotransferase

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

CDS_01179: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_01183: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

Hydrolases: dehalogenase

CDS_01187: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Lyases: cyclase dehydratase

CDS_01154: cyclase/dehydrase

smcogs: SMCOG1128: cyclase/dehydrase

CDS_01163: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_01170: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_01173: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase

CDS_01158: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_01181: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_01182: 3-oxoacyl-(acyl carrier protein) synthase III

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

CDS_01184: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transport

CDS_01188: MMPL domain-containing transport protein

smcogs: SMCOG1035: MMPL domain-containing transport protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000278.3	0.54	PKS	urdamycin	Streptomyces fradiae
BGC0001250.4	0.49	NRPS	epichloenin A	Epichloe festucae
BGC0002274.2	0.49	NRPS	aspulvinone H, aspulvinone B1	Aspergillus terreus NIH2624
BGC0002174.2	0.49	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0001251.4	0.48	NRPS	epichloenin A	Epichloe festucae
BGC0001817.5	0.47	other (other)	vancosamine	Streptomyces sp. WAC2288
BGC0002608.2	0.46	NRPS, PKS	ochratoxin A	Aspergillus steynii
BGC0002341.2	0.45	other (other)	3,5-dibromo-p-anisic acid	Planctomycetales bacterium 10988
BGC0000231.5	0.42	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0000749.3	0.41	saccharide	capsular polysaccharide	Escherichia coli

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002608.2	0.76	NRPS, PKS	ochratoxin A	Aspergillus steynii
BGC0002341.2	0.75	other (other)	3,5-dibromo-p-anisic acid	Planctomycetales bacterium 10988
BGC0002276.2	0.64	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000231.5	0.62	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0002164.2	0.61	NRPS	peramine	Epichloe festucae
BGC0000278.3	0.60	PKS	urdamycin	Streptomyces fradiae
BGC0001135.5	0.60	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.60	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
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
BGC0001250.4	0.60	NRPS	epichloenin A	Epichloe festucae

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: 20.47 out of 20.47

Confidence: strong

CRP

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

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.12 out of 27.78

Confidence: medium

VqsM

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

Additional weak hits (20):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 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

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.79 out of 32.74

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.53 out of 26.06

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.05 out of 27.55

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.26 out of 32.74

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.86 out of 20.97

Confidence: weak

MexT

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

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.20 out of 27.78

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.19 out of 29.25

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.32 out of 39.62

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.13 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.03 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.90 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.41 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.54 out of 28.19

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.76 out of 24.78

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: 20.83 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

TFBS Finder

NRPS/PKS substrate predictions

CDS_01158: Pro

Search NORINE for peptide: strict or relaxed

AMP-binding (19..426): 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:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DLFYVAWVCK
Nearest Stachelhaus code(s):: Pro DLFYVAWVCK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_01184: X

AMP-binding (37..436): 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:: PMNYLGGPSK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0002 - Region 4 - terpene-precursor

Download region GenBank file

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Location: 615,700 - 636,917 nt. (total: 21,218 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

Oxidoreductases: dehydrogenase

CDS_01278: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: dehydratase

CDS_01284: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthetase

CDS_01282: 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
BGC0000894.4	0.42	other (other)	citrinin	Monascus aurantiacus
BGC0000677.5	0.41	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0000866.5	0.41	other (other)	polyhydroxyalkanoate	Burkholderia sp. DSM 9242
BGC0002493.3	0.40	NRPS	parabactin	Paracoccus denitrificans PD1222
BGC0001077.4	0.39	PKS	6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone	Actinoplanes missouriensis 431
BGC0001911.3	0.37	terpene	raimonol	Streptomyces anulatus
BGC0000642.3	0.37	terpene	carotenoid	Enterobacteriaceae bacterium DC413
BGC0001264.3	0.36	PKS	betaenone A, betaenone B, betaenone C	Phoma betae
BGC0002309.2	0.36	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000657.5	0.44	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0000894.4	0.42	other (other)	citrinin	Monascus aurantiacus
BGC0000677.5	0.41	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0000866.5	0.41	other (other)	polyhydroxyalkanoate	Burkholderia sp. DSM 9242
BGC0002493.3	0.40	NRPS	parabactin	Paracoccus denitrificans PD1222
BGC0001077.4	0.39	PKS	6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone	Actinoplanes missouriensis 431
BGC0001911.3	0.37	terpene	raimonol	Streptomyces anulatus
BGC0000642.3	0.37	terpene	carotenoid	Enterobacteriaceae bacterium DC413
BGC0001264.3	0.36	PKS	betaenone A, betaenone B, betaenone C	Phoma betae
BGC0002309.2	0.36	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488

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_01282: PT_FPPS_like

Domain 1 (102 - 403): 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:

VqsM

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

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.80 out of 23.79

Confidence: strong

Additional weak hits (6):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.98 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.30 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.65 out of 29.38

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.79 out of 27.78

Confidence: weak

ZuR variant 1

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

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.25 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
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
GFPP	Geranylfarnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
HPP	Hexaprenyl diphosphate
IPP	Isopentenyl diphosphate
PP	Diphosphate

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0003 - Region 1 - terpene

Download region GenBank file

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Location: 219,692 - 242,016 nt. (total: 22,325 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

Transferases: aminotransferase glycosyltransferase

CDS_01643: aminotransferase

smcogs: SMCOG1019: aminotransferase

CDS_01655: glycosyl transferase group 1

smcogs: SMCOG1045: glycosyl transferase group 1

Hydrolases: esterase hydrolase

CDS_01652: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

smcogs: SMCOG1283: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

CDS_01656: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: cyclase

CDS_01644: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: ligase

CDS_01638: 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	0.81	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0001135.5	0.56	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.55	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000902.4	0.44	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0000597.4	0.42	ribosomal	SWA-2138	Streptomyces sp. e14
BGC0000595.3	0.41	ribosomal	SCO-2138	Streptomyces coelicolor A3(2)
BGC0001314.3	0.40	terpene	tirucalla	Arabidopsis thaliana
BGC0000285.5	0.39	PKS, saccharide	flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin	Saccharopolyspora erythraea
BGC0000632.5	0.38	saccharide, terpene	brasilicardin A	Nocardia terpenica
BGC0002387.2	0.37	PKS	yangpumicin A	Micromonospora yangpuensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001181.4	0.81	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0001135.5	0.56	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.55	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000902.4	0.44	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0000597.4	0.42	ribosomal	SWA-2138	Streptomyces sp. e14
BGC0000595.3	0.41	ribosomal	SCO-2138	Streptomyces coelicolor A3(2)
BGC0001314.3	0.40	terpene	tirucalla	Arabidopsis thaliana
BGC0000285.5	0.39	PKS, saccharide	flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin	Saccharopolyspora erythraea
BGC0000632.5	0.38	saccharide, terpene	brasilicardin A	Nocardia terpenica
BGC0002387.2	0.37	PKS	yangpumicin A	Micromonospora yangpuensis

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_01644: T1TS + T1TS

Domain 1 (3 - 326): Type 1 terpene synthase

Subtype: Geosmin synthase, N terminal domain

Reactions:: FPP → germacradienol

Domain 2 (327 - 705): Type 1 terpene synthase

Subtype: Geosmin synthase, C terminal domain

Reactions:: germacradienol → geosmin

Transcription Factor Binding Sites

Binding sites found:

AbrC3

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

Confidence: strong

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.05 out of 22.40

Confidence: strong

Additional weak hits (2):

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.56 out of 36.54

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.28 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
FPP	Farnesyl diphosphate

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
HypR	L-hydroxyproline utilization repressor

NPDC024463.ctg-0003 - Region 2 - NRPS,transAT-PKS

Download region GenBank file

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Location: 250,431 - 326,391 nt. (total: 75,961 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: 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_01684: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CDS_01687: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

Transferases: acylase

CDS_01679: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase phosphatase

CDS_01665: putative esterase

smcogs: SMCOG1104: putative esterase

CDS_01689: FkbH like protein

smcogs: SMCOG1256: FkbH like protein

Ligases: ligase synthase

CDS_01680: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_01681: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_01682: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_01683: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_01688: 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
BGC0000342.4	0.72	NRPS	enniatin	Fusarium equiseti
BGC0001275.3	0.69	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001276.3	0.68	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001135.5	0.63	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002192.3	0.63	PKS	FR901512	fungal sp. No.14919
BGC0002135.2	0.62	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.61	NRPS	AbT1	Aureobasidium pullulans
BGC0002191.2	0.61	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001164.3	0.61	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001268.4	0.60	NRPS, PKS	fusarin C	Fusarium fujikuroi

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0001275.3	0.67	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001276.3	0.67	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001135.5	0.65	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002192.3	0.65	PKS	FR901512	fungal sp. No.14919
BGC0002135.2	0.65	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.64	NRPS	AbT1	Aureobasidium pullulans
BGC0000037.4	0.64	PKS	cichorine	Aspergillus nidulans FGSC A4
BGC0002191.2	0.64	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001164.3	0.64	PKS	1-heptadecene	Cyanothece sp. PCC 7822

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

AbrC3

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

Confidence: strong

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.86 out of 18.57

Confidence: medium

Additional weak hits (20):

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.91 out of 28.14

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.65 out of 29.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.66 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.40 out of 30.25

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

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: 15.56 out of 21.84

Confidence: weak

MexT

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.04 out of 26.06

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.52 out of 29.38

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.91 out of 21.55

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.04 out of 26.85

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.49 out of 19.26

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.91 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.22 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.61 out of 26.06

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.54 out of 30.98

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.53 out of 35.63

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.02 out of 18.57

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.56 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 2, location 250430 - 326391:

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

Polymer prediction:: (mal - ccmal) + (mal - redmal) + (Me-mal) + (NMe-Ser)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_01679: mal - mal

PKS_AT (8..299): mal

ATSignature: (unknown)

No matches above 50%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 35.3
Isobutyryl-CoA: 28.9
Methylmalonyl-CoA: 23.3
fatty_acid: 16.6
inactive: 16.0
Benzoyl-CoA: 15.5
Propionyl-CoA: 11.0
Methoxymalonyl-CoA: 5.4
trans-1,2-CPDA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

PKS_AT (354..630): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 104.3
Methoxymalonyl-CoA: 33.8
inactive: 33.4
Methylmalonyl-CoA: 28.7
Propionyl-CoA: 24.8
Isobutyryl-CoA: 15.8
2-Methylbutyryl-CoA: 14.8
CHC-CoA: 14.1
fatty_acid: 11.5
Ethylmalonyl-CoA: 8.2
Acetyl-CoA: 7.6
trans-1,2-CPDA: 0.0
Benzoyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

CDS_01680: Ser

Search NORINE for peptide: strict or relaxed

AMP-binding (507..906): 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:: DVWHVSLVDK
Nearest Stachelhaus code(s):: Ser DVWHVSLVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
ToxT	Regulator of MSHA biosynthesis

NPDC024463.ctg-0003 - Region 3 - NAPAA

Download region GenBank file

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Location: 405,592 - 439,638 nt. (total: 34,047 nt) Show pHMM detection rules used

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: aminotransferase

CDS_01784: aminotransferase

smcogs: SMCOG1019: aminotransferase

Isomerases: isomerase

CDS_01775: isochorismate synthase

smcogs: SMCOG1018: isochorismate synthase

Ligases: ligase

CDS_01787: 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	0.74	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0001135.5	0.62	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.61	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.61	NRPS	AbT1	Aureobasidium pullulans
BGC0001758.4	0.61	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.60	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.60	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
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
BGC0001250.4	0.60	NRPS	epichloenin A	Epichloe festucae
BGC0001251.4	0.60	NRPS	epichloenin A	Epichloe festucae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002174.2	0.74	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0001135.5	0.62	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.61	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.61	NRPS	AbT1	Aureobasidium pullulans
BGC0001758.4	0.61	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.60	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.60	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
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
BGC0001250.4	0.60	NRPS	epichloenin A	Epichloe festucae
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:

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 (3):

ANR

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

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.09 out of 29.38

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.73 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 3, location 405591 - 439638:

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_01787: 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:: DFECLSAVSK
Nearest Stachelhaus code(s):: Val DFESLAAVYK (59% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein

NPDC024463.ctg-0003 - Region 4 - terpene-precursor

Download region GenBank file

Download region SVG

Location: 474,074 - 495,189 nt. (total: 21,116 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

Oxidoreductases: dehydrogenase oxidoreductase

CDS_01835: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

CDS_01841: pyridine nucleotide-disulfide oxidoreductase

smcogs: SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

CDS_01842: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

Transferases: phosphorylase

CDS_01839: thiamine-phosphate pyrophosphorylase

smcogs: SMCOG1280: thiamine-phosphate pyrophosphorylase

Hydrolases: dehalogenase

CDS_01834: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Ligases: synthetase

CDS_01838: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001456.3	0.46	terpene	isorenieratene	Streptomyces argillaceus
BGC0002345.2	0.43	other (other)	hydrogen cyanide	Pseudomonas fluorescens
BGC0000677.5	0.43	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0000843.5	0.43	other (non-nrp beta-lactam)	alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate	Streptomyces clavuligerus ATCC 27064
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
BGC0001521.3	0.41	NRPS	auriculamide	Herpetosiphon aurantiacus DSM 785
BGC0000648.3	0.41	terpene	carotenoid	Myxococcus xanthus
BGC0000649.3	0.40	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001227.3	0.40	terpene	isorenieratene	Streptomyces collinus Tu 365

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001456.3	0.46	terpene	isorenieratene	Streptomyces argillaceus
BGC0002345.2	0.43	other (other)	hydrogen cyanide	Pseudomonas fluorescens
BGC0000677.5	0.43	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0000843.5	0.43	other (non-nrp beta-lactam)	alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate	Streptomyces clavuligerus ATCC 27064
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
BGC0001521.3	0.41	NRPS	auriculamide	Herpetosiphon aurantiacus DSM 785
BGC0000648.3	0.41	terpene	carotenoid	Myxococcus xanthus
BGC0000649.3	0.40	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001227.3	0.40	terpene	isorenieratene	Streptomyces collinus Tu 365

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_01838: PT_FPPS_like

Domain 1 (49 - 369): 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:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.35 out of 23.79

Confidence: medium

Additional weak hits (9):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.41 out of 29.38

Confidence: weak

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: 16.86 out of 19.52

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.97 out of 27.78

Confidence: weak

LexA variant 1

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

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.10 out of 28.19

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.61 out of 32.93

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.84 out of 36.53

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
IolR	Regulator of the inositol catabolism

NPDC024463.ctg-0003 - Region 5 - crocagin

Download region GenBank file

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Location: 619,863 - 646,182 nt. (total: 26,320 nt) Show pHMM detection rules used

crocagin: (PhyH and Carbam_trans_N)

Legend:

core biosynthetic genes

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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

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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

CDS_01970: dehydrogenase

smcogs: SMCOG1072: dehydrogenase

CDS_01989: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

Transferases: methyltransferase

CDS_01975: methyltransferase

smcogs: SMCOG1089: methyltransferase

Ligases: ligase

CDS_01982: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_01990: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.63	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.63	NRPS	AbT1	Aureobasidium pullulans
BGC0001261.3	0.63	NRPS	AM-toxin	Alternaria alternata
BGC0001166.5	0.63	NRPS	HC-toxin	Alternaria jesenskae
BGC0001240.4	0.63	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0000357.5	0.63	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
BGC0000342.4	0.63	NRPS	enniatin	Fusarium equiseti
BGC0001251.4	0.62	NRPS	epichloenin A	Epichloe festucae
BGC0001250.4	0.62	NRPS	epichloenin A	Epichloe festucae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.63	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.63	NRPS	AbT1	Aureobasidium pullulans
BGC0001261.3	0.63	NRPS	AM-toxin	Alternaria alternata
BGC0001166.5	0.63	NRPS	HC-toxin	Alternaria jesenskae
BGC0001240.4	0.63	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0000357.5	0.63	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
BGC0000342.4	0.63	NRPS	enniatin	Fusarium equiseti
BGC0001251.4	0.62	NRPS	epichloenin A	Epichloe festucae
BGC0001250.4	0.62	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:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47

Confidence: medium

Additional weak hits (6):

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.47 out of 30.98

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.59 out of 29.65

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

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.72 out of 27.78

Confidence: weak

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.00 out of 32.38

Confidence: weak

MogR

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

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
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0003 - Region 6 - lanthipeptide-class-iv

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Location: 647,360 - 669,579 nt. (total: 22,220 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

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_02010: methyltransferase

smcogs: SMCOG1089: methyltransferase

Isomerases: mutase

CDS_01998: phosphoglycerate mutase

smcogs: SMCOG1101: phosphoglycerate mutase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000563.4	0.50	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0001226.4	0.49	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0001468.5	0.36	other (trna-derived)	bicyclomycin	Streptomyces cinnamoneus
BGC0002227.3	0.36	NRPS	AKML B, AKML D, AKML A, AKML C	Aspergillus luchuensis IFO 4308
BGC0000678.5	0.35	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002000.4	0.34	PKS	setomimycin	Streptomyces aurantiacus JA 4570
BGC0000874.5	0.34	other (other)	blasticidin S	Streptomyces griseochromogenes
BGC0001366.5	0.34	PKS	BE-24566B, zunyimycin A	Streptomyces sp. FJS31-2
BGC0001882.3	0.34	PKS	chrysoxanthone A, chrysoxanthone B, chrysoxanthone C	Penicillium rubens Wisconsin 54-1255
BGC0001582.4	0.34	NRPS	ecumicin	Nonomuraea sp. MJM5123

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000563.4	0.50	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0001226.4	0.49	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0001468.5	0.36	other (trna-derived)	bicyclomycin	Streptomyces cinnamoneus
BGC0002227.3	0.36	NRPS	AKML B, AKML D, AKML A, AKML C	Aspergillus luchuensis IFO 4308
BGC0000678.5	0.35	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002000.4	0.34	PKS	setomimycin	Streptomyces aurantiacus JA 4570
BGC0000874.5	0.34	other (other)	blasticidin S	Streptomyces griseochromogenes
BGC0001366.5	0.34	PKS	BE-24566B, zunyimycin A	Streptomyces sp. FJS31-2
BGC0001882.3	0.34	PKS	chrysoxanthone A, chrysoxanthone B, chrysoxanthone C	Penicillium rubens Wisconsin 54-1255
BGC0001582.4	0.34	NRPS	ecumicin	Nonomuraea sp. MJM5123

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: 17.72 out of 20.47

Confidence: medium

Additional weak hits (12):

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.18 out of 20.97

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.39 out of 29.38

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.68 out of 26.06

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.29 out of 18.57

Confidence: weak

MexT

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

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: 17.26 out of 24.78

Confidence: weak

HypR

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

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.10 out of 35.63

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: 17.24 out of 24.78

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

NPDC024463.ctg-0004 - Region 1 - T3PKS,azole-containing-RiPP

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Location: 235,211 - 276,701 nt. (total: 41,491 nt) Show pHMM detection rules used

T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
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

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

Azole RiPPs

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_02287: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02297: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Hydrolases: esterase

CDS_02311: thioesterase

smcogs: SMCOG1004: thioesterase

Lyases: dehydratase

CDS_02304: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

Ligases: ligase synthase

CDS_02298: chalcone and stilbene synthase domain protein

smcogs: SMCOG1024: chalcone and stilbene synthase domain protein

CDS_02312: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001310.5	1.14	PKS	naringenin	Streptomyces clavuligerus ATCC 27064
BGC0002127.3	0.78	PKS	flaviolin, 1,3,6,8-tetrahydroxynaphthalene	Streptomyces coelicolor A3(2)
BGC0000902.4	0.59	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0000016.4	0.43	other (other)	amphotericin B	Streptomyces nodosus
BGC0000282.3	0.42	PKS	2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000285.5	0.42	PKS, saccharide	flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin	Saccharopolyspora erythraea
BGC0001145.5	0.42	ribosomal	cyclothiazomycin b1	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001860.4	0.41	ribosomal	thiomuracin	Thermobispora bispora DSM 43833
BGC0000613.5	0.40	ribosomal	thiomuracin A	Nonomuraea sp. Bp3714-39
BGC0001201.3	0.39	terpene	eremophilene	Sorangium cellulosum So ce56

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	0.63	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0000016.4	0.54	other (other)	amphotericin B	Streptomyces nodosus
BGC0000282.3	0.54	PKS	2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000285.5	0.54	PKS, saccharide	flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin	Saccharopolyspora erythraea
BGC0001145.5	0.53	ribosomal	cyclothiazomycin b1	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001860.4	0.53	ribosomal	thiomuracin	Thermobispora bispora DSM 43833
BGC0000613.5	0.53	ribosomal	thiomuracin A	Nonomuraea sp. Bp3714-39
BGC0001201.3	0.52	terpene	eremophilene	Sorangium cellulosum So ce56

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: 18.51 out of 25.31

Confidence: medium

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.08 out of 23.43

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

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.85 out of 27.04

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31

Confidence: medium

Additional weak hits (10):

ANR

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

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.33 out of 27.18

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.56 out of 23.43

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.69 out of 19.26

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.69 out of 19.26

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.29 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.67 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

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.32 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

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS substrates

RREFinder

TFBS Finder

Azole RiPPs

NRPS/PKS substrate predictions

CDS_02312: X

AMP-binding (53..439): 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:: GLLFVAGHVK
Nearest Stachelhaus code(s):: Trp GALFFAAGVK (35% 8Å match); Ala DLLVVAGILK (29% 8Å match)
Stachelhaus code match:: 60% (weak)

Link to PARAS substrate predictor

RRE predictions

: RRE type: Thiopeptide_F_RRE; Location: 12 - 93; Score: 48.4; RRE type: Heterocycloanthracin_C_RRE; Location: 14 - 96; Score: 30.3; RRE type: Heterocycloanthracin_C_RRE; Location: 7 - 91; Score: 42.5; RRE type: Thiopeptide_F_RRE; Location: 0 - 79; Score: 42.4

TFBS definitions

Regulator	Description
BldD	Development and antibiotic global regulator
CRP	Cyclic AMP receptor protein
CatR	H2O2-responsive repressor
DasR	N-acetylglucosamine dependent repressor

Core peptide predictions

No core peptides found.

NPDC024463.ctg-0004 - Region 2 - lanthipeptide-class-i

Download region GenBank file

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Location: 280,835 - 305,654 nt. (total: 24,820 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

Oxidoreductases: dehydrogenase

CDS_02334: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02335: dehydrogenase

smcogs: SMCOG1072: dehydrogenase

Lyases: cyclase dehydratase

CDS_02327: Lanthionine synthetase C family protein

smcogs: SMCOG1140: Lanthionine synthetase C family protein

CDS_02328: 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.
BGC0002640.2	0.56	ribosomal	thalassomonasin A, thalassomonasin B	Thalassomonas actiniarum
BGC0002635.2	0.53	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0002316.2	0.49	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0000544.4	0.49	ribosomal	planosporicin	Planomonospora alba
BGC0001289.5	0.47	ribosomal	penisin	Paenibacillus ehimensis
BGC0000542.3	0.44	ribosomal	paenicidin B	Paenibacillus terrae
BGC0000541.5	0.44	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0001727.3	0.43	ribosomal	paenilan	Paenibacillus polymyxa E681
BGC0000529.5	0.43	ribosomal	microbisporicin A2	Microbispora corallina

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
BGC0002635.2	0.53	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0002316.2	0.49	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0000544.4	0.49	ribosomal	planosporicin	Planomonospora alba
BGC0001289.5	0.47	ribosomal	penisin	Paenibacillus ehimensis
BGC0000542.3	0.44	ribosomal	paenicidin B	Paenibacillus terrae
BGC0000541.5	0.44	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0001727.3	0.43	ribosomal	paenilan	Paenibacillus polymyxa E681
BGC0000529.5	0.43	ribosomal	microbisporicin A2	Microbispora corallina

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_02328

CDS_02329

Leader:

MSTATLPAAIDTVELEDLFDLDIRIEQTEHTAEDS

Core:

WTSIGCSIPCLPSYLPTGCCA

Core with dehydrations:

WDhbDhaIGCysDhaIPCysLPDhaYLPDhbGCysCysA

antiSMASH-DB 4.0 matches for CDS_02329

28.6%

NZ_QKTG01000020.1and 1 other:

NZ_QKTG01000020.1 Lanthipeptides: DEI99_RS08060_lanthipeptide

Lanthipeptides: DEI99_RS08060_lanthipeptide

11

LPSYLPTGCC

20

LP + PTG C

4

LPGFCPTGAC

13

23.1%

NZ_JANAVO010000004.1and 3 others:

NZ_JANAVO010000004.1 Lanthipeptides: NLX83_RS25550_lanthipeptideNZ_JANAVO010000004.1 Lanthipeptides: NLX83_RS25550_lanthipeptideNZ_JANAVO010000004.1 Lanthipeptides: NLX83_RS25550_lanthipeptide

Lanthipeptides: NLX83_RS25550_lanthipeptide

7

SIPCLPSYLPTGCCA

21

+ P + S +P GCC+

8

TFPSIRSMMPIGCCS

22

17.6%

NZ_JACSPO010000013.1and 1 other:

NZ_JACSPO010000013.1 Lanthipeptides: H9624_RS14885_lanthipeptide

Lanthipeptides: H9624_RS14885_lanthipeptide

11

LPSYLPTGCC

20

LP + PTG C

21

LPDFCPTGAC

30

with 2 more sequence matches

12.2%

NZ_SOCO01000001.1:

Lanthipeptides: allorf_1178421_1178636_lanthipeptide

1

WTSIGCSIPCL

11

W S+G S PC

32

WRSLGDSNPCF

42

11.5%

NZ_FWXM01000003.1:

Lanthipeptides: B8967_RS11230_lanthipeptide

5

GCSIPCLPSYLPT

17

GCS CL +++ T

23

GCSDGCLSNFMHT

35

MIBiG 4.0 matches for CDS_02329

10.7%

BGC0000517.4 (BAB04173.1):

Lanthipeptide: haloduracin β or haloduracin α

7

SIPCLPS

13

++ C+PS

20

TVECMPS

26

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.47 out of 27.04

Confidence: medium

Additional weak hits (3):

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.89 out of 25.75

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.45 out of 25.75

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.81 out of 30.22

Confidence: weak

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Lanthipeptides

RREFinder

TFBS Finder

Core peptide predictions

CDS_02329 - Class I

Cleavage pHMM score: 0.40

RODEO score: 19

Monoisotopic mass: 2081.0 Da

Molecular weight: 2082.5 Da

Number of bridges: 4

Alternative weights: (assuming N unmodified Ser/Thr residues); 2100.5 Da N = 1

RRE predictions

: RRE type: Lanthipeptide_LanB_RRE; Location: 187 - 271; Score: 40.1

TFBS definitions

Regulator	Description
DasR	N-acetylglucosamine dependent repressor

NPDC024463.ctg-0004 - Region 3 - RiPP-like

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Location: 387,157 - 399,073 nt. (total: 11,917 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))

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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 overview

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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

No tailoring functions detected.

