Actinosynnema_pretiosum_DSM_44132 - 37 region(s)

Identified secondary metabolite regions using strictness 'relaxed'

JAMTCF010000001.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 1.1	nucleoside	78,900	99,889	Medium	tunicamycin B1	other:nucleoside
Region 1.2	NRP-metallophore,NRPS	176,616	237,320	High	mirubactin	NRPS:Type I
Region 1.3	T1PKS	238,253	345,974	High	salinilactam	PKS
Region 1.4	betalactone	371,039	398,898
Region 1.5	ectoine	527,812	538,186
Region 1.6	hglE-KS,T1PKS,NRPS-like	614,212	673,439

JAMTCF010000002.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 2.1	terpene	70,333	92,582	High	geosmin	terpene:Sesquiterpene
Region 2.2	lanthipeptide-class-iii	426,605	449,169	Low	Ery-9/Ery-6/Ery-8/Ery-7/Ery-5/Ery-4/Ery-3	ribosomal:RiPP:Lanthipeptide
Region 2.3	terpene-precursor	513,795	534,865	Low	isorenieratene	terpene

JAMTCF010000005.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 5.1	T1PKS	1	84,258	High	sceliphrolactam	PKS
Region 5.2	lassopeptide,T1PKS,terpene	176,438	273,813	Medium	streptazone E	PKS
Region 5.3	T1PKS	281,438	347,793

JAMTCF010000006.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 6.1	opine-like-metallophore,PKS-like,2dos,NRPS	81,038	167,240	Low	rubiginone A2/rubiginone J/rubiginone K/rubiginone L/rubiginone M/rubiginone N/ochromycinone/rubiginone B2	PKS
Region 6.2	T1PKS	215,735	273,269
Region 6.3	T1PKS	314,162	359,921

JAMTCF010000008.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 8.1	RiPP-like	28,211	39,008

JAMTCF010000010.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 10.1	NRPS,azoxy-crosslink,nucleoside	159,309	311,234	High	detoxin P1/detoxin P2/detoxin P3	NRPS:Type I+PKS

JAMTCF010000011.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 11.1	hydrogen-cyanide	233,248	246,064
Region 11.2	bottromycin	257,937	278,755	High	bottromycin A2	ribosomal:RiPP:Bottromycin

JAMTCF010000013.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 13.1	indole	229,016	250,137

JAMTCF010000014.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 14.1	thioamitides	5,085	27,506
Region 14.2	NRPS	255,406	282,679

JAMTCF010000015.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 15.1	T1PKS,NRPS,NRPS-like	1	101,437	High	maytansine/ansamitocin P-3	PKS
Region 15.2	T1PKS,NRPS-like	140,262	222,826	High	macbecin/macbecin II	PKS
Region 15.3	lassopeptide	239,368	261,831	Low	felipeptin A2/felipeptin A1	ribosomal:RiPP

JAMTCF010000016.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 16.1	CDPS	4,493	25,194
Region 16.2	NRPS,T1PKS,betalactone,crocagin	67,564	198,804	High	tomaymycin	NRPS:Type I

JAMTCF010000018.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 18.1	azole-containing-RiPP	45,073	72,136
Region 18.2	terpene	96,062	132,801	High	isorenieratene	terpene

JAMTCF010000019.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 19.1	lanthipeptide-class-ii	12,486	35,623

JAMTCF010000021.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 21.1	NRP-metallophore,NRPS	1	37,911	High	saccharochelin A/saccharochelin B/saccharochelin C/saccharochelin D/saccharochelin E/saccharochelin F/saccharochelin G/saccharochelin H	NRPS:Type I
Region 21.2	T1PKS,NRPS	65,780	113,446

JAMTCF010000023.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 23.1	NRPS	21,685	66,052	Low	SF2768	NRPS:Type I

JAMTCF010000026.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 26.1	terpene	1	13,129

JAMTCF010000028.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 28.1	terpene-precursor	34,697	55,737

JAMTCF010000034.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 34.1	NRPS,T1PKS	3,784	51,981	Low	amipurimycin	PKS

JAMTCF010000041.1 (Actinosynnema pretiosum)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 41.1	lassopeptide	1	9,793

No secondary metabolite regions were found in these records:: JAMTCF010000003.1 (Actinosynnema pretiosum); JAMTCF010000004.1 (Actinosynnema pretiosum); JAMTCF010000007.1 (Actinosynnema pretiosum); JAMTCF010000009.1 (Actinosynnema pretiosum); JAMTCF010000012.1 (Actinosynnema pretiosum); JAMTCF010000017.1 (Actinosynnema pretiosum); JAMTCF010000020.1 (Actinosynnema pretiosum); JAMTCF010000022.1 (Actinosynnema pretiosum); JAMTCF010000024.1 (Actinosynnema pretiosum); JAMTCF010000025.1 (Actinosynnema pretiosum); JAMTCF010000027.1 (Actinosynnema pretiosum); JAMTCF010000029.1 (Actinosynnema pretiosum); JAMTCF010000030.1 (Actinosynnema pretiosum); JAMTCF010000031.1 (Actinosynnema pretiosum); JAMTCF010000032.1 (Actinosynnema pretiosum); JAMTCF010000033.1 (Actinosynnema pretiosum); JAMTCF010000035.1 (Actinosynnema pretiosum); JAMTCF010000036.1 (Actinosynnema pretiosum); JAMTCF010000037.1 (Actinosynnema pretiosum); JAMTCF010000038.1 (Actinosynnema pretiosum); JAMTCF010000039.1 (Actinosynnema pretiosum); JAMTCF010000040.1 (Actinosynnema pretiosum); JAMTCF010000042.1 (Actinosynnema pretiosum); JAMTCF010000043.1 (Actinosynnema pretiosum); JAMTCF010000044.1 (Actinosynnema pretiosum)

Compact view

JAMTCF010000001.1 - Region 1 - nucleoside

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Location: 78,900 - 99,889 nt. (total: 20,990 nt) Show pHMM detection rules used

nucleoside: (LipM or LipV or LipU or TunD or pur6 or pur10 or nikJ or nikO or truD)

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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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: glycosyltransferase methyltransferase

LV78_000069: glycosyl transferase group 1

smcogs: SMCOG1045: glycosyl transferase group 1

LV78_000073: methyltransferase

smcogs: SMCOG1089: methyltransferase

Lyases: dehydratase

LV78_000067: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

LV78_000072: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000880.4	0.69	other (nucleoside)	tunicamycin B1	Streptomyces chartreusis NRRL 3882
BGC0000786.3	0.46	saccharide	O-antigen	Edwardsiella ictaluri 93-146
BGC0000707.5	0.45	saccharide	kasugamycin	Streptomyces kasugaensis
BGC0000777.3	0.45	saccharide	lipopolysaccharide	Escherichia coli
BGC0002553.2	0.45	other (other)	tunicamycin	Rathayibacter iranicus
BGC0000916.5	0.43	other (other)	molybdenum cofactor	Staphylococcus carnosus
BGC0002316.2	0.43	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0000778.3	0.42	saccharide	lipopolysaccharide	Aeromonas piscicola
BGC0001374.5	0.42	other (other)	thienodolin	Streptomyces albogriseolus
BGC0001927.4	0.42	other (other)	A-94964	Streptomyces sp.

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000880.4	0.69	other (nucleoside)	tunicamycin B1	Streptomyces chartreusis NRRL 3882
BGC0000786.3	0.46	saccharide	O-antigen	Edwardsiella ictaluri 93-146
BGC0000707.5	0.45	saccharide	kasugamycin	Streptomyces kasugaensis
BGC0000777.3	0.45	saccharide	lipopolysaccharide	Escherichia coli
BGC0002553.2	0.45	other (other)	tunicamycin	Rathayibacter iranicus
BGC0000916.5	0.43	other (other)	molybdenum cofactor	Staphylococcus carnosus
BGC0002316.2	0.43	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0000778.3	0.42	saccharide	lipopolysaccharide	Aeromonas piscicola
BGC0001374.5	0.42	other (other)	thienodolin	Streptomyces albogriseolus
BGC0001927.4	0.42	other (other)	A-94964	Streptomyces sp.

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):

MatP

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

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.37 out of 19.26

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

JAMTCF010000001.1 - Region 2 - NRP-metallophore,NRPS

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Location: 176,616 - 237,320 nt. (total: 60,705 nt) Show pHMM detection rules used

NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

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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

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

LV78_000168: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

LV78_000183: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

Hydrolases: hydrolase

LV78_000171: isochorismatase

smcogs: SMCOG1027: isochorismatase

LV78_000189: metallo-beta-lactamase family protein

smcogs: SMCOG1170: metallo-beta-lactamase family protein

Isomerases: isomerase

LV78_000169: isochorismate synthase

smcogs: SMCOG1018: isochorismate synthase

Ligases: ligase

LV78_000170: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_000178: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000392.5	1.01	NRPS	mirubactin	Actinosynnema mirum DSM 43827
BGC0000357.5	0.69	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
BGC0001825.4	0.61	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001135.5	0.60	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.58	NRPS	HC-toxin	Alternaria jesenskae
BGC0000307.4	0.58	NRPS	AbT1	Aureobasidium pullulans
BGC0000343.5	0.58	NRPS	enterobactin	Pseudomonas sp. J465
BGC0001261.3	0.57	NRPS	AM-toxin	Alternaria alternata
BGC0001758.4	0.57	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.56	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000392.5	0.79	NRPS	mirubactin	Actinosynnema mirum DSM 43827
BGC0000357.5	0.67	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
BGC0001825.4	0.64	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.63	NRPS	HC-toxin	Alternaria jesenskae
BGC0000307.4	0.63	NRPS	AbT1	Aureobasidium pullulans
BGC0000343.5	0.62	NRPS	enterobactin	Pseudomonas sp. J465
BGC0001261.3	0.62	NRPS	AM-toxin	Alternaria alternata
BGC0001758.4	0.62	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.62	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: medium

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 24.49 out of 29.65

Confidence: medium

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.73 out of 36.53

Confidence: medium

DmdR1

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

Confidence: medium

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 27.53 out of 30.11

Confidence: strong

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.56 out of 30.11

Confidence: medium

Additional weak hits (12):

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.15 out of 20.97

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.85 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.83 out of 32.74

Confidence: weak

ZuR variant 1

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

Confidence: weak

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 17.94 out of 23.05

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.87 out of 21.55

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.34 out of 30.22

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 20.95 out of 36.53

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 23.05 out of 33.73

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.35 out of 29.38

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.91 out of 25.88

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.15 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 176615 - 237320:

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

Polymer prediction:: (D-Arg - D-Fo-OH-Orn)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

LV78_000170: diOH-Bz

Search NORINE for peptide: strict or relaxed

AMP-binding (62..472): diOH-Bz

nrpys: diOH-Bz

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
Small clusters prediction:: Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
Single AA prediction:: dhb (diOH-Bz)

Stachelhaus prediction details:

Stachelhaus sequence:: PMPGLGVVCK
Nearest Stachelhaus code(s):: diOH-Bz PMPGLGVVCK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

LV78_000178: Arg - Fo-OH-Orn

Search NORINE for peptide: strict or relaxed

AMP-binding (489..883): Arg

nrpys: Arg

SVM prediction details:

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

Stachelhaus prediction details:

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

AMP-binding (2112..2508): Fo-OH-Orn

nrpys: Fo-OH-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:: DVWNVGAVNK
Nearest Stachelhaus code(s):: Fo-OH-Orn DVWNVGAVNK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CelR	Cellobiose uptake repressor
DmdR1	Iron(II)-dependent repressor
LexA variant 1	Repressor of DNA damage response
VqsM	Regulator of quorum-sensing signalling systems

JAMTCF010000001.1 - Region 3 - T1PKS

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Location: 238,253 - 345,974 nt. (total: 107,722 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: dehydrogenase oxygenase

LV78_000212: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

LV78_000233: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

Transferases: acylase aminotransferase

LV78_000214: aminotransferase

smcogs: SMCOG1019: aminotransferase

LV78_000215: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

LV78_000221: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase hydrolase

LV78_000219: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

LV78_000226: thioesterase

smcogs: SMCOG1004: thioesterase

Ligases: ligase synthase

LV78_000210: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_000216: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_000217: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_000220: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_000222: Beta-ketoacyl synthase

smcogs: SMCOG1093: 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
BGC0001276.3	0.74	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.74	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0000142.3	0.65	PKS	salinilactam	Salinispora tropica CNB-440
BGC0000041.3	0.64	PKS	oronofacic acid	Pseudomonas syringae
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
BGC0002154.2	0.63	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001257.3	0.63	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245

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
BGC0001276.3	0.74	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.74	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0000142.3	0.65	PKS	salinilactam	Salinispora tropica CNB-440
BGC0000041.3	0.64	PKS	oronofacic acid	Pseudomonas syringae
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
BGC0002154.2	0.63	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001257.3	0.63	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245

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

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.16 out of 27.78

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.27 out of 23.79

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.60 out of 23.79

Confidence: medium

Additional weak hits (64):

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.85 out of 20.01

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.01 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.49 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.29 out of 28.14

Confidence: weak

CopR

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

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.00 out of 29.38

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.00 out of 27.78

Confidence: weak

MexT

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

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.09 out of 30.25

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.09 out of 32.74

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.00 out of 30.97

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 20.18 out of 31.73

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.28 out of 19.26

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.31 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.67 out of 28.19

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.61 out of 23.43

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.12 out of 26.85

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.24 out of 26.12

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.09 out of 27.78

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.20 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.42 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.99 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.70 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.54 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.56 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.06 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.37 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.79 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.33 out of 28.14

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.17 out of 18.57

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.91 out of 18.57

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.08 out of 30.97

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.75 out of 26.06

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.25 out of 30.97

Confidence: weak

MogR

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.86 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.76 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.32 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.58 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.88 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.06 out of 31.73

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.17 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

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.18 out of 27.78

Confidence: weak

MogR

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

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.11 out of 27.78

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.84 out of 29.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.66 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.26 out of 27.78

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.92 out of 28.14

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.44 out of 27.78

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.71 out of 28.14

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.37 out of 31.73

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.69 out of 25.88

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.01 out of 29.38

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.12 out of 27.55

Confidence: weak

ColR

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

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.68 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.29 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.67 out of 28.19

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.70 out of 36.53

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.51 out of 26.06

Confidence: weak

MntR

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

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 3, location 238252 - 345974:

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

Polymer prediction:: (ccmal - Me-ccmal - Me-ccmal - ccmal) + (ccmal) + (ohmal - ohmal) + (Me-ohmal) + (ccmal - ccmal - ccmal)
Non-colinear ordering:: LV78_000210 + LV78_000223 + LV78_000222 + LV78_000221 + LV78_000220

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

LV78_000210: mal - mmal - mmal - mal

PKS_AT (672..973): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 79.2%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 198.5
inactive: 107.0
Methoxymalonyl-CoA: 56.2
Methylmalonyl-CoA: 41.6
Isobutyryl-CoA: 28.6
Acetyl-CoA: 22.1
Propionyl-CoA: 17.9
Ethylmalonyl-CoA: 16.8
Benzoyl-CoA: 11.9
2-Methylbutyryl-CoA: 4.6
CHC-CoA: 1.6
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (2410..2705): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 95.8%; Methoxymalonyl-CoA: 91.7%; Malonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 188.3
Ethylmalonyl-CoA: 186.0
Methoxymalonyl-CoA: 153.5
trans-1,2-CPDA: 119.6
2-Methylbutyryl-CoA: 104.6
CHC-CoA: 87.0
Propionyl-CoA: 80.0
Malonyl-CoA: 78.9
Isobutyryl-CoA: 63.4
3-Methylbutyryl-CoA: 50.0
Benzoyl-CoA: 47.9
Acetyl-CoA: 42.0
fatty_acid: 41.7
inactive: 20.1

PKS_AT (4133..4428): 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: 211.3
Ethylmalonyl-CoA: 203.5
Methoxymalonyl-CoA: 172.1
trans-1,2-CPDA: 134.9
2-Methylbutyryl-CoA: 125.9
Malonyl-CoA: 97.1
CHC-CoA: 95.6
Propionyl-CoA: 90.9
Isobutyryl-CoA: 80.6
Benzoyl-CoA: 52.9
3-Methylbutyryl-CoA: 47.3
Acetyl-CoA: 36.0
fatty_acid: 28.3
inactive: 21.1

PKS_AT (5845..6136): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 79.2%; Isobutyryl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 187.7
inactive: 90.2
Methoxymalonyl-CoA: 64.9
Methylmalonyl-CoA: 62.1
Propionyl-CoA: 58.7
Isobutyryl-CoA: 31.8
Ethylmalonyl-CoA: 31.7
2-Methylbutyryl-CoA: 26.1
fatty_acid: 22.1
Acetyl-CoA: 20.7
Benzoyl-CoA: 20.3
CHC-CoA: 10.9
trans-1,2-CPDA: 6.1
3-Methylbutyryl-CoA: 0.0

LV78_000215: pk

PKS_AT (46..267): 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

LV78_000216: X

AMP-binding (18..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:: 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:: DCFFLAIITK
Nearest Stachelhaus code(s):: Ala DCFFFALITK (79% 8Å match); bMe-Asp DCFFFALITK (74% 8Å match)
Stachelhaus code match:: 80% (moderate)

LV78_000217: X

AMP-binding (23..432): X

nrpys: Val, Leu, Ile, Abu, Ival

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: 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:: DFLDLSCVAK
Nearest Stachelhaus code(s):: Gly DILQLGCVWK (44% 8Å match); Ile or Val DFLCLGVVIK (38% 8Å match)
Stachelhaus code match:: 60% (weak)