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.43	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0000558.5	0.42	ribosomal	sublancin 168	Bacillus subtilis subsp. subtilis str. 168
BGC0000554.4	0.41	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998
BGC0001639.3	0.40	ribosomal	klebsidin	Klebsiella pneumoniae
BGC0001887.3	0.38	ribosomal	huazacin	Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0001684.3	0.37	other (other)	N-acyloxyacyl glutamine	Klebsiella variicola
BGC0000551.5	0.37	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0002312.2	0.36	ribosomal	ubonodin	Burkholderia ubonensis
BGC0000571.3	0.36	ribosomal	burhizin	Paraburkholderia rhizoxinica HKI 454
BGC0000513.3	0.36	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.43	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0000558.5	0.42	ribosomal	sublancin 168	Bacillus subtilis subsp. subtilis str. 168
BGC0000554.4	0.41	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998
BGC0001639.3	0.40	ribosomal	klebsidin	Klebsiella pneumoniae
BGC0001887.3	0.38	ribosomal	huazacin	Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0001684.3	0.37	other (other)	N-acyloxyacyl glutamine	Klebsiella variicola
BGC0000551.5	0.37	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0002312.2	0.36	ribosomal	ubonodin	Burkholderia ubonensis
BGC0000571.3	0.36	ribosomal	burhizin	Paraburkholderia rhizoxinica HKI 454
BGC0000513.3	0.36	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338

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:

OsdR

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

Confidence: medium

Additional weak hits (1):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.61 out of 29.38

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
OsdR	Development and stress management regulator

NPDC024463.ctg-0004 - Region 4 - NRPS

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Location: 399,534 - 492,916 nt. (total: 93,383 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

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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 oxidase oxidoreductase

CDS_02417: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02422: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

CDS_02435: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02440: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_02441: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CDS_02442: pyruvate oxidase/decarboxylase

smcogs: SMCOG1055: pyruvate oxidase/decarboxylase

CDS_02466: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

Transferases: aminotransferase

CDS_02459: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Hydrolases: esterase hydrolase

CDS_02429: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

CDS_02446: thioesterase

smcogs: SMCOG1004: thioesterase

Lyases: decarboxylase hydratase

CDS_02420: diaminopimelate decarboxylase

smcogs: SMCOG1264: diaminopimelate decarboxylase

CDS_02465: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase

CDS_02431: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_02434: 1-deoxy-D-xylulose-5-phosphate synthase

smcogs: SMCOG1110: 1-deoxy-D-xylulose-5-phosphate synthase

CDS_02444: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_02445: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

CDS_02450: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_02451: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_02452: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_02463: 8-amino-7-oxononanoate synthase

smcogs: SMCOG1109: 8-amino-7-oxononanoate synthase

CDS_02467: 8-amino-7-oxononanoate synthase

smcogs: SMCOG1109: 8-amino-7-oxononanoate synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002286.3	0.76	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.75	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.75	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.75	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001249.5	0.74	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001261.3	0.74	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.73	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002286.3	0.76	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.75	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.75	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.75	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001249.5	0.74	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001261.3	0.74	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.73	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:

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.16 out of 20.01

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

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.06 out of 27.04

Confidence: medium

Additional weak hits (19):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.37 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.23 out of 30.25

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: 15.92 out of 27.78

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.77 out of 26.85

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.14 out of 31.73

Confidence: weak

MogR

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.53 out of 26.06

Confidence: weak

MexT

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

Confidence: weak

ANR

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

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.83 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.10 out of 28.19

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.08 out of 35.63

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.02 out of 29.65

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.41 out of 28.19

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.97 out of 24.78

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.61 out of 27.04

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.75 out of 35.63

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.78 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 6, location 399533 - 492916:

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

Polymer prediction:: (Glu - Pro - D-Gly) + (Thr - D-Thr - X) + (X) + (Thr)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_02431: Glu - Pro - Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (260..668): Glu

nrpys: Glu

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:: DLPKVASVSK
Nearest Stachelhaus code(s):: Glu DLVKVASVNK (62% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1321..1731): 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:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVYYTGGGVK
Nearest Stachelhaus code(s):: 4Me-Pro or Pro DVQYGGHLVK (74% 8Å match); Ala DVFWTGGIFK (50% 8Å match); Leu DGAYTGEVVK (47% 8Å match); Trp or Pro DVYFVGGICK (44% 8Å match)
Stachelhaus code match:: 60% (weak)

AMP-binding (2384..2779): 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_02444: Thr - Thr - X

Search NORINE for peptide: strict or relaxed

AMP-binding (467..872): 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 (91% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1530..1932): 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 (91% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3029..3426): 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:: DGGQSGIVNK
Nearest Stachelhaus code(s):: Lys DSGFSGAVDK (59% 8Å match); Cap DPQDIGIVNK (56% 8Å match); 3Me-Glu or Glu DLGKTGVVNK (50% 8Å match)
Stachelhaus code match:: 60% (weak)

CDS_02450: X

AMP-binding (288..677): 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:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVSFVGAVYK
Nearest Stachelhaus code(s):: Trp DVSQVGAVAK (68% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_02452: Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (466..872): 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 (88% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
ArgR	Regulator of arginine biosynthesis genes
CRP	Cyclic AMP receptor protein
DasR	N-acetylglucosamine dependent repressor

NPDC024463.ctg-0004 - Region 5 - NAPAA,guanidinotides,terpene

Download region GenBank file

Download region SVG

Location: 499,527 - 563,785 nt. (total: 64,259 nt) Show pHMM detection rules used

NAPAA: (AMP-binding and TIGR02353)
guanidinotides: (pgm1 and pgm_amidino)
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

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 oxygenase

CDS_02474: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_02481: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02498: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_02508: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

CDS_02513: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase

CDS_02500: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

Hydrolases: hydrolase

CDS_02494: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Lyases: cyclase

CDS_02516: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: ligase

CDS_02475: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_02485: 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	0.48	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0002631.2	0.43	ribosomal	Myxarylin	Pyxidicoccus fallax
BGC0001633.3	0.36	other (other)	ketomemicin B3, ketomemicin B4	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001849.4	0.34	ribosomal	thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D	Streptomyces varsoviensis
BGC0001510.5	0.29	other (other)	anisomycin	Streptomyces hygrospinosus
BGC0002706.2	0.29	NRPS	saframycin Mx1	Myxococcus xanthus
BGC0002293.2	0.29	NRPS	ohmyungsamycin A, ohmyungsamycin B	Streptomyces sp.
BGC0002000.4	0.28	PKS	setomimycin	Streptomyces aurantiacus JA 4570
BGC0001075.5	0.28	PKS, terpene	aurachin RE	Rhodococcus erythropolis
BGC0001135.5	0.27	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis

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
BGC0001261.3	0.60	NRPS	AM-toxin	Alternaria alternata
BGC0002276.2	0.60	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000307.4	0.60	NRPS	AbT1	Aureobasidium pullulans
BGC0001249.5	0.60	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001166.5	0.60	NRPS	HC-toxin	Alternaria jesenskae
BGC0001160.5	0.60	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002

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_02516: T1TS

Domain 1 (16 - 339): 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: 18.25 out of 20.47

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

CatR

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

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: 17.94 out of 23.79

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 22.20 out of 24.78

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 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 (23):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.37 out of 21.55

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.21 out of 18.57

Confidence: weak

CodY

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.55 out of 26.06

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.87 out of 25.88

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.23 out of 32.74

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.23 out of 36.54

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.91 out of 30.22

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.31 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.70 out of 32.74

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.05 out of 30.25

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: 17.39 out of 28.19

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.15 out of 24.78

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.36 out of 29.65

Confidence: weak

LexA variant 1

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

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: 16.96 out of 22.40

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.50 out of 35.63

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.55 out of 18.57

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.51 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.43 out of 29.65

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

Terpene

TFBS Finder

Predicted core structure(s)

For candidate cluster 7, location 499526 - 563785:

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 8, location 499526 - 533585:

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_02475: X

AMP-binding (24..429): 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:: GLLVRAGPAK
Nearest Stachelhaus code(s):: Ala DLLVVAGILK (24% 8Å match)
Stachelhaus code match:: 60% (weak)

CDS_02485: X

AMP-binding (42..415): 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
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
CatR	H2O2-responsive repressor
IolR	Regulator of the inositol catabolism
LexA variant 2	Repressor of DNA damage response
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0005 - Region 1 - terpene

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Location: 33,703 - 54,653 nt. (total: 20,951 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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Select a gene to view the details available for it

Gene overview

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SubClusterBlast

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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

No tailoring functions detected.

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0002700.2	0.41	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0000486.4	0.40	ribosomal	butyrivibriocin AR10	Butyrivibrio fibrisolvens
BGC0000616.4	0.40	ribosomal	amylocyclicin	Bacillus velezensis FZB42
BGC0000650.3	0.39	terpene	carotenoid	Algoriphagus sp. KK10202C
BGC0001743.3	0.39	ribosomal	plantaricyclin	Lactobacillus plantarum
BGC0001222.3	0.39	ribosomal	acidocin B	Lactobacillus acidophilus
BGC0000491.5	0.39	ribosomal	gassericin A	Lactobacillus gasseri
BGC0001887.3	0.39	ribosomal	huazacin	Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0002111.3	0.38	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0002700.2	0.41	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0000486.4	0.40	ribosomal	butyrivibriocin AR10	Butyrivibrio fibrisolvens
BGC0000616.4	0.40	ribosomal	amylocyclicin	Bacillus velezensis FZB42
BGC0000650.3	0.39	terpene	carotenoid	Algoriphagus sp. KK10202C
BGC0001743.3	0.39	ribosomal	plantaricyclin	Lactobacillus plantarum
BGC0001222.3	0.39	ribosomal	acidocin B	Lactobacillus acidophilus
BGC0000491.5	0.39	ribosomal	gassericin A	Lactobacillus gasseri
BGC0001887.3	0.39	ribosomal	huazacin	Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0002111.3	0.38	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139

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	C30 carotenoid	diapophytoene	C30	acyclic	none
triterpene		PSPP	C30	acyclic	PP
triterpene		squalene	C30	acyclic	none
tetraterpene	C40 carotenoid	phytoene	C40	acyclic	none
triterpene		hydroxysqualene	C30	acyclic	OH

Genes with terpene domains:

CDS_02570: PT_phytoene_like

Domain 1 (19 - 308): Prenyltransferase; Phytoene synthase like

Subtype: unknown

Reactions:: FPP → diapophytoene; FPP → PSPP; FPP → squalene; GGPP → phytoene; PSPP → hydroxysqualene

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: 19.37 out of 20.47

Confidence: strong

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.96 out of 27.18

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.91 out of 24.78

Confidence: medium

Additional weak hits (4):

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

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.37 out of 39.62

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.20 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.09 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
FPP	Farnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
PP	Diphosphate
PSPP	Presqualene diphosphate

TFBS definitions

Regulator	Description
LexA variant 2	Repressor of DNA damage response
NrdR	Represses ribonucleotide reductase encoding genes
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0005 - Region 2 - NRPS-like,terpene

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Location: 117,425 - 167,871 nt. (total: 50,447 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)

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

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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 oxidoreductase oxygenase

CDS_02647: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_02650: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_02669: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: acetyltransferase

CDS_02668: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Lyases: cyclase dehydratase

CDS_02663: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_02677: 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
BGC0000041.3	0.26	PKS	oronofacic acid	Pseudomonas syringae
BGC0001135.5	0.26	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001641.4	0.25	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.24	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.24	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001758.4	0.24	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001633.3	0.24	other (other)	ketomemicin B3, ketomemicin B4	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000067.5	0.23	PKS	geldanamycin	Streptomyces hygroscopicus subsp. duamyceticus
BGC0002514.3	0.19	PKS	julichrome Q6.6	Streptomyces sampsonii
BGC0000194.5	0.18	PKS	actinorhodin	Streptomyces coelicolor A3(2)

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.59	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001641.4	0.58	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.58	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.58	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001758.4	0.58	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002260.3	0.46	terpene	trichobrasilenol, xylarenic acid B, brasilane A, brasilane F, brasilane E, brasilane D	Annulohypoxylon truncatum
BGC0000351.5	0.45	NRPS	exochelin	Mycolicibacterium smegmatis MC2 155
BGC0002518.3	0.45	NRPS	syringafactin A, syringafactin C	Pseudomonas sp. SZ57
BGC0002150.2	0.43	ribosomal	triculamin	Streptomyces triculaminicus
BGC0002151.2	0.43	ribosomal	alboverticillin	Streptomyces griseocarneus

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	drimane-type		C15	C2-C7 + C6-C11	PP

Genes with terpene domains:

CDS_02677: T1TS

Domain 1 (2 - 315): Type 1 terpene synthase

Subtype: unknown

CDS_02679: T2TS

Domain 1 (7 - 504): Type 2 terpene synthase

Subtype: Sesquiterpene synthase, group b

Reactions:: FPP → sesquiterpene_C2-C7/C6-C11_PP

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

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.51 out of 25.31

Confidence: medium

CatR

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

Confidence: medium

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.50 out of 30.12

Confidence: medium

VqsM

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

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.98 out of 26.85

Confidence: medium

Additional weak hits (24):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.94 out of 27.78

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.13 out of 30.97

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.67 out of 30.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.16 out of 27.78

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75

Confidence: weak

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.67 out of 29.72

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.17 out of 36.54

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.56 out of 36.54

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.18 out of 31.73

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.36 out of 35.63

Confidence: weak

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.27 out of 30.12

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

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.90 out of 35.63

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.70 out of 33.14

Confidence: weak

HypR

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

Confidence: weak

HypR

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

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.73 out of 29.25

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.15 out of 28.19

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.83 out of 24.78

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.69 out of 26.85

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 20.08 out of 33.14

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.63 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

Terpene

TFBS Finder

Predicted core structure(s)

For candidate cluster 2, location 117424 - 167871:

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 117424 - 161042:

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_02663: X

AMP-binding (87..537): X

nrpys: (unknown)

SVM prediction details:

NOTE: uncertain match

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:: MIGLEA---K
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

Link to PARAS substrate predictor

Glossary

Acronym	Full name
FPP	Farnesyl diphosphate
PP	Diphosphate

TFBS definitions

Regulator	Description
CatR	H2O2-responsive repressor
OsdR	Development and stress management regulator
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0005 - Region 3 - terpene

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Location: 360,720 - 385,804 nt. (total: 25,085 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: oxygenase

CDS_02869: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_02872: Oxidation

MITE: MITE0000108Oxidation (identity: 67.10%)
smcogs: SMCOG1034: cytochrome P450

Transferases: kinase

CDS_02877: glycerol kinase

smcogs: SMCOG1210: glycerol kinase

Lyases: cyclase

CDS_02873: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthetase

CDS_02870: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001911.3	0.80	terpene	raimonol	Streptomyces anulatus
BGC0001910.4	0.76	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0000660.5	0.58	terpene	albaflavenone	Streptomyces coelicolor A3(2)
BGC0000677.5	0.57	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002043.3	0.54	ribosomal	cittilin A, cittilin B	Myxococcus xanthus DK 1622
BGC0000286.3	0.52	PKS	viguiepinol	Streptomyces sp. KO-3988
BGC0002309.2	0.52	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000675.5	0.49	terpene	(+)-T-muurolol	Streptomyces clavuligerus ATCC 27064
BGC0000674.5	0.48	terpene	(-)-δ-cadinene	Streptomyces clavuligerus ATCC 27064
BGC0000678.5	0.47	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001911.3	0.80	terpene	raimonol	Streptomyces anulatus
BGC0001910.4	0.76	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0000660.5	0.58	terpene	albaflavenone	Streptomyces coelicolor A3(2)
BGC0000677.5	0.57	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002043.3	0.54	ribosomal	cittilin A, cittilin B	Myxococcus xanthus DK 1622
BGC0000286.3	0.52	PKS	viguiepinol	Streptomyces sp. KO-3988
BGC0002309.2	0.52	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000675.5	0.49	terpene	(+)-T-muurolol	Streptomyces clavuligerus ATCC 27064
BGC0000674.5	0.48	terpene	(-)-δ-cadinene	Streptomyces clavuligerus ATCC 27064
BGC0000678.5	0.47	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893

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
diterpene			C20	C6-C11 + C10-C15	none

Genes with terpene domains:

CDS_02870: PT_FPPS_like

Domain 1 (52 - 359): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

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

CDS_02871: T2TS

Domain 1 (26 - 533): Type 2 terpene synthase

Subtype: Diterpene synthase

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

CDS_02873: T1TS

Domain 1 (7 - 319): 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 (1):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.29 out of 21.55

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

TFBS definitions

Regulator	Description

NPDC024463.ctg-0005 - Region 4 - T1PKS,T3PKS

Download region GenBank file

Download region SVG

Location: 436,924 - 493,964 nt. (total: 57,041 nt) Show pHMM detection rules used

T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
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

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: oxidoreductase oxygenase

CDS_02921: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

CDS_02935: oxidoreductase

smcogs: SMCOG1161: oxidoreductase

CDS_02941: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

CDS_02949: monooxygenase FAD-binding

smcogs: SMCOG1246: monooxygenase FAD-binding

CDS_02953: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

Transferases: acylase aminotransferase methyltransferase

CDS_02934: Methylation

MITE: MITE0000155Methylation (identity: 69.20%)
smcogs: SMCOG1150: isoprenylcysteine carboxyl methyltransferase

CDS_02940: DegT/DnrJ/EryC1/StrS aminotransferase

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

CDS_02946: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_02952: DegT/DnrJ/EryC1/StrS aminotransferase

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

Ligases: synthase

CDS_02933: 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
BGC0000282.3	1.12	PKS	2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001275.3	0.83	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001244.3	0.83	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001273.3	0.83	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.59	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001160.5	0.58	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002191.2	0.58	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001164.3	0.58	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0002192.3	0.55	PKS	FR901512	fungal sp. No.14919
BGC0002154.2	0.53	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
BGC0000282.3	0.82	PKS	2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001275.3	0.73	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001244.3	0.73	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001273.3	0.73	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.63	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001160.5	0.63	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002191.2	0.62	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001164.3	0.62	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0002192.3	0.61	PKS	FR901512	fungal sp. No.14919
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

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52

Confidence: strong

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: 18.87 out of 23.79

Confidence: medium

VqsM

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

Additional weak hits (13):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.54 out of 30.25

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.31 out of 26.85

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 26.33

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

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.57 out of 31.73

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.90 out of 24.78

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.81 out of 18.57

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.33 out of 26.06

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.91 out of 21.84

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.26 out of 27.18

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

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.35 out of 25.88

Confidence: weak

Module view

Legend

Detailed Pfam 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 6, location 436923 - 493964:

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

Polymer prediction:: (Me-ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 436923 - 477988:

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

Polymer prediction:: (Me-ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 8, location 448693 - 493964:

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

Polymer prediction:: (Me-ccmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_02946: mmal

PKS_AT (543..839): mmal

ATSignature: Ethylmalonyl-CoA, Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 121.2
Methoxymalonyl-CoA: 96.1
Ethylmalonyl-CoA: 94.9
Malonyl-CoA: 66.9
Isobutyryl-CoA: 65.2
fatty_acid: 58.8
trans-1,2-CPDA: 56.5
2-Methylbutyryl-CoA: 55.4
Propionyl-CoA: 55.1
Benzoyl-CoA: 40.0
CHC-CoA: 35.7
3-Methylbutyryl-CoA: 24.6
inactive: 19.5
Acetyl-CoA: -0.7

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0006 - Region 1 - lanthipeptide-class-ii

Download region GenBank file

Download region SVG

Location: 32,632 - 55,955 nt. (total: 23,324 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_03016: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase

CDS_03007: HAD-superfamily hydrolase, subfamily IA, variant

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

CDS_03008: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Lyases: cyclase

CDS_03011: lanthionine synthetase C family protein

smcogs: SMCOG1070: lanthionine synthetase C family protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002276.2	0.55	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000528.5	0.48	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002704.2	0.46	ribosomal	archalan β	Halorussus salinus
BGC0002404.2	0.46	other (other)	falcarindiol	Solanum lycopersicum
BGC0000903.3	0.45	other (other)	fluorometabolite	Streptomyces cattleya
BGC0000503.5	0.45	ribosomal	cinnamycin	Streptomyces cinnamoneus
BGC0002571.2	0.43	NRPS	pyoverdine DC3000	Pseudomonas syringae pv. tomato str. DC3000
BGC0001579.4	0.43	ribosomal	duramycin	Streptomyces cinnamoneus
BGC0000554.4	0.43	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998
BGC0002346.3	0.43	ribosomal	kyamicin	Saccharopolyspora sp.

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002276.2	0.55	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000528.5	0.48	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002704.2	0.46	ribosomal	archalan β	Halorussus salinus
BGC0002404.2	0.46	other (other)	falcarindiol	Solanum lycopersicum
BGC0000903.3	0.45	other (other)	fluorometabolite	Streptomyces cattleya
BGC0000503.5	0.45	ribosomal	cinnamycin	Streptomyces cinnamoneus
BGC0002571.2	0.43	NRPS	pyoverdine DC3000	Pseudomonas syringae pv. tomato str. DC3000
BGC0001579.4	0.43	ribosomal	duramycin	Streptomyces cinnamoneus
BGC0000554.4	0.43	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998
BGC0002346.3	0.43	ribosomal	kyamicin	Saccharopolyspora sp.

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_03011

CDS_03010

Leader:

MNVEELVRYWKDPEARADAATGHPAGEITLEERSRPGRRAALLAG

Core:

LSGSAFADHRGGNTLNPIGTSISSPC

Core with dehydrations:

LDhaGDhaAFADHRGGNDhbLNPIGDhbDhaIDhaDhaPCys

antiSMASH-DB 4.0 matches for CDS_03010

30.8%

NZ_JACHIP010000018.1:

Lanthipeptides: allorf_39691_39795_lanthipeptide

9

HRGGNTLNPIGTSISSP

25

HRG T + TS S P

7

HRGPQTFDCRCTSASGP

23

26.9%

NZ_CP114065.1:

Lanthipeptides: OX958_RS04450_lanthipeptide

9

HRGGNTLNPIGTSISSP

25

H GG+TL +G P

1

HHGGSTLTVLGCGSQRP

17

26.9%

NZ_PDKQ02000037.1:

Lanthipeptides: allorf_31549_31659_lanthipeptide

12

GNTLNPIGTSISSPC

26

GN + PIG +PC

3

GNVMGPIGIG-DAPC

16

with 4 more sequence matches

26.9%

NZ_SLWN01000005.1:

Lanthipeptides: EV652_RS16625_lanthipeptide

9

HRGGNTLNPIGTSISSP

25

H GG+TL +G + P

1

HHGGSTLTVLGCASQRP

17

25.9%

NZ_JACHWA010000004.1:

Lanthipeptides: FHS43_RS13815_lanthipeptide

9

HRGGNTLNPIGTSISSP

25

H GG+TL +G + + P

2

HGGGSTLTVLGCASAKP

18

25.9%

NZ_SLWR01000003.1:

Lanthipeptides: EV646_RS09945_lanthipeptide

8

DHRGGNTLNPIGTSISSP

25

H GG+TL +G + +P

1

HHPGGSTLTVLGCASQTP

18

17.5%

NZ_CP027306.1and 1 other:

NZ_JAINUL010000001.1 Lanthipeptides: K7B10_RS11240_lanthipeptide

Lanthipeptides: C5746_RS40385_lanthipeptide

14

TLNPIGTSISSP

25

TL+ I TS+S+P

28

TLSSIDTSVSAP

39

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.07 out of 23.79

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.91 out of 24.78

Confidence: medium

Additional weak hits (7):

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.47 out of 36.54

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.87 out of 36.54

Confidence: weak

ClgR

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

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.91 out of 19.26

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.47 out of 28.14

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.48 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_03010 - Class II

Cleavage pHMM score: -3.10

RODEO score: 0

Monoisotopic mass: 2432.2 Da

Molecular weight: 2433.6 Da

Number of bridges: 1

Alternative weights: (assuming N unmodified Ser/Thr residues); 2451.6 Da N = 1; 2469.7 Da N = 2; 2487.7 Da N = 3; 2505.7 Da N = 4; 2523.7 Da N = 5; 2541.7 Da N = 6

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism
LexA variant 2	Repressor of DNA damage response

NPDC024463.ctg-0006 - Region 2 - T1PKS

Download region GenBank file

Download region SVG

Location: 97,555 - 142,390 nt. (total: 44,836 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))

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

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: glycosyltransferase

CDS_03076: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

Hydrolases: hydrolase

CDS_03077: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Ligases: synthase

CDS_03079: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.63	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.63	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.62	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.62	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001164.3	0.60	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.59	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002171.2	0.45	NRPS, PKS	pyrophen, campyrone B	Aspergillus niger ATCC 1015
BGC0002275.2	0.45	NRPS, PKS	pyrophen, campyrone B	Aspergillus niger CBS 101883
BGC0001998.2	0.43	PKS	aspernidgulene A1, aspernidgulene A2, aspernidgulene B1	Aspergillus nidulans FGSC A4
BGC0001400.3	0.43	PKS	citreoviridin	Aspergillus terreus NIH2624

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.63	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.63	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.62	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.62	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001164.3	0.60	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.59	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002171.2	0.45	NRPS, PKS	pyrophen, campyrone B	Aspergillus niger ATCC 1015
BGC0002275.2	0.45	NRPS, PKS	pyrophen, campyrone B	Aspergillus niger CBS 101883
BGC0001998.2	0.43	PKS	aspernidgulene A1, aspernidgulene A2, aspernidgulene B1	Aspergillus nidulans FGSC A4
BGC0001400.3	0.43	PKS	citreoviridin	Aspergillus terreus NIH2624

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

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05

Confidence: medium

Additional weak hits (10):

ClgR

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

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.56 out of 26.85

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.28 out of 31.73

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.05 out of 30.22

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.07 out of 29.38

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.45 out of 35.63

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.23 out of 35.63

Confidence: weak

LexA variant 1

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

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.98 out of 27.18

Confidence: weak

Detailed Pfam 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_03079: mxmal

PKS_AT (655..884): mxmal

ATSignature: (unknown)

No matches above 50%

minowa: Methoxymalonyl-CoA

Prediction, score:

Methoxymalonyl-CoA: 9.9
Malonyl-CoA: 9.1
trans-1,2-CPDA: 0.0
inactive: 0.0
fatty_acid: 0.0
Propionyl-CoA: 0.0
Methylmalonyl-CoA: 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
AfsR	Pleiotropic regulatory for antibiotic production
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0006 - Region 3 - NRPS-like

Download region GenBank file

Download region SVG

Location: 152,805 - 196,038 nt. (total: 43,234 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

Transferases: methyltransferase

CDS_03132: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: peptidase

CDS_03128: gamma-glutamyltranspeptidase

smcogs: SMCOG1274: gamma-glutamyltranspeptidase

Lyases: dehydratase

CDS_03117: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase

CDS_03110: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

CDS_03114: 3-oxoacyl-(acyl carrier protein) synthase III

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

CDS_03115: 3-oxoacyl-(acyl carrier protein) synthase III

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

CDS_03116: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_03118: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000382.5	0.63	NRPS	lipstatin	Streptomyces toxytricini
BGC0002276.2	0.62	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0002135.2	0.61	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.61	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0000342.4	0.60	NRPS	enniatin	Fusarium equiseti
BGC0000307.4	0.60	NRPS	AbT1	Aureobasidium pullulans
BGC0002164.2	0.60	NRPS	peramine	Epichloe festucae
BGC0001758.4	0.60	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.60	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001250.4	0.60	NRPS	epichloenin A	Epichloe festucae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000382.5	0.63	NRPS	lipstatin	Streptomyces toxytricini
BGC0002276.2	0.62	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0002135.2	0.61	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.61	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0000342.4	0.60	NRPS	enniatin	Fusarium equiseti
BGC0000307.4	0.60	NRPS	AbT1	Aureobasidium pullulans
BGC0002164.2	0.60	NRPS	peramine	Epichloe festucae
BGC0001758.4	0.60	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.60	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001250.4	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:

CRP

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

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 (21):

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.57 out of 36.54

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.21 out of 36.54

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.90 out of 26.85

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

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.92 out of 30.97

Confidence: weak

ANR

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

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.69 out of 19.26

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.76 out of 27.18

Confidence: weak

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31

Confidence: weak

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.00 out of 32.38

Confidence: weak

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.72 out of 32.38

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.35 out of 26.06

Confidence: weak

MatP

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

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.84 out of 39.62

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.86 out of 29.38

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.21 out of 27.55

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.08 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.01 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.81 out of 33.14