LV78_000220: mal - mal - mal

PKS_AT (564..851): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 70.8%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 211.0
inactive: 101.1
Methoxymalonyl-CoA: 64.0
Methylmalonyl-CoA: 58.5
Propionyl-CoA: 28.6
Isobutyryl-CoA: 28.4
Ethylmalonyl-CoA: 28.0
Benzoyl-CoA: 23.6
2-Methylbutyryl-CoA: 21.2
Acetyl-CoA: 17.1
CHC-CoA: 11.9
trans-1,2-CPDA: 8.3
fatty_acid: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (2238..2524): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 209.6
inactive: 102.8
Methoxymalonyl-CoA: 64.8
Methylmalonyl-CoA: 57.4
Propionyl-CoA: 37.3
Isobutyryl-CoA: 29.7
Ethylmalonyl-CoA: 25.6
Benzoyl-CoA: 21.0
Acetyl-CoA: 17.5
trans-1,2-CPDA: 13.4
fatty_acid: 8.7
CHC-CoA: 7.2
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: -1.0

PKS_AT (3921..4199): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 208.0
inactive: 91.4
Methoxymalonyl-CoA: 69.0
Methylmalonyl-CoA: 57.0
Propionyl-CoA: 38.0
Isobutyryl-CoA: 34.8
Ethylmalonyl-CoA: 31.0
Benzoyl-CoA: 24.0
Acetyl-CoA: 19.4
CHC-CoA: 12.7
fatty_acid: 11.1
trans-1,2-CPDA: 8.1
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: -0.3

LV78_000221: mmal

PKS_AT (551..847): mmal

ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 191.8
Ethylmalonyl-CoA: 182.5
Methoxymalonyl-CoA: 157.5
2-Methylbutyryl-CoA: 118.9
trans-1,2-CPDA: 100.9
Isobutyryl-CoA: 91.2
Propionyl-CoA: 86.5
Malonyl-CoA: 85.8
CHC-CoA: 70.6
Benzoyl-CoA: 64.1
Acetyl-CoA: 59.8
3-Methylbutyryl-CoA: 54.6
inactive: 28.2
fatty_acid: 10.9

LV78_000222: mal - mal

PKS_AT (549..838): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 70.8%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 207.6
inactive: 90.0
Methoxymalonyl-CoA: 61.1
Methylmalonyl-CoA: 51.4
Propionyl-CoA: 40.5
Isobutyryl-CoA: 26.1
Ethylmalonyl-CoA: 23.9
Acetyl-CoA: 22.8
Benzoyl-CoA: 22.4
fatty_acid: 8.8
CHC-CoA: 7.4
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: -2.9

PKS_AT (2056..2327): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 209.1
inactive: 95.1
Methoxymalonyl-CoA: 62.2
Methylmalonyl-CoA: 51.8
Propionyl-CoA: 44.2
Isobutyryl-CoA: 26.8
Acetyl-CoA: 23.7
Ethylmalonyl-CoA: 23.1
2-Methylbutyryl-CoA: 21.5
Benzoyl-CoA: 21.1
fatty_acid: 11.8
CHC-CoA: 10.6
trans-1,2-CPDA: 10.2
3-Methylbutyryl-CoA: 0.0

LV78_000223: mal

PKS_AT (567..853): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 70.8%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 200.5
inactive: 87.5
Methoxymalonyl-CoA: 55.9
Methylmalonyl-CoA: 46.9
Propionyl-CoA: 27.6
Acetyl-CoA: 22.4
Benzoyl-CoA: 18.3
Ethylmalonyl-CoA: 15.4
2-Methylbutyryl-CoA: 15.3
Isobutyryl-CoA: 14.3
CHC-CoA: 7.3
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
3-Methylbutyryl-CoA: 0.0

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
IolR	Regulator of the inositol catabolism

JAMTCF010000001.1 - Region 4 - betalactone

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Location: 371,039 - 398,898 nt. (total: 27,860 nt) Show pHMM detection rules used

betalactone: (HMGL-like and AMP-binding)

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core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

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TTA codons

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Gene details

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Gene overview

Tailoring

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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

Oxidoreductases: dehydrogenase phosphate reductase

LV78_000266: N-acetyl-gamma-glutamyl-phosphate reductase

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

LV78_000273: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

LV78_000274: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

Transferases: aminotransferase kinase

LV78_000267: acetylglutamate kinase

smcogs: SMCOG1174: acetylglutamate kinase

LV78_000271: aminotransferase

smcogs: SMCOG1019: aminotransferase

Ligases: ligase synthase

LV78_000263: 2-isopropylmalate synthase

smcogs: SMCOG1271: 2-isopropylmalate synthase

LV78_000270: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.56	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001166.5	0.55	NRPS	HC-toxin	Alternaria jesenskae
BGC0001833.4	0.55	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.55	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001641.4	0.55	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.55	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.55	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.55	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.55	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0000131.5	0.45	PKS	pyrrolomycin	Streptomyces sp. UC 11065

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.56	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001166.5	0.55	NRPS	HC-toxin	Alternaria jesenskae
BGC0001833.4	0.55	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.55	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001641.4	0.55	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.55	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.55	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.55	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.55	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0000131.5	0.45	PKS	pyrrolomycin	Streptomyces sp. UC 11065

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: 16.75 out of 20.97

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.74 out of 20.97

Confidence: medium

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.67 out of 20.97

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.63 out of 28.19

Confidence: medium

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.84 out of 30.12

Confidence: medium

Additional weak hits (12):

ClgR

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

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.95 out of 25.88

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.15 out of 30.25

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: 14.96 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.12 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.24 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.11 out of 27.78

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

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.64 out of 27.04

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 18.77 out of 33.73

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

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
CcpA	Catabolite control protein A
MexT	Global virulence regulator
OsdR	Development and stress management regulator
ZuR variant 1	Zinc-responsive repressor

JAMTCF010000001.1 - Region 5 - ectoine

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Location: 527,812 - 538,186 nt. (total: 10,375 nt) Show pHMM detection rules used

ectoine: ectoine_synt

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Hydrolases: hydrolase

LV78_000403: HAD-superfamily hydrolase, subfamily IA, variant

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

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000859.3	0.50	other (other)	ectoine	Methylomicrobium alcaliphilum
BGC0000855.3	0.49	other (other)	ectoine	Methylomicrobium kenyense
BGC0000856.3	0.49	other (other)	ectoine	Methylophaga thalassica
BGC0000857.3	0.49	other (other)	ectoine	Methylophaga alcalica
BGC0000860.3	0.48	other (other)	ectoine	Methylarcula marina
BGC0000375.5	0.46	NRPS	indigoidine	Streptomyces chromofuscus
BGC0002295.3	0.46	NRPS, saccharide	minimycin, indigoidine	Streptomyces hygroscopicus
BGC0000854.3	0.43	other (other)	ectoine	Methylomicrobium alcaliphilum 20Z
BGC0001778.5	0.41	other (other)	showdomycin	Streptomyces showdoensis
BGC0002301.2	0.36	PKS	(P)-ustilaginoidin A	Aschersonia paraphysata

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000859.3	0.50	other (other)	ectoine	Methylomicrobium alcaliphilum
BGC0000855.3	0.49	other (other)	ectoine	Methylomicrobium kenyense
BGC0000856.3	0.49	other (other)	ectoine	Methylophaga thalassica
BGC0000857.3	0.49	other (other)	ectoine	Methylophaga alcalica
BGC0000860.3	0.48	other (other)	ectoine	Methylarcula marina
BGC0000375.5	0.46	NRPS	indigoidine	Streptomyces chromofuscus
BGC0002295.3	0.46	NRPS, saccharide	minimycin, indigoidine	Streptomyces hygroscopicus
BGC0000854.3	0.43	other (other)	ectoine	Methylomicrobium alcaliphilum 20Z
BGC0001778.5	0.41	other (other)	showdomycin	Streptomyces showdoensis
BGC0002301.2	0.36	PKS	(P)-ustilaginoidin A	Aschersonia paraphysata

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

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.84 out of 29.51

Confidence: medium

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.66 out of 23.43

Confidence: medium

Additional weak hits (2):

ANR

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

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.75 out of 23.43

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
BldD	Development and antibiotic global regulator
DosR	Hypoxia stress response regulator
VqsM	Regulator of quorum-sensing signalling systems

JAMTCF010000001.1 - Region 6 - NRPS-like,T1PKS,hglE-KS

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Location: 614,212 - 673,439 nt. (total: 59,228 nt) Show pHMM detection rules used

hglE-KS: (hglE or hglD)
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

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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

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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

LV78_000459: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

LV78_000476: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: glycosyltransferase

LV78_000469: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

Hydrolases: hydrolase

LV78_000470: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase synthase

LV78_000472: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_000473: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_000475: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	1.17	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002164.2	0.97	NRPS	peramine	Epichloe festucae
BGC0001135.5	0.92	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001261.3	0.92	NRPS	AM-toxin	Alternaria alternata
BGC0001132.4	0.90	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.88	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001276.3	0.88	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001273.3	0.88	PKS	asperlactone	Aspergillus ochraceus
BGC0002286.3	0.88	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001275.3	0.87	PKS	6-methylsalicyclic acid	Glarea lozoyensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.71	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002164.2	0.66	NRPS	peramine	Epichloe festucae
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001261.3	0.64	NRPS	AM-toxin	Alternaria alternata
BGC0001132.4	0.64	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.63	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001276.3	0.63	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001273.3	0.63	PKS	asperlactone	Aspergillus ochraceus
BGC0002286.3	0.63	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001275.3	0.63	PKS	6-methylsalicyclic acid	Glarea lozoyensis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.85 out of 23.79

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.31 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

VqsM

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

Confidence: medium

Additional weak hits (29):

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 21.81 out of 30.97

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.35 out of 30.97

Confidence: weak

ColR

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

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 26.33

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.32 out of 21.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.76 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.26 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.65 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.24 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.82 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.11 out of 30.25

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.57 out of 28.14

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: 17.67 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.83 out of 30.25

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.17 out of 32.93

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.39 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

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.07 out of 32.38

Confidence: weak

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.24 out of 32.38

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.77 out of 23.43

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.53 out of 25.88

Confidence: weak

CsoR

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

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.91 out of 32.93

Confidence: weak

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.30 out of 32.38

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.62 out of 26.85

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.54 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 6, location 614211 - 673439:

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

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 614211 - 665733:

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

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 8, location 631657 - 673439:

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

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

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

LV78_000472: pk

PKS_AT (601..807): pk

ATSignature: (unknown)

No matches above 50%

minowa: inactive

Prediction, score:

inactive: 16.5
3-Methylbutyryl-CoA: 9.0
Malonyl-CoA: 4.8
Methylmalonyl-CoA: 0.1
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Propionyl-CoA: 0.0
Methoxymalonyl-CoA: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

LV78_000473: mal

PKS_AT (1262..1551): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 70.8%; inactive: 62.5%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 81.1
Methoxymalonyl-CoA: 35.6
Methylmalonyl-CoA: 28.2
inactive: 27.3
CHC-CoA: 10.5
2-Methylbutyryl-CoA: 10.3
Benzoyl-CoA: 9.8
Propionyl-CoA: 8.5
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

LV78_000475: X

AMP-binding (10..391): X

nrpys: (unknown)

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DAWSVGAVCK
Nearest Stachelhaus code(s):: Trp DAWSVGSVCK (65% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
CcpA	Catabolite control protein A
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

JAMTCF010000002.1 - Region 1 - terpene

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Location: 70,333 - 92,582 nt. (total: 22,250 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

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SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

LV78_000719: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

Lyases: cyclase

LV78_000714: Terpene synthase/cyclase metal-binding domain protein

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

Translocases: transporter

LV78_000707: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001181.4	0.81	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0001364.3	0.37	ribosomal	cinnamycin B	Actinomadura atramentaria DSM 43919
BGC0002690.2	0.35	other (other)	FW0622	Verrucosispora sp. FIM060022
BGC0002285.2	0.35	ribosomal	aborycin	Streptomyces sp. ZS0098
BGC0001810.3	0.33	PKS	trehangelin	Polymorphospora rubra
BGC0000821.5	0.33	other (other)	rebeccamycin	Lechevalieria aerocolonigenes
BGC0001735.5	0.33	other (other)	pentostatine, vidarabine	Streptomyces antibioticus
BGC0000495.5	0.33	ribosomal	actagardine	Actinoplanes garbadinensis
BGC0002697.3	0.31	NRPS, PKS	clipibicyclene, azabicyclene B, azabicyclene C, azabicyclene D	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001647.3	0.31	PKS	lagunapyrone A, lagunapyrone B, lagunapyrone C	Streptomyces sp. MP131-18

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001181.4	0.81	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0001364.3	0.37	ribosomal	cinnamycin B	Actinomadura atramentaria DSM 43919
BGC0002690.2	0.35	other (other)	FW0622	Verrucosispora sp. FIM060022
BGC0002285.2	0.35	ribosomal	aborycin	Streptomyces sp. ZS0098
BGC0001810.3	0.33	PKS	trehangelin	Polymorphospora rubra
BGC0000821.5	0.33	other (other)	rebeccamycin	Lechevalieria aerocolonigenes
BGC0001735.5	0.33	other (other)	pentostatine, vidarabine	Streptomyces antibioticus
BGC0000495.5	0.33	ribosomal	actagardine	Actinoplanes garbadinensis
BGC0002697.3	0.31	NRPS, PKS	clipibicyclene, azabicyclene B, azabicyclene C, azabicyclene D	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001647.3	0.31	PKS	lagunapyrone A, lagunapyrone B, lagunapyrone C	Streptomyces sp. MP131-18

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:

LV78_000714: T1TS + T1TS

Domain 1 (2 - 329): Type 1 terpene synthase

Subtype: Geosmin synthase, N terminal domain

Reactions:: FPP → germacradienol

Domain 2 (330 - 699): Type 1 terpene synthase

Subtype: Geosmin synthase, C terminal domain

Reactions:: germacradienol → geosmin

Transcription Factor Binding Sites

Binding sites found:

OsdR

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

Confidence: medium

Additional weak hits (7):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.54 out of 21.55

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.67 out of 26.33

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.10 out of 20.01

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.90 out of 30.22

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.87 out of 32.74

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.38 out of 28.19

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.55 out of 27.18

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
FPP	Farnesyl diphosphate

TFBS definitions

Regulator	Description
OsdR	Development and stress management regulator

JAMTCF010000002.1 - Region 2 - lanthipeptide-class-iii

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Location: 426,605 - 449,169 nt. (total: 22,565 nt) Show pHMM detection rules used

lanthipeptide-class-iii: (micKC and not PKS_KS)

Legend:

core biosynthetic genes

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resistance

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Gene overview

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MIBiG comparison

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Lanthipeptides

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: oxidoreductase

LV78_001031: pyridine nucleotide-disulfide oxidoreductase

smcogs: SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: acylase

LV78_001043: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: synthase

LV78_001040: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_001042: 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
BGC0000551.5	0.60	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000496.5	0.59	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3	0.58	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0001164.3	0.58	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.57	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0000519.4	0.57	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000501.3	0.57	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0002698.2	0.51	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0000518.3	0.49	ribosomal	informatipeptin	Streptomyces viridochromogenes DSM 40736
BGC0002700.2	0.49	ribosomal	bacinapeptin	Bacillus nakamurai

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000551.5	0.60	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000496.5	0.59	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3	0.58	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0001164.3	0.58	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.57	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0000519.4	0.57	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000501.3	0.57	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0002698.2	0.51	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0000518.3	0.49	ribosomal	informatipeptin	Streptomyces viridochromogenes DSM 40736
BGC0002700.2	0.49	ribosomal	bacinapeptin	Bacillus nakamurai

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:

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.59 out of 23.05

Confidence: medium

Additional weak hits (11):

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.35 out of 26.85

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.27 out of 19.26

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.26 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.51 out of 26.06

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.99 out of 26.33

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: 19.63 out of 29.38

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.39 out of 25.88

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.89 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.14 out of 31.73

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.14 out of 35.63

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lanthipeptides

TFBS Finder

Core peptide predictions

No core peptides found.