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.40 out of 36.53

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.56 out of 36.53

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 152804 - 196038:

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_03116: X

AMP-binding (19..466): 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:: --YFVGTPIK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

CDS_03118: X

AMP-binding (440..848): X

nrpys: Gly, 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:: N/A

Stachelhaus prediction details:

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

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
CRP	Cyclic AMP receptor protein

NPDC024463.ctg-0006 - Region 4 - NRPS,transAT-PKS-like

Download region GenBank file

Download region SVG

Location: 199,704 - 248,473 nt. (total: 48,770 nt) Show pHMM detection rules used

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

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: oxidoreductase

CDS_03160: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

Transferases: methyltransferase

CDS_03173: methyltransferase

smcogs: SMCOG1248: methyltransferase

Hydrolases: esterase

CDS_03156: thioesterase

smcogs: SMCOG1004: thioesterase

Lyases: dehydratase

CDS_03172: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase

CDS_03153: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_03154: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_03155: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_03158: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_03159: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.84	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.79	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.77	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001050.5	0.77	NRPS, PKS	thalassospiramide A	Tistrella bauzanensis
BGC0001825.4	0.77	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001261.3	0.75	NRPS	AM-toxin	Alternaria alternata
BGC0001128.4	0.75	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.73	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0000342.4	0.73	NRPS	enniatin	Fusarium equiseti
BGC0002286.3	0.73	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.73	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.72	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.71	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001050.5	0.71	NRPS, PKS	thalassospiramide A	Tistrella bauzanensis
BGC0001825.4	0.71	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001261.3	0.70	NRPS	AM-toxin	Alternaria alternata
BGC0001128.4	0.70	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.69	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
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:

VqsM

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

Confidence: medium

VqsM

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

Confidence: medium

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46

Confidence: strong

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.03 out of 29.72

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.91 out of 27.04

Confidence: medium

OsdR

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

Confidence: medium

Additional weak hits (20):

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.30 out of 29.25

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.80 out of 26.12

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.21 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.21 out of 27.78

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.41 out of 19.26

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.59 out of 29.65

Confidence: weak

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.50 out of 29.72

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: 15.53 out of 21.84

Confidence: weak

MexT

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

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.04 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.51 out of 29.38

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.66 out of 26.85

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: 16.85 out of 31.73

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 17.67 out of 22.40

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.08 out of 26.06

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.57 out of 33.14

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.61 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

TFBS Finder

Predicted core structure(s)

For candidate cluster 4, location 199703 - 248473:

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

Polymer prediction:: (Leu) + (mal) + (Ser)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_03153: Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (474..881): 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:: DAWFLGNVVK
Nearest Stachelhaus code(s):: Leu DAWFLGNVVK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_03155: Ser

Search NORINE for peptide: strict or relaxed

AMP-binding (485..893): 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:: DVQHFSFIEK
Nearest Stachelhaus code(s):: Ser DVPHFSLIEK (82% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_03158: Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (14..435): 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:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: thr (Thr)
Single AA prediction:: thr (Thr)

Stachelhaus prediction details:

Stachelhaus sequence:: DFWNIGMVFK
Nearest Stachelhaus code(s):: Thr DFWNIGMVFK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
DasR	N-acetylglucosamine dependent repressor
NtrC	Nitrogen regulatory protein C
OsdR	Development and stress management regulator
RpoN	Regulator of nitrogen assimilation and virulence
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0006 - Region 5 - NRPS,indole

Download region GenBank file

Download region SVG

Location: 265,674 - 313,155 nt. (total: 47,482 nt) Show pHMM detection rules used

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
indole: (indsynth or dmat or indole_PTase)

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: oxidoreductase oxygenase

CDS_03196: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

CDS_03197: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_03214: pyridine nucleotide-disulfide oxidoreductase

smcogs: SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Ligases: ligase

CDS_03199: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Translocases: transporter

CDS_03189: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.63	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.62	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.61	NRPS	AbT1	Aureobasidium pullulans
BGC0000342.4	0.60	NRPS	enniatin	Fusarium equiseti
BGC0002164.2	0.60	NRPS	peramine	Epichloe festucae
BGC0001833.4	0.59	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001261.3	0.58	NRPS	AM-toxin	Alternaria alternata
BGC0001825.4	0.58	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001166.5	0.57	NRPS	HC-toxin	Alternaria jesenskae
BGC0001758.4	0.57	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.65	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.65	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.64	NRPS	AbT1	Aureobasidium pullulans
BGC0000342.4	0.64	NRPS	enniatin	Fusarium equiseti
BGC0002164.2	0.64	NRPS	peramine	Epichloe festucae
BGC0001833.4	0.63	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001261.3	0.62	NRPS	AM-toxin	Alternaria alternata
BGC0001825.4	0.62	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001166.5	0.62	NRPS	HC-toxin	Alternaria jesenskae
BGC0001758.4	0.62	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:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.16 out of 23.79

Confidence: medium

Additional weak hits (15):

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 14.94 out of 20.97

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.28 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.61 out of 28.14

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.59 out of 21.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.96 out of 27.78

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.15 out of 27.04

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.35 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.87 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.10 out of 29.38

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.44 out of 33.14

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.79 out of 30.98

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.91 out of 28.14

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.02 out of 36.53

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.78 out of 32.93

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 5, location 265673 - 313155:

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

Polymer prediction:: (NMe-Val - Trp)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_03199: Val - Trp

Search NORINE for peptide: strict or relaxed

AMP-binding (17..424): 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:: DAYWWGGTFK
Nearest Stachelhaus code(s):: Val DAYWWGGTFK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1489..1893): Trp

nrpys: Trp

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:: DGWTISGVCK
Nearest Stachelhaus code(s):: Trp DGWTISGVCK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism

NPDC024463.ctg-0006 - Region 6 - NI-siderophore

Download region GenBank file

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Location: 361,610 - 394,428 nt. (total: 32,819 nt) Show pHMM detection rules used

NI-siderophore: IucA_IucC

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core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

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

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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

Lyases: decarboxylase

CDS_03280: diaminopimelate decarboxylase

smcogs: SMCOG1264: diaminopimelate decarboxylase

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
BGC0000947.5	0.63	other (other)	vibrioferrin	Vibrio alginolyticus
BGC0002073.3	0.57	NRPS	dehydroxynocardamine	Corynebacterium propinquum
BGC0001870.3	0.56	other (other)	putrebactin, avaroferrin	Xenorhabdus budapestensis
BGC0002682.2	0.55	other (other)	aerobactin	Vibrio mimicus
BGC0000939.5	0.55	other (other)	aerobactin	Grimontia hollisae
BGC0001498.5	0.51	other (other)	aerobactin	Xenorhabdus szentirmaii DSM 16338
BGC0002683.2	0.50	NRPS	schizokinen	Nostoc sp. PCC 7120 = FACHB-418

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
BGC0000947.5	0.63	other (other)	vibrioferrin	Vibrio alginolyticus
BGC0002073.3	0.57	NRPS	dehydroxynocardamine	Corynebacterium propinquum
BGC0001870.3	0.56	other (other)	putrebactin, avaroferrin	Xenorhabdus budapestensis
BGC0002682.2	0.55	other (other)	aerobactin	Vibrio mimicus
BGC0000939.5	0.55	other (other)	aerobactin	Grimontia hollisae
BGC0001498.5	0.51	other (other)	aerobactin	Xenorhabdus szentirmaii DSM 16338
BGC0002683.2	0.50	NRPS	schizokinen	Nostoc sp. PCC 7120 = FACHB-418

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: 31.20 out of 36.53

Confidence: medium

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.90 out of 36.53

Confidence: medium

Additional weak hits (5):

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.74 out of 25.31

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.60 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.23 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.02 out of 32.74

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.19 out of 29.38

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
DmdR1	Iron(II)-dependent repressor

NPDC024463.ctg-0006 - Region 7 - lanthipeptide-class-ii

Download region GenBank file

Download region SVG

Location: 428,227 - 451,316 nt. (total: 23,090 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

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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

Hydrolases: hydrolase

CDS_03329: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Lyases: cyclase

CDS_03332: lanthionine synthetase C family protein

smcogs: SMCOG1070: lanthionine synthetase C family protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000525.5	0.50	ribosomal	lichenicidin VK21 A1, lichenicidin VK21 A2	Bacillus licheniformis
BGC0000528.5	0.50	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001210.5	0.47	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0000504.5	0.46	ribosomal	cytolysin ClyLl, cytolysin ClyLs	Plasmid pAD1
BGC0000517.4	0.46	ribosomal	haloduracin β, haloduracin α	Bacillus halodurans C-125
BGC0000500.5	0.45	ribosomal	carnolysin A1, carnolysin A2	Carnobacterium maltaromaticum
BGC0002698.2	0.44	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0000516.4	0.43	ribosomal	geobacillin II	Geobacillus thermodenitrificans
BGC0000527.5	0.43	ribosomal	mersacidin	Bacillus sp. HIL-Y85/54728
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000525.5	0.50	ribosomal	lichenicidin VK21 A1, lichenicidin VK21 A2	Bacillus licheniformis
BGC0000528.5	0.50	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001210.5	0.47	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0000504.5	0.46	ribosomal	cytolysin ClyLl, cytolysin ClyLs	Plasmid pAD1
BGC0000517.4	0.46	ribosomal	haloduracin β, haloduracin α	Bacillus halodurans C-125
BGC0000500.5	0.45	ribosomal	carnolysin A1, carnolysin A2	Carnobacterium maltaromaticum
BGC0002698.2	0.44	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0000516.4	0.43	ribosomal	geobacillin II	Geobacillus thermodenitrificans
BGC0000527.5	0.43	ribosomal	mersacidin	Bacillus sp. HIL-Y85/54728
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842

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: 17.80 out of 20.47

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47

Confidence: medium

Additional weak hits (5):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.62 out of 30.22

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.47 out of 26.06

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.36 out of 29.38

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.78 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.81 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

Lanthipeptides

TFBS Finder

Core peptide predictions

No core peptides found.

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0007 - Region 1 - NRPS

Download region GenBank file

Download region SVG

Location: 29,200 - 108,149 nt. (total: 78,950 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

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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

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_03395: Dioxygenase TauD/TfdA

smcogs: SMCOG1046: Dioxygenase TauD/TfdA

CDS_03398: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: acetyltransferase acyltransferase

CDS_03400: polyketide synthase associated protein papA3

smcogs: SMCOG1209: polyketide synthase associated protein papA3

CDS_03403: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: amidase hydrolase

CDS_03391: amidase

smcogs: SMCOG1105: amidase

CDS_03399: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: ligase

CDS_03401: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.73	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
BGC0001133.4	0.71	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.70	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002286.3	0.70	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001825.4	0.70	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001132.4	0.70	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.73	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
BGC0001133.4	0.71	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.70	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002286.3	0.70	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001825.4	0.70	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001132.4	0.70	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

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: 18.39 out of 19.26

Confidence: strong

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.49 out of 25.31

Confidence: medium

Additional weak hits (17):

ClgR

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

Confidence: weak

ANR

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

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.97 out of 28.19

Confidence: weak

CatR

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

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.67 out of 20.01

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.96 out of 20.97

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.08 out of 27.04

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.95 out of 27.04

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.21 out of 29.38

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.16 out of 33.14

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.71 out of 29.65

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.75 out of 23.43

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.88 out of 27.55

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.73 out of 29.25

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.06 out of 28.19

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 17.67 out of 22.40

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.08 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

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 29199 - 108149:

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

Polymer prediction:: (Leu - D-X - D-Val - 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_03400: Leu - X - Val - Ala - Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (40..453): 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 (1119..1469): X

nrpys: (unknown)

SVM prediction details:

NOTE: uncertain match

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:: GVF-WA-VGK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

AMP-binding (2625..3019): 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:: DAYWWGGTFK
Nearest Stachelhaus code(s):: Val DAYWWGGTFK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4137..4546): 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:: DVFSVAIVYK
Nearest Stachelhaus code(s):: Ala DVFSVAIVYK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (5669..6054): 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:: 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:: DALLVGAVVK
Nearest Stachelhaus code(s):: Leu DALLVGAVVK (76% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_03401: Orn - Thr - X - Val - Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (509..896): Orn

nrpys: Orn

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:: DTEDMGFVDK
Nearest Stachelhaus code(s):: Orn DTEDMGFVDK (82% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2069..2480): 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 (3139..3532): 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:: DTENLGVVDK
Nearest Stachelhaus code(s):: Orn DTEDMGYVDK (76% 8Å match); Ile DAQDLGVVDK (65% 8Å match); Asp DSWKLGVVDK (50% 8Å match)
Stachelhaus code match:: 70% (weak)

AMP-binding (4645..5026): 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 (5681..6062): 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:: DALLIGSVVK
Nearest Stachelhaus code(s):: Leu DALLIGAVVK (71% 8Å match); Leu or 3OH-Leu DALLIGAVVK (68% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
CatR	H2O2-responsive repressor

NPDC024463.ctg-0007 - Region 2 - terpene

Download region GenBank file

Download region SVG

Location: 208,680 - 229,657 nt. (total: 20,978 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: dehydrogenase oxygenase

CDS_03507: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_03512: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_03514: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

CDS_03519: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: methyltransferase

CDS_03520: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: hydrolase

CDS_03511: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

CDS_03517: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: cyclase

CDS_03513: 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
BGC0002391.2	0.56	terpene	zealexin B3, zealexin C2	Zea mays
BGC0001160.5	0.55	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002320.3	0.53	terpene	conidiogenone	Penicillium rubens Wisconsin 54-1255
BGC0000675.5	0.52	terpene	(+)-T-muurolol	Streptomyces clavuligerus ATCC 27064
BGC0000798.3	0.51	saccharide	dhurrin	Sorghum bicolor
BGC0002721.2	0.49	saccharide	α-hydroxynitrile glucoside, β-hydroxynitrile glucoside, γ-hydroxynitrile glucoside	Hordeum vulgare subsp. vulgare
BGC0000677.5	0.48	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0001605.3	0.44	terpene	gibberellin	Sinorhizobium fredii NGR234
BGC0002347.3	0.44	other (other)	cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D	Actinoalloteichus caeruleus WH1-2216-6
BGC0002406.2	0.44	other (other)	hydroxycinnamoyltyramine	Oryza sativa Japonica Group

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002391.2	0.56	terpene	zealexin B3, zealexin C2	Zea mays
BGC0001160.5	0.55	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002320.3	0.53	terpene	conidiogenone	Penicillium rubens Wisconsin 54-1255
BGC0000675.5	0.52	terpene	(+)-T-muurolol	Streptomyces clavuligerus ATCC 27064
BGC0000798.3	0.51	saccharide	dhurrin	Sorghum bicolor
BGC0002721.2	0.49	saccharide	α-hydroxynitrile glucoside, β-hydroxynitrile glucoside, γ-hydroxynitrile glucoside	Hordeum vulgare subsp. vulgare
BGC0000677.5	0.48	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0001605.3	0.44	terpene	gibberellin	Sinorhizobium fredii NGR234
BGC0002347.3	0.44	other (other)	cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D	Actinoalloteichus caeruleus WH1-2216-6
BGC0002406.2	0.44	other (other)	hydroxycinnamoyltyramine	Oryza sativa Japonica Group

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_03513: T1TS

Domain 1 (16 - 323): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.63 out of 27.55

Confidence: medium

Additional weak hits (8):

ANR

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

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.05 out of 32.93

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.35 out of 39.62

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.09 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.07 out of 26.06

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.45 out of 20.01

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.88 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

Terpene

TFBS Finder

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
GnfM	Regulator of nitrogen-fixation genes

NPDC024463.ctg-0007 - Region 3 - T1PKS,lanthipeptide-class-i

Download region GenBank file

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Location: 417,609 - 469,042 nt. (total: 51,434 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))
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 oxidoreductase

CDS_03695: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

CDS_03720: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase acylase

CDS_03709: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

CDS_03718: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase

CDS_03706: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: cyclase dehydratase

CDS_03701: Lanthionine synthetase C family protein

smcogs: SMCOG1140: Lanthionine synthetase C family protein

CDS_03702: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

Ligases: synthase

CDS_03719: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.46	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0002635.2	0.36	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0001289.5	0.32	ribosomal	penisin	Paenibacillus ehimensis
BGC0001257.3	0.30	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0002154.2	0.30	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001276.3	0.30	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002191.2	0.30	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0000041.3	0.30	PKS	oronofacic acid	Pseudomonas syringae
BGC0001273.3	0.30	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.30	PKS	6-methylsalicyclic acid	Glarea lozoyensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.76	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0001257.3	0.63	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
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
BGC0001276.3	0.63	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0000041.3	0.63	PKS	oronofacic acid	Pseudomonas syringae
BGC0001273.3	0.63	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.63	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001258.3	0.63	PKS	1,3,6,8-tetrahydroxynaphthalene	Glarea lozoyensis
BGC0000107.3	0.63	PKS	naphthopyrone	Aspergillus nidulans FGSC A4

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for CDS_03702

CDS_03703

Leader:

MTIPKESTMPTTATEIMDGTLLDLDAEIDALFDLDVQIEVTETQAEGN

Core:

AMTWSITGYTCNCTHWTQCC

Core with dehydrations:

AMDhbWDhaIDhbGYDhbCysNCysDhbHWDhbQCysCys

antiSMASH-DB 4.0 matches for CDS_03703

25.0%

NZ_CP022685.1and 3 others:

NZ_CP022685.1 Lanthipeptides: KY5_RS01355_lanthipeptideNZ_CP023699.1 Lanthipeptides: CP970_RS41395_lanthipeptideNZ_CP023699.1 Lanthipeptides: CP970_RS41395_lanthipeptide

Lanthipeptides: KY5_RS01355_lanthipeptide

2

MTWSITGYTCNCTHWTQC

19

+T I G T CT T+C

7

LTVGIVGTTQGCTAATKC

24

22.2%

NZ_CP071875.1:

Lanthipeptides: J4I02_RS02880_lanthipeptide

9

YTCNCTHWTQCC

20

+ C THW CC

16

HECAGTHWYSCC

27

14.3%

NZ_CP072384.1:

Lanthipeptides: allorf_0337653_0337835_lanthipeptide

4

WSITGYTCNCT

14

W+I GY CT

16

WNIAGYLIICT

26

with 2 more sequence matches

8.6%

NZ_JALATU010000001.1:

Lanthipeptides: allorf_0123772_0124005_lanthipeptide

7

TGYTCNCTHWTQC

19

GY C+ +T C

37

AGYVVPCSPFTNC

49

8.6%

NZ_JANVAG010000003.1:

Lanthipeptides: allorf_432453_432671_lanthipeptide

6

ITGYTCNCTHWT

17

++G+TC+C T

37

LSGFTCDCLRAT

48

MIBiG 4.0 matches for CDS_03703

15.0%

BGC0001155.5 (AGY49587.1):

Thiopeptide: GE2270

6

ITGYTCNCT

14

+ G+ C+C+

5

VCGFCCSCS

13

8.8%

BGC0000535.4 (ADJ56352.1):

Lanthipeptide: nisin A

10

TCNCT

14

TC+C+

25

TCHCS

29

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.87 out of 27.04

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.84 out of 28.19

Confidence: medium

Additional weak hits (22):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.30 out of 31.73

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.32 out of 29.25

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.17 out of 26.12

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.50 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.08 out of 29.38

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.66 out of 26.85

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.65 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.17 out of 30.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.05 out of 27.78

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.87 out of 36.54

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 21.84

Confidence: weak

MogR

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

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.39 out of 30.25

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.09 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.55 out of 28.19

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.78 out of 24.78

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.39 out of 20.01

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.93 out of 23.43

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.09 out of 20.97

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.33 out of 24.78

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 20.94 out of 32.93

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

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

RREFinder

TFBS Finder

Core peptide predictions

CDS_03703 - Class I

Cleavage pHMM score: 5.50

RODEO score: 20

Monoisotopic mass: 2154.9 Da

Molecular weight: 2156.5 Da

Number of bridges: 3

Additional modifications: AviCys

Alternative weights: (assuming N unmodified Ser/Thr residues); 2174.5 Da N = 1; 2192.6 Da N = 2

Predicted core structure(s)

For candidate cluster 3, location 417608 - 469042:

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

Polymer prediction:: (ohmal) + (Me-ccmal - ccmal)
Non-colinear ordering:: CDS_03719 + CDS_03718

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 430894 - 469042:

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

Polymer prediction:: (ohmal) + (Me-ccmal - ccmal)
Non-colinear ordering:: CDS_03719 + CDS_03718

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_03717: X

AMP-binding (92..303): 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:: DPVMRSMFGK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

CDS_03718: mmal - mal

PKS_AT (551..856): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 95.8%; Methoxymalonyl-CoA: 87.5%; Ethylmalonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 222.2
Ethylmalonyl-CoA: 220.2
Methoxymalonyl-CoA: 182.3
2-Methylbutyryl-CoA: 166.8
trans-1,2-CPDA: 124.5
Propionyl-CoA: 120.4
Malonyl-CoA: 105.5
CHC-CoA: 104.3
Isobutyryl-CoA: 84.9
Benzoyl-CoA: 70.6
Acetyl-CoA: 49.1
3-Methylbutyryl-CoA: 44.4
fatty_acid: 43.9
inactive: 36.2

PKS_AT (2005..2302): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 200.6
inactive: 110.8
Methylmalonyl-CoA: 56.8
Methoxymalonyl-CoA: 55.9
Propionyl-CoA: 27.9
Benzoyl-CoA: 24.3
Isobutyryl-CoA: 23.9
2-Methylbutyryl-CoA: 17.9
Acetyl-CoA: 15.6
CHC-CoA: 14.4
fatty_acid: 12.2
trans-1,2-CPDA: 10.2
3-Methylbutyryl-CoA: 0.0
Ethylmalonyl-CoA: -2.4

CDS_03719: mal

PKS_AT (553..836): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 87.5%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 203.1
inactive: 119.0
Methoxymalonyl-CoA: 62.3
Methylmalonyl-CoA: 42.7
Propionyl-CoA: 23.4
Isobutyryl-CoA: 22.1
Acetyl-CoA: 18.1
Benzoyl-CoA: 17.3
Ethylmalonyl-CoA: 9.6
CHC-CoA: 3.8
2-Methylbutyryl-CoA: 3.5
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

RRE predictions

: RRE type: Lanthipeptide_LanB_RRE; Location: 188 - 273; Score: 48.6

TFBS definitions

Regulator	Description
DasR	N-acetylglucosamine dependent repressor
ZuR variant 1	Zinc-responsive repressor

NPDC024463.ctg-0008 - Region 1 - T1PKS

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Location: 1 - 54,397 nt. (total: 54,397 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

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Gene details

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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: acetyltransferase acylase

CDS_03721: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_03734: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

CDS_03735: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: hydrolase

CDS_03731: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Isomerases: mutase

CDS_03742: phosphoglycerate mutase

smcogs: SMCOG1101: phosphoglycerate mutase

Ligases: synthase

CDS_03723: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_03724: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_03725: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

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	0.74	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001276.3	0.64	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002191.2	0.64	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0002192.3	0.62	PKS	FR901512	fungal sp. No.14919
BGC0001160.5	0.62	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001254.3	0.62	PKS	ACT-Toxin II	Alternaria alternata
BGC0001164.3	0.62	PKS	1-heptadecene	Cyanothece sp. PCC 7822

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	0.74	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001276.3	0.64	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002191.2	0.64	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0002192.3	0.62	PKS	FR901512	fungal sp. No.14919
BGC0001160.5	0.62	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001254.3	0.62	PKS	ACT-Toxin II	Alternaria alternata
BGC0001164.3	0.62	PKS	1-heptadecene	Cyanothece sp. PCC 7822

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: 18.04 out of 23.79

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.61 out of 26.85

Confidence: medium

Additional weak hits (7):

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.25 out of 27.55

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.28 out of 27.55

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.32 out of 30.22

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.68 out of 28.19

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.64 out of 35.63

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 20.07 out of 22.40

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

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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 0 - 54397:

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

Polymer prediction:: (ohmal) + (ohmal - ccmal) + (ccmal - ohmal - ccmal) + (mal)
Non-colinear ordering:: CDS_03721 + CDS_03723 + CDS_03724 + CDS_03725

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_03721: mal

PKS_AT (906..1186): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 87.5%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 210.8
inactive: 103.1
Methoxymalonyl-CoA: 60.2
Methylmalonyl-CoA: 55.9
Propionyl-CoA: 35.3
Isobutyryl-CoA: 34.8
Acetyl-CoA: 23.4
Benzoyl-CoA: 21.1
Ethylmalonyl-CoA: 18.9
2-Methylbutyryl-CoA: 16.9
trans-1,2-CPDA: 11.8
CHC-CoA: 11.2
fatty_acid: 9.0
3-Methylbutyryl-CoA: 0.0

CDS_03723: mal - mal

PKS_AT (599..879): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 87.5%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 203.3
inactive: 98.4
Methoxymalonyl-CoA: 61.4
Methylmalonyl-CoA: 58.5
Propionyl-CoA: 31.8
Isobutyryl-CoA: 31.0
Ethylmalonyl-CoA: 26.5
Acetyl-CoA: 25.7
Benzoyl-CoA: 21.3
2-Methylbutyryl-CoA: 17.5
CHC-CoA: 14.8
fatty_acid: 12.2
trans-1,2-CPDA: 11.2
3-Methylbutyryl-CoA: 0.0

PKS_AT (2159..2443): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 87.5%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 205.8
inactive: 99.4
Methoxymalonyl-CoA: 64.9
Methylmalonyl-CoA: 64.3
Propionyl-CoA: 39.1
Isobutyryl-CoA: 36.2
Acetyl-CoA: 24.4
Ethylmalonyl-CoA: 23.2
2-Methylbutyryl-CoA: 22.1
Benzoyl-CoA: 18.4
fatty_acid: 12.6
CHC-CoA: 11.6
trans-1,2-CPDA: 11.4
3-Methylbutyryl-CoA: 9.6

CDS_03724: mal - mal - mal

PKS_AT (572..851): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 87.5%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 201.8
inactive: 101.7
Methoxymalonyl-CoA: 61.6
Methylmalonyl-CoA: 56.1
Propionyl-CoA: 35.8
Isobutyryl-CoA: 35.8
Acetyl-CoA: 22.3
Benzoyl-CoA: 21.2
Ethylmalonyl-CoA: 19.6
2-Methylbutyryl-CoA: 16.5
trans-1,2-CPDA: 11.1
CHC-CoA: 10.7
fatty_acid: 9.3
3-Methylbutyryl-CoA: 0.0

PKS_AT (2334..2615): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 87.5%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 215.4
inactive: 105.6
Methoxymalonyl-CoA: 63.9
Methylmalonyl-CoA: 62.1
Isobutyryl-CoA: 40.8
Acetyl-CoA: 29.2
Propionyl-CoA: 29.1
Ethylmalonyl-CoA: 20.5
Benzoyl-CoA: 20.4
2-Methylbutyryl-CoA: 14.6
CHC-CoA: 13.9
fatty_acid: 11.8
trans-1,2-CPDA: 11.2
3-Methylbutyryl-CoA: 0.0

PKS_AT (3860..4144): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 87.5%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 210.5
inactive: 98.8
Methoxymalonyl-CoA: 63.8
Methylmalonyl-CoA: 63.5
Propionyl-CoA: 42.7
Isobutyryl-CoA: 40.1
Acetyl-CoA: 31.0
Ethylmalonyl-CoA: 20.7
2-Methylbutyryl-CoA: 20.7
Benzoyl-CoA: 20.4
fatty_acid: 13.5
CHC-CoA: 13.2
trans-1,2-CPDA: 10.5
3-Methylbutyryl-CoA: 0.0