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production

JAMTCF010000002.1 - Region 3 - terpene-precursor

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Location: 513,795 - 534,865 nt. (total: 21,071 nt) Show pHMM detection rules used

terpene-precursor: (PT_FPPS_like and not PT_HPP)

Legend:

core biosynthetic genes

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Select a gene to view the details available for it

Gene overview

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MIBiG comparison

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KnownClusterBlast

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Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

LV78_001116: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

Lyases: decarboxylase

LV78_001119: putative carboxymuconolactone decarboxylase

smcogs: SMCOG1298: putative carboxymuconolactone decarboxylase

Ligases: synthetase

LV78_001117: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001456.3	0.47	terpene	isorenieratene	Streptomyces argillaceus
BGC0000664.5	0.46	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3	0.44	terpene	carotenoid	Streptomyces avermitilis
BGC0001227.3	0.44	terpene	isorenieratene	Streptomyces collinus Tu 365
BGC0000677.5	0.43	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0000649.3	0.43	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000648.3	0.40	terpene	carotenoid	Myxococcus xanthus
BGC0001911.3	0.38	terpene	raimonol	Streptomyces anulatus
BGC0002309.2	0.37	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000936.5	0.37	other (other)	pyocyanine	Pseudomonas aeruginosa PAO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001456.3	0.47	terpene	isorenieratene	Streptomyces argillaceus
BGC0000664.5	0.46	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3	0.44	terpene	carotenoid	Streptomyces avermitilis
BGC0001227.3	0.44	terpene	isorenieratene	Streptomyces collinus Tu 365
BGC0000677.5	0.43	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0000649.3	0.43	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000648.3	0.40	terpene	carotenoid	Myxococcus xanthus
BGC0001911.3	0.38	terpene	raimonol	Streptomyces anulatus
BGC0002309.2	0.37	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000936.5	0.37	other (other)	pyocyanine	Pseudomonas aeruginosa PAO1

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:

LV78_001117: PT_FPPS_like

Domain 1 (46 - 349): 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: 18.07 out of 20.47

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.02 out of 26.85

Confidence: medium

LexA variant 1

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

Confidence: medium

Additional weak hits (4):

ColR

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

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.09 out of 30.11

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.78 out of 29.38

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.72 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

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
LexA variant 1	Repressor of DNA damage response
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems

JAMTCF010000005.1 - Region 1 - T1PKS

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Location: 1 - 84,258 nt. (total: 84,258 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

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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: acylase

LV78_002289: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

LV78_002299: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

LV78_002304: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: dehalogenase protease

LV78_002288: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

LV78_002311: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

Lyases: decarboxylase

LV78_002293: diaminopimelate decarboxylase

smcogs: SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase

LV78_002291: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_002292: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_002298: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

LV78_002301: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_002302: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_002303: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_002316: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.74	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.74	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001275.3	0.74	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001244.3	0.74	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001770.4	0.71	PKS	sceliphrolactam	Streptomyces sp. SD85
BGC0000067.5	0.66	PKS	geldanamycin	Streptomyces hygroscopicus subsp. duamyceticus
BGC0002192.3	0.64	PKS	FR901512	fungal sp. No.14919
BGC0001641.4	0.64	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.64	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001132.4	0.64	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.74	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.74	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001275.3	0.74	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001244.3	0.74	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001770.4	0.71	PKS	sceliphrolactam	Streptomyces sp. SD85
BGC0000067.5	0.66	PKS	geldanamycin	Streptomyces hygroscopicus subsp. duamyceticus
BGC0002192.3	0.64	PKS	FR901512	fungal sp. No.14919
BGC0001641.4	0.64	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.64	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001132.4	0.64	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.34 out of 20.97

Confidence: medium

Additional weak hits (11):

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 19.99 out of 32.74

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.58 out of 29.25

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.76 out of 26.33

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.75 out of 32.74

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

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.01 out of 29.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.49 out of 26.06

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.66 out of 29.38

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.29 out of 30.98

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.16 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 0 - 84258:

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

Polymer prediction:: (ccmal - ccmal) + (Me-ccmal - ccmal) + (ccmal) + (ohmal) + (ccmal - Me-ccmal - ccmal) + (mal)
Non-colinear ordering:: LV78_002298 + LV78_002299 + LV78_002301 + LV78_002302 + LV78_002303 + LV78_002304

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

LV78_002289: pk

PKS_AT (39..290): 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

LV78_002291: X

AMP-binding (21..419): X

nrpys: bMe-Asp

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: 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:: DCFFFALITK
Nearest Stachelhaus code(s):: bMe-Asp DCFFFALITK (94% 8Å match); Ala DCFFFALITK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

LV78_002292: X

AMP-binding (21..416): X

nrpys: (unknown)

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DYYPTTQRVK
Nearest Stachelhaus code(s):: 3S-Abu DYYPTTQRIK (88% 8Å match); Asp DYYPTTMRVK (65% 8Å match)
Stachelhaus code match:: 90% (moderate)

LV78_002298: mal - mal

PKS_AT (644..939): 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: 181.3
inactive: 88.5
Methoxymalonyl-CoA: 53.7
Methylmalonyl-CoA: 47.2
Isobutyryl-CoA: 27.7
Propionyl-CoA: 25.3
CHC-CoA: 21.7
Ethylmalonyl-CoA: 17.5
Benzoyl-CoA: 14.5
Acetyl-CoA: 13.9
fatty_acid: 11.0
2-Methylbutyryl-CoA: 8.3
trans-1,2-CPDA: 3.6
3-Methylbutyryl-CoA: 0.0

PKS_AT (2313..2603): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 87.5%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 196.3
inactive: 110.4
Methoxymalonyl-CoA: 64.4
Methylmalonyl-CoA: 53.1
Ethylmalonyl-CoA: 20.4
Acetyl-CoA: 20.0
Propionyl-CoA: 19.6
Isobutyryl-CoA: 16.3
Benzoyl-CoA: 11.5
fatty_acid: 9.6
2-Methylbutyryl-CoA: 8.9
trans-1,2-CPDA: 0.0
CHC-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

LV78_002299: mmal - mal

PKS_AT (559..854): 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: 223.3
Ethylmalonyl-CoA: 214.2
Methoxymalonyl-CoA: 182.4
2-Methylbutyryl-CoA: 147.7
CHC-CoA: 120.1
trans-1,2-CPDA: 119.6
Propionyl-CoA: 111.2
Malonyl-CoA: 97.8
Isobutyryl-CoA: 90.6
Benzoyl-CoA: 71.1
3-Methylbutyryl-CoA: 53.7
Acetyl-CoA: 46.3
fatty_acid: 36.9
inactive: 23.8

PKS_AT (2253..2550): 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: 206.1
inactive: 108.6
Methoxymalonyl-CoA: 66.3
Methylmalonyl-CoA: 48.3
Propionyl-CoA: 42.1
Acetyl-CoA: 13.3
Isobutyryl-CoA: 12.6
Benzoyl-CoA: 8.8
trans-1,2-CPDA: 8.1
CHC-CoA: 7.8
2-Methylbutyryl-CoA: 5.2
Ethylmalonyl-CoA: 2.1
fatty_acid: 0.0
3-Methylbutyryl-CoA: 0.0

LV78_002301: mal

PKS_AT (553..837): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 79.2%; Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 173.7
inactive: 76.5
Methoxymalonyl-CoA: 56.6
Methylmalonyl-CoA: 49.8
CHC-CoA: 21.2
Propionyl-CoA: 20.5
Ethylmalonyl-CoA: 20.4
Isobutyryl-CoA: 18.0
Benzoyl-CoA: 18.0
fatty_acid: 16.9
2-Methylbutyryl-CoA: 8.5
trans-1,2-CPDA: 8.2
3-Methylbutyryl-CoA: 0.0
Acetyl-CoA: -1.7

LV78_002302: mal

PKS_AT (551..841): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 87.5%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 203.3
inactive: 114.8
Methoxymalonyl-CoA: 60.3
Methylmalonyl-CoA: 44.5
Isobutyryl-CoA: 39.9
Propionyl-CoA: 29.9
Ethylmalonyl-CoA: 19.4
Benzoyl-CoA: 18.2
Acetyl-CoA: 14.0
2-Methylbutyryl-CoA: 8.5
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
CHC-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

LV78_002303: mal - mmal - mal

PKS_AT (563..859): 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: 210.1
inactive: 111.7
Methoxymalonyl-CoA: 61.5
Methylmalonyl-CoA: 55.5
Propionyl-CoA: 35.2
Benzoyl-CoA: 30.3
Isobutyryl-CoA: 27.6
Ethylmalonyl-CoA: 25.5
2-Methylbutyryl-CoA: 19.0
Acetyl-CoA: 16.8
fatty_acid: 12.8
CHC-CoA: 9.5
trans-1,2-CPDA: 8.8
3-Methylbutyryl-CoA: 0.0

PKS_AT (2262..2551): 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: 211.5
Ethylmalonyl-CoA: 198.2
Methoxymalonyl-CoA: 176.5
2-Methylbutyryl-CoA: 143.6
trans-1,2-CPDA: 116.6
CHC-CoA: 114.3
Propionyl-CoA: 114.1
Malonyl-CoA: 109.8
Isobutyryl-CoA: 84.1
Benzoyl-CoA: 66.2
Acetyl-CoA: 45.5
fatty_acid: 36.9
3-Methylbutyryl-CoA: 32.2
inactive: 28.3

PKS_AT (3937..4222): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 75.0%; Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 175.1
inactive: 66.2
Methoxymalonyl-CoA: 58.6
Methylmalonyl-CoA: 48.7
Propionyl-CoA: 37.4
fatty_acid: 19.4
Acetyl-CoA: 19.3
trans-1,2-CPDA: 15.3
CHC-CoA: 15.3
Benzoyl-CoA: 14.1
Isobutyryl-CoA: 13.3
Ethylmalonyl-CoA: 12.2
2-Methylbutyryl-CoA: 6.4
3-Methylbutyryl-CoA: 0.0

LV78_002304: mal

PKS_AT (557..835): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 187.3
inactive: 88.2
Methoxymalonyl-CoA: 52.8
Methylmalonyl-CoA: 50.9
Propionyl-CoA: 32.3
Isobutyryl-CoA: 20.2
Acetyl-CoA: 15.2
CHC-CoA: 12.2
Benzoyl-CoA: 10.5
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
3-Methylbutyryl-CoA: 0.0
Ethylmalonyl-CoA: -0.5
2-Methylbutyryl-CoA: -2.2

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
CcpA	Catabolite control protein A

JAMTCF010000005.1 - Region 2 - T1PKS,lassopeptide,terpene

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Location: 176,438 - 273,813 nt. (total: 97,376 nt) Show pHMM detection rules used

lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)
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

Lasso peptides

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

LV78_002420: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

LV78_002429: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

LV78_002432: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

LV78_002433: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

LV78_002434: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

LV78_002437: flavin reductase domain protein FMN-binding

smcogs: SMCOG1160: flavin reductase domain protein FMN-binding

LV78_002451: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

LV78_002452: dioxygenase, TauD/TfdA

smcogs: SMCOG1121: dioxygenase, TauD/TfdA

LV78_002454: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

LV78_002458: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase methyltransferase

LV78_002431: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

LV78_002438: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

LV78_002448: aminotransferase

smcogs: SMCOG1019: aminotransferase

LV78_002453: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

Hydrolases: hydrolase

LV78_002412: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Ligases: synthase synthetase

LV78_002440: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_002441: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

LV78_002442: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_002456: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.43	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001550.3	0.42	ribosomal	citrulassin D	Streptomyces katrae
BGC0002631.2	0.42	ribosomal	Myxarylin	Pyxidicoccus fallax
BGC0001552.3	0.41	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001336.5	0.36	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0002825.2	0.36	ribosomal	nocapeptin A	Nocardia terpenica IFM 0406
BGC0001549.3	0.36	ribosomal	citrulassin B	Streptomyces aurantiacus JA 4570
BGC0001485.4	0.35	other (other)	chuangxinmycin	Actinoplanes tsinanensis
BGC0002425.3	0.35	ribosomal	stlassin	Streptomyces sp.
BGC0000677.5	0.35	terpene	cyclooctatin	Streptomyces melanosporofaciens

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.74	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001550.3	0.73	ribosomal	citrulassin D	Streptomyces katrae
BGC0001552.3	0.73	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001549.3	0.68	ribosomal	citrulassin B	Streptomyces aurantiacus JA 4570
BGC0001551.4	0.66	ribosomal	citrulassin E	Streptomyces glaucescens
BGC0000041.3	0.65	PKS	oronofacic acid	Pseudomonas syringae
BGC0001164.3	0.64	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0001160.5	0.64	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Lasso peptide predictions

Lassopeptides - No core peptides 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:

LV78_002450: T2TS

Domain 1 (282 - 553): Type 2 terpene synthase

Subtype: unknown

LV78_002456: PT_FPPS_like

Domain 1 (281 - 564): 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:

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.73 out of 20.97

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.06 out of 23.79

Confidence: medium

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 23.03 out of 26.33

Confidence: medium

AfsR

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

Confidence: medium

VqsM

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

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.22 out of 27.04

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 17.96 out of 23.79

Confidence: medium

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.29 out of 30.11

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.42 out of 20.47

Confidence: medium

Additional weak hits (17):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.54 out of 21.55

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.78 out of 25.88

Confidence: weak

HipB

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

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.40 out of 20.97

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.10 out of 20.97

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.22 out of 29.38

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.28 out of 27.78

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 18.77 out of 33.73

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.28 out of 26.85

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84

Confidence: weak

ZuR variant 1

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

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.20 out of 35.63

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.03 out of 28.19

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.20 out of 30.11

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.29 out of 24.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 11.66 out of 26.06

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.30 out of 24.78

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

Lasso peptides

NRPS/PKS products

NRPS/PKS substrates

RREFinder

Terpene

TFBS Finder

Core peptide predictions

No core peptides found.

Predicted core structure(s)

For candidate cluster 2, location 176437 - 273813:

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

Polymer prediction:: (mal - ccmal - ccmal) + (ccmal - ohmal) + (ccmal)
Non-colinear ordering:: LV78_002440 + LV78_002441 + LV78_002442

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 198634 - 267263:

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

Polymer prediction:: (mal - ccmal - ccmal) + (ccmal - ohmal) + (ccmal)
Non-colinear ordering:: LV78_002440 + LV78_002441 + LV78_002442

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

LV78_002440: mal - mal - mal

PKS_AT (546..810): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 70.8%; 2-Methylbutyryl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 164.4
inactive: 67.6
Methylmalonyl-CoA: 55.1
Methoxymalonyl-CoA: 55.1
Propionyl-CoA: 34.4
Acetyl-CoA: 30.9
Isobutyryl-CoA: 28.0
Ethylmalonyl-CoA: 22.2
fatty_acid: 21.4
Benzoyl-CoA: 19.6
CHC-CoA: 18.2
2-Methylbutyryl-CoA: 16.1
trans-1,2-CPDA: 14.6
3-Methylbutyryl-CoA: 0.0

PKS_AT (1517..1781): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 75.0%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 162.7
inactive: 83.8
Methoxymalonyl-CoA: 50.7
Methylmalonyl-CoA: 36.3
Propionyl-CoA: 19.2
Isobutyryl-CoA: 13.0
Acetyl-CoA: 11.9
fatty_acid: 9.5
Ethylmalonyl-CoA: 6.4
2-Methylbutyryl-CoA: 2.7
trans-1,2-CPDA: 0.0
Benzoyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
CHC-CoA: -3.8

PKS_AT (3165..3459): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 182.4
inactive: 93.6
Methoxymalonyl-CoA: 56.1
Methylmalonyl-CoA: 49.6
Propionyl-CoA: 37.5
Isobutyryl-CoA: 24.6
Ethylmalonyl-CoA: 16.2
CHC-CoA: 15.1
Benzoyl-CoA: 9.6
Acetyl-CoA: 8.4
2-Methylbutyryl-CoA: 8.3
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
3-Methylbutyryl-CoA: 0.0

LV78_002441: mal - mal

PKS_AT (537..800): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 83.3%; inactive: 66.7%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 166.5
Methoxymalonyl-CoA: 77.0
inactive: 69.1
Methylmalonyl-CoA: 62.6
Isobutyryl-CoA: 32.0
Propionyl-CoA: 31.7
Benzoyl-CoA: 30.9
Acetyl-CoA: 29.7
Ethylmalonyl-CoA: 26.5
fatty_acid: 16.9
trans-1,2-CPDA: 16.2
CHC-CoA: 14.4
2-Methylbutyryl-CoA: 8.9
3-Methylbutyryl-CoA: 0.0

PKS_AT (2089..2362): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 79.2%; Propionyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 156.7
Methoxymalonyl-CoA: 70.8
Methylmalonyl-CoA: 66.7
inactive: 56.8
Propionyl-CoA: 33.1
Isobutyryl-CoA: 26.3
Acetyl-CoA: 25.6
Benzoyl-CoA: 25.4
Ethylmalonyl-CoA: 25.0
CHC-CoA: 16.8
fatty_acid: 14.6
trans-1,2-CPDA: 11.6
2-Methylbutyryl-CoA: 10.7
3-Methylbutyryl-CoA: 0.0

LV78_002442: mal

PKS_AT (562..847): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 75.0%; Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 194.1
inactive: 90.1
Methoxymalonyl-CoA: 56.2
Methylmalonyl-CoA: 37.7
Propionyl-CoA: 20.0
Acetyl-CoA: 15.0
Isobutyryl-CoA: 14.0
fatty_acid: 10.5
trans-1,2-CPDA: 9.1
2-Methylbutyryl-CoA: 8.8
Benzoyl-CoA: 8.6
Ethylmalonyl-CoA: 7.8
CHC-CoA: 7.3
3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

RRE predictions

: RRE type: Stand_Alone_Lasso_RRE; Location: 1 - 82; Score: 87.7

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
ANR	Anaerobic transcriptional regulator
AfsR	Pleiotropic regulatory for antibiotic production
CcpA	Catabolite control protein A
CelR	Cellobiose uptake repressor
DasR	N-acetylglucosamine dependent repressor
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

JAMTCF010000005.1 - Region 3 - T1PKS

Download region GenBank file

Download region SVG

Location: 281,438 - 347,793 nt. (total: 66,356 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: dehydrogenase oxygenase

LV78_002475: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

LV78_002486: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

LV78_002487: monooxygenase FAD-binding

smcogs: SMCOG1246: monooxygenase FAD-binding

Transferases: acetyltransferase glycosyltransferase methyltransferase

LV78_002472: acetyl-CoA acetyltransferase

smcogs: SMCOG1124: acetyl-CoA acetyltransferase

LV78_002483: methyltransferase

smcogs: SMCOG1248: methyltransferase

LV78_002484: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

LV78_002485: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

Lyases: hydratase

LV78_002471: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase

LV78_002473: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_002488: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_002491: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000041.3	0.61	PKS	oronofacic acid	Pseudomonas syringae
BGC0001164.3	0.60	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.60	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002277.2	0.60	NRPS	atromentin	Suillus grevillei
BGC0001135.5	0.59	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002075.3	0.58	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001132.4	0.58	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001641.4	0.58	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.58	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000067.5	0.54	PKS	geldanamycin	Streptomyces hygroscopicus subsp. duamyceticus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000041.3	0.61	PKS	oronofacic acid	Pseudomonas syringae
BGC0001164.3	0.60	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.60	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002277.2	0.60	NRPS	atromentin	Suillus grevillei
BGC0001135.5	0.59	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002075.3	0.58	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001132.4	0.58	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001641.4	0.58	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.58	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000067.5	0.54	PKS	geldanamycin	Streptomyces hygroscopicus subsp. duamyceticus

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (28):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.90 out of 21.55

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.90 out of 21.55

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.25 out of 20.97

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.73 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.33 out of 28.14

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.67 out of 27.78

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 14.65 out of 20.97

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.13 out of 32.74

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.65 out of 19.26

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.01 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.40 out of 26.06

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.11 out of 30.22

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.81 out of 29.65

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 20.86 out of 36.53

Confidence: weak

ZuR variant 1

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

Confidence: weak

HypR

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 11.55 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.48 out of 28.14

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.83 out of 25.75

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.71 out of 26.06

Confidence: weak

MogR

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.96 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 11.68 out of 28.14

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 14.52 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 15.83 out of 28.19

Confidence: weak

ZuR variant 1

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

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.75 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.03 out of 28.19

Confidence: weak

Module view

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Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 6, location 281437 - 347793:

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

Polymer prediction:: (Me-mal) + (Me-ohmal)
Non-colinear ordering:: LV78_002486 + LV78_002489

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

LV78_002473: X

AMP-binding (21..472): X

nrpys: (unknown)

SVM prediction details:

NOTE: uncertain match

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:: IALF---FEK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

LV78_002486: mmal - mmal - mmal

PKS_AT (124..418): mmal

ATSignature: Isobutyryl-CoA

Top 3 matches:: Isobutyryl-CoA: 75.0%; 2-Methylbutyryl-CoA: 70.8%; Propionyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 148.8
Methoxymalonyl-CoA: 131.1
Ethylmalonyl-CoA: 131.1
2-Methylbutyryl-CoA: 124.3
CHC-CoA: 107.4
Propionyl-CoA: 102.7
Malonyl-CoA: 86.7
trans-1,2-CPDA: 82.3
Isobutyryl-CoA: 59.6
Benzoyl-CoA: 48.7
3-Methylbutyryl-CoA: 39.0
inactive: 32.9
Acetyl-CoA: 26.9
fatty_acid: 17.9

PKS_AT (1070..1279): mmal

ATSignature: (unknown)

No matches above 50%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 61.1
Methoxymalonyl-CoA: 55.5
Ethylmalonyl-CoA: 47.5
2-Methylbutyryl-CoA: 44.5
Propionyl-CoA: 40.2
trans-1,2-CPDA: 39.1
CHC-CoA: 36.6
Isobutyryl-CoA: 23.5
Benzoyl-CoA: 21.5
Malonyl-CoA: 18.4
Acetyl-CoA: 16.6
3-Methylbutyryl-CoA: 13.1
fatty_acid: 11.6
inactive: 0.0

PKS_AT (1956..2249): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 66.7%; Malonyl-CoA: 62.5%; Methoxymalonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 133.5
Methoxymalonyl-CoA: 120.5
Ethylmalonyl-CoA: 112.2
Malonyl-CoA: 102.9
2-Methylbutyryl-CoA: 74.2
trans-1,2-CPDA: 67.8
CHC-CoA: 64.9
Propionyl-CoA: 59.2
Isobutyryl-CoA: 53.6
Benzoyl-CoA: 40.9
inactive: 36.8
fatty_acid: 34.8
Acetyl-CoA: 22.6
3-Methylbutyryl-CoA: 16.7

LV78_002489: mmal - mal

PKS_AT (1039..1331): mmal

ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA, 2-Methylbutyryl-CoA

Top 3 matches:: Methylmalonyl-CoA: 66.7%; Methoxymalonyl-CoA: 66.7%; 2-Methylbutyryl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 147.6
Ethylmalonyl-CoA: 143.8
Methoxymalonyl-CoA: 130.0
2-Methylbutyryl-CoA: 124.3
Propionyl-CoA: 103.8
trans-1,2-CPDA: 102.6
CHC-CoA: 81.8
Malonyl-CoA: 76.1
Benzoyl-CoA: 46.4
Isobutyryl-CoA: 36.5
Acetyl-CoA: 36.5
3-Methylbutyryl-CoA: 25.6
inactive: 18.7
fatty_acid: 16.7

PKS_AT (2680..2971): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 66.7%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 126.8
Methoxymalonyl-CoA: 59.1
Methylmalonyl-CoA: 56.9
Propionyl-CoA: 44.3
inactive: 34.1
CHC-CoA: 27.5
2-Methylbutyryl-CoA: 25.3
fatty_acid: 21.6
Acetyl-CoA: 20.8
Ethylmalonyl-CoA: 20.0
trans-1,2-CPDA: 14.6
Benzoyl-CoA: 12.0
Isobutyryl-CoA: 8.9
3-Methylbutyryl-CoA: 0.0

LV78_002491: X

AMP-binding (12..380): 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:: QVEVLSGTIK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description

JAMTCF010000006.1 - Region 1 - 2dos,NRPS,PKS-like,opine-like-metallophore

Download region GenBank file

Download region SVG

Location: 81,038 - 167,240 nt. (total: 86,203 nt) Show pHMM detection rules used

opine-like-metallophore: (CntL and CntM)
PKS-like: (t2pks2 or ksIII)
2dos: ((DOIS or DHQ_synthase or ValA or salQ) and DegT_DnrJ_EryC1 and (LipV or ADSI-DH or cds(ADH_N and ADH_zinc_N)))
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 oxidase oxidoreductase oxygenase

LV78_002758: monooxygenase FAD-binding

smcogs: SMCOG1246: monooxygenase FAD-binding

LV78_002762: FAD linked oxidase domain protein

smcogs: SMCOG1138: FAD linked oxidase domain protein

LV78_002765: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

LV78_002766: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

LV78_002771: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

LV78_002785: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: carboxylase methyltransferase sulfhydrylase

LV78_002753: methyltransferase

smcogs: SMCOG1089: methyltransferase

LV78_002774: O-succinylhomoserine sulfhydrylase

smcogs: SMCOG1168: O-succinylhomoserine sulfhydrylase

LV78_002776: acetyl-CoA carboxylase biotin carboxylase

smcogs: SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Hydrolases: deaminase dehalogenase hydrolase

LV78_002744: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

LV78_002754: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

LV78_002772: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

LV78_002778: ornithine cyclodeaminase

smcogs: SMCOG1158: ornithine cyclodeaminase

Ligases: ligase synthase

LV78_002763: 3-oxoacyl-(acyl carrier protein) synthase III

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

LV78_002769: 3-dehydroquinate synthase

smcogs: SMCOG1183: 3-dehydroquinate synthase

LV78_002775: carbamoyl phosphate synthase small subunit

smcogs: SMCOG1249: carbamoyl phosphate synthase small subunit

LV78_002777: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

LV78_002781: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002276.2	0.72	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000895.5	0.59	other (other)	citrulline	Lactobacillus plantarum subsp. plantarum
BGC0000701.5	0.58	saccharide	jinggangmycin	Streptomyces hygroscopicus subsp. yingchengensis
BGC0002510.2	0.56	PKS	youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4	Streptomyces sp.
BGC0002458.3	0.52	NRPS	alazopeptin	Streptacidiphilus griseoplanus
BGC0002404.2	0.47	other (other)	falcarindiol	Solanum lycopersicum
BGC0000723.5	0.47	other (cyclitol), saccharide	validamycin A	Streptomyces hygroscopicus subsp. limoneus
BGC0000234.5	0.47	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0001343.3	0.47	PKS	aurachin A, aurachin D	Stigmatella aurantiaca Sg a15
BGC0002047.2	0.46	PKS	brasiliquinone A, brasiliquinone B	Nocardia brasiliensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002135.2	0.68	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.68	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.67	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001135.5	0.67	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001261.3	0.66	NRPS	AM-toxin	Alternaria alternata
BGC0001758.4	0.66	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.66	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: strong

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: 17.13 out of 19.26

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.58 out of 20.97

Confidence: medium

AfsR

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

Confidence: medium

Additional weak hits (17):

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.54 out of 29.25

Confidence: weak

CcpA

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

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.38 out of 20.97

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.65 out of 19.26

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.49 out of 29.65

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 30.11

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11

Confidence: weak

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

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.29 out of 33.73

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 18.77 out of 33.73

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.05 out of 29.38

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: 15.11 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.16 out of 27.78

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.29 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.77 out of 28.19

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.62 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 1, location 81037 - 167240:

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 5, location 124072 - 167240:

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

LV78_002781: X

AMP-binding (474..871): X

nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DMGGMGLIGK
Nearest Stachelhaus code(s):: E-ahmohOrn DVGGGGVIGK (50% 8Å match); OH-Orn DMENMGLINK (44% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
CRP	Cyclic AMP receptor protein
CcpA	Catabolite control protein A
RpoN	Regulator of nitrogen assimilation and virulence
VqsM	Regulator of quorum-sensing signalling systems

JAMTCF010000006.1 - Region 2 - T1PKS

Download region GenBank file

Download region SVG

Location: 215,735 - 273,269 nt. (total: 57,535 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: dehydrogenase oxidoreductase

LV78_002848: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

LV78_002856: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

LV78_002859: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

Transferases: acylase sulfhydrylase

LV78_002855: O-succinylhomoserine sulfhydrylase

smcogs: SMCOG1168: O-succinylhomoserine sulfhydrylase

LV78_002858: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase hydrolase

LV78_002842: thioesterase

smcogs: SMCOG1004: thioesterase

LV78_002852: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000016.4	0.57	other (other)	amphotericin B	Streptomyces nodosus
BGC0000843.5	0.43	other (non-nrp beta-lactam)	alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate	Streptomyces clavuligerus ATCC 27064
BGC0000815.4	0.42	other (other)	loline, N-acetylnorloline, N-formylloline	Epichloe uncinata
BGC0000467.5	0.41	NRPS	yersiniabactin	Yersinia enterocolitica
BGC0000122.5	0.41	PKS	phenylnannolone A, phenylnannolone B, phenylnannolone C	Nannocystis pusilla
BGC0001521.3	0.41	NRPS	auriculamide	Herpetosiphon aurantiacus DSM 785
BGC0000899.4	0.40	saccharide	desosamine	Streptomyces narbonensis
BGC0000829.5	0.40	other (other)	violacein	Chromobacterium violaceum
BGC0001483.4	0.40	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8
BGC0001513.3	0.39	PKS	anthrabenzoxocinone	Actinobacteria bacterium

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000016.4	0.57	other (other)	amphotericin B	Streptomyces nodosus
BGC0000843.5	0.43	other (non-nrp beta-lactam)	alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate	Streptomyces clavuligerus ATCC 27064
BGC0000815.4	0.42	other (other)	loline, N-acetylnorloline, N-formylloline	Epichloe uncinata
BGC0000467.5	0.41	NRPS	yersiniabactin	Yersinia enterocolitica
BGC0000122.5	0.41	PKS	phenylnannolone A, phenylnannolone B, phenylnannolone C	Nannocystis pusilla
BGC0001521.3	0.41	NRPS	auriculamide	Herpetosiphon aurantiacus DSM 785
BGC0000899.4	0.40	saccharide	desosamine	Streptomyces narbonensis
BGC0000829.5	0.40	other (other)	violacein	Chromobacterium violaceum
BGC0001483.4	0.40	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8
BGC0001513.3	0.39	PKS	anthrabenzoxocinone	Actinobacteria bacterium

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:

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.53 out of 20.97

Confidence: medium

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.67 out of 30.11

Confidence: medium

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.73 out of 30.22

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.82 out of 27.04

Confidence: medium

Additional weak hits (27):

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.71 out of 20.97

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84

Confidence: weak

FuR variant 1

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

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.53 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.04 out of 29.38

Confidence: weak

MexT

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

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.71 out of 30.25

Confidence: weak

HipB

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

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.81 out of 21.84

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 14.83 out of 31.73

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.40 out of 20.97

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.21 out of 30.22

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.88 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.02 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.38 out of 28.14

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.88 out of 31.73

Confidence: weak

HgtR

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

Confidence: weak

ZuR variant 1

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

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.88 out of 32.93

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 18.84 out of 27.04

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.14 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.86 out of 28.14

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.32 out of 36.54

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 15.67 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 15.82 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.57 out of 29.65

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.30 out of 30.11

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 6, location 215734 - 273269:

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

LV78_002858: mal - mal - mmal - mal

PKS_AT (503..754): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 83.3%; Methylmalonyl-CoA: 66.7%; inactive: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 127.1
Methoxymalonyl-CoA: 80.9
Methylmalonyl-CoA: 61.9
inactive: 42.5
Isobutyryl-CoA: 42.4
Benzoyl-CoA: 28.0
Propionyl-CoA: 27.1
Acetyl-CoA: 26.7
Ethylmalonyl-CoA: 25.5
fatty_acid: 23.5
2-Methylbutyryl-CoA: 15.6
CHC-CoA: 12.9
trans-1,2-CPDA: 11.3
3-Methylbutyryl-CoA: 4.2

PKS_AT (1579..1822): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 70.8%; Methylmalonyl-CoA: 62.5%; Ethylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 89.0
Methylmalonyl-CoA: 58.2
Propionyl-CoA: 55.5
Methoxymalonyl-CoA: 53.8
inactive: 37.9
CHC-CoA: 30.0
Ethylmalonyl-CoA: 27.3
Isobutyryl-CoA: 22.1
2-Methylbutyryl-CoA: 19.5
trans-1,2-CPDA: 18.9
fatty_acid: 13.6
Benzoyl-CoA: 13.5
Acetyl-CoA: 8.9
3-Methylbutyryl-CoA: 3.6

PKS_AT (3836..4047): mmal

ATSignature: (unknown)

No matches above 50%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 84.7
Methoxymalonyl-CoA: 59.0
Ethylmalonyl-CoA: 46.8
trans-1,2-CPDA: 37.1
2-Methylbutyryl-CoA: 32.2
Isobutyryl-CoA: 30.7
Malonyl-CoA: 29.2
Propionyl-CoA: 28.9
Benzoyl-CoA: 26.0
CHC-CoA: 18.1
Acetyl-CoA: 17.5
fatty_acid: 14.8
inactive: 13.3
3-Methylbutyryl-CoA: 10.2

PKS_AT (4563..4809): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 66.7%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 106.5
Methoxymalonyl-CoA: 50.0
Methylmalonyl-CoA: 44.4
inactive: 41.9
Propionyl-CoA: 21.2
Isobutyryl-CoA: 19.1
Acetyl-CoA: 14.7
CHC-CoA: 14.6
fatty_acid: 13.4
Benzoyl-CoA: 13.3
Ethylmalonyl-CoA: 10.7
3-Methylbutyryl-CoA: 7.7
trans-1,2-CPDA: 6.5
2-Methylbutyryl-CoA: -1.7

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
CelR	Cellobiose uptake repressor
ClgR	Caseinolytic protease gene regulator
DasR	N-acetylglucosamine dependent repressor

JAMTCF010000006.1 - Region 3 - T1PKS

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Location: 314,162 - 359,921 nt. (total: 45,760 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

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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

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

LV78_002905: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

LV78_002922: flavin reductase domain protein FMN-binding

smcogs: SMCOG1160: flavin reductase domain protein FMN-binding

LV78_002925: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

LV78_002926: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

LV78_002927: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

LV78_002935: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

LV78_002938: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

Transferases: acylase aminotransferase methyltransferase

LV78_002916: aminotransferase class V

smcogs: SMCOG1139: aminotransferase class V

LV78_002918: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

LV78_002924: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: dehalogenase

LV78_002932: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Lyases: dehydratase

LV78_002921: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase

LV78_002934: polyprenol-monophosphomannose synthase ppm1

smcogs: SMCOG1123: polyprenol-monophosphomannose synthase ppm1

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001160.5	0.57	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.57	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001273.3	0.56	PKS	asperlactone	Aspergillus ochraceus
BGC0002175.3	0.56	PKS	YWA1	Aspergillus oryzae RIB40
BGC0000056.3	0.55	PKS	esperamicin	Actinomadura verrucosospora
BGC0002387.2	0.51	PKS	yangpumicin A	Micromonospora yangpuensis
BGC0001377.5	0.46	PKS	uncialamycin	Streptomyces uncialis
BGC0000584.5	0.46	ribosomal	colicin V	Escherichia coli
BGC0002372.3	0.46	PKS, other (other), terpene	marinoterpin B, marinoterpin A, marinoterpin C	Streptomyces sp.
BGC0000265.5	0.45	PKS	rhodomycin	Streptomyces purpurascens

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001160.5	0.57	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.57	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001273.3	0.56	PKS	asperlactone	Aspergillus ochraceus
BGC0002175.3	0.56	PKS	YWA1	Aspergillus oryzae RIB40
BGC0000056.3	0.55	PKS	esperamicin	Actinomadura verrucosospora
BGC0002387.2	0.51	PKS	yangpumicin A	Micromonospora yangpuensis
BGC0001377.5	0.46	PKS	uncialamycin	Streptomyces uncialis
BGC0000584.5	0.46	ribosomal	colicin V	Escherichia coli
BGC0002372.3	0.46	PKS, other (other), terpene	marinoterpin B, marinoterpin A, marinoterpin C	Streptomyces sp.
BGC0000265.5	0.45	PKS	rhodomycin	Streptomyces purpurascens