CDS_03725: mal

PKS_AT (586..869): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 87.5%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 209.1
inactive: 96.6
Methoxymalonyl-CoA: 63.4
Methylmalonyl-CoA: 62.2
Propionyl-CoA: 40.2
Isobutyryl-CoA: 33.2
Acetyl-CoA: 24.7
2-Methylbutyryl-CoA: 23.9
Ethylmalonyl-CoA: 22.1
Benzoyl-CoA: 19.2
CHC-CoA: 14.5
fatty_acid: 12.3
trans-1,2-CPDA: 8.1
3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism
RutR	Regulator of the pyrimidine and purine metabolism

NPDC024463.ctg-0008 - Region 2 - RiPP-like

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Location: 99,062 - 109,862 nt. (total: 10,801 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

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

CDS_03787: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0000554.4	0.41	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998
BGC0000504.5	0.40	ribosomal	cytolysin ClyLl, cytolysin ClyLs	Plasmid pAD1
BGC0000500.5	0.40	ribosomal	carnolysin A1, carnolysin A2	Carnobacterium maltaromaticum
BGC0001887.3	0.38	ribosomal	huazacin	Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0001684.3	0.38	other (other)	N-acyloxyacyl glutamine	Klebsiella variicola
BGC0001526.4	0.37	other (other)	bartoloside E, bartoloside F, bartoloside G, bartoloside H, bartoloside I, bartoloside J, bartoloside K	Synechocystis salina LEGE 06099
BGC0000517.4	0.37	ribosomal	haloduracin β, haloduracin α	Bacillus halodurans C-125
BGC0000496.5	0.37	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000520.5	0.37	ribosomal	lacticin 3147 A1, lacticin 3147 A2	Lactococcus lactis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0000554.4	0.41	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998
BGC0000504.5	0.40	ribosomal	cytolysin ClyLl, cytolysin ClyLs	Plasmid pAD1
BGC0000500.5	0.40	ribosomal	carnolysin A1, carnolysin A2	Carnobacterium maltaromaticum
BGC0001887.3	0.38	ribosomal	huazacin	Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0001684.3	0.38	other (other)	N-acyloxyacyl glutamine	Klebsiella variicola
BGC0001526.4	0.37	other (other)	bartoloside E, bartoloside F, bartoloside G, bartoloside H, bartoloside I, bartoloside J, bartoloside K	Synechocystis salina LEGE 06099
BGC0000517.4	0.37	ribosomal	haloduracin β, haloduracin α	Bacillus halodurans C-125
BGC0000496.5	0.37	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000520.5	0.37	ribosomal	lacticin 3147 A1, lacticin 3147 A2	Lactococcus lactis

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (2):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.63 out of 30.22

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.53 out of 30.25

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

NPDC024463.ctg-0008 - Region 3 - T3PKS,amglyccycl

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Location: 113,860 - 156,040 nt. (total: 42,181 nt) Show pHMM detection rules used

T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
amglyccycl: (DOIS or ValA or salQ or strH or strK1 or strK2 or NeoL or SpcFG or SpcDK_glyc)

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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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_03825: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

CDS_03826: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

Transferases: aminotransferase methyltransferase

CDS_03837: aminotransferase class V

smcogs: SMCOG1139: aminotransferase class V

CDS_03838: methyltransferase

smcogs: SMCOG1089: methyltransferase

Lyases: decarboxylase

CDS_03835: diaminopimelate decarboxylase

smcogs: SMCOG1264: diaminopimelate decarboxylase

Ligases: synthase

CDS_03821: chalcone and stilbene synthase domain protein

smcogs: SMCOG1024: chalcone and stilbene synthase domain protein

CDS_03831: 3-dehydroquinate synthase

smcogs: SMCOG1183: 3-dehydroquinate synthase

CDS_03836: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

Translocases: permease

CDS_03806: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000701.5	0.39	saccharide	jinggangmycin	Streptomyces hygroscopicus subsp. yingchengensis
BGC0000723.5	0.31	other (cyclitol), saccharide	validamycin A	Streptomyces hygroscopicus subsp. limoneus
BGC0000722.5	0.29	other (cyclitol), saccharide	validamycin A	Streptomyces hygroscopicus subsp. jinggangensis
BGC0000720.3	0.28	saccharide	tobramycin	Streptoalloteichus tenebrarius
BGC0000719.5	0.27	saccharide	tobramycin	Streptoalloteichus hindustanus
BGC0000721.4	0.26	saccharide	tobramycin	Streptoalloteichus tenebrarius
BGC0000466.5	0.25	NRPS	yatakemycin	Streptomyces sp. TP-A2060
BGC0000903.3	0.25	other (other)	fluorometabolite	Streptomyces cattleya
BGC0001610.5	0.25	other (other)	gougerotin	Streptomyces ahygroscopicus subsp. wuzhouensis
BGC0002439.3	0.25	other (other)	diastaphenazine, izumiphenazine C	Streptomyces diastaticus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000701.5	0.52	saccharide	jinggangmycin	Streptomyces hygroscopicus subsp. yingchengensis
BGC0000723.5	0.47	other (cyclitol), saccharide	validamycin A	Streptomyces hygroscopicus subsp. limoneus
BGC0001905.4	0.47	PKS	violapyrone B	Streptomyces somaliensis
BGC0000722.5	0.47	other (cyclitol), saccharide	validamycin A	Streptomyces hygroscopicus subsp. jinggangensis
BGC0000903.3	0.45	other (other)	fluorometabolite	Streptomyces cattleya
BGC0000719.5	0.44	saccharide	tobramycin	Streptoalloteichus hindustanus
BGC0000720.3	0.44	saccharide	tobramycin	Streptoalloteichus tenebrarius
BGC0002332.2	0.43	PKS	4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A	Candidatus Entotheonella sp.
BGC0000721.4	0.43	saccharide	tobramycin	Streptoalloteichus tenebrarius
BGC0000466.5	0.42	NRPS	yatakemycin	Streptomyces sp. TP-A2060

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: 17.80 out of 20.47

Confidence: medium

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.71 out of 26.33

Confidence: medium

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 21.80 out of 23.43

Confidence: strong

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 27.00 out of 27.04

Confidence: strong

AfsR

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

Confidence: medium

Additional weak hits (15):

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.04 out of 29.25

Confidence: weak

ANR

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

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.13 out of 29.25

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 27.17 out of 39.62

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.31 out of 30.22

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.85 out of 30.97

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.56 out of 35.63

Confidence: weak

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.12 out of 32.93

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.16 out of 36.53

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.11 out of 26.06

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.78 out of 27.55

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.54 out of 26.85

Confidence: weak

HypR

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

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.45 out of 23.43

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

TFBS Finder

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
AfsR	Pleiotropic regulatory for antibiotic production
BldD	Development and antibiotic global regulator
DasR	N-acetylglucosamine dependent repressor
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0008 - Region 4 - T2PKS

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Location: 183,361 - 255,885 nt. (total: 72,525 nt) Show pHMM detection rules used

T2PKS: (t2ks and t2clf)

Legend:

core biosynthetic genes

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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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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_03868: aldehyde oxidase and xanthine dehydrogenase

smcogs: SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

CDS_03885: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_03903: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_03906: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

Transferases: carboxylase methyltransferase transferase

CDS_03892: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

CDS_03893: acetyl-CoA carboxylase biotin carboxylase

smcogs: SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

CDS_03895: acetyl-CoA carboxylase, carboxyl transferase,

smcogs: SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Hydrolases: dehalogenase hydrolase

CDS_03879: HAD-superfamily hydrolase, subfamily IA, variant

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

CDS_03882: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Lyases: cyclase dehydratase

CDS_03896: Polyketide synthesis cyclase

smcogs: SMCOG1225: Polyketide synthesis cyclase

CDS_03897: cyclase/dehydrase

smcogs: SMCOG1128: cyclase/dehydrase

CDS_03928: L-carnitine dehydratase/bile acid-inducible

smcogs: SMCOG1189: L-carnitine dehydratase/bile acid-inducible

Ligases: ligase synthase

CDS_03899: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_03900: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_03907: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter

CDS_03917: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000272.3	0.74	PKS	spore pigment	Streptomyces collinus
BGC0000271.5	0.73	PKS	spore pigment	Streptomyces avermitilis
BGC0000215.5	0.69	PKS	curamycin	Streptomyces cyaneus
BGC0000231.5	0.61	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0000234.5	0.59	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0001197.5	0.57	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0001273.3	0.56	PKS	asperlactone	Aspergillus ochraceus
BGC0001513.3	0.55	PKS	anthrabenzoxocinone	Actinobacteria bacterium
BGC0002000.4	0.55	PKS	setomimycin	Streptomyces aurantiacus JA 4570
BGC0000275.4	0.55	PKS	tetracenomycin C	Streptomyces glaucescens

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000272.3	0.74	PKS	spore pigment	Streptomyces collinus
BGC0000271.5	0.73	PKS	spore pigment	Streptomyces avermitilis
BGC0000215.5	0.69	PKS	curamycin	Streptomyces cyaneus
BGC0000231.5	0.61	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0000234.5	0.59	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0001197.5	0.57	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0001273.3	0.56	PKS	asperlactone	Aspergillus ochraceus
BGC0001513.3	0.55	PKS	anthrabenzoxocinone	Actinobacteria bacterium
BGC0002000.4	0.55	PKS	setomimycin	Streptomyces aurantiacus JA 4570
BGC0000275.4	0.55	PKS	tetracenomycin C	Streptomyces glaucescens

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05

Confidence: medium

Additional weak hits (17):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.82 out of 27.78

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.35 out of 21.55

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.35 out of 32.93

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.50 out of 23.43

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

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.69 out of 19.26

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.33 out of 20.97

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.90 out of 26.06

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.43 out of 32.74

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.80 out of 20.97

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.10 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.22 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: 22.23 out of 29.65

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.40 out of 35.63

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.37 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

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS substrates

Type II PKS

TFBS Finder

NRPS/PKS substrate predictions

CDS_03907: X

AMP-binding (25..417): 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:: AAMFSGLIIK
Nearest Stachelhaus code(s):: Leu or Trp DAMFSGAIFK (35% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

Type II PKS gene cluster prediction details

Cluster section:: 183360 to 255885
Starter unit(s):: acetyl-CoA (Score: 0.0; E-value: 0)
Product class(es):: pentangular polyphenol
tetracenomycin

CDS_03885: OXY (Score: 261.3; E-value: 4.5e-80)
CDS_03892: MET C6|C8 (Score: 526.0; E-value: 7.2e-161)
CDS_03896: CYC C4-C21/C2-C23|C2-C19 (Score: 155.5; E-value: 9e-49)
CDS_03897: CYC C9-C14 (Score: 248.2; E-value: 5.4e-77)
CDS_03898: ACP (Score: 62.3; E-value: 7.9e-20)
CDS_03899: CLF (Score: 543.6; E-value: 6.2e-166)
CDS_03900: KS (Score: 718.9; E-value: 4e-219)
CDS_03901: CYC C5-C18 (Score: 214.6; E-value: 8.7e-67)
CDS_03903: OXY (Score: 298.3; E-value: 2.6e-91)

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production

NPDC024463.ctg-0008 - Region 5 - terpene

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Location: 279,426 - 300,646 nt. (total: 21,221 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

Transferases: methyltransferase

CDS_03953: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: back translocase protease

CDS_03944: GTP-binding protein LepA

smcogs: SMCOG1190: GTP-binding protein LepA

CDS_03949: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

Lyases: cyclase

CDS_03952: 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
BGC0000659.3	0.80	terpene	2-methylisoborneol	Saccharopolyspora erythraea NRRL 2338
BGC0000657.5	0.73	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0000658.3	0.61	terpene	2-methylisoborneol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000583.5	0.40	ribosomal	grisemycin	Streptomyces griseus subsp. griseus NBRC 13350
BGC0002666.2	0.33	NRPS, other (other)	Legonmycin A, Legonmycin B, Legonindolizine A, Legonindolizine B	Streptomyces sp. MA37
BGC0000843.5	0.33	other (non-nrp beta-lactam)	alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate	Streptomyces clavuligerus ATCC 27064
BGC0001151.5	0.33	other (non-nrp beta-lactam)	valclavam, (-)-2-(2-hydroxyethyl)clavam	Streptomyces antibioticus
BGC0000821.5	0.31	other (other)	rebeccamycin	Lechevalieria aerocolonigenes
BGC0002363.3	0.31	ribosomal	berninamycin K, berninamycin J, berninamycin A, berninamycin B	Streptomyces sp.
BGC0000711.5	0.31	saccharide	neomycin	Streptomyces fradiae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000659.3	0.80	terpene	2-methylisoborneol	Saccharopolyspora erythraea NRRL 2338
BGC0000657.5	0.73	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0000658.3	0.61	terpene	2-methylisoborneol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000583.5	0.40	ribosomal	grisemycin	Streptomyces griseus subsp. griseus NBRC 13350
BGC0002666.2	0.33	NRPS, other (other)	Legonmycin A, Legonmycin B, Legonindolizine A, Legonindolizine B	Streptomyces sp. MA37
BGC0000843.5	0.33	other (non-nrp beta-lactam)	alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate	Streptomyces clavuligerus ATCC 27064
BGC0001151.5	0.33	other (non-nrp beta-lactam)	valclavam, (-)-2-(2-hydroxyethyl)clavam	Streptomyces antibioticus
BGC0000821.5	0.31	other (other)	rebeccamycin	Lechevalieria aerocolonigenes
BGC0002363.3	0.31	ribosomal	berninamycin K, berninamycin J, berninamycin A, berninamycin B	Streptomyces sp.
BGC0000711.5	0.31	saccharide	neomycin	Streptomyces fradiae

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
monoterpene		2-methylisoborneol	C11	C1-C6	OH
monoterpene		2-methylenebornane	C11	C1-C6	none

Genes with terpene domains:

CDS_03952: T1TS

Domain 1 (37 - 403): Type 1 terpene synthase

Subtype: 2-Methylisoborneol synthase type

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

Transcription Factor Binding Sites

Binding sites found:

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.89 out of 29.72

Confidence: medium

AbrC3

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

Confidence: strong

Additional weak hits (4):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 13.99 out of 21.55

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.37 out of 29.65

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.37 out of 23.43

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
2-MeGPP	2-methylgeranyl diphosphate

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
NtrC	Nitrogen regulatory protein C

NPDC024463.ctg-0009 - Region 1 - lassopeptide

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Location: 139,597 - 162,158 nt. (total: 22,562 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_04155: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Hydrolases: hydrolase

CDS_04153: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: dehydratase

CDS_04148: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001548.4	0.72	ribosomal	citrulassin A	Streptomyces albulus
BGC0001552.3	0.72	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002053.3	0.71	ribosomal	ulleungdin	Streptomyces sp.
BGC0001889.2	0.69	ribosomal	fusilassin	Thermobifida fusca YX
BGC0001551.4	0.68	ribosomal	citrulassin E	Streptomyces glaucescens
BGC0001550.3	0.68	ribosomal	citrulassin D	Streptomyces katrae
BGC0001507.3	0.64	ribosomal	anantin C	Streptomyces olindensis
BGC0001549.3	0.64	ribosomal	citrulassin B	Streptomyces aurantiacus JA 4570
BGC0001493.5	0.63	ribosomal	achromosin	Streptomyces achromogenes subsp. achromogenes
BGC0001781.4	0.59	ribosomal	sphaericin	Planomonospora sphaerica

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001548.4	0.72	ribosomal	citrulassin A	Streptomyces albulus
BGC0001552.3	0.72	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002053.3	0.71	ribosomal	ulleungdin	Streptomyces sp.
BGC0001889.2	0.69	ribosomal	fusilassin	Thermobifida fusca YX
BGC0001551.4	0.68	ribosomal	citrulassin E	Streptomyces glaucescens
BGC0001550.3	0.68	ribosomal	citrulassin D	Streptomyces katrae
BGC0001507.3	0.64	ribosomal	anantin C	Streptomyces olindensis
BGC0001549.3	0.64	ribosomal	citrulassin B	Streptomyces aurantiacus JA 4570
BGC0001493.5	0.63	ribosomal	achromosin	Streptomyces achromogenes subsp. achromogenes
BGC0001781.4	0.59	ribosomal	sphaericin	Planomonospora sphaerica

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lasso peptide predictions

Lassopeptides - No core peptides found.

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.19 out of 23.79

Confidence: medium

AbrC3

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

Confidence: strong

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.45 out of 27.04

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.00 out of 20.47

Confidence: medium

Additional weak hits (4):

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.79 out of 30.97

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: 18.16 out of 30.25

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84

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

No core peptides found.

RRE predictions

: RRE type: Stand_Alone_Lasso_RRE; Location: 0 - 84; Score: 74.8; RRE type: Lasso_Fused_RRE; Location: 0 - 52; Score: 39.1

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
DasR	N-acetylglucosamine dependent repressor
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0009 - Region 2 - T1PKS

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Location: 310,025 - 338,671 nt. (total: 28,647 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

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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_04312: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Lyases: decarboxylase

CDS_04307: diaminopimelate decarboxylase

smcogs: SMCOG1264: diaminopimelate decarboxylase

Translocases: transport

CDS_04306: MMPL domain-containing transport protein

smcogs: SMCOG1035: MMPL domain-containing transport protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001275.3	0.64	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.63	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.63	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001244.3	0.63	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0002192.3	0.62	PKS	FR901512	fungal sp. No.14919
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
BGC0001254.3	0.61	PKS	ACT-Toxin II	Alternaria alternata

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001275.3	0.64	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.63	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.63	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001244.3	0.63	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0002192.3	0.62	PKS	FR901512	fungal sp. No.14919
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
BGC0001254.3	0.61	PKS	ACT-Toxin II	Alternaria alternata

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.53 out of 20.97

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.77 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.00 out of 28.19

Confidence: medium

OsdR

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

Confidence: medium

AbrC3

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

Confidence: strong

Additional weak hits (12):

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.23 out of 27.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.61 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.31 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.27 out of 32.74

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.22 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.36 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.34 out of 28.14

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.61 out of 20.97

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.22 out of 26.12

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.14 out of 30.22

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.60 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 2, location 310024 - 338671:

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

Polymer prediction:: (Me-redmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_04312: mmal

PKS_AT (564..859): 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: 214.9
Ethylmalonyl-CoA: 207.8
Methoxymalonyl-CoA: 176.9
trans-1,2-CPDA: 139.9
2-Methylbutyryl-CoA: 136.7
Malonyl-CoA: 124.8
Propionyl-CoA: 117.5
CHC-CoA: 100.1
Isobutyryl-CoA: 67.1
Benzoyl-CoA: 60.8
inactive: 52.1
Acetyl-CoA: 49.3
fatty_acid: 38.6
3-Methylbutyryl-CoA: 37.4

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
CcpA	Catabolite control protein A
OsdR	Development and stress management regulator
ZuR variant 1	Zinc-responsive repressor

NPDC024463.ctg-0010 - Region 1 - T1PKS

Download region GenBank file

Download region SVG

Location: 1 - 66,232 nt. (total: 66,232 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

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_04319: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Hydrolases: esterase

CDS_04325: thioesterase

smcogs: SMCOG1004: thioesterase

Ligases: synthase

CDS_04321: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_04322: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_04323: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.73	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0000041.3	0.65	PKS	oronofacic acid	Pseudomonas syringae
BGC0001275.3	0.63	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.63	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.62	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0000067.5	0.62	PKS	geldanamycin	Streptomyces hygroscopicus subsp. duamyceticus
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
BGC0000037.4	0.60	PKS	cichorine	Aspergillus nidulans FGSC A4
BGC0001051.5	0.59	NRPS, PKS	thuggacin A	Sorangium cellulosum

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.73	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0000041.3	0.65	PKS	oronofacic acid	Pseudomonas syringae
BGC0001275.3	0.63	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.63	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.62	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0000067.5	0.62	PKS	geldanamycin	Streptomyces hygroscopicus subsp. duamyceticus
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
BGC0000037.4	0.60	PKS	cichorine	Aspergillus nidulans FGSC A4
BGC0001051.5	0.59	NRPS, PKS	thuggacin A	Sorangium cellulosum

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

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.22 out of 18.46

Confidence: strong

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.27 out of 23.79

Confidence: medium

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.50 out of 30.12

Confidence: medium

Additional weak hits (15):

ClgR

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

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

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.75 out of 32.93

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.01 out of 29.25

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.42 out of 18.57

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.78 out of 28.14

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.73 out of 29.25

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.47 out of 28.14

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.92 out of 23.43

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.77 out of 23.43

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.68 out of 20.97

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.21 out of 32.74

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.34 out of 32.74

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.17 out of 27.55

Confidence: weak

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.70 out of 30.12

Confidence: weak

Module view

Legend

Detailed Pfam 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 - 66232:

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

Polymer prediction:: (Me-mal - ohmal - redmal) + (mal - Me-ohmal - ohmal) + (Me-ohmal - ccmal)
Non-colinear ordering:: CDS_04323 + CDS_04322 + CDS_04321

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_04317: pk

PKS_AT (14..251): pk

ATSignature: (unknown)

No matches above 50%

minowa: trans-1,2-CPDA

Prediction, score:

trans-1,2-CPDA: 0.0
inactive: 0.0
fatty_acid: 0.0
Propionyl-CoA: 0.0
Methylmalonyl-CoA: 0.0
Methoxymalonyl-CoA: 0.0
Malonyl-CoA: 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

CDS_04321: mmal - mal

PKS_AT (555..848): 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: 215.0
Ethylmalonyl-CoA: 209.6
Methoxymalonyl-CoA: 173.2
2-Methylbutyryl-CoA: 167.6
CHC-CoA: 126.1
Propionyl-CoA: 119.8
Malonyl-CoA: 114.2
trans-1,2-CPDA: 113.5
Benzoyl-CoA: 88.7
Isobutyryl-CoA: 86.5
Acetyl-CoA: 62.6
3-Methylbutyryl-CoA: 37.7
fatty_acid: 31.6
inactive: 31.0

PKS_AT (2074..2353): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 83.3%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 214.8
inactive: 103.4
Methoxymalonyl-CoA: 65.7
Methylmalonyl-CoA: 56.9
Propionyl-CoA: 33.4
Isobutyryl-CoA: 29.8
Acetyl-CoA: 21.3
Benzoyl-CoA: 14.9
Ethylmalonyl-CoA: 13.6
CHC-CoA: 13.0
fatty_acid: 12.0
2-Methylbutyryl-CoA: 11.9
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

CDS_04322: mal - mmal - mal

PKS_AT (560..817): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 156.9
inactive: 87.3
Methylmalonyl-CoA: 61.2
Methoxymalonyl-CoA: 61.1
Ethylmalonyl-CoA: 28.1
Isobutyryl-CoA: 25.3
Acetyl-CoA: 18.3
fatty_acid: 16.4
Propionyl-CoA: 12.9
2-Methylbutyryl-CoA: 8.2
trans-1,2-CPDA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (1507..1802): 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: 208.7
Ethylmalonyl-CoA: 206.9
Methoxymalonyl-CoA: 163.8
2-Methylbutyryl-CoA: 128.5
trans-1,2-CPDA: 112.2
Propionyl-CoA: 104.9
Malonyl-CoA: 99.3
CHC-CoA: 91.9
Isobutyryl-CoA: 71.2
Benzoyl-CoA: 59.7
Acetyl-CoA: 48.7
fatty_acid: 40.5
inactive: 25.0
3-Methylbutyryl-CoA: 21.9

PKS_AT (2964..3255): 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: 198.2
inactive: 106.9
Methoxymalonyl-CoA: 70.7
Methylmalonyl-CoA: 64.0
Isobutyryl-CoA: 37.9
Propionyl-CoA: 29.1
Ethylmalonyl-CoA: 26.1
Acetyl-CoA: 21.3
fatty_acid: 19.9
CHC-CoA: 18.0
Benzoyl-CoA: 17.9
2-Methylbutyryl-CoA: 9.5
3-Methylbutyryl-CoA: 8.3
trans-1,2-CPDA: 6.8

CDS_04323: mmal - mal - mal

PKS_AT (28..313): mmal

ATSignature: Isobutyryl-CoA, 2-Methylbutyryl-CoA

Top 3 matches:: Isobutyryl-CoA: 66.7%; 2-Methylbutyryl-CoA: 66.7%; Methylmalonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 145.0
Ethylmalonyl-CoA: 138.7
2-Methylbutyryl-CoA: 131.9
Methoxymalonyl-CoA: 113.1
Propionyl-CoA: 112.0
trans-1,2-CPDA: 101.7
CHC-CoA: 95.4
Malonyl-CoA: 79.1
Isobutyryl-CoA: 73.1
Benzoyl-CoA: 49.3
inactive: 38.6
fatty_acid: 27.4
Acetyl-CoA: 22.6
3-Methylbutyryl-CoA: 20.0

PKS_AT (987..1268): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 83.3%; inactive: 66.7%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 191.7
inactive: 80.7
Methylmalonyl-CoA: 57.6
Methoxymalonyl-CoA: 57.5
Propionyl-CoA: 32.5
Isobutyryl-CoA: 22.8
fatty_acid: 19.4
Ethylmalonyl-CoA: 15.7
CHC-CoA: 15.3
Benzoyl-CoA: 12.9
2-Methylbutyryl-CoA: 9.7
Acetyl-CoA: 9.6
trans-1,2-CPDA: 9.1
3-Methylbutyryl-CoA: 0.0

PKS_AT (2442..2699): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 87.5%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 158.1
inactive: 89.9
Methylmalonyl-CoA: 60.4
Methoxymalonyl-CoA: 60.3
Ethylmalonyl-CoA: 28.5
Isobutyryl-CoA: 22.7
Acetyl-CoA: 16.3
fatty_acid: 12.7
Propionyl-CoA: 12.6
Benzoyl-CoA: 11.3
CHC-CoA: 9.0
2-Methylbutyryl-CoA: 7.9
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
IolR	Regulator of the inositol catabolism
OsdR	Development and stress management regulator
RpoN	Regulator of nitrogen assimilation and virulence

NPDC024463.ctg-0010 - Region 2 - NRPS,T1PKS

Download region GenBank file

Download region SVG

Location: 92,959 - 178,117 nt. (total: 85,159 nt) Show pHMM detection rules used

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

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 oxygenase

CDS_04399: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

CDS_04402: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_04405: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

CDS_04418: NADH:flavin oxidoreductase/NADH oxidase

smcogs: SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

CDS_04419: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: methyltransferase

CDS_04377: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_04378: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: hydrolase

CDS_04415: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

CDS_04424: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

CDS_04433: alpha/beta hydrolase domain-containing protein

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

Ligases: ligase synthase

CDS_04400: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_04401: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_04423: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_04436: 2-isopropylmalate synthase

smcogs: SMCOG1271: 2-isopropylmalate synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.74	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.73	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.73	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.70	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0002286.3	0.69	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.67	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002135.2	0.67	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.65	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.69	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.69	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.69	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.68	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4	0.68	NRPS	enniatin	Fusarium equiseti
BGC0002286.3	0.68	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.67	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002135.2	0.67	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.66	NRPS	AM-toxin	Alternaria alternata
BGC0001273.3	0.66	PKS	asperlactone	Aspergillus ochraceus

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

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.03 out of 29.72

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26

Confidence: strong

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05

Confidence: medium

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.56 out of 23.43

Confidence: medium

VqsM

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

Confidence: medium

Additional weak hits (24):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.19 out of 27.78

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.98 out of 21.55

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.25 out of 36.53

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.90 out of 18.57

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.77 out of 26.06

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.65 out of 22.40

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.39 out of 23.43

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.41 out of 24.78

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.22 out of 23.43

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 23.43

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.13 out of 23.43

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.14 out of 27.78

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.85 out of 20.01

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.61 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.96 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.61 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.12 out of 28.14