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

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: 25.64 out of 26.85

Confidence: strong

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.86 out of 18.57

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.56 out of 23.79

Confidence: medium

AbrC3

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

Confidence: strong

Additional weak hits (16):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.17 out of 21.55

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.88 out of 23.43

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.18 out of 27.55

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.18 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.44 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.52 out of 30.25

Confidence: weak

LexA variant 1

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.24 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.04 out of 26.06

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.68 out of 26.12

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.08 out of 33.14

Confidence: weak

HypR

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

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.07 out of 33.14

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.91 out of 30.98

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.42 out of 27.04

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.23 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

TFBS Finder

NRPS/PKS substrate predictions

LV78_002924: mal

PKS_AT (612..846): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 75.0%; inactive: 58.3%; Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 66.5
Methoxymalonyl-CoA: 46.4
Methylmalonyl-CoA: 34.5
inactive: 31.6
Propionyl-CoA: 25.4
Isobutyryl-CoA: 20.1
trans-1,2-CPDA: 13.6
fatty_acid: 11.1
Ethylmalonyl-CoA: 9.6
2-Methylbutyryl-CoA: 0.9
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
AbrC3	Antibiotic production activator
IolR	Regulator of the inositol catabolism
RutR	Regulator of the pyrimidine and purine metabolism
ToxT	Regulator of MSHA biosynthesis

JAMTCF010000008.1 - Region 1 - RiPP-like

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Location: 28,211 - 39,008 nt. (total: 10,798 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

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transport-related genes

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resistance

TTA codons

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

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Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Hydrolases: protease

LV78_003473: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000595.3	0.32	ribosomal	SCO-2138	Streptomyces coelicolor A3(2)
BGC0000597.4	0.29	ribosomal	SWA-2138	Streptomyces sp. e14
BGC0000842.5	0.26	other (non-nrp beta-lactam)	carbapenem MM4550	Streptomyces argenteolus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000595.3	0.32	ribosomal	SCO-2138	Streptomyces coelicolor A3(2)
BGC0000597.4	0.29	ribosomal	SWA-2138	Streptomyces sp. e14
BGC0000842.5	0.26	other (non-nrp beta-lactam)	carbapenem MM4550	Streptomyces argenteolus

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):

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.83 out of 20.97

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.47 out of 27.78

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description

JAMTCF010000010.1 - Region 1 - NRPS,azoxy-crosslink,nucleoside

Download region GenBank file

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Location: 159,309 - 311,234 nt. (total: 151,926 nt) Show pHMM detection rules used

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
azoxy-crosslink: (azdH and LPG_synthase_C and azdO and vlmB)
nucleoside: (LipM or LipV or LipU or TunD or pur6 or pur10 or nikJ or nikO or truD)

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

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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 electron transfer oxidoreductase oxygenase

LV78_004299: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

LV78_004309: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

LV78_004333: flavodoxin

smcogs: SMCOG1134: flavodoxin

LV78_004335: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

LV78_004339: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

LV78_004357: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

LV78_004358: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

LV78_004362: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

LV78_004369: dioxygenase, TauD/TfdA

smcogs: SMCOG1121: dioxygenase, TauD/TfdA

LV78_004370: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

LV78_004388: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: acetyltransferase aminotransferase glycosyltransferase methyltransferase

LV78_004356: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

LV78_004365: Chloramphenicol acetyltransferase

smcogs: SMCOG1156: Chloramphenicol acetyltransferase

LV78_004373: glycosyltransferase

smcogs: SMCOG1102: glycosyltransferase

LV78_004378: methyltransferase

smcogs: SMCOG1089: methyltransferase

LV78_004382: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: deaminase hydrolase protease

LV78_004295: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

LV78_004300: alpha/beta hydrolase domain-containing protein

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

LV78_004318: ornithine cyclodeaminase

smcogs: SMCOG1158: ornithine cyclodeaminase

LV78_004372: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: dehydratase

LV78_004349: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase

LV78_004311: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

LV78_004314: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_004315: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

LV78_004341: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

LV78_004364: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_004367: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

LV78_004368: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Translocases: transporter

LV78_004351: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001128.4	1.40	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	1.38	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002286.3	1.37	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	1.26	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	1.23	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	1.21	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001132.4	1.18	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001758.4	1.17	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	1.10	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	1.05	NRPS	HC-toxin	Alternaria jesenskae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001841.2	0.81	NRPS, PKS	detoxin P1, detoxin P2, detoxin P3	Amycolatopsis jejuensis
BGC0002135.2	0.77	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.76	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0000342.4	0.74	NRPS	enniatin	Fusarium equiseti
BGC0001128.4	0.74	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001135.5	0.73	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.73	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.73	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

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: 16.16 out of 18.46

Confidence: medium

VqsM

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

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.71 out of 23.79

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

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.20 out of 26.33

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.39 out of 27.04

Confidence: medium

Additional weak hits (76):

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.62 out of 39.62

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.58 out of 27.78

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.48 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.44 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.86 out of 31.73

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.19 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.22 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.47 out of 26.06

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.37 out of 18.57

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.03 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.21 out of 26.06

Confidence: weak

MogR

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

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.46 out of 28.14

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.38 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.14 out of 26.06

Confidence: weak

MogR

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

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.06 out of 28.14

Confidence: weak

ColR

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

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.46 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.99 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.26 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.27 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.44 out of 26.06

Confidence: weak

MogR

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

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.67 out of 30.97

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 18.77 out of 33.73

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.47 out of 21.55

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 13.97 out of 21.55

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.55 out of 30.25

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.63 out of 26.85

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

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.46 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.74 out of 27.78

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 14.98 out of 31.73

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.22 out of 25.75

Confidence: weak

CodY

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

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.10 out of 28.14

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.94 out of 30.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.01 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.87 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.12 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.92 out of 31.73

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.40 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.59 out of 28.14

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.90 out of 18.57

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.86 out of 26.33

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.62 out of 21.55

Confidence: weak

MntR

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

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 12.77 out of 18.57

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.08 out of 29.38

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.65 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.51 out of 26.06

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.46 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.24 out of 29.38

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.41 out of 21.55

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 11.94 out of 28.14

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.42 out of 27.78

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 20.96 out of 36.53

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.13 out of 24.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.57 out of 26.06

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 12.89 out of 18.57

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 14.66 out of 33.14

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.43 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.29 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.31 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 15.93 out of 28.19

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.89 out of 27.04

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.08 out of 28.19

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.11 out of 35.63

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.45 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.24 out of 28.19

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.59 out of 32.93

Confidence: weak

ZuR variant 1

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

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 18.92 out of 27.04

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.41 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 1, location 159308 - 311234:

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

Polymer prediction:: (Thr - Val) + (X - X) + (X - Thr - Thr - Pro - Phe - NMe-Tyr - Val) + (Val) + (Val - Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 159308 - 212936:

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

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 203774 - 268785:

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

Polymer prediction:: (X - Thr - Thr - Pro - Phe - NMe-Tyr - Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 258995 - 311234:

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

Polymer prediction:: (Val - Pro) + (Val)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

LV78_004310: Thr - Val

Search NORINE for peptide: strict or relaxed

AMP-binding (518..920): Thr

nrpys: Thr

SVM prediction details:

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

Stachelhaus prediction details:

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

AMP-binding (1570..1960): 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:: N/A
Single AA prediction:: val (Val)

Stachelhaus prediction details:

Stachelhaus sequence:: DALMQAVVWK
Nearest Stachelhaus code(s):: Phe DAYVGAAVWK (59% 8Å match); Dpr DAQDLAVVNK (53% 8Å match); aIle DALVFGVVLK (47% 8Å match)
Stachelhaus code match:: 60% (weak)

LV78_004311: X - X

AMP-binding (462..842): X

nrpys: Asp, Asn, Glu, Gln, Aad

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DADNIGAVTK
Nearest Stachelhaus code(s):: Arg DAEDIGAITK (68% 8Å match); Tyr DAMSIGAVIK (44% 8Å match)
Stachelhaus code match:: 70% (weak)

AMP-binding (1537..1922): X

nrpys: (unknown)

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DAEEVGSIAK
Nearest Stachelhaus code(s):: Arg DAEGVGAIAK (59% 8Å match)
Stachelhaus code match:: 80% (moderate)

LV78_004314: X

AMP-binding (2..395): 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:: DARLASQMTK
Nearest Stachelhaus code(s):: Glu DPRSLSQMAK (59% 8Å match)
Stachelhaus code match:: 60% (weak)

LV78_004341: X - Thr - Thr - Pro - Phe - Tyr - Val

Search NORINE for peptide: strict or relaxed

AMP-binding (500..970): X

nrpys: (unknown)

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DADEVGHVDK
Nearest Stachelhaus code(s):: Arg DADDVGLVDK (62% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1792..2189): Thr

nrpys: Thr

SVM prediction details:

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

Stachelhaus prediction details:

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

AMP-binding (2845..3240): Thr

nrpys: Thr

SVM prediction details:

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

Stachelhaus prediction details:

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

AMP-binding (3893..4295): 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:: DVQYAAHVVK
Nearest Stachelhaus code(s):: Pro DVQYAAHVVK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4951..5317): 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 (88% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (5965..6324): Tyr

nrpys: Tyr

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DASTVAAVCK
Nearest Stachelhaus code(s):: Tyr DASTVAAVCK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (7465..7844): 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:: N/A
Single AA prediction:: val (Val)

Stachelhaus prediction details:

Stachelhaus sequence:: DLYVIAAVYK
Nearest Stachelhaus code(s):: Ala DVWVIAAVIK (71% 8Å match); Phe DAYVGAAVWK (59% 8Å match)
Stachelhaus code match:: 70% (weak)

LV78_004364: X

AMP-binding (23..464): 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:: VLPHLGGSTK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

LV78_004367: Val

Search NORINE for peptide: strict or relaxed

AMP-binding (468..847): 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:: N/A
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: val (Val)

Stachelhaus prediction details:

Stachelhaus sequence:: DAHFLGGLYK
Nearest Stachelhaus code(s):: Val DALFLGGTFK (59% 8Å match); Ile DAMFLGCTYK (56% 8Å match)
Stachelhaus code match:: 70% (weak)

LV78_004368: Val - Pro

Search NORINE for peptide: strict or relaxed

AMP-binding (9..383): Val

nrpys: Val

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DAFFVGGTFK
Nearest Stachelhaus code(s):: Val DAFFVGGTFK (68% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (960..1338): 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:: DVQFIAHVVK
Nearest Stachelhaus code(s):: Pro DVQFIAHVVK (85% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
CRP	Cyclic AMP receptor protein
DasR	N-acetylglucosamine dependent repressor
IolR	Regulator of the inositol catabolism
RpoN	Regulator of nitrogen assimilation and virulence
VqsM	Regulator of quorum-sensing signalling systems

JAMTCF010000011.1 - Region 1 - hydrogen-cyanide

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Location: 233,248 - 246,064 nt. (total: 12,817 nt) Show pHMM detection rules used

hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)

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

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase reductase

LV78_004625: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

LV78_004627: alkyl hydroperoxide reductase subunit

smcogs: SMCOG1176: alkyl hydroperoxide reductase subunit

LV78_004630: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002345.2	0.54	other (other)	hydrogen cyanide	Pseudomonas fluorescens
BGC0002285.2	0.34	ribosomal	aborycin	Streptomyces sp. ZS0098
BGC0000875.4	0.29	other (nucleoside), saccharide	caprazamycin, caprazamycin aglycon	Streptomyces sp. MK730-62F2
BGC0001735.5	0.29	other (other)	pentostatine, vidarabine	Streptomyces antibioticus
BGC0000872.5	0.28	other (other)	A-90289 A, A-90289 B	Streptomyces sp. SANK 60405
BGC0001076.5	0.28	other (nucleoside)	liposidomycin B, liposidomycin A, liposidomycin C, liposidomycin Z, liposidomycin H, liposidomycin G, liposidomycin L, liposidomycin M, liposidomycin K, liposidomycin N	Streptomyces sp. SN-1061M
BGC0002359.3	0.25	NRPS	dudomycin A	Streptomyces albus subsp. chlorinus
BGC0001783.5	0.22	other (other)	streptonigrin	Streptomyces flocculus
BGC0002336.2	0.21	NRPS	bolagladin A, bolagladin B	Burkholderia gladioli
BGC0001020.5	0.20	NRPS, PKS	muraymycin C1	Streptomyces sp. NRRL 30471

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002345.2	0.54	other (other)	hydrogen cyanide	Pseudomonas fluorescens
BGC0002285.2	0.34	ribosomal	aborycin	Streptomyces sp. ZS0098
BGC0000875.4	0.29	other (nucleoside), saccharide	caprazamycin, caprazamycin aglycon	Streptomyces sp. MK730-62F2
BGC0001735.5	0.29	other (other)	pentostatine, vidarabine	Streptomyces antibioticus
BGC0000872.5	0.28	other (other)	A-90289 A, A-90289 B	Streptomyces sp. SANK 60405
BGC0001076.5	0.28	other (nucleoside)	liposidomycin B, liposidomycin A, liposidomycin C, liposidomycin Z, liposidomycin H, liposidomycin G, liposidomycin L, liposidomycin M, liposidomycin K, liposidomycin N	Streptomyces sp. SN-1061M
BGC0002359.3	0.25	NRPS	dudomycin A	Streptomyces albus subsp. chlorinus
BGC0001783.5	0.22	other (other)	streptonigrin	Streptomyces flocculus
BGC0002336.2	0.21	NRPS	bolagladin A, bolagladin B	Burkholderia gladioli
BGC0001020.5	0.20	NRPS, PKS	muraymycin C1	Streptomyces sp. NRRL 30471

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 (7):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.41 out of 31.73

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.60 out of 21.55

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.93 out of 26.85

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.51 out of 33.14

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.65 out of 33.14

Confidence: weak

HypR

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

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

JAMTCF010000011.1 - Region 2 - bottromycin

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Location: 257,937 - 278,755 nt. (total: 20,819 nt) Show pHMM detection rules used

bottromycin: botH

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

Tailoring functions

Oxidoreductases: Cyclization oxygenase

LV78_004646: Decarboxylation, Oxidation

MITE: MITE0000044Decarboxylation, Oxidation (identity: 64.70%)
smcogs: SMCOG1007: cytochrome P450

LV78_004650: Cyclization

MITE: MITE0000053Cyclization (identity: 71.10%)

Transferases: Methylation

LV78_004645: Methylation

MITE: MITE0000047Methylation (identity: 69.00%)

LV78_004649: Methylation

MITE: MITE0000046Methylation (identity: 69.20%)

LV78_004653: Methylation

MITE: MITE0000049Methylation (identity: 72.30%)

LV78_004655: Methylation

MITE: MITE0000045Methylation (identity: 63.40%)

Hydrolases: Hydrolysis hydrolase

LV78_004643: Hydrolysis

MITE: MITE0000048Hydrolysis (identity: 61.50%)

LV78_004648: Epimerization

MITE: MITE0000051Epimerization (identity: 62.70%)
smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Lyases: oxygenase

LV78_004646: Decarboxylation, Oxidation

MITE: MITE0000044Decarboxylation, Oxidation (identity: 64.70%)
smcogs: SMCOG1007: cytochrome P450

Isomerases: hydrolase

LV78_004648: Epimerization

MITE: MITE0000051Epimerization (identity: 62.70%)
smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000468.5	0.77	ribosomal	bottromycin A2	Streptomyces bottropensis DSM40262
BGC0001157.6	0.77	ribosomal	bottromycin A2	Streptomyces scabiei 87.22
BGC0000470.6	0.75	ribosomal	bottromycin D	Streptomyces sp. WMMB272
BGC0000469.6	0.75	ribosomal	bottromycin A2	Streptomyces sp. BC16019
BGC0001485.4	0.45	other (other)	chuangxinmycin	Actinoplanes tsinanensis
BGC0002103.2	0.45	other (other)	pulcherriminic acid	Bacillus subtilis subsp. subtilis str. 168
BGC0001986.3	0.45	other (other)	purincyclamide	Streptomyces chrestomyceticus
BGC0000275.4	0.39	PKS	tetracenomycin C	Streptomyces glaucescens
BGC0001377.5	0.39	PKS	uncialamycin	Streptomyces uncialis
BGC0002387.2	0.39	PKS	yangpumicin A	Micromonospora yangpuensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000468.5	0.77	ribosomal	bottromycin A2	Streptomyces bottropensis DSM40262
BGC0001157.6	0.77	ribosomal	bottromycin A2	Streptomyces scabiei 87.22
BGC0000470.6	0.75	ribosomal	bottromycin D	Streptomyces sp. WMMB272
BGC0000469.6	0.75	ribosomal	bottromycin A2	Streptomyces sp. BC16019
BGC0001485.4	0.45	other (other)	chuangxinmycin	Actinoplanes tsinanensis
BGC0002103.2	0.45	other (other)	pulcherriminic acid	Bacillus subtilis subsp. subtilis str. 168
BGC0001986.3	0.45	other (other)	purincyclamide	Streptomyces chrestomyceticus
BGC0000275.4	0.39	PKS	tetracenomycin C	Streptomyces glaucescens
BGC0001377.5	0.39	PKS	uncialamycin	Streptomyces uncialis
BGC0002387.2	0.39	PKS	yangpumicin A	Micromonospora yangpuensis

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: 18.89 out of 23.79

Confidence: medium

Additional weak hits (5):

FuR variant 1

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

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.52 out of 27.78

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.77 out of 27.55

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.44 out of 29.65

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.09 out of 33.14

Confidence: weak

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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RREFinder

TFBS Finder

RRE predictions

: RRE type: Bottromycin_Methyltransferase_RRE; Location: 529 - 604; Score: 97.8; RRE type: Bottromycin_Methyltransferase_RRE; Location: 540 - 615; Score: 79.3; RRE type: Bottromycin_Methyltransferase_RRE; Location: 494 - 570; Score: 105.4

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism

JAMTCF010000013.1 - Region 1 - indole

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Location: 229,016 - 250,137 nt. (total: 21,122 nt) Show pHMM detection rules used

indole: (indsynth or dmat or indole_PTase)

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

Tailoring functions

Oxidoreductases: dehydrogenase

LV78_005206: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

LV78_005207: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

LV78_005212: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Translocases: permease

LV78_005210: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001294.5	0.50	other (other)	7-prenylisatin	Streptomyces sp. MBT28
BGC0002128.3	0.48	other (other)	5-dimethylallylindole-3-acetonitrile	Streptomyces coelicolor A3(2)
BGC0001483.4	0.48	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8
BGC0001197.5	0.45	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0001924.3	0.42	terpene	ascofuranone	Acremonium egyptiacum
BGC0000706.3	0.40	saccharide	kanamycin	Streptomyces kanamyceticus
BGC0001267.3	0.39	terpene	elymoclavine, Agroclavine I	Claviceps fusiformis
BGC0001910.4	0.38	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0000671.3	0.38	terpene	momilactone B	Oryza sativa Japonica Group
BGC0001605.3	0.38	terpene	gibberellin	Sinorhizobium fredii NGR234

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001294.5	0.50	other (other)	7-prenylisatin	Streptomyces sp. MBT28
BGC0002128.3	0.48	other (other)	5-dimethylallylindole-3-acetonitrile	Streptomyces coelicolor A3(2)
BGC0001483.4	0.48	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8
BGC0001197.5	0.45	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0001924.3	0.42	terpene	ascofuranone	Acremonium egyptiacum
BGC0000706.3	0.40	saccharide	kanamycin	Streptomyces kanamyceticus
BGC0001267.3	0.39	terpene	elymoclavine, Agroclavine I	Claviceps fusiformis
BGC0001910.4	0.38	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0000671.3	0.38	terpene	momilactone B	Oryza sativa Japonica Group
BGC0001605.3	0.38	terpene	gibberellin	Sinorhizobium fredii NGR234

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (3):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.22 out of 30.22

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.28 out of 26.85

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.07 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

JAMTCF010000014.1 - Region 1 - thioamitides

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Location: 5,085 - 27,506 nt. (total: 22,422 nt) Show pHMM detection rules used

Region on contig edge.

thioamitides: ((YcaO or TIGR03604) and TfuA)

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Pfam domains

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Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Transferases: methyltransferase

LV78_005272: methyltransferase

smcogs: SMCOG1089: methyltransferase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001849.4	0.53	ribosomal	thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D	Streptomyces varsoviensis
BGC0002560.3	0.39	ribosomal	thiostreptamide S4	Streptomyces sp. NRRL S-4
BGC0002120.3	0.35	ribosomal	nocathioamide A	Nocardia terpenica IFM 0706
BGC0001802.5	0.34	ribosomal	thioholgamide A, thioholgamide B	Streptomyces malaysiense
BGC0001696.5	0.34	ribosomal	neothioviridamide	Streptomyces sp.
BGC0000625.5	0.33	ribosomal	thioviridamide	Streptomyces olivoviridis
BGC0002669.2	0.30	ribosomal	TVA-YJ-2	Streptomyces sp. NRRL S-87
BGC0001474.4	0.29	ribosomal	thiopeptin	Streptomyces tateyamensis
BGC0001471.5	0.28	ribosomal	saalfelduracin	Amycolatopsis saalfeldensis
BGC0001473.4	0.28	ribosomal	Sch 18640	Micromonospora arborensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001849.4	0.53	ribosomal	thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D	Streptomyces varsoviensis
BGC0002560.3	0.39	ribosomal	thiostreptamide S4	Streptomyces sp. NRRL S-4
BGC0002120.3	0.35	ribosomal	nocathioamide A	Nocardia terpenica IFM 0706
BGC0001802.5	0.34	ribosomal	thioholgamide A, thioholgamide B	Streptomyces malaysiense
BGC0001696.5	0.34	ribosomal	neothioviridamide	Streptomyces sp.
BGC0000625.5	0.33	ribosomal	thioviridamide	Streptomyces olivoviridis
BGC0002669.2	0.30	ribosomal	TVA-YJ-2	Streptomyces sp. NRRL S-87
BGC0001474.4	0.29	ribosomal	thiopeptin	Streptomyces tateyamensis
BGC0001471.5	0.28	ribosomal	saalfelduracin	Amycolatopsis saalfeldensis
BGC0001473.4	0.28	ribosomal	Sch 18640	Micromonospora arborensis

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:

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 19.87 out of 20.97

Confidence: strong

Additional weak hits (4):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.35 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.12 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.85 out of 28.14

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.79 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
CcpA	Catabolite control protein A

JAMTCF010000014.1 - Region 2 - NRPS

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Location: 255,406 - 282,679 nt. (total: 27,274 nt) Show pHMM detection rules used

Region on contig edge.

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

Legend:

core biosynthetic genes

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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

LV78_005514: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Ligases: ligase

LV78_005531: 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	0.67	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.66	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.65	NRPS	HC-toxin	Alternaria jesenskae
BGC0001132.4	0.65	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.65	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0000307.4	0.64	NRPS	AbT1	Aureobasidium pullulans
BGC0001128.4	0.64	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.64	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001758.4	0.64	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.63	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.67	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.66	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.65	NRPS	HC-toxin	Alternaria jesenskae
BGC0001132.4	0.65	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.65	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0000307.4	0.64	NRPS	AbT1	Aureobasidium pullulans
BGC0001128.4	0.64	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.64	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001758.4	0.64	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.63	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

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 (6):

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.68 out of 20.97

Confidence: weak

FuR variant 2

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

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.15 out of 25.75

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.88 out of 39.62

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.29 out of 36.54

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.22 out of 30.22

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 255405 - 282679:

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

LV78_005531: X

AMP-binding (601..837): 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:: ASVFVGASTK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description

JAMTCF010000015.1 - Region 1 - NRPS,NRPS-like,T1PKS

Download region GenBank file

Download region SVG

Location: 1 - 101,437 nt. (total: 101,437 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)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

LV78_005541: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

LV78_005543: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

LV78_005545: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

LV78_005562: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

LV78_005567: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

LV78_005570: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

LV78_005572: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

Transferases: acyltransferase aminotransferase glycosyltransferase halogenase methyltransferase

LV78_005542: flavin-dependent cycline orsellinic halogenase

halogenases: flavin-dependent cycline orsellinic halogenase
smcogs: SMCOG1119: halogenase

LV78_005549: acyltransferase 3

smcogs: SMCOG1088: acyltransferase 3

LV78_005561: DegT/DnrJ/EryC1/StrS aminotransferase

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

LV78_005566: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

LV78_005574: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: hydrolase phosphatase

LV78_005546: FkbH like protein

smcogs: SMCOG1256: FkbH like protein

LV78_005563: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: ligase synthase

LV78_005538: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_005555: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

LV78_005556: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

LV78_005558: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_005559: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_005564: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_005565: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	1.68	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	1.67	NRPS	AM-toxin	Alternaria alternata
BGC0001249.5	1.67	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001135.5	1.61	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	1.56	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	1.54	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	1.53	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	1.50	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	1.50	NRPS	HC-toxin	Alternaria jesenskae
BGC0001825.4	1.42	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002341.2	0.76	other (other)	3,5-dibromo-p-anisic acid	Planctomycetales bacterium 10988
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001273.3	0.74	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.74	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0000020.3	0.74	PKS	maytansine, ansamitocin P-3	Actinosynnema pretiosum subsp. auranticum
BGC0001275.3	0.74	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001261.3	0.73	NRPS	AM-toxin	Alternaria alternata
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001135.5	0.73	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001511.5	0.73	PKS	ansamitocin P-3	Actinosynnema pretiosum subsp. pretiosum

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.35 out of 18.57

Confidence: medium

IolR

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

Confidence: strong

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.41 out of 23.43

Confidence: medium

AfsR

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

Confidence: medium

VqsM

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

Confidence: medium

CatR

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

Confidence: medium

Additional weak hits (15):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.17 out of 21.55

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

ANR

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

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.00 out of 21.55

Confidence: weak

ColR

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

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.93 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.02 out of 27.78

Confidence: weak

CcpA

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

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

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.06 out of 29.65

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 15.38 out of 28.19

Confidence: weak

HypR

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

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.51 out of 24.78

Confidence: weak

PerR

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

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.83 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 1, location 0 - 36363:

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

Polymer prediction:: (Me-ohmal) + (Me-ccmal - ccmal) + (X - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 15036 - 101437:

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

Polymer prediction:: (Me-ccmal - ccmal) + (X - X) + (Ser - X) + (Cys) + (AHBA - Me-redmal - ccmal) + (ccmxmal - mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 15036 - 70906:

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

Polymer prediction:: (AHBA - Me-redmal - ccmal) + (Cys) + (Ser - X) + (X - X) + (Me-ccmal - ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 30913 - 72857:

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

Polymer prediction:: (ccmxmal - mal) + (AHBA - Me-redmal - ccmal) + (Cys) + (Ser - X) + (X - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 37483 - 101437:

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

Polymer prediction:: (ccmxmal - mal) + (AHBA - Me-redmal - ccmal) + (Cys) + (Ser - X) + (X - X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

LV78_005537: mmal

PKS_AT (559..841): 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: 196.4
Ethylmalonyl-CoA: 172.5
Methoxymalonyl-CoA: 153.8
2-Methylbutyryl-CoA: 113.6
trans-1,2-CPDA: 112.4
Malonyl-CoA: 106.7
CHC-CoA: 91.6
Propionyl-CoA: 85.4
Isobutyryl-CoA: 75.9
Benzoyl-CoA: 54.7
inactive: 49.5
3-Methylbutyryl-CoA: 35.5
Acetyl-CoA: 24.7
fatty_acid: 16.5

LV78_005538: mmal - mal

PKS_AT (557..843): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 100.0%; Methoxymalonyl-CoA: 79.2%; Malonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 185.1
Ethylmalonyl-CoA: 150.5
Methoxymalonyl-CoA: 138.5
2-Methylbutyryl-CoA: 103.3
CHC-CoA: 102.4
trans-1,2-CPDA: 93.9
Propionyl-CoA: 91.3
Malonyl-CoA: 76.1
Isobutyryl-CoA: 55.7
Benzoyl-CoA: 49.1
fatty_acid: 37.1
3-Methylbutyryl-CoA: 32.3
Acetyl-CoA: 28.9
inactive: 14.3

PKS_AT (2270..2545): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 100.0%; inactive: 62.5%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 123.5
Methoxymalonyl-CoA: 59.9
Methylmalonyl-CoA: 56.4
inactive: 36.2
Propionyl-CoA: 30.8
Ethylmalonyl-CoA: 19.7
Isobutyryl-CoA: 18.9
fatty_acid: 9.6
Benzoyl-CoA: 5.3
CHC-CoA: 4.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
trans-1,2-CPDA: -0.5
2-Methylbutyryl-CoA: -1.1

LV78_005555: X - X

AMP-binding (30..432): 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:: DPAQVSMINK
Nearest Stachelhaus code(s):: Gly DILQVGMIWK (53% 8Å match)
Stachelhaus code match:: 60% (weak)

AMP-binding (1080..1476): 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:: DARALSMMTK
Nearest Stachelhaus code(s):: Glu DPRSLSQMAK (56% 8Å match); Dpr DVRHLSMVEK (53% 8Å match); Leu DAFYLGMMCK (50% 8Å match)
Stachelhaus code match:: 60% (weak)

LV78_005558: Ser - X

Search NORINE for peptide: strict or relaxed

AMP-binding (476..875): 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:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVWHLSLIHK
Nearest Stachelhaus code(s):: Ser DVWHLSLIDK (76% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1511..1898): 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:: DARARSLMTK
Nearest Stachelhaus code(s):: Ala DAWHISLMDK (44% 8Å match)
Stachelhaus code match:: 60% (weak)

LV78_005559: Cys

Search NORINE for peptide: strict or relaxed

AMP-binding (45..439): Cys

nrpys: Cys

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:: Polar, uncharged (aliphatic with -SH) (Cys)
Small clusters prediction:: Polar, uncharged (aliphatic with -SH) (Cys)
Single AA prediction:: Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:

Stachelhaus sequence:: DLYNLSLIWK
Nearest Stachelhaus code(s):: Cys DLYNLSLIWK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

LV78_005564: AHBA - mmal - mal

CAL_domain (34..434): AHBA

minowa: AHBA

Prediction, score:

AHBA: 509.2
shikimic_acid: 244.0
Acetyl-CoA: 10.0
fatty_acid: 0.0
NH2: -1.4

PKS_AT (1501..1784): 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: 198.7
Ethylmalonyl-CoA: 178.8
Methoxymalonyl-CoA: 160.9
trans-1,2-CPDA: 121.6
2-Methylbutyryl-CoA: 111.0
Malonyl-CoA: 105.8
Propionyl-CoA: 89.0
CHC-CoA: 86.4
Isobutyryl-CoA: 69.3
Benzoyl-CoA: 55.5
inactive: 47.9
3-Methylbutyryl-CoA: 31.5
Acetyl-CoA: 26.0
fatty_acid: 21.5

PKS_AT (3556..3835): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 66.7%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 143.6
inactive: 52.7
Methoxymalonyl-CoA: 51.8
Methylmalonyl-CoA: 43.5
fatty_acid: 15.2
Ethylmalonyl-CoA: 14.4
Isobutyryl-CoA: 11.7
Benzoyl-CoA: 9.3
Propionyl-CoA: 7.5
2-Methylbutyryl-CoA: 5.6
CHC-CoA: 3.7
trans-1,2-CPDA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

LV78_005565: mxmal - mal

PKS_AT (864..1156): mxmal

ATSignature: Methoxymalonyl-CoA

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

minowa: Methoxymalonyl-CoA

Prediction, score:

Methoxymalonyl-CoA: 186.1
Methylmalonyl-CoA: 181.8
Ethylmalonyl-CoA: 173.3
trans-1,2-CPDA: 112.4
Malonyl-CoA: 100.6
2-Methylbutyryl-CoA: 98.3
Propionyl-CoA: 83.9
CHC-CoA: 82.8
Isobutyryl-CoA: 74.8
Acetyl-CoA: 49.5
3-Methylbutyryl-CoA: 48.9
Benzoyl-CoA: 44.5
inactive: 37.7
fatty_acid: 20.5

PKS_AT (2520..2803): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 79.2%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 159.5
inactive: 70.0
Methoxymalonyl-CoA: 57.1
Methylmalonyl-CoA: 50.2
Propionyl-CoA: 32.5
Ethylmalonyl-CoA: 24.6
2-Methylbutyryl-CoA: 18.7
fatty_acid: 16.0
CHC-CoA: 15.7
Benzoyl-CoA: 9.8
trans-1,2-CPDA: 9.4
Isobutyryl-CoA: 7.1
Acetyl-CoA: 6.2
3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
BldD	Development and antibiotic global regulator
CatR	H2O2-responsive repressor
IolR	Regulator of the inositol catabolism
ToxT	Regulator of MSHA biosynthesis
VqsM	Regulator of quorum-sensing signalling systems

JAMTCF010000015.1 - Region 2 - NRPS-like,T1PKS

Download region GenBank file

Download region SVG

Location: 140,262 - 222,826 nt. (total: 82,565 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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

LV78_005619: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

LV78_005620: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

LV78_005622: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

LV78_005624: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

LV78_005631: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

LV78_005633: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

Transferases: aminotransferase methyltransferase

LV78_005617: methyltransferase

smcogs: SMCOG1089: methyltransferase

LV78_005618: methyltransferase

smcogs: SMCOG1089: methyltransferase

LV78_005630: DegT/DnrJ/EryC1/StrS aminotransferase

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

Hydrolases: hydrolase phosphatase

LV78_005625: FkbH like protein

smcogs: SMCOG1256: FkbH like protein

LV78_005632: HAD-superfamily hydrolase, subfamily IA, variant

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

LV78_005650: isochorismatase

smcogs: SMCOG1027: isochorismatase

Ligases: synthase

LV78_005635: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

LV78_005636: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_005637: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

LV78_005639: 3-dehydroquinate synthase

smcogs: SMCOG1183: 3-dehydroquinate synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000090.4	0.89	PKS	macbecin, macbecin II	Actinosynnema pretiosum subsp. pretiosum
BGC0001275.3	0.84	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.83	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.83	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0000041.3	0.77	PKS	oronofacic acid	Pseudomonas syringae
BGC0000067.5	0.77	PKS	geldanamycin	Streptomyces hygroscopicus subsp. duamyceticus
BGC0001276.3	0.59	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002192.3	0.55	PKS	FR901512	fungal sp. No.14919
BGC0001268.4	0.53	NRPS, PKS	fusarin C	Fusarium fujikuroi
BGC0001012.3	0.44	NRPS, PKS	meridamycin	Streptomyces violaceusniger

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000090.4	0.88	PKS	macbecin, macbecin II	Actinosynnema pretiosum subsp. pretiosum
BGC0000067.5	0.79	PKS	geldanamycin	Streptomyces hygroscopicus subsp. duamyceticus
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	0.71	PKS	oronofacic acid	Pseudomonas syringae
BGC0001276.3	0.63	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002192.3	0.61	PKS	FR901512	fungal sp. No.14919
BGC0000068.5	0.61	PKS	geldanamycin	Streptomyces hygroscopicus
BGC0001268.4	0.60	NRPS, PKS	fusarin C	Fusarium fujikuroi