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.66 out of 31.73

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.69 out of 19.26

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.81 out of 21.84

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.63 out of 30.22

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.80 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

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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 2, location 92958 - 178117:

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

Polymer prediction:: (Me-ccmal) + (Me-redmal - Ser - Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 92958 - 146668:

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

Polymer prediction:: (Me-redmal - Ser - Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 131718 - 178117:

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

Polymer prediction:: (Me-ccmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_04400: mmal - Ser - Pro

Search NORINE for peptide: strict or relaxed

PKS_AT (565..864): mmal

ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 201.3
Ethylmalonyl-CoA: 195.0
Methoxymalonyl-CoA: 173.9
2-Methylbutyryl-CoA: 130.9
Malonyl-CoA: 113.9
trans-1,2-CPDA: 111.8
Propionyl-CoA: 100.9
Isobutyryl-CoA: 89.0
CHC-CoA: 77.4
Benzoyl-CoA: 65.0
Acetyl-CoA: 41.6
3-Methylbutyryl-CoA: 32.4
inactive: 28.0
fatty_acid: 23.4

AMP-binding (2625..3035): 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)

AMP-binding (3688..4085): 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:: DVQFVSQVVK
Nearest Stachelhaus code(s):: Pro DVQFVAQVVK (79% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_04423: mmal

PKS_AT (545..839): mmal

ATSignature: Methylmalonyl-CoA, Malonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 66.7%; Malonyl-CoA: 66.7%; 2-Methylbutyryl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 140.5
Ethylmalonyl-CoA: 125.7
Methoxymalonyl-CoA: 114.6
Malonyl-CoA: 78.8
trans-1,2-CPDA: 71.8
2-Methylbutyryl-CoA: 71.2
Propionyl-CoA: 70.4
Isobutyryl-CoA: 51.3
CHC-CoA: 48.7
Benzoyl-CoA: 41.0
Acetyl-CoA: 29.6
3-Methylbutyryl-CoA: 29.2
inactive: 19.4
fatty_acid: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
BldD	Development and antibiotic global regulator
CRP	Cyclic AMP receptor protein
NtrC	Nitrogen regulatory protein C
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0010 - Region 3 - NRPS-like,T1PKS

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Location: 225,662 - 271,895 nt. (total: 46,234 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)
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

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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 oxidoreductase oxygenase

CDS_04486: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_04512: dihydropteridine reductase

smcogs: SMCOG1159: dihydropteridine reductase

CDS_04515: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase

CDS_04513: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: hydrolase

CDS_04505: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Lyases: dehydratase

CDS_04483: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_04492: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase

CDS_04498: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001164.3	0.60	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0002276.2	0.58	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0001160.5	0.57	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002171.2	0.37	NRPS, PKS	pyrophen, campyrone B	Aspergillus niger ATCC 1015
BGC0002275.2	0.37	NRPS, PKS	pyrophen, campyrone B	Aspergillus niger CBS 101883
BGC0001928.2	0.33	other (other)	(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid	Streptomyces sp. MA37
BGC0000043.5	0.30	PKS	curacin A	Moorea producens 19L
BGC0001895.4	0.29	PKS	huanglongmycin A, huanglongmycin B, huanglongmycin C	Streptomyces sp. CB09001
BGC0002749.2	0.29	NRPS, PKS	aspcandine	Aspergillus candidus
BGC0000122.5	0.29	PKS	phenylnannolone A, phenylnannolone B, phenylnannolone C	Nannocystis pusilla

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001164.3	0.63	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0002276.2	0.62	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0001160.5	0.62	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002171.2	0.50	NRPS, PKS	pyrophen, campyrone B	Aspergillus niger ATCC 1015
BGC0002275.2	0.50	NRPS, PKS	pyrophen, campyrone B	Aspergillus niger CBS 101883
BGC0001928.2	0.48	other (other)	(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid	Streptomyces sp. MA37
BGC0000043.5	0.45	PKS	curacin A	Moorea producens 19L
BGC0001895.4	0.44	PKS	huanglongmycin A, huanglongmycin B, huanglongmycin C	Streptomyces sp. CB09001
BGC0002749.2	0.44	NRPS, PKS	aspcandine	Aspergillus candidus
BGC0000122.5	0.44	PKS	phenylnannolone A, phenylnannolone B, phenylnannolone C	Nannocystis pusilla

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.57 out of 25.88

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

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.39 out of 28.19

Confidence: medium

Additional weak hits (21):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.19 out of 30.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.74 out of 29.38

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.56 out of 20.97

Confidence: weak

FuR variant 1

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

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.74 out of 29.38

Confidence: weak

HipB

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

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.86 out of 21.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.81 out of 27.78

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.64 out of 30.25

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.88 out of 29.65

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.97 out of 39.62

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.29 out of 30.98

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.65 out of 29.25

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.29 out of 33.14

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.41 out of 24.78

Confidence: weak

ZuR variant 1

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

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

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.97 out of 20.01

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.64 out of 26.06

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.59 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 5, location 225661 - 271895:

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

Polymer prediction:: (AHBA)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_04498: AHBA

CAL_domain (25..368): AHBA

minowa: AHBA

Prediction, score:

AHBA: 117.6
shikimic_acid: 110.7
fatty_acid: 0.0
NH2: 0.0
Acetyl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
PsrA	Oleic acid responsive regulator
ZuR variant 1	Zinc-responsive repressor

NPDC024463.ctg-0011 - Region 1 - terpene

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Location: 129,929 - 150,360 nt. (total: 20,432 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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regulatory genes

other genes

resistance

TTA codons

binding site

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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: dehydrogenase

CDS_04706: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

Transferases: acetyltransferase acyltransferase

CDS_04700: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

CDS_04703: acyltransferase 3

smcogs: SMCOG1088: acyltransferase 3

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000313.4	0.36	NRPS	beauvericin	Beauveria bassiana
BGC0000274.5	0.26	PKS	tetarimycin A, tetarimycin B	uncultured bacterium
BGC0001902.3	0.26	NRPS, PKS	bengamide	Myxococcus virescens
BGC0001589.3	0.26	saccharide	exopolysaccharides	Burkholderia cenocepacia J2315
BGC0000806.5	0.25	saccharide	phosphonoglycans	Glycomyces sp. NRRL B-16210
BGC0002104.3	0.24	NRPS, PKS	eurocidin D, eurocidin E	Streptomyces eurocidicus ATCC 27428
BGC0001653.3	0.24	PKS	linfuranone B, linfuranone C	Microbispora sp. GMKU363
BGC0001533.5	0.22	PKS	borrelidin	Streptomyces rochei
BGC0000031.5	0.22	PKS	borrelidin	Streptomyces parvulus
BGC0002686.2	0.21	NRPS	madurastatin D1, madurastatin D2, (-)-Madurastatin C1	Actinomadura sp. WMMA1423

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000313.4	0.36	NRPS	beauvericin	Beauveria bassiana
BGC0000274.5	0.26	PKS	tetarimycin A, tetarimycin B	uncultured bacterium
BGC0001902.3	0.26	NRPS, PKS	bengamide	Myxococcus virescens
BGC0001589.3	0.26	saccharide	exopolysaccharides	Burkholderia cenocepacia J2315
BGC0000806.5	0.25	saccharide	phosphonoglycans	Glycomyces sp. NRRL B-16210
BGC0002104.3	0.24	NRPS, PKS	eurocidin D, eurocidin E	Streptomyces eurocidicus ATCC 27428
BGC0001653.3	0.24	PKS	linfuranone B, linfuranone C	Microbispora sp. GMKU363
BGC0001533.5	0.22	PKS	borrelidin	Streptomyces rochei
BGC0000031.5	0.22	PKS	borrelidin	Streptomyces parvulus
BGC0002686.2	0.21	NRPS	madurastatin D1, madurastatin D2, (-)-Madurastatin C1	Actinomadura sp. WMMA1423

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:

No domains found

Transcription Factor Binding Sites

Binding sites found:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26

Confidence: medium

Additional weak hits (9):

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.49 out of 36.54

Confidence: weak

ANR

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

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.55 out of 32.93

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

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.21 out of 29.25

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 32.93

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.94 out of 32.93

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.57 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

Terpene

TFBS Finder

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein

NPDC024463.ctg-0013 - Region 1 - melanin

Download region GenBank file

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Location: 170,897 - 181,307 nt. (total: 10,411 nt) Show pHMM detection rules used

melanin: melC

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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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: back translocase

CDS_05287: GTP-binding protein LepA

smcogs: SMCOG1190: GTP-binding protein LepA

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000911.3	0.79	other (other)	melanin	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3	0.79	other (other)	melanin	Streptomyces coelicolor A3(2)
BGC0000909.3	0.63	other (other)	melanin	Streptomyces avermitilis
BGC0000912.3	0.60	other (other)	melanin	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3	0.57	other (other)	melanin	Streptomyces avermitilis
BGC0000662.5	0.37	terpene	grixazone A	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3	0.37	other (other)	4-hydroxy-3-nitrosobenzamide	Streptomyces murayamaensis
BGC0000889.5	0.36	other (other)	bagremycin A, bagremycin B	Streptomyces sp. WK-5344
BGC0001624.3	0.35	other (other)	iso-A82775C	Pestalotiopsis fici
BGC0002525.3	0.35	PKS	fusarubin, 1233A, 1233B, NG-391, lucilactaene	Fusarium sp.

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000911.3	0.79	other (other)	melanin	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3	0.79	other (other)	melanin	Streptomyces coelicolor A3(2)
BGC0000909.3	0.63	other (other)	melanin	Streptomyces avermitilis
BGC0000912.3	0.60	other (other)	melanin	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3	0.57	other (other)	melanin	Streptomyces avermitilis
BGC0000662.5	0.37	terpene	grixazone A	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3	0.37	other (other)	4-hydroxy-3-nitrosobenzamide	Streptomyces murayamaensis
BGC0000889.5	0.36	other (other)	bagremycin A, bagremycin B	Streptomyces sp. WK-5344
BGC0001624.3	0.35	other (other)	iso-A82775C	Pestalotiopsis fici
BGC0002525.3	0.35	PKS	fusarubin, 1233A, 1233B, NG-391, lucilactaene	Fusarium sp.

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: 20.71 out of 26.33

Confidence: medium

Additional weak hits (5):

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.05 out of 19.26

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.37 out of 27.04

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: 16.99 out of 29.25

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.16 out of 29.25

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
ANR	Anaerobic transcriptional regulator

NPDC024463.ctg-0015 - Region 1 - terpene

Download region GenBank file

Download region SVG

Location: 1 - 14,965 nt. (total: 14,965 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

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

Hydrolases: amidase hydrolase

CDS_05599: HAD-superfamily hydrolase, subfamily IA, variant

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

CDS_05604: metallo-beta-lactamase family protein

smcogs: SMCOG1170: metallo-beta-lactamase family protein

CDS_05610: amidase

smcogs: SMCOG1105: amidase

Lyases: cyclase

CDS_05601: 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
BGC0002535.2	0.38	NRPS	γ-poly-L-2,4-diaminobutyric acid	Streptomyces celluloflavus
BGC0000678.5	0.37	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001954.2	0.35	NRPS, PKS	wortmanamide A, wortmanamide B	Talaromyces wortmannii
BGC0002434.2	0.34	NRPS, PKS	clifednamide D, clifednamide E, clifednamide F, clifednamide G, clifednamide H, clifednamide I, clifednamide J	Kitasatospora sp.
BGC0001468.5	0.34	other (trna-derived)	bicyclomycin	Streptomyces cinnamoneus
BGC0000194.5	0.33	PKS	actinorhodin	Streptomyces coelicolor A3(2)
BGC0001782.3	0.33	other (other)	spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G	Streptomyces sp. SCSIO 03032
BGC0002514.3	0.32	PKS	julichrome Q6.6	Streptomyces sampsonii
BGC0000219.4	0.31	PKS, saccharide	elloramycin	Streptomyces olivaceus
BGC0002591.2	0.31	PKS, terpene	aurachin C, aurachin D, aurachin SS	Streptomyces sp.

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002535.2	0.38	NRPS	γ-poly-L-2,4-diaminobutyric acid	Streptomyces celluloflavus
BGC0000678.5	0.37	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001954.2	0.35	NRPS, PKS	wortmanamide A, wortmanamide B	Talaromyces wortmannii
BGC0002434.2	0.34	NRPS, PKS	clifednamide D, clifednamide E, clifednamide F, clifednamide G, clifednamide H, clifednamide I, clifednamide J	Kitasatospora sp.
BGC0001468.5	0.34	other (trna-derived)	bicyclomycin	Streptomyces cinnamoneus
BGC0000194.5	0.33	PKS	actinorhodin	Streptomyces coelicolor A3(2)
BGC0001782.3	0.33	other (other)	spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G	Streptomyces sp. SCSIO 03032
BGC0002514.3	0.32	PKS	julichrome Q6.6	Streptomyces sampsonii
BGC0000219.4	0.31	PKS, saccharide	elloramycin	Streptomyces olivaceus
BGC0002591.2	0.31	PKS, terpene	aurachin C, aurachin D, aurachin SS	Streptomyces sp.

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_05601: T1TS

Domain 1 (28 - 288): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.86 out of 25.31

Confidence: medium

Additional weak hits (9):

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.41 out of 27.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.97 out of 27.78

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.90 out of 30.22

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.39 out of 31.73

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.26 out of 21.55

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.71 out of 24.78

Confidence: weak

HypR

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

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.32 out of 26.85

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.75 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

No acronyms to display

TFBS definitions

Regulator	Description
CatR	H2O2-responsive repressor

NPDC024463.ctg-0015 - Region 2 - PKS-like,T1PKS,terpene

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Location: 135,936 - 192,956 nt. (total: 57,021 nt) Show pHMM detection rules used

PKS-like: (t2pks2 or ksIII)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
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: Oxidation dehydrogenase oxidoreductase oxygenase

CDS_05752: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_05755: flavin reductase domain protein FMN-binding

smcogs: SMCOG1160: flavin reductase domain protein FMN-binding

CDS_05760: Oxidation

MITE: MITE0000060Oxidation (identity: 91.20%)
smcogs: SMCOG1034: cytochrome P450

CDS_05763: Dehydration, Oxidation

MITE: MITE0000058Dehydration, Oxidation (identity: 84.90%)
smcogs: SMCOG1121: dioxygenase, TauD/TfdA

CDS_05764: Oxidation

MITE: MITE0000057Oxidation (identity: 90.30%)

CDS_05765: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_05768: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Hydrolases: esterase hydrolase

CDS_05753: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

CDS_05756: thioesterase

smcogs: SMCOG1004: thioesterase

Lyases: cyclase decarboxylase oxygenase

CDS_05751: putative carboxymuconolactone decarboxylase

smcogs: SMCOG1298: putative carboxymuconolactone decarboxylase

CDS_05761: Terpene synthase/cyclase metal-binding domain protein

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

CDS_05763: Dehydration, Oxidation

MITE: MITE0000058Dehydration, Oxidation (identity: 84.90%)
smcogs: SMCOG1121: dioxygenase, TauD/TfdA

CDS_05772: putative carboxymuconolactone decarboxylase

smcogs: SMCOG1298: putative carboxymuconolactone decarboxylase

Ligases: ligase synthase synthetase

CDS_05745: 3-oxoacyl-(acyl carrier protein) synthase III

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

CDS_05757: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_05758: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_05762: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000683.3	1.41	terpene	avermitilol	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001275.3	0.99	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001244.3	0.99	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001273.3	0.99	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.99	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0000678.5	0.96	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000653.5	0.94	terpene	pentalenolactone	Streptomyces arenae
BGC0001163.3	0.92	PKS	1-heptadecene	Moorea producens 3L
BGC0002191.2	0.88	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0000107.3	0.87	PKS	naphthopyrone	Aspergillus nidulans FGSC A4

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000683.3	0.77	terpene	avermitilol	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000678.5	0.71	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000653.5	0.70	terpene	pentalenolactone	Streptomyces arenae
BGC0001275.3	0.66	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001244.3	0.66	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001273.3	0.66	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.66	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001163.3	0.65	PKS	1-heptadecene	Moorea producens 3L
BGC0000107.3	0.64	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
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:

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_05761: T1TS

Domain 1 (3 - 315): Type 1 terpene synthase

Subtype: unknown

CDS_05762: PT_FPPS_like

Domain 1 (52 - 321): 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

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.86 out of 29.51

Confidence: medium

OsdR

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

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

IolR

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

Confidence: medium

OsdR

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

Confidence: medium

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.37 out of 30.12

Confidence: medium

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.90 out of 30.12

Confidence: medium

Additional weak hits (11):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.04 out of 27.78

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.77 out of 39.62

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.79 out of 30.22

Confidence: weak

MexT

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

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.42 out of 39.62

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.84 out of 26.85

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.96 out of 25.75

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.96 out of 25.75

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.34 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.02 out of 33.14

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

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 2, location 135935 - 192956:

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

Polymer prediction:: (ohmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 135935 - 176961:

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

Polymer prediction:: (ohmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 148381 - 192956:

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

Polymer prediction:: (ohmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_05757: X

AMP-binding (13..418): 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:: SIMFAGITVK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

CDS_05758: mal

PKS_AT (579..873): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 91.7%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 166.3
inactive: 106.7
Methoxymalonyl-CoA: 68.6
Methylmalonyl-CoA: 66.9
Isobutyryl-CoA: 49.2
Ethylmalonyl-CoA: 37.8
Propionyl-CoA: 34.9
2-Methylbutyryl-CoA: 24.4
CHC-CoA: 23.9
Acetyl-CoA: 16.0
fatty_acid: 15.1
Benzoyl-CoA: 14.7
trans-1,2-CPDA: 10.8
3-Methylbutyryl-CoA: 0.0

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
PP	Diphosphate

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
DosR	Hypoxia stress response regulator
IolR	Regulator of the inositol catabolism
OsdR	Development and stress management regulator

NPDC024463.ctg-0015 - Region 3 - NRPS

Download region GenBank file

Download region SVG

Location: 193,139 - 241,310 nt. (total: 48,172 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

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 oxidase oxidoreductase oxygenase

CDS_05780: flavin reductase domain protein FMN-binding

smcogs: SMCOG1160: flavin reductase domain protein FMN-binding

CDS_05781: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_05782: dioxygenase, TauD/TfdA

smcogs: SMCOG1121: dioxygenase, TauD/TfdA

CDS_05794: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_05795: dehydrogenase

smcogs: SMCOG1072: dehydrogenase

CDS_05796: pyruvate oxidase/decarboxylase

smcogs: SMCOG1055: pyruvate oxidase/decarboxylase

CDS_05797: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

Ligases: ligase synthase

CDS_05789: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_05791: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_05792: 8-amino-7-oxononanoate synthase

smcogs: SMCOG1109: 8-amino-7-oxononanoate synthase

CDS_05793: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

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
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
BGC0001833.4	0.68	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.67	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.67	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002286.3	0.67	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.66	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

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
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
BGC0001833.4	0.68	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.67	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.67	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002286.3	0.67	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.66	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.11 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

VqsM

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

Confidence: medium

Additional weak hits (14):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.48 out of 29.38

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.06 out of 27.78

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.99 out of 32.74

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.27 out of 33.14

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.72 out of 36.53

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.30 out of 20.01

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.44 out of 29.25

Confidence: weak

MexT

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

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.95 out of 28.19

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 30.98

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.92 out of 35.63

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.87 out of 35.63

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.79 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 6, location 193138 - 241310:

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

Polymer prediction:: (Ser - X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_05789: Ser - X

Search NORINE for peptide: strict or relaxed

AMP-binding (528..937): 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)

AMP-binding (1642..2021): 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:: DIPYEVGAVK
Nearest Stachelhaus code(s):: Tyr DVPYEVGAVK (91% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_05791: Hpr

Search NORINE for peptide: strict or relaxed

AMP-binding (10..410): Hpr

nrpys: 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:: pip (Hpr)

Stachelhaus prediction details:

Stachelhaus sequence:: TFCMFGGPVK
Nearest Stachelhaus code(s):: nLev GFCMYGGCSK (79% 8Å match)
Stachelhaus code match:: 60% (weak)

CDS_05793: X

AMP-binding (25..426): 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:: --GFITLMVK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0016 - Region 1 - azole-containing-RiPP

Download region GenBank file

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Location: 163,854 - 187,854 nt. (total: 24,001 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

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

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 oxygenase

CDS_05952: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_05965: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

Lyases: dehydratase

CDS_05955: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000565.5	0.49	ribosomal	goadsporin	Streptomyces sp. TP-A0584
BGC0002551.2	0.48	other (other), ribosomal, terpene	muscoride A, muscoride B	Nostoc sp. UHCC-0398
BGC0002485.2	0.48	other (other), ribosomal	muscoride A, muscoride B	Desmonostoc sp. PCC 7906
BGC0000483.5	0.47	ribosomal	aeruginosamide B, aeruginosamide C	Microcystis aeruginosa PCC 9432
BGC0002584.2	0.47	ribosomal	azolemycin B, azolemycin A, azolemycin D, azolemycin C	Streptomyces sp. FXJ1.264
BGC0000221.5	0.44	PKS	erdacin	uncultured soil bacterium V167
BGC0000480.5	0.44	ribosomal	tenuecyclamide A, tenuecyclamide C	Nostoc spongiaeforme var. tenue str. Carmeli
BGC0000475.5	0.44	ribosomal	patellamide A, patellamide C	Prochloron didemni
BGC0000193.3	0.44	PKS	aclacinomycin	Streptomyces galilaeus
BGC0000197.5	0.43	PKS, saccharide	aranciamycin	Streptomyces echinatus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000565.5	0.49	ribosomal	goadsporin	Streptomyces sp. TP-A0584
BGC0002551.2	0.48	other (other), ribosomal, terpene	muscoride A, muscoride B	Nostoc sp. UHCC-0398
BGC0002485.2	0.48	other (other), ribosomal	muscoride A, muscoride B	Desmonostoc sp. PCC 7906
BGC0000483.5	0.47	ribosomal	aeruginosamide B, aeruginosamide C	Microcystis aeruginosa PCC 9432
BGC0002584.2	0.47	ribosomal	azolemycin B, azolemycin A, azolemycin D, azolemycin C	Streptomyces sp. FXJ1.264
BGC0000221.5	0.44	PKS	erdacin	uncultured soil bacterium V167
BGC0000480.5	0.44	ribosomal	tenuecyclamide A, tenuecyclamide C	Nostoc spongiaeforme var. tenue str. Carmeli
BGC0000475.5	0.44	ribosomal	patellamide A, patellamide C	Prochloron didemni
BGC0000193.3	0.44	PKS	aclacinomycin	Streptomyces galilaeus
BGC0000197.5	0.43	PKS, saccharide	aranciamycin	Streptomyces echinatus

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

AfsQ1

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

Confidence: strong

AfsQ1

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

Confidence: strong

Additional weak hits (13):

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.41 out of 19.26

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.65 out of 27.78

Confidence: weak

MatP

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

Confidence: weak

HexR

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

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.39 out of 30.97

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.10 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.95 out of 28.14

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

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.48 out of 25.88

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.26 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.28 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: Goadsporin_CD_RRE; Location: 11 - 110; Score: 55.8; RRE type: NHLP_CD_RRE; Location: 11 - 95; Score: 51.6; RRE type: Cyanobactin_D_RRE; Location: 9 - 86; Score: 46.3

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production

Core peptide predictions

No core peptides found.

NPDC024463.ctg-0017 - Region 1 - NRPS,NRPS-like

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Location: 1 - 32,834 nt. (total: 32,834 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)
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: oxygenase

CDS_06001: Dioxygenase TauD/TfdA

smcogs: SMCOG1046: Dioxygenase TauD/TfdA

Hydrolases: deaminase

CDS_06002: ornithine cyclodeaminase

smcogs: SMCOG1158: ornithine cyclodeaminase

Ligases: ligase synthase

CDS_05998: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_06000: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_06003: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

CDS_06004: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_06006: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.82	NRPS	dimethylcoprogen	Alternaria alternata
BGC0000342.4	0.72	NRPS	enniatin	Fusarium equiseti
BGC0000307.4	0.69	NRPS	AbT1	Aureobasidium pullulans
BGC0002164.2	0.67	NRPS	peramine	Epichloe festucae
BGC0001261.3	0.67	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.67	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.63	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.62	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.62	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4	0.62	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0000307.4	0.67	NRPS	AbT1	Aureobasidium pullulans
BGC0002164.2	0.67	NRPS	peramine	Epichloe festucae
BGC0001261.3	0.67	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.66	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.65	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.65	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4	0.64	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii

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: 20.80 out of 26.33

Confidence: medium

OsdR

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

Additional weak hits (6):

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.15 out of 36.54

Confidence: weak

MexT

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

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.96 out of 30.22

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.21 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.21 out of 27.78

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.75 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 0 - 32834:

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

Polymer prediction:: (NMe-X - NMe-X) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 0 - 29864:

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

Polymer prediction:: (NMe-X - NMe-X) + (X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_05998: X - X

AMP-binding (869..1271): 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:: DSLQWSLIQK
Nearest Stachelhaus code(s):: Ala DILQISLIYK (53% 8Å match)
Stachelhaus code match:: 70% (weak)

AMP-binding (2316..2690): X

nrpys: (unknown)

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:: DAWLVGAVAK
Nearest Stachelhaus code(s):: Leu DALLVGAVAK (68% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_06000: X

AMP-binding (242..662): X

nrpys: Dpr

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:: DIWQSTADDK
Nearest Stachelhaus code(s):: Dpr DIWQSTADDK (91% 8Å match); dnmeProp or Dab DIWQSTADDK (79% 8Å match); Asp DIWQSTADDK (79% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_06004: X

AMP-binding (7..406): 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:: DLNYLALISK
Nearest Stachelhaus code(s):: Pro DLLYLALVCK (76% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
OsdR	Development and stress management regulator

NPDC024463.ctg-0017 - Region 2 - terpene-precursor

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Location: 171,059 - 192,207 nt. (total: 21,149 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

Oxidoreductases: oxidoreductase oxygenase

CDS_06145: monooxygenase FAD-binding

smcogs: SMCOG1246: monooxygenase FAD-binding

CDS_06152: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

Ligases: synthetase

CDS_06147: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000677.5	0.41	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0001456.3	0.38	terpene	isorenieratene	Streptomyces argillaceus
BGC0001910.4	0.38	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0000664.5	0.38	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3	0.38	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000678.5	0.37	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000906.3	0.37	other (other)	heme D1	Heliophilum fasciatum
BGC0001458.4	0.37	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
BGC0000905.5	0.37	other (other)	heme D1	Heliobacillus mobilis
BGC0002309.2	0.36	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000677.5	0.41	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0001456.3	0.38	terpene	isorenieratene	Streptomyces argillaceus
BGC0001910.4	0.38	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0000664.5	0.38	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3	0.38	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000678.5	0.37	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000906.3	0.37	other (other)	heme D1	Heliophilum fasciatum
BGC0001458.4	0.37	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
BGC0000905.5	0.37	other (other)	heme D1	Heliobacillus mobilis
BGC0002309.2	0.36	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488

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_06147: PT_FPPS_like

Domain 1 (75 - 359): 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 (2):

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.60 out of 28.14

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.10 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

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

NPDC024463.ctg-0018 - Region 1 - terpene

Download region GenBank file

Download region SVG

Location: 3,970 - 25,133 nt. (total: 21,164 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

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: dehydrogenase oxygenase

CDS_06183: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CDS_06184: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CDS_06185: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: methyltransferase

CDS_06189: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: esterase hydrolase