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.93 out of 20.97

Confidence: medium

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 27.04 out of 30.11

Confidence: strong

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.56 out of 30.11

Confidence: medium

Additional weak hits (18):

ClgR

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

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 12.56 out of 18.57

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.41 out of 26.85

Confidence: weak

CodY

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

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 11.53 out of 28.14

Confidence: weak

ANR

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

Confidence: weak

ANR

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

Confidence: weak

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.46 out of 29.51

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 14.67 out of 20.97

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.82 out of 21.55

Confidence: weak

CopR

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

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.67 out of 24.78

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.57 out of 23.43

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.78 out of 20.97

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.79 out of 30.25

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.20 out of 29.65

Confidence: weak

ToxT

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.52 out of 26.06

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 6, location 140261 - 222826:

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

Polymer prediction:: (AHBA - Me-redmal - pk - Me-ohmal) + (Me-ccmal - Me-ohmal) + (redmal - Me-ccmal)
Non-colinear ordering:: LV78_005637 + LV78_005636 + LV78_005635

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

LV78_005635: mal - mmal

PKS_AT (651..946): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 83.3%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 190.0
inactive: 94.1
Methylmalonyl-CoA: 67.1
Methoxymalonyl-CoA: 66.8
Propionyl-CoA: 29.7
Isobutyryl-CoA: 26.9
Ethylmalonyl-CoA: 22.4
Acetyl-CoA: 21.7
CHC-CoA: 11.6
Benzoyl-CoA: 10.5
2-Methylbutyryl-CoA: 6.1
trans-1,2-CPDA: 4.9
fatty_acid: 0.0
3-Methylbutyryl-CoA: -0.6

PKS_AT (2737..3030): 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: 199.9
Ethylmalonyl-CoA: 176.6
Methoxymalonyl-CoA: 169.6
Malonyl-CoA: 109.4
2-Methylbutyryl-CoA: 104.1
Propionyl-CoA: 87.4
trans-1,2-CPDA: 87.0
Benzoyl-CoA: 64.4
Isobutyryl-CoA: 60.6
CHC-CoA: 59.7
fatty_acid: 42.6
Acetyl-CoA: 35.4
inactive: 32.5
3-Methylbutyryl-CoA: 24.2

LV78_005636: mmal - mmal

PKS_AT (562..854): 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: 209.5
Ethylmalonyl-CoA: 189.8
Methoxymalonyl-CoA: 170.1
2-Methylbutyryl-CoA: 129.3
trans-1,2-CPDA: 108.7
Propionyl-CoA: 99.9
CHC-CoA: 96.2
Malonyl-CoA: 95.1
Isobutyryl-CoA: 84.4
Benzoyl-CoA: 61.7
3-Methylbutyryl-CoA: 39.2
Acetyl-CoA: 38.0
fatty_acid: 31.8
inactive: 20.2

PKS_AT (2277..2570): 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: 194.6
Ethylmalonyl-CoA: 173.5
Methoxymalonyl-CoA: 166.8
Malonyl-CoA: 105.7
2-Methylbutyryl-CoA: 104.9
Propionyl-CoA: 89.3
trans-1,2-CPDA: 88.5
CHC-CoA: 71.7
Isobutyryl-CoA: 69.4
Benzoyl-CoA: 54.3
Acetyl-CoA: 46.6
fatty_acid: 36.9
inactive: 36.4
3-Methylbutyryl-CoA: 35.6

LV78_005637: AHBA - mmal - pk - mmal

CAL_domain (35..443): AHBA

minowa: AHBA

Prediction, score:

AHBA: 491.6
shikimic_acid: 283.1
Acetyl-CoA: 22.5
NH2: 9.2
fatty_acid: 0.0

PKS_AT (1734..2030): 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: 194.4
Ethylmalonyl-CoA: 185.5
Methoxymalonyl-CoA: 157.2
2-Methylbutyryl-CoA: 113.2
Propionyl-CoA: 106.5
trans-1,2-CPDA: 98.7
Malonyl-CoA: 98.1
CHC-CoA: 82.0
Isobutyryl-CoA: 66.2
Benzoyl-CoA: 54.8
Acetyl-CoA: 51.3
inactive: 31.7
fatty_acid: 26.2
3-Methylbutyryl-CoA: 22.4

PKS_AT (3779..4079): pk

ATSignature: Methoxymalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 192.8
Methoxymalonyl-CoA: 183.9
Ethylmalonyl-CoA: 183.3
2-Methylbutyryl-CoA: 139.1
trans-1,2-CPDA: 120.9
Malonyl-CoA: 110.3
Propionyl-CoA: 103.9
CHC-CoA: 85.0
Isobutyryl-CoA: 64.7
Benzoyl-CoA: 55.6
Acetyl-CoA: 51.7
fatty_acid: 31.8
inactive: 30.8
3-Methylbutyryl-CoA: 29.3

PKS_AT (5787..6079): 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: 205.4
Ethylmalonyl-CoA: 192.6
Methoxymalonyl-CoA: 163.7
2-Methylbutyryl-CoA: 117.5
trans-1,2-CPDA: 105.2
CHC-CoA: 101.4
Propionyl-CoA: 95.2
Malonyl-CoA: 90.6
Isobutyryl-CoA: 87.8
Benzoyl-CoA: 62.6
Acetyl-CoA: 39.5
3-Methylbutyryl-CoA: 31.8
fatty_acid: 25.4
inactive: 14.3

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
CelR	Cellobiose uptake repressor
VqsM	Regulator of quorum-sensing signalling systems

JAMTCF010000015.1 - Region 3 - lassopeptide

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Location: 239,368 - 261,831 nt. (total: 22,464 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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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

LV78_005688: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase

LV78_005681: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001551.4	0.65	ribosomal	citrulassin E	Streptomyces glaucescens
BGC0001889.2	0.64	ribosomal	fusilassin	Thermobifida fusca YX
BGC0001493.5	0.62	ribosomal	achromosin	Streptomyces achromogenes subsp. achromogenes
BGC0001539.4	0.60	ribosomal	cattlecin	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001548.4	0.60	ribosomal	citrulassin A	Streptomyces albulus
BGC0002074.2	0.60	ribosomal	huascopeptin	Streptomyces huasconensis
BGC0002053.3	0.60	ribosomal	ulleungdin	Streptomyces sp.
BGC0001506.5	0.60	ribosomal	anantin B1, anantin B2	Streptomyces sp. NRRL S-146
BGC0002064.2	0.59	ribosomal	felipeptin A2, felipeptin A1	Amycolatopsis sp. YIM 10
BGC0001507.3	0.58	ribosomal	anantin C	Streptomyces olindensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001551.4	0.65	ribosomal	citrulassin E	Streptomyces glaucescens
BGC0001889.2	0.64	ribosomal	fusilassin	Thermobifida fusca YX
BGC0001493.5	0.62	ribosomal	achromosin	Streptomyces achromogenes subsp. achromogenes
BGC0001539.4	0.60	ribosomal	cattlecin	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001548.4	0.60	ribosomal	citrulassin A	Streptomyces albulus
BGC0002074.2	0.60	ribosomal	huascopeptin	Streptomyces huasconensis
BGC0002053.3	0.60	ribosomal	ulleungdin	Streptomyces sp.
BGC0001506.5	0.60	ribosomal	anantin B1, anantin B2	Streptomyces sp. NRRL S-146
BGC0002064.2	0.59	ribosomal	felipeptin A2, felipeptin A1	Amycolatopsis sp. YIM 10
BGC0001507.3	0.58	ribosomal	anantin C	Streptomyces olindensis

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: 20.80 out of 23.79

Confidence: strong

VqsM

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

Confidence: medium

AbrC3

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

Confidence: strong

Additional weak hits (20):

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.29 out of 25.88

Confidence: weak

MntR

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

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.01 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.75 out of 29.38

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.56 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.12 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.66 out of 30.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.77 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.46 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.38 out of 28.14

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.59 out of 27.78

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.82 out of 27.55

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.45 out of 35.63

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.17 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.19 out of 28.19

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.09 out of 30.98

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.82 out of 30.98

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.17 out of 28.19

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.33 out of 35.63

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.98 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

Lasso peptides

RREFinder

TFBS Finder

Core peptide predictions

No core peptides found.

RRE predictions

: RRE type: Stand_Alone_Lasso_RRE; Location: 0 - 82; Score: 69.2; RRE type: Lasso_Fused_RRE; Location: 0 - 51; Score: 28.9

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

JAMTCF010000016.1 - Region 1 - CDPS

Download region GenBank file

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Location: 4,493 - 25,194 nt. (total: 20,702 nt) Show pHMM detection rules used

CDPS: CDPS

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

LV78_005714: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase

LV78_005711: methyltransferase

smcogs: SMCOG1089: methyltransferase

Ligases: ligase synthase

LV78_005707: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

LV78_005713: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000851.5	0.46	other (other)	albonoursin	Streptomyces noursei ATCC 11455
BGC0001948.3	0.45	other (other)	naseseazine C, C3-aryl pyrroloindolines	Streptomyces sp.
BGC0002103.2	0.42	other (other)	pulcherriminic acid	Bacillus subtilis subsp. subtilis str. 168
BGC0001197.5	0.41	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0000231.5	0.41	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0001294.5	0.41	other (other)	7-prenylisatin	Streptomyces sp. MBT28
BGC0001295.5	0.38	other (other)	cremeomycin	Streptomyces cremeus
BGC0000234.5	0.38	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0000218.5	0.38	PKS	doxorubicin	Streptomyces peucetius
BGC0000204.5	0.38	PKS	benastatin A, benastatin B, BE-43767, TAN1532B	Streptomyces sp. A2991200

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000851.5	0.46	other (other)	albonoursin	Streptomyces noursei ATCC 11455
BGC0001948.3	0.45	other (other)	naseseazine C, C3-aryl pyrroloindolines	Streptomyces sp.
BGC0002103.2	0.42	other (other)	pulcherriminic acid	Bacillus subtilis subsp. subtilis str. 168
BGC0001197.5	0.41	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0000231.5	0.41	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0001294.5	0.41	other (other)	7-prenylisatin	Streptomyces sp. MBT28
BGC0001295.5	0.38	other (other)	cremeomycin	Streptomyces cremeus
BGC0000234.5	0.38	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0000218.5	0.38	PKS	doxorubicin	Streptomyces peucetius
BGC0000204.5	0.38	PKS	benastatin A, benastatin B, BE-43767, TAN1532B	Streptomyces sp. A2991200

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.69 out of 30.11

Confidence: medium

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 24.01 out of 30.11

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 (7):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.47 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.51 out of 26.06

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.11 out of 32.74

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.36 out of 26.06

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.14 out of 35.63

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.81 out of 23.43

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.20 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

NRPS/PKS substrates

TFBS Finder

NRPS/PKS substrate predictions

LV78_005713: X

AMP-binding (47..434): 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:: AAWEINGGMK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CelR	Cellobiose uptake repressor
VqsM	Regulator of quorum-sensing signalling systems

JAMTCF010000016.1 - Region 2 - NRPS,T1PKS,betalactone,crocagin

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Location: 67,564 - 198,804 nt. (total: 131,241 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))
betalactone: (HMGL-like and AMP-binding)
crocagin: (PhyH and Carbam_trans_N)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

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

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

LV78_005760: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

LV78_005766: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

LV78_005771: flavin reductase domain protein FMN-binding

smcogs: SMCOG1160: flavin reductase domain protein FMN-binding

LV78_005787: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

LV78_005811: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

LV78_005820: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

LV78_005834: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: acyltransferase glycosyltransferase

LV78_005785: polyketide synthase associated protein papA3

smcogs: SMCOG1209: polyketide synthase associated protein papA3

LV78_005819: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

Hydrolases: esterase peptidase protease

LV78_005764: gamma-glutamyltranspeptidase

smcogs: SMCOG1274: gamma-glutamyltranspeptidase

LV78_005779: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

LV78_005796: thioesterase

smcogs: SMCOG1004: thioesterase

LV78_005801: thioesterase

smcogs: SMCOG1004: thioesterase

Lyases: lyase

LV78_005783: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Isomerases: isomerase

LV78_005772: isochorismate synthase

smcogs: SMCOG1018: isochorismate synthase

LV78_005776: isochorismate synthase

smcogs: SMCOG1018: isochorismate synthase

Ligases: ligase synthase

LV78_005774: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

LV78_005775: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_005799: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_005800: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_005802: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_005804: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_005806: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_005812: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_005821: polyprenol-monophosphomannose synthase ppm1

smcogs: SMCOG1123: polyprenol-monophosphomannose synthase ppm1

LV78_005823: 2-isopropylmalate synthase

smcogs: SMCOG1271: 2-isopropylmalate synthase

LV78_005826: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_005827: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

LV78_005836: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001132.4	1.17	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0000357.5	1.16	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
BGC0001261.3	1.16	NRPS	AM-toxin	Alternaria alternata
BGC0002135.2	1.15	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002286.3	1.14	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	1.14	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	1.13	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001135.5	1.12	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001249.5	1.11	NRPS	dimethylcoprogen	Alternaria alternata
BGC0000342.4	1.08	NRPS	enniatin	Fusarium equiseti

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
BGC0001128.4	0.73	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.73	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.73	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.73	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001135.5	0.73	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0000448.5	0.71	NRPS	tomaymycin	Streptomyces achromogenes
BGC0001166.5	0.71	NRPS	HC-toxin	Alternaria jesenskae

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: 19.35 out of 20.47

Confidence: strong

VqsM

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

Confidence: medium

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 23.16 out of 26.33

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

CRP

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

Confidence: medium

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.15 out of 29.72

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.85 out of 23.79

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.37 out of 23.79

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 (36):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.03 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.46 out of 28.14

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.93 out of 29.25

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.90 out of 31.73

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.59 out of 27.78

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: 18.31 out of 27.78

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.33 out of 30.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.62 out of 26.06

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.46 out of 20.97

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.17 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.56 out of 29.38

Confidence: weak

ANR

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

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.28 out of 20.97

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.85 out of 36.53

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.13 out of 28.19

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.29 out of 32.93

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.74 out of 20.01

Confidence: weak

MexT

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

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.57 out of 23.43

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.28 out of 30.25

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.80 out of 28.14

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.93 out of 27.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.82 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.33 out of 27.78

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.93 out of 20.97

Confidence: weak

ColR

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

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.78 out of 25.88

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.60 out of 20.97

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.47 out of 32.93

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.21 out of 35.63

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.64 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.46 out of 29.65

Confidence: weak

HypR

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

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.16 out of 24.78

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.75 out of 27.18

Confidence: weak

Module view

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Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 2, location 67563 - 198804:

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

Polymer prediction:: (ccmal) + (Arg - X) + (ccmal) + (Gly) + (Gly) + (ccmal) + (X) + (X) + (Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 67563 - 131467:

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

Polymer prediction:: (ccmal) + (X) + (X) + (Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 106259 - 183211:

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

Polymer prediction:: (X) + (ccmal) + (Gly) + (Gly) + (ccmal) + (Arg - X) + (ccmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

LV78_005774: Pro

Search NORINE for peptide: strict or relaxed

AMP-binding (560..959): 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:: DVMYAVMLAK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

LV78_005775: X

AMP-binding (33..426): 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:: AAISLSGTIK
Nearest Stachelhaus code(s):: diOH-Bz AANFVSGAIK (62% 8Å match); mxAnt AATHLSATLK (56% 8Å match)
Stachelhaus code match:: 60% (weak)

LV78_005784: X

AMP-binding (80..469): 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:: DSHEIGGVAK
Nearest Stachelhaus code(s):: Lys DVFESGGVAK (47% 8Å match)
Stachelhaus code match:: 70% (weak)

LV78_005785: X

AMP-binding (474..865): 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:: DVLKVGSVLK
Nearest Stachelhaus code(s):: Glu DVLKVGAVNK (62% 8Å match)
Stachelhaus code match:: 80% (moderate)

LV78_005799: mal

PKS_AT (545..824): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 79.2%; inactive: 66.7%; Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 118.2
Methoxymalonyl-CoA: 65.9
Methylmalonyl-CoA: 61.8
Propionyl-CoA: 51.8
inactive: 50.4
CHC-CoA: 37.5
2-Methylbutyryl-CoA: 30.5
Ethylmalonyl-CoA: 25.0
trans-1,2-CPDA: 19.4
fatty_acid: 16.1
Benzoyl-CoA: 13.5
Acetyl-CoA: 12.0
Isobutyryl-CoA: 8.1
3-Methylbutyryl-CoA: 0.0

LV78_005800: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (460..838): 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:: DILQLGVIWK
Nearest Stachelhaus code(s):: Gly DILQLGVIWK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

LV78_005802: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (451..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:: DILQLGVIWK
Nearest Stachelhaus code(s):: Gly DILQLGVIWK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

LV78_005804: mal

PKS_AT (531..807): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 83.3%; inactive: 70.8%; Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 98.4
Methylmalonyl-CoA: 53.8
Propionyl-CoA: 49.9
Methoxymalonyl-CoA: 47.7
2-Methylbutyryl-CoA: 39.3
inactive: 34.4
CHC-CoA: 26.9
Ethylmalonyl-CoA: 26.7
trans-1,2-CPDA: 19.7
Benzoyl-CoA: 19.5
Acetyl-CoA: 19.3
fatty_acid: 13.2
Isobutyryl-CoA: 13.1
3-Methylbutyryl-CoA: 0.0