CDS_06186: thioesterase

smcogs: SMCOG1004: thioesterase

CDS_06188: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: cyclase

CDS_06190: 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
BGC0000658.3	0.85	terpene	2-methylisoborneol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3	0.79	terpene	2-methylisoborneol	Saccharopolyspora erythraea NRRL 2338
BGC0000657.5	0.55	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0000016.4	0.54	other (other)	amphotericin B	Streptomyces nodosus
BGC0002631.2	0.53	ribosomal	Myxarylin	Pyxidicoccus fallax
BGC0000706.3	0.46	saccharide	kanamycin	Streptomyces kanamyceticus
BGC0000876.5	0.44	other (other)	neopolyoxin C	Streptomyces tendae
BGC0000019.5	0.42	PKS	angolamycin	Streptomyces eurythermus
BGC0002482.2	0.42	other (other)	tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M	Symphyonema bifilamentata 97.28
BGC0002103.2	0.42	other (other)	pulcherriminic acid	Bacillus subtilis subsp. subtilis str. 168

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
BGC0000657.5	0.55	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0000016.4	0.54	other (other)	amphotericin B	Streptomyces nodosus
BGC0002631.2	0.53	ribosomal	Myxarylin	Pyxidicoccus fallax
BGC0000706.3	0.46	saccharide	kanamycin	Streptomyces kanamyceticus
BGC0000876.5	0.44	other (other)	neopolyoxin C	Streptomyces tendae
BGC0000019.5	0.42	PKS	angolamycin	Streptomyces eurythermus
BGC0002482.2	0.42	other (other)	tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M	Symphyonema bifilamentata 97.28
BGC0002103.2	0.42	other (other)	pulcherriminic acid	Bacillus subtilis subsp. subtilis str. 168

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
monoterpene		2-methylisoborneol	C11	C1-C6	OH
monoterpene		2-methylenebornane	C11	C1-C6	none

Genes with terpene domains:

CDS_06190: T1TS

Domain 1 (5 - 381): Type 1 terpene synthase

Subtype: 2-Methylisoborneol synthase type

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

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

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.36 out of 20.97

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.36 out of 25.31

Confidence: medium

Additional weak hits (7):

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.48 out of 27.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.22 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.04 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.69 out of 29.38

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.68 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.65 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.01 out of 28.19

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

Terpene

TFBS Finder

Glossary

Acronym	Full name
2-MeGPP	2-methylgeranyl diphosphate

TFBS definitions

Regulator	Description
CatR	H2O2-responsive repressor
CcpA	Catabolite control protein A
VqsM	Regulator of quorum-sensing signalling systems

NPDC024463.ctg-0018 - Region 2 - hydrogen-cyanide

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Location: 123,994 - 137,028 nt. (total: 13,035 nt) Show pHMM detection rules used

hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)

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core biosynthetic genes

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Gene details

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Gene overview

Tailoring

MIBiG comparison

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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 reductase

CDS_06278: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

CDS_06281: alkyl hydroperoxide reductase subunit

smcogs: SMCOG1176: alkyl hydroperoxide reductase subunit

CDS_06283: 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
BGC0001427.4	0.33	NRPS, PKS	myxochromide A	Myxococcus xanthus
BGC0001424.4	0.33	NRPS, PKS	myxochromide C	Myxococcus virescens
BGC0001423.4	0.33	NRPS, PKS	myxochromide C	Myxococcus hansupus
BGC0001428.4	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	0.27	PKS	gladiofungin A, gladiofungin B	Burkholderia gladioli

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002345.2	0.63	other (other)	hydrogen cyanide	Pseudomonas fluorescens
BGC0001427.4	0.33	NRPS, PKS	myxochromide A	Myxococcus xanthus
BGC0001424.4	0.33	NRPS, PKS	myxochromide C	Myxococcus virescens
BGC0001423.4	0.33	NRPS, PKS	myxochromide C	Myxococcus hansupus
BGC0001428.4	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	0.27	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):

HexR

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

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.43 out of 27.78

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.55 out of 18.57

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.60 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.01 out of 26.06

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.16 out of 35.63

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.16 out of 33.14

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

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Detailed TIGRFAM domain annotation

Selected features only

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TFBS Finder

TFBS definitions

Regulator	Description

NPDC024463.ctg-0019 - Region 1 - T1PKS

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Location: 1 - 40,052 nt. (total: 40,052 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

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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

Oxidoreductases: dehydrogenase oxygenase

CDS_06332: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_06348: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

Ligases: synthase

CDS_06333: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.73	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.73	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.73	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001276.3	0.63	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0000041.3	0.56	PKS	oronofacic acid	Pseudomonas syringae
BGC0001298.4	0.48	PKS	4-Z-annimycin, 4-E-annimycin	Streptomyces calvus
BGC0000143.5	0.47	PKS	salinomycin	Streptomyces albus
BGC0002229.2	0.47	PKS	6-MSA, aculin A	Aspergillus aculeatus ATCC 16872
BGC0000122.5	0.46	PKS	phenylnannolone A, phenylnannolone B, phenylnannolone C	Nannocystis pusilla
BGC0001065.5	0.46	PKS	herboxidiene	Streptomyces chromofuscus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.73	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.73	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.73	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001276.3	0.63	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0000041.3	0.56	PKS	oronofacic acid	Pseudomonas syringae
BGC0001298.4	0.48	PKS	4-Z-annimycin, 4-E-annimycin	Streptomyces calvus
BGC0000143.5	0.47	PKS	salinomycin	Streptomyces albus
BGC0002229.2	0.47	PKS	6-MSA, aculin A	Aspergillus aculeatus ATCC 16872
BGC0000122.5	0.46	PKS	phenylnannolone A, phenylnannolone B, phenylnannolone C	Nannocystis pusilla
BGC0001065.5	0.46	PKS	herboxidiene	Streptomyces chromofuscus

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):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.66 out of 29.38

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.98 out of 27.78

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.61 out of 24.78

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.61 out of 28.14

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.13 out of 29.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.58 out of 26.06

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 - 40052:

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

Polymer prediction:: (ccmal) + (ccmal - Me-ccmal - ccmal)
Non-colinear ordering:: CDS_06332 + CDS_06333

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_06332: mal

PKS_AT (0..259): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 177.6
inactive: 104.9
Methoxymalonyl-CoA: 57.6
Methylmalonyl-CoA: 45.1
Propionyl-CoA: 26.0
Isobutyryl-CoA: 17.7
Ethylmalonyl-CoA: 14.8
Acetyl-CoA: 14.3
CHC-CoA: 1.4
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Benzoyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

CDS_06333: mal - mmal - mal

PKS_AT (560..846): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 87.5%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 190.1
inactive: 109.2
Methoxymalonyl-CoA: 56.6
Methylmalonyl-CoA: 47.5
Propionyl-CoA: 30.3
Isobutyryl-CoA: 20.6
Acetyl-CoA: 16.4
Ethylmalonyl-CoA: 15.7
fatty_acid: 10.3
Benzoyl-CoA: 10.2
2-Methylbutyryl-CoA: 8.5
CHC-CoA: 1.4
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (2282..2577): 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: 211.2
Ethylmalonyl-CoA: 204.0
Methoxymalonyl-CoA: 169.4
2-Methylbutyryl-CoA: 146.0
trans-1,2-CPDA: 141.3
Propionyl-CoA: 122.0
CHC-CoA: 109.8
Malonyl-CoA: 106.8
Isobutyryl-CoA: 66.4
Benzoyl-CoA: 51.8
Acetyl-CoA: 44.1
inactive: 37.8
fatty_acid: 31.5
3-Methylbutyryl-CoA: 28.1

PKS_AT (4004..4274): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 87.5%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 190.4
inactive: 108.6
Methoxymalonyl-CoA: 58.9
Methylmalonyl-CoA: 48.4
Propionyl-CoA: 31.2
Isobutyryl-CoA: 21.5
Acetyl-CoA: 16.6
Ethylmalonyl-CoA: 15.9
Benzoyl-CoA: 10.2
fatty_acid: 10.1
2-Methylbutyryl-CoA: 3.2
CHC-CoA: 2.1
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description

NPDC024463.ctg-0020 - Region 1 - NI-siderophore

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Location: 66,011 - 99,550 nt. (total: 33,540 nt) Show pHMM detection rules used

NI-siderophore: IucA_IucC

Legend:

core biosynthetic genes

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Gene details

Select a gene to view the details available for it

Gene overview

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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_06485: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_06486: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_06496: lysine/ornithine N-monooxygenase

smcogs: SMCOG1080: lysine/ornithine N-monooxygenase

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	0.56	other (other)	ochrobactin	Ochrobactrum anthropi
BGC0002305.2	0.55	other (other)	legonoxamine A, desferrioxamine B, legonoxamine B	Streptomyces sp.
BGC0000295.5	0.54	NRPS	acinetoferrin	Acinetobacter haemolyticus
BGC0001478.5	0.53	other (other)	desferrioxamine E	Streptomyces sp. ID38640
BGC0000941.3	0.52	other (other)	desferrioxamin B	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001531.5	0.51	other (other)	bisucaberin B	Tenacibaculum mesophilum
BGC0001870.3	0.51	other (other)	putrebactin, avaroferrin	Xenorhabdus budapestensis

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	0.56	other (other)	ochrobactin	Ochrobactrum anthropi
BGC0002305.2	0.55	other (other)	legonoxamine A, desferrioxamine B, legonoxamine B	Streptomyces sp.
BGC0000295.5	0.54	NRPS	acinetoferrin	Acinetobacter haemolyticus
BGC0001478.5	0.53	other (other)	desferrioxamine E	Streptomyces sp. ID38640
BGC0000941.3	0.52	other (other)	desferrioxamin B	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001531.5	0.51	other (other)	bisucaberin B	Tenacibaculum mesophilum
BGC0001870.3	0.51	other (other)	putrebactin, avaroferrin	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:

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 20.10 out of 21.84

Confidence: medium

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.09 out of 27.18

Confidence: medium

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.17 out of 27.18

Confidence: medium

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 (9):

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.22 out of 20.97

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.78 out of 26.85

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.77 out of 25.88

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.73 out of 19.26

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.70 out of 19.26

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.69 out of 31.73

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

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.09 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
LexA variant 2	Repressor of DNA damage response
MexT	Global virulence regulator
NrdR	Represses ribonucleotide reductase encoding genes

NPDC024463.ctg-0021 - Region 1 - RRE-containing,azole-containing-RiPP

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Location: 12,053 - 38,516 nt. (total: 26,464 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)
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

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 oxidoreductase

CDS_06541: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_06547: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: methyltransferase

CDS_06544: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: amidase hydrolase

CDS_06546: amidase

smcogs: SMCOG1105: amidase

CDS_06563: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: dehydratase

CDS_06554: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002311.3	0.35	ribosomal	cutimycin	Cutibacterium acnes KPA171202
BGC0001146.5	0.33	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0000606.5	0.31	ribosomal	lactazole	Streptomyces lactacystinaeus
BGC0001145.5	0.29	ribosomal	cyclothiazomycin b1	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5	0.28	ribosomal	cyclothiazomycin	Streptomyces hygroscopicus
BGC0000605.5	0.27	ribosomal	GE37468	Streptomyces sp. ATCC 55365
BGC0001640.3	0.27	ribosomal	kocurin	Kocuria rosea
BGC0001753.3	0.26	ribosomal	radamycin, globimycin	Streptomyces globisporus subsp. globisporus
BGC0002363.3	0.26	ribosomal	berninamycin K, berninamycin J, berninamycin A, berninamycin B	Streptomyces sp.
BGC0000613.5	0.25	ribosomal	thiomuracin A	Nonomuraea sp. Bp3714-39

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002311.3	0.49	ribosomal	cutimycin	Cutibacterium acnes KPA171202
BGC0001146.5	0.47	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0000606.5	0.46	ribosomal	lactazole	Streptomyces lactacystinaeus
BGC0002404.2	0.46	other (other)	falcarindiol	Solanum lycopersicum
BGC0000894.4	0.45	other (other)	citrinin	Monascus aurantiacus
BGC0001145.5	0.44	ribosomal	cyclothiazomycin b1	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5	0.44	ribosomal	cyclothiazomycin	Streptomyces hygroscopicus
BGC0001640.3	0.43	ribosomal	kocurin	Kocuria rosea
BGC0000605.5	0.43	ribosomal	GE37468	Streptomyces sp. ATCC 55365
BGC0001197.5	0.42	PKS	frankiamicin	Frankia sp. EAN1pec

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: 18.01 out of 23.79

Confidence: medium

Additional weak hits (8):

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.57 out of 29.51

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.14 out of 32.93

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.43 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.49 out of 29.38

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.12 out of 27.55

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.53 out of 31.73

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.45 out of 29.65

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 15.98 out of 28.19

Confidence: weak

(Thi)azol(in)e containing peptide predictions

(Thi)azol(in)e containing peptide(s)

CDS_06555

Leader:

MSVDFATFDLTELAVLDAADTAAMAALRASHTERFVDDLEDLIGKPGMEVVGP

Core:

MCCSCATSVSCCCCS

Core with dehydrations:

MCysCysDhaCysADhbDhaVDhaCysCysCysCysDha

CDS_06555

Cleaved off residues:

Q

MIBiG 4.0 matches for CDS_06555

26.7%

BGC0001155.5 (AGY49587.1):

Thiopeptide: GE2270

1

MCCSCAT

7

CCSC+

8

FCCSCSP

14

11.8%

BGC0000535.4 (ADJ56352.1):

Lanthipeptide: nisin A

7

TSVSCC

12

TS+S C

2

TSISLC

7

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Types:

Type I: Featuring genes encoding indolic acid side ring (series e)
Type II: Featuring the gene coding for quinaldic acid moiety formation (series a, b, and c)
Type III: No genes for synthesizing L-Trp derivatives (series d)

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: Thiopeptide_F_RRE; Location: 0 - 82; Score: 37.1
: RRE type: Thiopeptide_F_RRE; Location: 0 - 82; Score: 37.1

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism

Core peptide predictions

CDS_06555

Putative Type III

Cleavage pHMM score: 3.50

RODEO score: 25

Monoisotopic mass: 1489.4 Da

Molecular weight: 1490.8 Da

Predicted peptide features:
Central ring: pyridine trisubstituted

Alternative weights: (assuming N unmodified Ser/Thr residues); 1508.9 Da N = 1; 1526.9 Da N = 2; 1544.9 Da N = 3; 1562.9 Da N = 4; 1580.9 Da N = 5

NPDC024463.ctg-0021 - Region 2 - T1PKS

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Location: 49,963 - 106,801 nt. (total: 56,839 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))

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

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_06581: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

CDS_06587: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

Ligases: synthase

CDS_06592: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000041.3	0.65	PKS	oronofacic acid	Pseudomonas syringae
BGC0001276.3	0.64	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.64	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.64	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002191.2	0.64	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001254.3	0.62	PKS	ACT-Toxin II	Alternaria alternata
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0002192.3	0.62	PKS	FR901512	fungal sp. No.14919
BGC0001164.3	0.61	PKS	1-heptadecene	Cyanothece sp. PCC 7822

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000041.3	0.65	PKS	oronofacic acid	Pseudomonas syringae
BGC0001276.3	0.64	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.64	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.64	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002191.2	0.64	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001254.3	0.62	PKS	ACT-Toxin II	Alternaria alternata
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0002192.3	0.62	PKS	FR901512	fungal sp. No.14919
BGC0001164.3	0.61	PKS	1-heptadecene	Cyanothece sp. PCC 7822

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

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 25.52 out of 27.04

Confidence: strong

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.58 out of 27.04

Confidence: medium

Additional weak hits (17):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.09 out of 31.73

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.36 out of 24.78

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.65 out of 18.57

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.01 out of 26.06

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.06 out of 32.93

Confidence: weak

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 23.11 out of 32.38

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.06 out of 29.25

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.47 out of 20.01

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 20.97 out of 32.93

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.89 out of 27.78

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.02 out of 26.85

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.34 out of 26.12

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: 15.64 out of 27.78

Confidence: weak

MexT

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

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.06 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.09 out of 28.19

Confidence: weak

Module view

Legend

Detailed Pfam 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 49962 - 106801:

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

Polymer prediction:: (Me-ohmal - pk) + (pk)
Non-colinear ordering:: CDS_06592 + CDS_06593

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_06592: mmal - pk

PKS_AT (581..877): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 87.5%; Methoxymalonyl-CoA: 79.2%; Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 191.9
Ethylmalonyl-CoA: 183.1
Methoxymalonyl-CoA: 161.8
2-Methylbutyryl-CoA: 119.4
trans-1,2-CPDA: 111.1
Propionyl-CoA: 105.7
CHC-CoA: 92.9
Malonyl-CoA: 91.5
Benzoyl-CoA: 71.6
Isobutyryl-CoA: 69.7
fatty_acid: 43.4
Acetyl-CoA: 41.6
3-Methylbutyryl-CoA: 36.3
inactive: 34.6

PKS_AT (2200..2506): pk

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 95.8%; Methoxymalonyl-CoA: 87.5%; Ethylmalonyl-CoA: 83.3%

minowa: Ethylmalonyl-CoA

Prediction, score:

Ethylmalonyl-CoA: 221.9
Methylmalonyl-CoA: 216.2
Methoxymalonyl-CoA: 182.3
2-Methylbutyryl-CoA: 137.4
trans-1,2-CPDA: 134.2
Propionyl-CoA: 112.3
Malonyl-CoA: 95.9
CHC-CoA: 95.4
Isobutyryl-CoA: 80.5
Benzoyl-CoA: 70.1
3-Methylbutyryl-CoA: 37.6
Acetyl-CoA: 35.3
fatty_acid: 32.3
inactive: 23.4

CDS_06593: pk

PKS_AT (574..883): pk

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

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

minowa: Ethylmalonyl-CoA

Prediction, score:

Ethylmalonyl-CoA: 168.0
Methylmalonyl-CoA: 166.4
Methoxymalonyl-CoA: 145.2
2-Methylbutyryl-CoA: 112.9
trans-1,2-CPDA: 95.4
Propionyl-CoA: 89.5
Malonyl-CoA: 80.8
Isobutyryl-CoA: 64.2
CHC-CoA: 64.0
Benzoyl-CoA: 59.5
Acetyl-CoA: 41.0
3-Methylbutyryl-CoA: 39.0
fatty_acid: 34.3
inactive: 18.9

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
DasR	N-acetylglucosamine dependent repressor
OsdR	Development and stress management regulator

NPDC024463.ctg-0022 - Region 1 - NRPS,linaridin,transAT-PKS

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Location: 87,057 - 127,952 nt. (total: 40,896 nt) Show pHMM detection rules used

Region on contig edge.

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)))
linaridin: (cypemycin or cypI)
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

Oxidoreductases: dehydrogenase

CDS_06714: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase

CDS_06726: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: back translocase hydrolase

CDS_06711: GTP-binding protein LepA

smcogs: SMCOG1190: GTP-binding protein LepA

CDS_06719: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001735.5	0.51	other (other)	pentostatine, vidarabine	Streptomyces antibioticus
BGC0002332.2	0.46	PKS	4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A	Candidatus Entotheonella sp.
BGC0001188.3	0.37	ribosomal	legonaridin	Streptomyces sp. CT34
BGC0001906.2	0.36	PKS	2-acetyl-1,3,6,8-tetrahydroxynaphthalene, 1,3,6,8-tetrahydroxynaphthalene	Daldinia eschscholzii IFB-TL01
BGC0002609.2	0.36	NRPS, PKS	ochratoxin A	Aspergillus welwitschiae
BGC0000888.5	0.35	other (other)	bacilysin	Bacillus sp. CS93
BGC0002474.2	0.34	NRPS	agrobactin	Agrobacterium tumefaciens
BGC0002477.3	0.33	PKS	thioangucycline A, thioangucycline B	Streptomyces sp. CB00072
BGC0001895.4	0.33	PKS	huanglongmycin A, huanglongmycin B, huanglongmycin C	Streptomyces sp. CB09001
BGC0001904.2	0.32	PKS	fluostatin L, fluostatin D, difluostatin A, fluostatin C, fluostatin F, fluostatin G/H, fluostatin J, fluostatin K, rabelomycin	Micromonospora rosaria

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001735.5	0.48	other (other)	pentostatine, vidarabine	Streptomyces antibioticus
BGC0001050.5	0.46	NRPS, PKS	thalassospiramide A	Tistrella bauzanensis
BGC0002332.2	0.45	PKS	4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A	Candidatus Entotheonella sp.
BGC0002474.2	0.42	NRPS	agrobactin	Agrobacterium tumefaciens
BGC0000353.5	0.42	NRPS	tacrolimus	Streptomyces sp. MA6548
BGC0001188.3	0.42	ribosomal	legonaridin	Streptomyces sp. CT34
BGC0002451.2	0.42	PKS	inthomycin B	Streptomyces sp.
BGC0001906.2	0.41	PKS	2-acetyl-1,3,6,8-tetrahydroxynaphthalene, 1,3,6,8-tetrahydroxynaphthalene	Daldinia eschscholzii IFB-TL01
BGC0002477.3	0.41	PKS	thioangucycline A, thioangucycline B	Streptomyces sp. CB00072
BGC0000888.5	0.41	other (other)	bacilysin	Bacillus sp. CS93

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

Additional weak hits (3):

MexT

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

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.85 out of 29.25

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.48 out of 25.88

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 87056 - 127952:

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

Polymer prediction:: (Gly - ccmal - ohmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_06726: mal - mal

PKS_AT (41..329): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 31.0
Methylmalonyl-CoA: 23.8
Methoxymalonyl-CoA: 20.4
Isobutyryl-CoA: 18.9
Benzoyl-CoA: 18.2
fatty_acid: 13.9
inactive: 13.3
Propionyl-CoA: 13.3
2-Methylbutyryl-CoA: 8.7
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 (393..670): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 103.0
inactive: 37.9
Methoxymalonyl-CoA: 33.6
Methylmalonyl-CoA: 30.5
Propionyl-CoA: 23.6
fatty_acid: 17.0
2-Methylbutyryl-CoA: 12.0
trans-1,2-CPDA: 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

CDS_06727: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (1912..2307): 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 (100% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator

NPDC024463.ctg-0023 - Region 1 - NAPAA

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Location: 29,368 - 63,291 nt. (total: 33,924 nt) Show pHMM detection rules used

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

Oxidoreductases: oxidoreductase

CDS_06770: NADH:flavin oxidoreductase/NADH oxidase

smcogs: SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

Transferases: acetyltransferase

CDS_06755: Chloramphenicol acetyltransferase

smcogs: SMCOG1156: Chloramphenicol acetyltransferase

Hydrolases: deformylase dehalogenase

CDS_06760: peptide deformylase

smcogs: SMCOG1275: peptide deformylase

CDS_06761: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Ligases: ligase

CDS_06772: 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	0.60	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001250.4	0.60	NRPS	epichloenin A	Epichloe festucae
BGC0001251.4	0.60	NRPS	epichloenin A	Epichloe festucae
BGC0000342.4	0.60	NRPS	enniatin	Fusarium equiseti
BGC0000307.4	0.60	NRPS	AbT1	Aureobasidium pullulans
BGC0001166.5	0.60	NRPS	HC-toxin	Alternaria jesenskae
BGC0001261.3	0.60	NRPS	AM-toxin	Alternaria alternata
BGC0001758.4	0.59	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

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	0.60	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001250.4	0.60	NRPS	epichloenin A	Epichloe festucae
BGC0001251.4	0.60	NRPS	epichloenin A	Epichloe festucae
BGC0000342.4	0.60	NRPS	enniatin	Fusarium equiseti
BGC0000307.4	0.60	NRPS	AbT1	Aureobasidium pullulans
BGC0001166.5	0.60	NRPS	HC-toxin	Alternaria jesenskae
BGC0001261.3	0.60	NRPS	AM-toxin	Alternaria alternata
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.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (5):

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.00 out of 20.97

Confidence: weak

HipB

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

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.83 out of 30.22

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.55 out of 35.63

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.61 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 29367 - 63291:

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_06772: X

AMP-binding (41..429): 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

NPDC024463.ctg-0024 - Region 1 - lanthipeptide-class-iii

Download region GenBank file

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Location: 51,347 - 73,941 nt. (total: 22,595 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

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

No tailoring functions detected.

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000496.5	0.48	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3	0.47	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000551.5	0.47	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000519.4	0.46	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000501.3	0.46	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0000553.3	0.46	ribosomal	SRO15-2212	Streptomyces filamentosus NRRL 15998
BGC0001226.4	0.46	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0000563.4	0.45	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0002700.2	0.45	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0002111.3	0.42	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000496.5	0.48	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3	0.47	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000551.5	0.47	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000519.4	0.46	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000501.3	0.46	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0000553.3	0.46	ribosomal	SRO15-2212	Streptomyces filamentosus NRRL 15998
BGC0001226.4	0.46	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0000563.4	0.45	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0002700.2	0.45	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0002111.3	0.42	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139

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_06906

CDS_06905

Leader:

MAFILDLQGLHEESESYVE

Core:

SLFCSHWSSRTCM

Core with dehydrations:

DhaLFCysDhaHWDhaDhaRDhbCysM

antiSMASH-DB 4.0 matches for CDS_06905

84.6%

NZ_CP026498.1and 1 other:

NZ_JAGIYX010000019.1 Lanthipeptides: allorf_139216_139377_lanthipeptide

Lanthipeptides: allorf_09763889_09763999_lanthipeptide

1

SLFCSHWSSRTCM

13

SL+CSHWSSR CM

1

SLWCSHWSSRACM

13

31.2%

NZ_CP023466.1and 2 others:

NZ_JHVT01000005.1 Lanthipeptides: allorf_225959_226054_lanthipeptideNZ_KB906329.1 Lanthipeptides: allorf_148726_148821_lanthipeptide

Lanthipeptides: allorf_0913536_0913631_lanthipeptide

6

HWSSRTCM

13

HWS R+C

3

HWSDRSCQ

10

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.36 out of 20.97

Confidence: medium

CRP

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

Confidence: strong

AfsQ1

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

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

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.27 out of 26.85

Confidence: medium

Additional weak hits (11):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.42 out of 21.55

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.07 out of 23.43

Confidence: weak

HipB

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

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.68 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.01 out of 29.38

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.36 out of 18.57

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.07 out of 23.43

Confidence: weak

CopR

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

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.94 out of 31.73

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.69 out of 19.26

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.40 out of 30.11

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_06905 - Class III

Cleavage pHMM score: -1.70

RODEO score: 0

Monoisotopic mass: 1453.6 Da

Molecular weight: 1454.7 Da

Number of bridges: 2

Alternative weights: (assuming N unmodified Ser/Thr residues); 1472.7 Da N = 1; 1490.7 Da N = 2; 1508.7 Da N = 3

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
CRP	Cyclic AMP receptor protein
CcpA	Catabolite control protein A
RutR	Regulator of the pyrimidine and purine metabolism

NPDC024463.ctg-0025 - Region 1 - NRPS,transAT-PKS

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Location: 1 - 32,714 nt. (total: 32,714 nt) Show pHMM detection rules used

Region on contig edge.

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

Legend:

core biosynthetic genes

additional biosynthetic 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

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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: acetyltransferase acylase

CDS_06957: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_06961: acetyl-CoA acetyltransferase

smcogs: SMCOG1124: acetyl-CoA acetyltransferase

Ligases: ligase

CDS_06956: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.60	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.59	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.58	NRPS	AbT1	Aureobasidium pullulans
BGC0001240.4	0.58	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001128.4	0.57	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.57	NRPS	AM-toxin	Alternaria alternata
BGC0001833.4	0.57	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.56	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001641.4	0.56	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.56	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.63	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.63	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.63	NRPS	AbT1	Aureobasidium pullulans
BGC0001240.4	0.62	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001128.4	0.62	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.62	NRPS	AM-toxin	Alternaria alternata
BGC0001833.4	0.62	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.62	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001641.4	0.62	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.61	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:

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.64 out of 26.33

Confidence: medium

CRP

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

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

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31

Confidence: medium

Additional weak hits (9):

HipB

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

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.30 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.71 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.17 out of 29.38

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.49 out of 29.65

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.95 out of 28.19

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.56 out of 23.43

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.92 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 - 32714:

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

Polymer prediction:: (Gly)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_06956: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (1844..2248): 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)

CDS_06957: mal - mal

PKS_AT (12..302): mal

ATSignature: (unknown)

No matches above 50%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 32.6
Methylmalonyl-CoA: 21.6
Propionyl-CoA: 17.4
Benzoyl-CoA: 16.4
Methoxymalonyl-CoA: 16.3
inactive: 14.4
Isobutyryl-CoA: 13.9
Ethylmalonyl-CoA: 12.7
fatty_acid: 9.4
trans-1,2-CPDA: 0.0
CHC-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

PKS_AT (338..615): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 126.9
inactive: 54.6
Methoxymalonyl-CoA: 51.2
Methylmalonyl-CoA: 42.8
Propionyl-CoA: 37.6
trans-1,2-CPDA: 18.1
Isobutyryl-CoA: 16.9
2-Methylbutyryl-CoA: 15.9
fatty_acid: 12.4
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
CRP	Cyclic AMP receptor protein
CatR	H2O2-responsive repressor

NPDC024463.ctg-0026 - Region 1 - azole-containing-RiPP

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Location: 75,151 - 104,853 nt. (total: 29,703 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

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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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: oxygenase

CDS_07090: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_07106: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Lyases: dehydratase

CDS_07100: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000606.5	0.67	ribosomal	lactazole	Streptomyces lactacystinaeus
BGC0001146.5	0.52	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0002311.3	0.51	ribosomal	cutimycin	Cutibacterium acnes KPA171202
BGC0001145.5	0.50	ribosomal	cyclothiazomycin b1	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5	0.48	ribosomal	cyclothiazomycin	Streptomyces hygroscopicus
BGC0001640.3	0.48	ribosomal	kocurin	Kocuria rosea
BGC0001986.3	0.48	other (other)	purincyclamide	Streptomyces chrestomyceticus
BGC0001174.4	0.47	ribosomal	corynazolicin	Corynebacterium urealyticum DSM 7111
BGC0002127.3	0.47	PKS	flaviolin, 1,3,6,8-tetrahydroxynaphthalene	Streptomyces coelicolor A3(2)
BGC0001860.4	0.46	ribosomal	thiomuracin	Thermobispora bispora DSM 43833

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000606.5	0.67	ribosomal	lactazole	Streptomyces lactacystinaeus
BGC0001146.5	0.52	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0002311.3	0.51	ribosomal	cutimycin	Cutibacterium acnes KPA171202
BGC0001145.5	0.50	ribosomal	cyclothiazomycin b1	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5	0.48	ribosomal	cyclothiazomycin	Streptomyces hygroscopicus
BGC0001640.3	0.48	ribosomal	kocurin	Kocuria rosea
BGC0001986.3	0.48	other (other)	purincyclamide	Streptomyces chrestomyceticus
BGC0001174.4	0.47	ribosomal	corynazolicin	Corynebacterium urealyticum DSM 7111
BGC0002127.3	0.47	PKS	flaviolin, 1,3,6,8-tetrahydroxynaphthalene	Streptomyces coelicolor A3(2)
BGC0001860.4	0.46	ribosomal	thiomuracin	Thermobispora bispora DSM 43833

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: 23.51 out of 30.11

Confidence: medium

Additional weak hits (14):

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.82 out of 18.57

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.52 out of 23.43

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.52 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.83 out of 29.38

Confidence: weak

PsrA

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

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.24 out of 39.62

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.67 out of 39.62

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.69 out of 19.26

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.14 out of 19.26

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.09 out of 26.06

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.22 out of 33.14

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.04 out of 30.11

Confidence: weak

(Thi)azol(in)e containing peptide predictions

(Thi)azol(in)e containing peptide(s)

CDS_07101

Leader:

MSDLHETPSFELQDLDLSDLTVTSLRDSAALPEGGA

Core:

SWGSSSCQGSSSCATQEPRPVAL

Core with dehydrations:

DhaWGDhaDhaDhaCysQGDhaDhaDhaCysADhbQEPRPVAL

antiSMASH-DB 4.0 matches for CDS_07101

50.0%

NZ_CP023701.1and 1 other:

NZ_CP023701.1 Thiopeptides: CP968_RS31565_thiopeptide

Thiopeptides: CP968_RS31560_thiopeptide

1

SWGSSSCQGSSSCA

14

SWG+ SCQGSSSCA

1

SWGTCSCQGSSSCA

14

26.1%

NZ_CP011420.1:

Lanthipeptides: allorf_2444072_2444176_lanthipeptide

13

CATQEPRP

20

C+T EPRP

3

CSTAEPRP

10

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Types:

Type I: Featuring genes encoding indolic acid side ring (series e)
Type II: Featuring the gene coding for quinaldic acid moiety formation (series a, b, and c)
Type III: No genes for synthesizing L-Trp derivatives (series d)

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: Thiopeptide_F_RRE; Location: 40 - 122; Score: 45.2

TFBS definitions

Regulator	Description
CelR	Cellobiose uptake repressor

Core peptide predictions

CDS_07101

Putative Type III

Cleavage pHMM score: 3.10

RODEO score: 25

Monoisotopic mass: 2324.0 Da

Molecular weight: 2325.5 Da

Predicted peptide features:
Central ring: pyridine trisubstituted

Alternative weights: (assuming N unmodified Ser/Thr residues); 2343.5 Da N = 1; 2361.5 Da N = 2; 2379.6 Da N = 3; 2397.6 Da N = 4; 2415.6 Da N = 5; 2433.6 Da N = 6; 2451.6 Da N = 7; 2469.7 Da N = 8

NPDC024463.ctg-0027 - Region 1 - lanthipeptide-class-iv

Download region GenBank file

Download region SVG

Location: 21,397 - 43,994 nt. (total: 22,598 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

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_07133: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

Hydrolases: hydrolase

CDS_07136: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002337.2	0.60	ribosomal	class IV lanthipeptide, SflA	Streptomyces sp. NRRL S-1022
BGC0000528.5	0.53	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000563.4	0.52	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0001226.4	0.50	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0002700.2	0.49	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0002316.2	0.48	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0002111.3	0.46	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000503.5	0.45	ribosomal	cinnamycin	Streptomyces cinnamoneus
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0001579.4	0.42	ribosomal	duramycin	Streptomyces cinnamoneus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002337.2	0.60	ribosomal	class IV lanthipeptide, SflA	Streptomyces sp. NRRL S-1022
BGC0000528.5	0.53	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000563.4	0.52	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0001226.4	0.50	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0002700.2	0.49	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0002316.2	0.48	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0002111.3	0.46	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000503.5	0.45	ribosomal	cinnamycin	Streptomyces cinnamoneus
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0001579.4	0.42	ribosomal	duramycin	Streptomyces cinnamoneus

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

No hits above weak threshold.

Weak hits (1):

MexT

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

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

NPDC024463.ctg-0028 - Region 1 - NRPS,T2PKS,arylpolyene

Download region GenBank file

Download region SVG

Location: 1 - 89,682 nt. (total: 89,682 nt) Show pHMM detection rules used

Region on contig edge.

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
arylpolyene: (APE_KS1 or APE_KS2)
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

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_07187: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

CDS_07188: pyruvate oxidase/decarboxylase

smcogs: SMCOG1055: pyruvate oxidase/decarboxylase

CDS_07192: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_07198: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

CDS_07208: monooxygenase FAD-binding

smcogs: SMCOG1246: monooxygenase FAD-binding

CDS_07216: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_07228: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: acylase methyltransferase

CDS_07193: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_07194: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_07232: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

Hydrolases: deacetylase hydrolase phosphatase

CDS_07197: polysaccharide deacetylase

smcogs: SMCOG1235: polysaccharide deacetylase

CDS_07201: alpha/beta hydrolase domain-containing protein

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

CDS_07204: inositol monophosphatase

smcogs: SMCOG1207: inositol monophosphatase

CDS_07239: amidohydrolase

smcogs: SMCOG1244: amidohydrolase

Lyases: cyclase

CDS_07221: Polyketide synthesis cyclase

smcogs: SMCOG1225: Polyketide synthesis cyclase

CDS_07223: cyclase/dehydrase

smcogs: SMCOG1128: cyclase/dehydrase

Ligases: ligase synthase

CDS_07181: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07182: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07186: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07189: 3-oxoacyl-(acyl carrier protein) synthase III

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

CDS_07196: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_07224: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_07225: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.61	NRPS	enniatin	Fusarium equiseti
BGC0001135.5	0.59	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.57	NRPS	icosalide A, icosalide B	Burkholderia gladioli
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
BGC0001825.4	0.56	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002286.3	0.56	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.56	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	0.55	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001160.5	0.53	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.68	NRPS	enniatin	Fusarium equiseti
BGC0002135.2	0.68	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.67	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001050.5	0.67	NRPS, PKS	thalassospiramide A	Tistrella bauzanensis
BGC0001261.3	0.67	NRPS	AM-toxin	Alternaria alternata
BGC0000426.5	0.66	NRPS	sevadicin	Paenibacillus larvae
BGC0001133.4	0.66	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001166.5	0.66	NRPS	HC-toxin	Alternaria jesenskae
BGC0001833.4	0.66	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001758.4	0.66	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

AbrC3

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

Confidence: strong

AfsQ1

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

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.64 out of 23.79

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.42 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

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.09 out of 23.79

Confidence: medium

Additional weak hits (24):

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.07 out of 26.85

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

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.76 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.27 out of 30.25

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

AfsQ1

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

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.64 out of 36.54

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.33 out of 20.97

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.91 out of 19.26

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.24 out of 36.54

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.39 out of 36.54

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.93 out of 39.62

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84

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: 15.56 out of 21.84

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.30 out of 26.85

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.40 out of 36.54

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.23 out of 21.55

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.13 out of 36.53

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.01 out of 32.74

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.16 out of 30.98

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.83 out of 32.93

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.46 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

Type II PKS

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 89682:

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

Polymer prediction:: (D-Val) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 0 - 29813:

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

Polymer prediction:: (D-Val) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 6708 - 47848:

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

Polymer prediction:: (D-Val)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07181: X

AMP-binding (468..868): X

nrpys: Ala, 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):: Ala or Ser DVWHFSLVDK (97% 8Å match); Ser DVWHFSLVDK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_07182: Val

Search NORINE for peptide: strict or relaxed

AMP-binding (460..856): 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:: DLYWWGGTFK
Nearest Stachelhaus code(s):: Val DAYWWGGTFK (82% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_07186: X

AMP-binding (20..422): 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:: QYSDCGGNIK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

CDS_07193: mal

PKS_AT (37..309): mal

ATSignature: (unknown)

No matches above 50%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 30.1
Methoxymalonyl-CoA: 10.3
inactive: 10.0
Methylmalonyl-CoA: 6.3
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Propionyl-CoA: 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

CDS_07194: mal

PKS_AT (37..283): mal

ATSignature: (unknown)

No matches above 50%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 12.0
Methoxymalonyl-CoA: 8.5
trans-1,2-CPDA: 0.0
inactive: 0.0
fatty_acid: 0.0
Propionyl-CoA: 0.0
Methylmalonyl-CoA: 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

Type II PKS gene cluster prediction details

Cluster section:: 17160 to 89682
Starter unit(s):: acetyl-CoA (Score: 0.0; E-value: 0)
Product class(es):: pentangular polyphenol
tetracenomycin

CDS_07192: KR (Score: 186.4; E-value: 1.8e-57)
CDS_07198: OXY (Score: 21.9; E-value: 1.8e-07)
CDS_07206: OXY (Score: 46.9; E-value: 4.7e-15)
CDS_07208: OXY (Score: 10.8; E-value: 0.00042)
CDS_07216: KR (Score: 93.4; E-value: 4.2e-29)
CDS_07221: CYC C4-C21/C2-C23|C2-C19 (Score: 132.6; E-value: 1.2e-41)
CDS_07222: ACP (Score: 46.7; E-value: 5.5e-15)
CDS_07223: CYC C9-C14 (Score: 235.8; E-value: 3.6e-73); CYC C5-C18 (Score: 181.9; E-value: 1e-56)
CDS_07224: KS (Score: 708.5; E-value: 6e-216)
CDS_07225: CLF (Score: 525.6; E-value: 1.8e-160)
CDS_07231: OXY (Score: 48.8; E-value: 1.3e-15)
CDS_07232: MET (Score: 280.2; E-value: 5.1e-86)

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

NPDC024463.ctg-0030 - Region 1 - terpene

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Location: 19,054 - 40,148 nt. (total: 21,095 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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TFBS Finder

Pfam domains

TIGRFAM 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 oxygenase

CDS_07396: monooxygenase FAD-binding

smcogs: SMCOG1246: monooxygenase FAD-binding

CDS_07397: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

CDS_07398: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Hydrolases: deacetylase dehalogenase hydrolase

CDS_07387: polysaccharide deacetylase

smcogs: SMCOG1235: polysaccharide deacetylase

CDS_07399: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

CDS_07401: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Lyases: cyclase

CDS_07395: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthase

CDS_07390: cobalamin synthesis protein/P47K family protein

smcogs: SMCOG1178: cobalamin synthesis protein/P47K family protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000660.5	0.58	terpene	albaflavenone	Streptomyces coelicolor A3(2)
BGC0000675.5	0.56	terpene	(+)-T-muurolol	Streptomyces clavuligerus ATCC 27064
BGC0000674.5	0.47	terpene	(-)-δ-cadinene	Streptomyces clavuligerus ATCC 27064
BGC0000677.5	0.46	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002571.2	0.45	NRPS	pyoverdine DC3000	Pseudomonas syringae pv. tomato str. DC3000
BGC0000842.5	0.44	other (non-nrp beta-lactam)	carbapenem MM4550	Streptomyces argenteolus
BGC0002000.4	0.43	PKS	setomimycin	Streptomyces aurantiacus JA 4570
BGC0002007.2	0.43	terpene	atolypene A, atolypene B	Amycolatopsis tolypomycina
BGC0002150.2	0.43	ribosomal	triculamin	Streptomyces triculaminicus
BGC0002151.2	0.43	ribosomal	alboverticillin	Streptomyces griseocarneus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000660.5	0.58	terpene	albaflavenone	Streptomyces coelicolor A3(2)
BGC0000675.5	0.56	terpene	(+)-T-muurolol	Streptomyces clavuligerus ATCC 27064
BGC0000674.5	0.47	terpene	(-)-δ-cadinene	Streptomyces clavuligerus ATCC 27064
BGC0000677.5	0.46	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002571.2	0.45	NRPS	pyoverdine DC3000	Pseudomonas syringae pv. tomato str. DC3000
BGC0000842.5	0.44	other (non-nrp beta-lactam)	carbapenem MM4550	Streptomyces argenteolus
BGC0002000.4	0.43	PKS	setomimycin	Streptomyces aurantiacus JA 4570
BGC0002007.2	0.43	terpene	atolypene A, atolypene B	Amycolatopsis tolypomycina
BGC0002150.2	0.43	ribosomal	triculamin	Streptomyces triculaminicus
BGC0002151.2	0.43	ribosomal	alboverticillin	Streptomyces griseocarneus

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_07395: T1TS

Domain 1 (5 - 306): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 26.66 out of 28.19

Confidence: strong

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05

Confidence: medium

Additional weak hits (13):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.99 out of 29.38

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.91 out of 20.97

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.41 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.85 out of 29.38

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.32 out of 31.73

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.20 out of 26.12

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.27 out of 36.54

Confidence: weak

ClgR

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

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.00 out of 29.65

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.68 out of 28.14

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 26.85

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.54 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

No acronyms to display

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
ZuR variant 1	Zinc-responsive repressor

NPDC024463.ctg-0031 - Region 1 - terpene

Download region GenBank file

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Location: 27,127 - 48,074 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

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

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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_07484: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

Hydrolases: hydrolase

CDS_07486: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: cyclase

CDS_07483: 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
BGC0000683.3	0.78	terpene	avermitilol	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001873.3	0.39	NRPS	pyrrolizixenamide A	Xenorhabdus szentirmaii DSM 16338
BGC0001911.3	0.38	terpene	raimonol	Streptomyces anulatus
BGC0001910.4	0.37	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0001197.5	0.36	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0002255.3	0.34	PKS	lijiquinone	Ascomycota sp. F53
BGC0000678.5	0.34	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001972.4	0.33	other (other)	toxoflavin, fervenulin	Streptomyces hiroshimensis
BGC0002561.3	0.32	other (other)	phenazine SA, phenazine SB, phenazine SC	Streptomyces sp.
BGC0001483.4	0.32	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000683.3	0.78	terpene	avermitilol	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001873.3	0.39	NRPS	pyrrolizixenamide A	Xenorhabdus szentirmaii DSM 16338
BGC0001911.3	0.38	terpene	raimonol	Streptomyces anulatus
BGC0001910.4	0.37	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0001197.5	0.36	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0002255.3	0.34	PKS	lijiquinone	Ascomycota sp. F53
BGC0000678.5	0.34	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001972.4	0.33	other (other)	toxoflavin, fervenulin	Streptomyces hiroshimensis
BGC0002561.3	0.32	other (other)	phenazine SA, phenazine SB, phenazine SC	Streptomyces sp.
BGC0001483.4	0.32	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8

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_07483: T1TS

Domain 1 (6 - 313): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.82 out of 21.84

Confidence: medium

Additional weak hits (4):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.17 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.44 out of 28.14

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 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

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
MexT	Global virulence regulator

NPDC024463.ctg-0031 - Region 2 - terpene

Download region GenBank file

Download region SVG

Location: 49,576 - 76,280 nt. (total: 26,705 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

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

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_07497: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_07508: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

CDS_07515: dehydrogenase

smcogs: SMCOG1181: dehydrogenase

Transferases: aminotransferase transferase

CDS_07501: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

CDS_07516: glucose-1-phosphate adenylyl/thymidylyltransferase

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

Ligases: synthase synthetase

CDS_07502: 1-deoxy-D-xylulose-5-phosphate synthase

smcogs: SMCOG1110: 1-deoxy-D-xylulose-5-phosphate synthase

CDS_07507: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000663.5	0.74	terpene	hopene	Streptomyces coelicolor A3(2)
BGC0001248.3	0.74	terpene	clavaric acid	Hypholoma sublateritium
BGC0000647.3	0.58	terpene	carotenoid	Rhodobacter sphaeroides
BGC0002276.2	0.55	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000648.3	0.52	terpene	carotenoid	Myxococcus xanthus
BGC0002591.2	0.51	PKS, terpene	aurachin C, aurachin D, aurachin SS	Streptomyces sp.
BGC0001839.3	0.51	terpene	squalestatin S1	Aspergillus sp. Z5
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

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000663.5	0.74	terpene	hopene	Streptomyces coelicolor A3(2)
BGC0001248.3	0.74	terpene	clavaric acid	Hypholoma sublateritium
BGC0000647.3	0.58	terpene	carotenoid	Rhodobacter sphaeroides
BGC0002276.2	0.55	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000648.3	0.52	terpene	carotenoid	Myxococcus xanthus
BGC0002591.2	0.51	PKS, terpene	aurachin C, aurachin D, aurachin SS	Streptomyces sp.
BGC0001839.3	0.51	terpene	squalestatin S1	Aspergillus sp. Z5
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

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
triterpene	hopanoid		C30	hopanoid skeleton	unknown
triterpene	polypodane		C30	polypodane skeleton	unknown

Genes with terpene domains:

CDS_07506: T2TS

Domain 1 (80 - 711): Type 2 terpene synthase

Subtype: Squalene substrate

Reactions:: squalene → hopanoid; squalene → polypodane

CDS_07507: PT_FPPS_like

Domain 1 (66 - 354): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

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

CDS_07509: PT_phytoene_like

Domain 1 (2 - 279): Prenyltransferase; Phytoene synthase like

Subtype: unknown

Reactions:: FPP → diapophytoene; FPP → PSPP; FPP → squalene; GGPP → phytoene; PSPP → hydroxysqualene

CDS_07510: PT_phytoene_like

Domain 1 (27 - 309): Prenyltransferase; Phytoene synthase like

Subtype: unknown

Reactions:: FPP → diapophytoene; FPP → PSPP; FPP → squalene; GGPP → phytoene; PSPP → hydroxysqualene

Transcription Factor Binding Sites

Binding sites found:

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.03 out of 29.72

Confidence: medium

Additional weak hits (10):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.58 out of 27.78

Confidence: weak

CodY

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

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.43 out of 36.54

Confidence: weak

HypR

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

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.54 out of 29.25

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.79 out of 28.14

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.16 out of 29.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.53 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.51 out of 26.06

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
NtrC	Nitrogen regulatory protein C

NPDC024463.ctg-0032 - Region 1 - NRPS,phosphonate

Download region GenBank file

Download region SVG

Location: 1 - 35,436 nt. (total: 35,436 nt) Show pHMM detection rules used

Region on contig edge.

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
phosphonate: (phosphonates and minimum(1, [2-Hacid_dh_C, Aldedh, Aminotran_1_2, Aminotran_5, AurF, CTP_transf_like, DUF4992, Fe-ADH, HMGL-like, Metallophos_2, NTP_transf_3, NTP_transf_5, PALP, PEP_mutase, TPP_enzyme_C, TPP_enzyme_N, phosphonates]) and not (phosphonatesHydrolase or phosphonatesMeIsocitrateLyase))

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

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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 carboxylase

CDS_07535: aminotransferase class V

smcogs: SMCOG1139: aminotransferase class V

CDS_07545: acetyl-CoA carboxylase biotin carboxylase

smcogs: SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Hydrolases: deaminase

CDS_07539: ornithine cyclodeaminase

smcogs: SMCOG1158: ornithine cyclodeaminase

Ligases: ligase synthase

CDS_07538: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07540: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

CDS_07544: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.72	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001132.4	0.64	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.64	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.64	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.63	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001825.4	0.63	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001641.4	0.62	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.62	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.60	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004

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	0.68	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.68	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.67	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001825.4	0.67	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002286.3	0.67	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	0.66	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.65	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.64	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:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.61 out of 23.79

Confidence: medium

Additional weak hits (13):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.22 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.16 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.71 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.40 out of 30.25

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.44 out of 29.25

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.92 out of 18.57

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.50 out of 32.74

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.31 out of 32.74

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.35 out of 21.55

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.27 out of 28.19

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.25 out of 36.53

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.32 out of 32.93

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.62 out of 33.14

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 0 - 35436:

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

Polymer prediction:: (Gln)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 0 - 23939:

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

Polymer prediction:: (Gln)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07525: Gln

Search NORINE for peptide: strict or relaxed

AMP-binding (442..848): Gln

nrpys: Gln

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:: DAWQFGLIQK
Nearest Stachelhaus code(s):: Gln DAWQFGLIQK (85% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_07538: X

AMP-binding (40..452): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
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:: DIWEITADDK
Nearest Stachelhaus code(s):: Dpr DIWELTADDK (88% 8Å match); Dab DIWELTADDK (74% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism

NPDC024463.ctg-0034 - Region 1 - terpene

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Location: 1 - 11,351 nt. (total: 11,351 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

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other genes

resistance

TTA codons

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Terpene

TFBS Finder

Pfam domains

Gene/CDS overview

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Automatically zoom to filtered/selected features

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

Tailoring functions

Lyases: cyclase

CDS_07637: Terpene synthase/cyclase metal-binding domain protein

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

Similar gene clusters

No matches found.

Similar known clusters

No significant matches found.

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_07637: T1TS

Domain 1 (1 - 307): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.11 out of 20.97

Confidence: medium

Additional weak hits (4):

ANR

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

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.65 out of 23.43

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.34 out of 27.18

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.30 out of 26.85

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
CcpA	Catabolite control protein A

NPDC024463.ctg-0035 - Region 1 - T1PKS

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Location: 1 - 40,276 nt. (total: 40,276 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

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other genes

resistance

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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_07692: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase

CDS_07698: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase

CDS_07693: thioesterase

smcogs: SMCOG1004: thioesterase

Lyases: hydratase

CDS_07697: Nitrilase/cyanide hydratase and apolipoprotein

smcogs: SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

Ligases: ligase synthase

CDS_07691: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_07699: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001275.3	0.73	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.73	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.73	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0000041.3	0.70	PKS	oronofacic acid	Pseudomonas syringae
BGC0001160.5	0.64	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
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
BGC0001257.3	0.64	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0002175.3	0.63	PKS	YWA1	Aspergillus oryzae RIB40
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0000107.3	0.63	PKS	naphthopyrone	Aspergillus nidulans FGSC A4

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001275.3	0.73	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.73	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.73	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0000041.3	0.70	PKS	oronofacic acid	Pseudomonas syringae
BGC0001160.5	0.64	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
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
BGC0001257.3	0.64	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0002175.3	0.63	PKS	YWA1	Aspergillus oryzae RIB40
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0000107.3	0.63	PKS	naphthopyrone	Aspergillus nidulans FGSC A4

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ToxT

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

Confidence: medium

OsdR

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

Confidence: strong

Additional weak hits (4):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.09 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

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.13 out of 33.14

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.47 out of 23.43

Confidence: weak

Module view

Legend

Detailed Pfam 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 - 40276:

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

Polymer prediction:: (ccmal) + (ccmal - Me-ccmal)
Non-colinear ordering:: CDS_07691 + CDS_07692

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07691: mal

PKS_AT (1543..1829): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 83.3%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 206.0
inactive: 91.5
Methylmalonyl-CoA: 62.9
Methoxymalonyl-CoA: 60.1
Propionyl-CoA: 40.3
Isobutyryl-CoA: 35.2
Acetyl-CoA: 28.5
Ethylmalonyl-CoA: 24.6
2-Methylbutyryl-CoA: 18.8
Benzoyl-CoA: 17.7
CHC-CoA: 14.2
fatty_acid: 13.6
trans-1,2-CPDA: 9.1
3-Methylbutyryl-CoA: 0.0

CDS_07692: mal - mmal

PKS_AT (583..869): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 83.3%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 211.1
inactive: 90.4
Methylmalonyl-CoA: 62.8
Methoxymalonyl-CoA: 59.4
Propionyl-CoA: 43.9
Isobutyryl-CoA: 32.5
Acetyl-CoA: 31.3
Ethylmalonyl-CoA: 27.6
Benzoyl-CoA: 21.0
2-Methylbutyryl-CoA: 17.4
fatty_acid: 13.9
CHC-CoA: 13.7
trans-1,2-CPDA: 11.5
3-Methylbutyryl-CoA: 0.0

PKS_AT (2377..2676): 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: 207.8
Ethylmalonyl-CoA: 199.4
Methoxymalonyl-CoA: 165.7
2-Methylbutyryl-CoA: 121.2
trans-1,2-CPDA: 115.4
Propionyl-CoA: 96.5
CHC-CoA: 93.4
Malonyl-CoA: 87.1
Isobutyryl-CoA: 63.8
Benzoyl-CoA: 60.5
Acetyl-CoA: 42.4
3-Methylbutyryl-CoA: 41.8
fatty_acid: 37.3
inactive: 30.4

CDS_07698: mmal

PKS_AT (27..285): mmal

ATSignature: (unknown)

No matches above 50%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 15.2
CHC-CoA: 14.4
2-Methylbutyryl-CoA: 11.7
Methoxymalonyl-CoA: 11.3
trans-1,2-CPDA: 10.6
Benzoyl-CoA: 9.9
Malonyl-CoA: 8.7
inactive: 0.0
fatty_acid: 0.0
Propionyl-CoA: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

CDS_07699: X

AMP-binding (7..370): 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:: QYSDCGSNVK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
OsdR	Development and stress management regulator
ToxT	Regulator of MSHA biosynthesis

NPDC024463.ctg-0036 - Region 1 - NRPS,T1PKS

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Location: 1 - 46,297 nt. (total: 46,297 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))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

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Select a gene to view the details available for it

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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: oxygenase

CDS_07705: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_07711: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Hydrolases: esterase

CDS_07719: thioesterase

smcogs: SMCOG1004: thioesterase

Lyases: cyclase

CDS_07708: Diels-Alderase cyclase

extras: DA_cyclase: Diels-Alderase cyclase

Ligases: ligase synthase

CDS_07703: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_07704: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_07715: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

CDS_07718: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001164.3	0.49	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001273.3	0.44	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.43	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.43	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002631.2	0.42	ribosomal	Myxarylin	Pyxidicoccus fallax
BGC0000844.5	0.36	other (other)	clavulanic acid	Streptomyces clavuligerus
BGC0000342.4	0.35	NRPS	enniatin	Fusarium equiseti
BGC0001833.4	0.33	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	0.33	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002171.2	0.33	NRPS, PKS	pyrophen, campyrone B	Aspergillus niger ATCC 1015

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.74	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.74	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.74	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0000342.4	0.68	NRPS	enniatin	Fusarium equiseti
BGC0000041.3	0.67	PKS	oronofacic acid	Pseudomonas syringae
BGC0001833.4	0.66	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	0.66	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001132.4	0.66	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001261.3	0.66	NRPS	AM-toxin	Alternaria alternata
BGC0001825.4	0.66	NRPS	xenematide	Xenorhabdus nematophila AN6/1

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):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.06 out of 29.38

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.32 out of 26.06

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.95 out of 27.55

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.16 out of 30.98

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.30 out of 26.85

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.16 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.91 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.16 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 - 46297:

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

Polymer prediction:: (Me-ccmal) + (ohmal) + (Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 0 - 34159:

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

Polymer prediction:: (Me-ccmal) + (ohmal) + (Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 11363 - 46297:

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

Polymer prediction:: (ohmal) + (Gly)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07703: mmal

PKS_AT (1764..2059): 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: 211.0
Ethylmalonyl-CoA: 204.6
Methoxymalonyl-CoA: 169.5
2-Methylbutyryl-CoA: 145.2
trans-1,2-CPDA: 141.0
Propionyl-CoA: 120.2
CHC-CoA: 108.8
Malonyl-CoA: 108.6
Isobutyryl-CoA: 65.5
Benzoyl-CoA: 50.9
Acetyl-CoA: 43.2
inactive: 41.2
fatty_acid: 30.9
3-Methylbutyryl-CoA: 27.7

CDS_07704: mal

PKS_AT (585..876): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 91.7%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 199.4
inactive: 112.4
Methoxymalonyl-CoA: 57.2
Methylmalonyl-CoA: 51.8
Propionyl-CoA: 38.5
Isobutyryl-CoA: 32.8
Ethylmalonyl-CoA: 16.1
Acetyl-CoA: 15.7
fatty_acid: 13.2
Benzoyl-CoA: 11.5
trans-1,2-CPDA: 11.3
2-Methylbutyryl-CoA: 9.5
CHC-CoA: 8.5
3-Methylbutyryl-CoA: 0.0

CDS_07718: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (447..835): 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:: DMLQVGATWK
Nearest Stachelhaus code(s):: Ala DMTQIGWTWK (62% 8Å match); Gly DILQVGMIWK (62% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description

NPDC024463.ctg-0037 - Region 1 - NRPS-like,T1PKS

Download region GenBank file

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Location: 1 - 46,176 nt. (total: 46,176 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))
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

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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

Ligases: ligase synthase

CDS_07727: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_07728: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_07729: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_07730: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07732: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07733: 8-amino-7-oxononanoate synthase

smcogs: SMCOG1109: 8-amino-7-oxononanoate synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.83	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.83	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001244.3	0.83	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001276.3	0.59	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002135.2	0.55	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.55	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001160.5	0.54	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.54	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0000307.4	0.53	NRPS	AbT1	Aureobasidium pullulans
BGC0000342.4	0.53	NRPS	enniatin	Fusarium equiseti

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.73	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.73	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001244.3	0.73	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0000067.5	0.63	PKS	geldanamycin	Streptomyces hygroscopicus subsp. duamyceticus
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001276.3	0.63	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001164.3	0.62	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.62	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001254.3	0.61	PKS	ACT-Toxin II	Alternaria alternata

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (2):

SypG

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

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.19 out of 32.74

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 - 46176:

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

Polymer prediction:: (ccmal) + (Me-ohmal - Me-ohmal) + (ccmal - redmal) + (Asn)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 10063 - 46176:

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

Polymer prediction:: (Me-ohmal - Me-ohmal) + (ccmal - redmal) + (Asn)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07727: mal

PKS_AT (1459..1743): 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: 215.7
inactive: 95.1
Methoxymalonyl-CoA: 66.1
Methylmalonyl-CoA: 65.3
Propionyl-CoA: 51.5
Isobutyryl-CoA: 31.3
Acetyl-CoA: 26.8
2-Methylbutyryl-CoA: 25.9
Ethylmalonyl-CoA: 24.5
Benzoyl-CoA: 17.3
CHC-CoA: 15.8
trans-1,2-CPDA: 15.5
fatty_acid: 13.0
3-Methylbutyryl-CoA: 0.0

CDS_07728: mmal - mmal

PKS_AT (578..878): mmal

ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 200.6
Ethylmalonyl-CoA: 182.0
Methoxymalonyl-CoA: 165.5
2-Methylbutyryl-CoA: 116.6
trans-1,2-CPDA: 112.7
Malonyl-CoA: 108.0
Propionyl-CoA: 99.7
CHC-CoA: 92.0
Isobutyryl-CoA: 75.5
Benzoyl-CoA: 55.8
inactive: 54.7
3-Methylbutyryl-CoA: 54.7
Acetyl-CoA: 40.3
fatty_acid: 24.0

PKS_AT (2130..2429): 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: 204.3
Ethylmalonyl-CoA: 192.2
Methoxymalonyl-CoA: 170.0
trans-1,2-CPDA: 123.5
2-Methylbutyryl-CoA: 118.9
Malonyl-CoA: 103.3
Propionyl-CoA: 103.0
CHC-CoA: 97.4
Isobutyryl-CoA: 65.7
Benzoyl-CoA: 63.9
3-Methylbutyryl-CoA: 46.4
Acetyl-CoA: 46.0
inactive: 38.7
fatty_acid: 26.1

CDS_07729: mal - mal

PKS_AT (568..858): 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: 203.5
inactive: 86.3
Methylmalonyl-CoA: 56.1
Methoxymalonyl-CoA: 55.5
Propionyl-CoA: 34.0
Acetyl-CoA: 27.5
2-Methylbutyryl-CoA: 20.5
Isobutyryl-CoA: 20.3
Benzoyl-CoA: 19.9
Ethylmalonyl-CoA: 15.3
CHC-CoA: 8.5
trans-1,2-CPDA: 6.4
fatty_acid: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (2337..2622): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 79.2%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 202.8
inactive: 91.6
Methylmalonyl-CoA: 61.7
Methoxymalonyl-CoA: 59.9
Propionyl-CoA: 39.3
Isobutyryl-CoA: 28.4
Acetyl-CoA: 25.6
Benzoyl-CoA: 23.2
2-Methylbutyryl-CoA: 22.0
Ethylmalonyl-CoA: 20.1
CHC-CoA: 13.3
fatty_acid: 12.7
trans-1,2-CPDA: 8.5
3-Methylbutyryl-CoA: 5.6

CDS_07730: Asn

Search NORINE for peptide: strict or relaxed

AMP-binding (407..803): 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:: DVTNLIEIGK
Nearest Stachelhaus code(s):: Asn DLTKLGEVGK (59% 8Å match)
Stachelhaus code match:: 60% (weak)

CDS_07732: X

AMP-binding (9..417): 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:: TFCMFGGPSK
Nearest Stachelhaus code(s):: nLev GFCMYGGCSK (79% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_07733: X

AMP-binding (20..424): 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:: TVMFITARIK
Nearest Stachelhaus code(s):: Trp or Pro DVMFIGAVNK (29% 8Å match)
Stachelhaus code match:: 60% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description

NPDC024463.ctg-0038 - Region 1 - azole-containing-RiPP

Download region GenBank file

Download region SVG

Location: 12,036 - 45,533 nt. (total: 33,498 nt) Show pHMM detection rules used

Region on contig edge.

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

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

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 oxidoreductase

CDS_07749: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

CDS_07765: aldehyde oxidase and xanthine dehydrogenase

smcogs: SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

Hydrolases: back translocase hydrolase

CDS_07762: amidohydrolase

smcogs: SMCOG1244: amidohydrolase

CDS_07768: GTP-binding protein LepA

smcogs: SMCOG1190: GTP-binding protein LepA

Lyases: dehydratase

CDS_07755: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

CDS_07756: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001146.5	0.57	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0001145.5	0.54	ribosomal	cyclothiazomycin b1	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5	0.51	ribosomal	cyclothiazomycin	Streptomyces hygroscopicus
BGC0001860.4	0.50	ribosomal	thiomuracin	Thermobispora bispora DSM 43833
BGC0002120.3	0.49	ribosomal	nocathioamide A	Nocardia terpenica IFM 0706
BGC0001753.3	0.48	ribosomal	radamycin, globimycin	Streptomyces globisporus subsp. globisporus
BGC0002144.3	0.48	ribosomal	phazolicin	Rhizobium sp. Pop5
BGC0001640.3	0.48	ribosomal	kocurin	Kocuria rosea
BGC0000607.5	0.47	ribosomal	micrococcin P1	Macrococcus caseolyticus
BGC0001174.4	0.47	ribosomal	corynazolicin	Corynebacterium urealyticum DSM 7111

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001146.5	0.57	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0001145.5	0.54	ribosomal	cyclothiazomycin b1	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5	0.51	ribosomal	cyclothiazomycin	Streptomyces hygroscopicus
BGC0001860.4	0.50	ribosomal	thiomuracin	Thermobispora bispora DSM 43833
BGC0002120.3	0.49	ribosomal	nocathioamide A	Nocardia terpenica IFM 0706
BGC0001753.3	0.48	ribosomal	radamycin, globimycin	Streptomyces globisporus subsp. globisporus
BGC0002144.3	0.48	ribosomal	phazolicin	Rhizobium sp. Pop5
BGC0001640.3	0.48	ribosomal	kocurin	Kocuria rosea
BGC0000607.5	0.47	ribosomal	micrococcin P1	Macrococcus caseolyticus
BGC0001174.4	0.47	ribosomal	corynazolicin	Corynebacterium urealyticum DSM 7111

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: 18.58 out of 23.79

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.68 out of 20.47

Confidence: medium

Additional weak hits (9):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.28 out of 27.78

Confidence: weak

ANR

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

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.15 out of 27.78

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.73 out of 19.26

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.81 out of 27.78

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.80 out of 36.54

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.32 out of 27.18

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.75 out of 27.18

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.10 out of 27.04

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: Thiopeptide_F_RRE; Location: 9 - 88; Score: 60.6; RRE type: Heterocycloanthracin_C_RRE; Location: 8 - 91; Score: 39.5

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

Core peptide predictions

No core peptides found.

NPDC024463.ctg-0040 - Region 1 - T1PKS

Download region GenBank file

Download region SVG

Location: 1 - 41,493 nt. (total: 41,493 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

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: synthase

CDS_07803: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_07804: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_07805: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.74	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.73	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.73	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.73	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0000041.3	0.71	PKS	oronofacic acid	Pseudomonas syringae
BGC0000067.5	0.66	PKS	geldanamycin	Streptomyces hygroscopicus subsp. duamyceticus
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001160.5	0.62	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.62	PKS	1-heptadecene	Cyanothece sp. PCC 7822

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.74	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.73	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.73	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.73	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0000041.3	0.71	PKS	oronofacic acid	Pseudomonas syringae
BGC0000067.5	0.66	PKS	geldanamycin	Streptomyces hygroscopicus subsp. duamyceticus
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001160.5	0.62	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.62	PKS	1-heptadecene	Cyanothece sp. PCC 7822

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):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.34 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.94 out of 29.38

Confidence: weak

Module view

Legend

Detailed Pfam 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 - 41493:

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

Polymer prediction:: (redmal) + (ohmal - Me-ohmal - ccmal) + (redemal - ccmal)
Non-colinear ordering:: CDS_07803 + CDS_07804 + CDS_07805

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07803: mal

PKS_AT (570..870): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 215.0
inactive: 99.5
Methoxymalonyl-CoA: 67.5
Methylmalonyl-CoA: 58.0
Propionyl-CoA: 36.3
Benzoyl-CoA: 31.8
Isobutyryl-CoA: 28.6
Ethylmalonyl-CoA: 26.7
Acetyl-CoA: 20.4
2-Methylbutyryl-CoA: 17.5
CHC-CoA: 17.3
fatty_acid: 13.3
trans-1,2-CPDA: 7.4
3-Methylbutyryl-CoA: 0.0

CDS_07804: mal - mmal - mal

PKS_AT (577..878): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 79.2%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 211.4
inactive: 101.7
Methoxymalonyl-CoA: 59.9
Methylmalonyl-CoA: 45.5
Propionyl-CoA: 30.5
Isobutyryl-CoA: 21.7
Acetyl-CoA: 19.4
Ethylmalonyl-CoA: 15.7
Benzoyl-CoA: 13.7
2-Methylbutyryl-CoA: 11.8
CHC-CoA: 9.7
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (2075..2371): 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: 226.6
Ethylmalonyl-CoA: 219.0
Methoxymalonyl-CoA: 188.3
trans-1,2-CPDA: 148.6
2-Methylbutyryl-CoA: 145.1
CHC-CoA: 116.3
Propionyl-CoA: 110.4
Malonyl-CoA: 98.7
Isobutyryl-CoA: 89.6
Benzoyl-CoA: 74.4
Acetyl-CoA: 53.8
3-Methylbutyryl-CoA: 51.5
fatty_acid: 35.6
inactive: 35.4

PKS_AT (3629..3934): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 209.8
inactive: 86.1
Methoxymalonyl-CoA: 65.2
Methylmalonyl-CoA: 61.1
Propionyl-CoA: 34.1
Isobutyryl-CoA: 27.2
Ethylmalonyl-CoA: 24.0
Acetyl-CoA: 20.8
2-Methylbutyryl-CoA: 15.9
fatty_acid: 15.2
trans-1,2-CPDA: 13.2
CHC-CoA: 13.1
Benzoyl-CoA: 12.4
3-Methylbutyryl-CoA: 0.0

CDS_07805: emal - mal

PKS_AT (575..873): emal

ATSignature: Ethylmalonyl-CoA, Methylmalonyl-CoA, Methoxymalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:

Ethylmalonyl-CoA: 209.1
Methylmalonyl-CoA: 190.3
Methoxymalonyl-CoA: 169.7
trans-1,2-CPDA: 144.3
2-Methylbutyryl-CoA: 140.5
Propionyl-CoA: 116.0
CHC-CoA: 98.3
Malonyl-CoA: 88.5
Benzoyl-CoA: 62.1
Isobutyryl-CoA: 60.3
fatty_acid: 52.9
Acetyl-CoA: 39.6
inactive: 31.7
3-Methylbutyryl-CoA: 31.4

PKS_AT (2645..2951): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 79.2%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 207.3
inactive: 115.1
Methoxymalonyl-CoA: 77.0
Methylmalonyl-CoA: 59.6
Propionyl-CoA: 36.4
Isobutyryl-CoA: 27.3
Ethylmalonyl-CoA: 25.2
2-Methylbutyryl-CoA: 23.5
fatty_acid: 19.6
Benzoyl-CoA: 16.3
CHC-CoA: 15.3
Acetyl-CoA: 14.4
trans-1,2-CPDA: 14.3
3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description

NPDC024463.ctg-0041 - Region 1 - PKS-like,butyrolactone

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Location: 3,702 - 31,898 nt. (total: 28,197 nt) Show pHMM detection rules used

Region on contig edge.

PKS-like: (t2pks2 or ksIII)
butyrolactone: AfsA

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core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

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Gene overview

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TFBS Finder

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

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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_07817: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_07822: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CDS_07823: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

CDS_07827: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

Transferases: acylase transferase

CDS_07831: acetyl-CoA carboxylase, carboxyl transferase,

smcogs: SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

CDS_07832: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: synthase

CDS_07824: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_07826: 3-oxoacyl-(acyl carrier protein) synthase III

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

CDS_07828: 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
BGC0000849.4	0.95	other (butyrolactone)	SCB1, SCB2, SCB3	Streptomyces coelicolor A3(2)
BGC0000848.5	0.94	other (other)	A-factor	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5	0.69	other (other)	γ-butyrolactone	Streptomyces acidiscabies
BGC0000107.3	0.52	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0002276.2	0.50	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000217.5	0.37	PKS	daunorubicin	Streptomyces sp.
BGC0000218.5	0.36	PKS	doxorubicin	Streptomyces peucetius
BGC0002578.2	0.33	other (other)	gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F	Streptomyces venezuelae ATCC 10712
BGC0000013.3	0.33	PKS	alternariol	Aspergillus nidulans FGSC A4
BGC0002504.2	0.32	PKS	nocardiopsistin A, nocardiopsistin B, nocardiopsistin C	Nocardiopsis sp.

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000849.4	0.77	other (butyrolactone)	SCB1, SCB2, SCB3	Streptomyces coelicolor A3(2)
BGC0000848.5	0.77	other (other)	A-factor	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5	0.68	other (other)	γ-butyrolactone	Streptomyces acidiscabies
BGC0000107.3	0.59	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0002276.2	0.58	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000217.5	0.50	PKS	daunorubicin	Streptomyces sp.
BGC0000218.5	0.50	PKS	doxorubicin	Streptomyces peucetius
BGC0002578.2	0.48	other (other)	gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F	Streptomyces venezuelae ATCC 10712
BGC0000013.3	0.47	PKS	alternariol	Aspergillus nidulans FGSC A4
BGC0002504.2	0.47	PKS	nocardiopsistin A, nocardiopsistin B, nocardiopsistin C	Nocardiopsis sp.

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

AfsR

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

Confidence: medium

Additional weak hits (13):

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.77 out of 32.74

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.04 out of 29.38

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.69 out of 29.38

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 21.84

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.35 out of 27.04

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.60 out of 39.62

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

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.56 out of 29.65

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.98 out of 27.04

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.56 out of 35.63

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.63 out of 29.65

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.58 out of 29.65

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

NRPS/PKS substrates

TFBS Finder

NRPS/PKS substrate predictions

CDS_07832: mal

PKS_AT (9..296): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 70.8%; Methoxymalonyl-CoA: 58.3%; Ethylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 72.4
Methoxymalonyl-CoA: 47.5
Methylmalonyl-CoA: 44.1
Propionyl-CoA: 24.2
inactive: 23.9
Isobutyryl-CoA: 22.5
Acetyl-CoA: 19.0
3-Methylbutyryl-CoA: 18.4
2-Methylbutyryl-CoA: 16.5
trans-1,2-CPDA: 14.4
fatty_acid: 11.2
Ethylmalonyl-CoA: 9.6
CHC-CoA: 8.3
Benzoyl-CoA: 5.7

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production

NPDC024463.ctg-0044 - Region 1 - NRPS

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Location: 1 - 19,973 nt. (total: 19,973 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

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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_07888: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.74	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000342.4	0.73	NRPS	enniatin	Fusarium equiseti
BGC0001128.4	0.73	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.72	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.72	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001758.4	0.71	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.70	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.74	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000342.4	0.73	NRPS	enniatin	Fusarium equiseti
BGC0001128.4	0.73	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.72	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.72	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001758.4	0.71	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.70	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae

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 - 19973:

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

Polymer prediction:: (X - Phe - X - NMe-Gly - X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07888: X - Phe - X - Gly - X

Search NORINE for peptide: strict or relaxed

AMP-binding (597..977): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: N/A
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:: DVGQVGAVCK
Nearest Stachelhaus code(s):: Trp DVGMVGAVAK (56% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1638..2012): 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:: Unpolar aromatic ring (Phe, Trp)
Single AA prediction:: phe (Phe)

Stachelhaus prediction details:

Stachelhaus sequence:: DAWTVAAVCK
Nearest Stachelhaus code(s):: Phe DAWTVAAVCK (82% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2672..3047): X

nrpys: OH-Asp, OMe-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:: asn (Asn)

Stachelhaus prediction details:

Stachelhaus sequence:: DLTKIGAVNK
Nearest Stachelhaus code(s):: OH-Asp or OMe-Asp DLTKIGAVNK (88% 8Å match); Asp DLTKIGAVNK (74% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3714..4113): 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:: DIVQLGLVWK
Nearest Stachelhaus code(s):: Gly DILQLGLVWK (76% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (5175..5577): X

nrpys: OH-Asp, OMe-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:: asn (Asn)

Stachelhaus prediction details:

Stachelhaus sequence:: DLTKIGAVNK
Nearest Stachelhaus code(s):: OH-Asp or OMe-Asp DLTKIGAVNK (82% 8Å match); Asp DLTKIGAVNK (74% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

NPDC024463.ctg-0045 - Region 1 - T1PKS

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Location: 1 - 16,836 nt. (total: 16,836 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

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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

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_07891: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: acylase

CDS_07892: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: ligase synthase

CDS_07889: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_07890: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.73	PKS	6-methylsalicyclic acid	Aspergillus terreus
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
BGC0001254.3	0.64	PKS	ACT-Toxin II	Alternaria alternata
BGC0001164.3	0.64	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.64	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001257.3	0.63	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0000107.3	0.63	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0001275.3	0.63	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0002175.3	0.63	PKS	YWA1	Aspergillus oryzae RIB40

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.73	PKS	6-methylsalicyclic acid	Aspergillus terreus
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
BGC0001254.3	0.64	PKS	ACT-Toxin II	Alternaria alternata
BGC0001164.3	0.64	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.64	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001257.3	0.63	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0000107.3	0.63	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0001275.3	0.63	PKS	6-methylsalicyclic acid	Glarea lozoyensis
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.

Module view

Legend

Detailed Pfam 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 - 16836:

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

Polymer prediction:: (Me-ccmal) + (ccmal)
Non-colinear ordering:: CDS_07892 + CDS_07889

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07889: mal

PKS_AT (838..1123): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 100.0%; inactive: 79.2%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 219.9
inactive: 115.2
Methoxymalonyl-CoA: 72.5
Methylmalonyl-CoA: 64.7
Propionyl-CoA: 46.8
Isobutyryl-CoA: 23.0
Ethylmalonyl-CoA: 22.6
Acetyl-CoA: 18.0
fatty_acid: 17.4
Benzoyl-CoA: 13.8
2-Methylbutyryl-CoA: 13.8
CHC-CoA: 7.8
3-Methylbutyryl-CoA: 7.7
trans-1,2-CPDA: 0.0

CDS_07890: Acetyl-CoA

CAL_domain (46..505): Acetyl-CoA

minowa: Acetyl-CoA

Prediction, score:

Acetyl-CoA: 38.7
AHBA: 13.3
fatty_acid: 11.6
NH2: 9.8
shikimic_acid: 0.0

CDS_07892: mmal

PKS_AT (573..874): 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: 214.0
Ethylmalonyl-CoA: 207.9
Methoxymalonyl-CoA: 174.9
2-Methylbutyryl-CoA: 126.4
trans-1,2-CPDA: 122.4
Propionyl-CoA: 106.5
CHC-CoA: 105.8
Malonyl-CoA: 104.1
Isobutyryl-CoA: 92.6
Benzoyl-CoA: 73.1
Acetyl-CoA: 52.3
fatty_acid: 42.2
3-Methylbutyryl-CoA: 41.6
inactive: 35.2

Link to PARAS substrate predictor

NPDC024463.ctg-0048 - Region 1 - NRPS-like

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Location: 1 - 8,799 nt. (total: 8,799 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

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

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: formyltransferase

CDS_07910: methionyl-tRNA formyltransferase

smcogs: SMCOG1228: methionyl-tRNA formyltransferase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.71	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002164.2	0.64	NRPS	peramine	Epichloe festucae
BGC0001261.3	0.64	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.63	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.63	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.62	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.62	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.62	NRPS	AbT1	Aureobasidium pullulans
BGC0001240.4	0.62	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001641.4	0.61	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.71	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002164.2	0.64	NRPS	peramine	Epichloe festucae
BGC0001261.3	0.64	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.63	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.63	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.62	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.62	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.62	NRPS	AbT1	Aureobasidium pullulans
BGC0001240.4	0.62	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001641.4	0.61	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

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

Predicted core structure(s)

For candidate cluster 1, location 0 - 8799:

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

Polymer prediction:: (Gly)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07910: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (569..970): 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)

Link to PARAS substrate predictor

NPDC024463.ctg-0050 - Region 1 - NRPS-like

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Location: 1 - 8,324 nt. (total: 8,324 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

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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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Automatically zoom to filtered/selected features

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

Tailoring functions

Transferases: formyltransferase

CDS_07917: methionyl-tRNA formyltransferase

smcogs: SMCOG1228: methionyl-tRNA formyltransferase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.71	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002164.2	0.64	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
BGC0001128.4	0.62	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.62	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.62	NRPS	AbT1	Aureobasidium pullulans
BGC0001240.4	0.62	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
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	0.64	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
BGC0001128.4	0.62	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.62	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.62	NRPS	AbT1	Aureobasidium pullulans
BGC0001240.4	0.62	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
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:

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.20 out of 26.85

Confidence: medium

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05

Confidence: medium

Additional weak hits (2):

LexA variant 1

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

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.16 out of 26.85

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 1, location 0 - 8324:

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

Polymer prediction:: (Gly)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07917: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (577..969): 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)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
RutR	Regulator of the pyrimidine and purine metabolism

NPDC024463.ctg-0062 - Region 1 - T1PKS

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Location: 1 - 1,988 nt. (total: 1,988 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

Pfam 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: synthase

ctg62_1: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000056.3	0.62	PKS	esperamicin	Actinomadura verrucosospora
BGC0001284.4	0.57	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001244.3	0.57	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001164.3	0.56	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0002154.2	0.56	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001257.3	0.56	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0001276.3	0.56	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001275.3	0.56	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002171.2	0.56	NRPS, PKS	pyrophen, campyrone B	Aspergillus niger ATCC 1015
BGC0002275.2	0.56	NRPS, PKS	pyrophen, campyrone B	Aspergillus niger CBS 101883

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000056.3	0.62	PKS	esperamicin	Actinomadura verrucosospora
BGC0001284.4	0.57	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001244.3	0.57	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001164.3	0.56	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0002154.2	0.56	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001257.3	0.56	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0001276.3	0.56	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001275.3	0.56	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002171.2	0.56	NRPS, PKS	pyrophen, campyrone B	Aspergillus niger ATCC 1015
BGC0002275.2	0.56	NRPS, PKS	pyrophen, campyrone B	Aspergillus niger CBS 101883

Similar known clusters

No significant matches found.

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS substrates

NRPS/PKS substrate predictions

ctg62_1: mal

PKS_AT (318..615): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 75.0%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 171.5
inactive: 94.5
Methoxymalonyl-CoA: 79.3
Methylmalonyl-CoA: 65.0
Propionyl-CoA: 32.0
fatty_acid: 28.3
Isobutyryl-CoA: 25.6
Ethylmalonyl-CoA: 21.5
3-Methylbutyryl-CoA: 18.6
Acetyl-CoA: 16.6
trans-1,2-CPDA: 14.9
2-Methylbutyryl-CoA: 6.8
CHC-CoA: 0.0
Benzoyl-CoA: 0.0

Link to PARAS substrate predictor