LV78_005806: Arg - X

Search NORINE for peptide: strict or relaxed

AMP-binding (0..393): Arg

nrpys: Arg

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DVGDIGAVEK
Nearest Stachelhaus code(s):: Arg DVGDIGAVTK (59% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1036..1414): X

nrpys: Asp, Asn, Glu, Gln, Aad

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DPRHVGAVAK
Nearest Stachelhaus code(s):: Asp DPRHVSLLAK (56% 8Å match); D-Asp DPRHVGIFIK (50% 8Å match); Leu DALLVGAVAK (47% 8Å match); Trp DVGMVGAVAK (44% 8Å match)
Stachelhaus code match:: 70% (weak)

LV78_005812: mal

PKS_AT (541..826): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 77.3
Methoxymalonyl-CoA: 42.3
Methylmalonyl-CoA: 38.2
Propionyl-CoA: 34.4
inactive: 23.4
Isobutyryl-CoA: 23.4
CHC-CoA: 8.8
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Ethylmalonyl-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

LV78_005826: X

AMP-binding (1..368): 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:: AALTNAGPLK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
CRP	Cyclic AMP receptor protein
IolR	Regulator of the inositol catabolism
NtrC	Nitrogen regulatory protein C
VqsM	Regulator of quorum-sensing signalling systems

JAMTCF010000018.1 - Region 1 - azole-containing-RiPP

Download region GenBank file

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Location: 45,073 - 72,136 nt. (total: 27,064 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)

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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

Azole RiPPs

Pfam domains

TIGRFAM 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

Hydrolases: hydrolase

LV78_006132: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000606.5	0.55	ribosomal	lactazole	Streptomyces lactacystinaeus
BGC0002311.3	0.46	ribosomal	cutimycin	Cutibacterium acnes KPA171202
BGC0002013.4	0.46	ribosomal	curacozole	Streptomyces curacoi
BGC0001174.4	0.45	ribosomal	corynazolicin	Corynebacterium urealyticum DSM 7111
BGC0002316.2	0.44	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0001146.5	0.43	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0001145.5	0.42	ribosomal	cyclothiazomycin b1	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001640.3	0.41	ribosomal	kocurin	Kocuria rosea
BGC0000603.5	0.41	ribosomal	cyclothiazomycin	Streptomyces hygroscopicus
BGC0001860.4	0.40	ribosomal	thiomuracin	Thermobispora bispora DSM 43833

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000606.5	0.55	ribosomal	lactazole	Streptomyces lactacystinaeus
BGC0002311.3	0.46	ribosomal	cutimycin	Cutibacterium acnes KPA171202
BGC0002013.4	0.46	ribosomal	curacozole	Streptomyces curacoi
BGC0001174.4	0.45	ribosomal	corynazolicin	Corynebacterium urealyticum DSM 7111
BGC0002316.2	0.44	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0001146.5	0.43	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0001145.5	0.42	ribosomal	cyclothiazomycin b1	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001640.3	0.41	ribosomal	kocurin	Kocuria rosea
BGC0000603.5	0.41	ribosomal	cyclothiazomycin	Streptomyces hygroscopicus
BGC0001860.4	0.40	ribosomal	thiomuracin	Thermobispora bispora DSM 43833

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: medium

Additional weak hits (15):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.65 out of 29.38

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.41 out of 29.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.34 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.13 out of 26.06

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.81 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.05 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.79 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.84 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.93 out of 27.78

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.79 out of 20.97

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.23 out of 29.65

Confidence: weak

ToxT

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

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.82 out of 28.19

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.35 out of 24.78

Confidence: weak

(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: 1 - 87; Score: 40.8

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

Core peptide predictions

No core peptides found.

JAMTCF010000018.1 - Region 2 - terpene

Download region GenBank file

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Location: 96,062 - 132,801 nt. (total: 36,740 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 oxidoreductase

LV78_006158: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

LV78_006164: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

LV78_006168: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

LV78_006174: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: methyltransferase

LV78_006163: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: protease

LV78_006182: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

Lyases: cyclase

LV78_006177: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthase synthetase

LV78_006167: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

LV78_006178: 1-deoxy-D-xylulose-5-phosphate synthase

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

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000664.5	0.70	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3	0.65	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3	0.60	terpene	isorenieratene	Streptomyces argillaceus
BGC0000633.3	0.59	terpene	carotenoid	Streptomyces avermitilis
BGC0001227.3	0.59	terpene	isorenieratene	Streptomyces collinus Tu 365
BGC0001361.3	0.58	terpene	sodorifen	Serratia plymuthica 4Rx13
BGC0002283.2	0.58	terpene	sodorifen	Serratia plymuthica
BGC0000636.3	0.54	terpene	carotenoid	Brevibacterium linens
BGC0000648.3	0.53	terpene	carotenoid	Myxococcus xanthus
BGC0002309.2	0.50	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000664.5	0.70	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3	0.65	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3	0.60	terpene	isorenieratene	Streptomyces argillaceus
BGC0000633.3	0.59	terpene	carotenoid	Streptomyces avermitilis
BGC0001227.3	0.59	terpene	isorenieratene	Streptomyces collinus Tu 365
BGC0001361.3	0.58	terpene	sodorifen	Serratia plymuthica 4Rx13
BGC0002283.2	0.58	terpene	sodorifen	Serratia plymuthica
BGC0000636.3	0.54	terpene	carotenoid	Brevibacterium linens
BGC0000648.3	0.53	terpene	carotenoid	Myxococcus xanthus
BGC0002309.2	0.50	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	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
tetraterpene	C40 carotenoid		C40	unknown	unknown

Genes with terpene domains:

LV78_006161: Lycopene_cycl

Domain 1 (5 - 94): Lycopene cyclase

Reactions:: C40_carotenoid → C40_carotenoid

LV78_006162: Lycopene_cycl

Domain 1 (11 - 94): Lycopene cyclase

Reactions:: C40_carotenoid → C40_carotenoid

LV78_006166: PT_phytoene_like

Domain 1 (17 - 308): Prenyltransferase; Phytoene synthase like

Subtype: unknown

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

LV78_006167: PT_FPPS_like

Domain 1 (50 - 352): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

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

LV78_006177: T1TS

Domain 1 (4 - 288): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: medium

AfsQ1

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

Confidence: medium

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.95 out of 29.51

Confidence: medium

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.86 out of 30.25

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.00 out of 23.79

Confidence: medium

Additional weak hits (14):

MogR

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

Confidence: weak

MogR

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

Confidence: weak

NtrC

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

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.21 out of 31.73

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.58 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.38 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.81 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.93 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.38 out of 29.38

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.48 out of 30.25

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.54 out of 18.57

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.09 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.67 out of 28.19

Confidence: weak

AfsQ1

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

Confidence: weak

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
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
ColR	Phenol-responsive regulator
DosR	Hypoxia stress response regulator
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

JAMTCF010000019.1 - Region 1 - lanthipeptide-class-ii

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Location: 12,486 - 35,623 nt. (total: 23,138 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 oxidoreductase

LV78_006270: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

LV78_006281: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

Lyases: cyclase

LV78_006277: lanthionine synthetase C family protein

smcogs: SMCOG1070: lanthionine synthetase C family protein

Translocases: transporter

LV78_006273: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

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
BGC0002703.2	0.49	ribosomal	archalan α	Halorussus salinus
BGC0000554.4	0.48	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998
BGC0002704.2	0.47	ribosomal	archalan β	Halorussus salinus
BGC0001660.3	0.47	ribosomal	mathermycin	Marinactinospora thermotolerans
BGC0001210.5	0.45	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0001407.5	0.43	ribosomal	bicereucin	Bacillus cereus SJ1
BGC0002699.2	0.43	ribosomal	nostolysamide A, nostolysamide B	Nostoc punctiforme PCC 73102
BGC0000527.5	0.43	ribosomal	mersacidin	Bacillus sp. HIL-Y85/54728
BGC0000517.4	0.41	ribosomal	haloduracin β, haloduracin α	Bacillus halodurans C-125

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000525.5	0.50	ribosomal	lichenicidin VK21 A1, lichenicidin VK21 A2	Bacillus licheniformis
BGC0002703.2	0.49	ribosomal	archalan α	Halorussus salinus
BGC0000554.4	0.48	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998
BGC0002704.2	0.47	ribosomal	archalan β	Halorussus salinus
BGC0001660.3	0.47	ribosomal	mathermycin	Marinactinospora thermotolerans
BGC0001210.5	0.45	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0001407.5	0.43	ribosomal	bicereucin	Bacillus cereus SJ1
BGC0002699.2	0.43	ribosomal	nostolysamide A, nostolysamide B	Nostoc punctiforme PCC 73102
BGC0000527.5	0.43	ribosomal	mersacidin	Bacillus sp. HIL-Y85/54728
BGC0000517.4	0.41	ribosomal	haloduracin β, haloduracin α	Bacillus halodurans C-125

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for LV78_006277

allorf_013843_014079

Leader:

MALAGLRERVGDPVGA

Core:

GRKTTLVRCHAPKNRQTRCVTTGNGVQPSCNRRPSAFRPFRYPDAAGQIRNDPTALLITLRK

Core with dehydrations:

GRKDhbDhbLVRCysHAPKNRQDhbRCysVDhbDhbGNGVQPDhaCysNRRPDhaAFRPFRYPDAAGQIRNDPDhbALLIDhbLRK

antiSMASH-DB 4.0 matches for allorf_013843_014079

16.1%

NZ_GG657757.1and 1 other:

NZ_GG657757.1 Lanthipeptides: allorf_4712210_4712371_lanthipeptide

Lanthipeptides: allorf_4712210_4712371_lanthipeptide

36

AFRPFRYPDAAGQIRNDPTA

55

A RP RYP N PTA

12

ALRPVRYPACVLSSANQPTA

31

12.9%

NZ_AQRJ01000038.1and 1 other:

NZ_AQRJ01000038.1 Lanthipeptides: YW7_RS06850_lanthipeptide

Lanthipeptides: YW7_RS06850_lanthipeptide

20

VTTGNGVQPSCNRRPSAFRPF

40

+TG+G P+C SA F

5

CSTGDGCGPTCQGGASACNSF

25

12.9%

NZ_BKZV01000001.1:

Lanthipeptides: allorf_0679543_0679704_lanthipeptide

13

KNRQTRCVTTGN

24

KNR RC TGN

20

KNRGERCEKTGN

31

with 3 more sequence matches

12.9%

NZ_CP011131.1:

Lanthipeptides: allorf_2170870_2171055_lanthipeptide

13

KNRQTRCVTTGNGVQPSCNRR

33

+ R+ R + TG PS +RR

14

ETRRPRAIKTGGSPTPSLDRR

34

11.3%

NZ_CP054019.1:

Lanthipeptides: allorf_9072958_9073107_lanthipeptide

9

CHAPKNRQTRCVTTG

23

CHAP + Q ++TG

9

CHAPPHAQRESLSTG

23

11.3%

NZ_FNVU01000016.1and 1 other:

NZ_FNVU01000016.1 Lanthipeptides: C4U44_RS29500_lanthipeptide

Lanthipeptides: C4U44_RS29500_lanthipeptide

20

VTTGNGVQPSCNRRPSAFRPF

40

+TG+G +C+ SA F

5

CSTGDGCGSTCSNGASACNSF

25

MIBiG 4.0 matches for allorf_013843_014079

8.1%

BGC0001229.4 (SBI_06990):

Lanthipeptide: SBI-06990 A1 or SBI-06989 A2

21

TTGNGVQPSCN

31

T QP+CN

29

TLSKECQPNCN

39

6.5%

BGC0002110.3 (QKV49893.1):

Lanthipeptide: birimositide

26

VQPSCN

31

QP+CN

25

CQPNCN

30

allorf_020699_020893

Leader:

MGGARSWRGEGSAGCRRSAGRRLGERALGWTGGRRDRVGGERGRVAVG

Core:

GCGRGARAGVTQASGG

Core with dehydrations:

GCysGRGARAGVDhbQADhaGG

allorf_027129_027332

Leader:

MTIARWEGERRRVKGG

Core:

AGGGGGWLGPVGGAGGCERGELGGGGVMGVVAGGDGCWLSGELHPWLLCRP

Core with dehydrations:

AGGGGGWLGPVGGAGGCysERGELGGGGVMGVVAGGDGCysWLDhaGELHPWLLCysRP

antiSMASH-DB 4.0 matches for allorf_027129_027332

11.8%

NZ_JAQCXO010000012.1:

Lanthipeptides: allorf_079305_079412_lanthipeptide

39

LSGELHPWLLC

49

L+ E+H WL C

4

LNSEIHKWLSC

14

MIBiG 4.0 matches for allorf_027129_027332

7.8%

BGC0000580.3 (EGD17355.1):

Lasso peptide: xanthomonin II or xanthomonin I

21

ELGGGGVMGV

30

E+GG +G+

8

EMGGITTLGI

17

7.8%

BGC0001229.4 (SBI_06989):

Lanthipeptide: SBI-06990 A1 or SBI-06989 A2

25

GGVMGVVA

32

G ++G+VA

7

GLILGIVA

14

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

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

AfsQ1

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

Confidence: strong

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 21.26 out of 23.43

Confidence: medium

Additional weak hits (10):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.54 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.77 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.57 out of 29.38

Confidence: weak

HexR

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

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.66 out of 29.65

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.78 out of 23.43

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.37 out of 30.98

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.09 out of 23.43

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.16 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.17 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

allorf_013843_014079 - Class II

Cleavage pHMM score: -7.20

RODEO score: 0

Monoisotopic mass: 6797.7 Da

Molecular weight: 6801.8 Da

Number of bridges: 3

Alternative weights: (assuming N unmodified Ser/Thr residues); 6819.8 Da N = 1; 6837.8 Da N = 2; 6855.8 Da N = 3; 6873.9 Da N = 4; 6891.9 Da N = 5; 6909.9 Da N = 6

allorf_020699_020893 - Class II

Cleavage pHMM score: -4.80

RODEO score: 0

Monoisotopic mass: 1367.7 Da

Molecular weight: 1368.5 Da

Number of bridges: 1

Alternative weights: (assuming N unmodified Ser/Thr residues); 1386.5 Da N = 1

allorf_027129_027332 - Class II

Cleavage pHMM score: -1.10

RODEO score: 0

Monoisotopic mass: 4756.2 Da

Molecular weight: 4759.3 Da

Number of bridges: 1

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR	Pleiotropic regulatory for antibiotic production
BldD	Development and antibiotic global regulator

JAMTCF010000021.1 - Region 1 - NRP-metallophore,NRPS

Download region GenBank file

Download region SVG

Location: 1 - 37,911 nt. (total: 37,911 nt) Show pHMM detection rules used

Region on contig edge.

NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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 oxygenase

LV78_006565: lysine/ornithine N-monooxygenase

smcogs: SMCOG1080: lysine/ornithine N-monooxygenase

LV78_006569: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

Ligases: ligase

LV78_006563: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002424.3	1.12	NRPS	saccharochelin A, saccharochelin B, saccharochelin C, saccharochelin D, saccharochelin E, saccharochelin F, saccharochelin G, saccharochelin H	Saccharothrix sp.
BGC0002135.2	0.86	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.80	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.76	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.75	NRPS	HC-toxin	Alternaria jesenskae
BGC0001261.3	0.74	NRPS	AM-toxin	Alternaria alternata
BGC0001758.4	0.72	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001128.4	0.72	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4	0.71	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002424.3	0.82	NRPS	saccharochelin A, saccharochelin B, saccharochelin C, saccharochelin D, saccharochelin E, saccharochelin F, saccharochelin G, saccharochelin H	Saccharothrix sp.
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.72	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.70	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0001758.4	0.69	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001128.4	0.69	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4	0.68	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0002286.3	0.68	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.44 out of 36.53

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.17 out of 27.04

Confidence: medium

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.45 out of 36.53

Confidence: medium

AfsQ1

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

Confidence: strong

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 30.11

Confidence: strong

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 30.11

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

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: 17.68 out of 20.47

Confidence: medium

Additional weak hits (9):

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.72 out of 32.74

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.49 out of 21.55

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 20.98 out of 36.53

Confidence: weak

AfsQ1

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

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.68 out of 20.97

Confidence: weak

ClgR

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

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.36 out of 30.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.90 out of 26.06

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.46 out of 28.19

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 37911:

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

Polymer prediction:: (Fo-OH-Orn - Ser - OH-Orn - X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

LV78_006563: Fo-OH-Orn - Ser - OH-Orn - X

Search NORINE for peptide: strict or relaxed

AMP-binding (424..798): Fo-OH-Orn

nrpys: Fo-OH-Orn

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:: DVWIVGAVNK
Nearest Stachelhaus code(s):: Fo-OH-Orn DVWIIGAVNK (94% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1402..1781): 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 (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2426..2817): OH-Orn

nrpys: OH-Orn

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Long positively charged side chain (Orn, Lys, Arg)
Small clusters prediction:: Orn and hydroxy-Orn specific (Orn, OH-Orn)
Single AA prediction:: orn (Orn)

Stachelhaus prediction details:

Stachelhaus sequence:: DMENLGLINK
Nearest Stachelhaus code(s):: OH-Orn DMENLGLINK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3464..3855): X

nrpys: Ac-OH-Orn, OH-Orn

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:: DVFVLGAVNK
Nearest Stachelhaus code(s):: Ac-OH-Orn DVFALGAVNK (91% 8Å match); OH-Orn DVFILGAVNK (88% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
CelR	Cellobiose uptake repressor
DasR	N-acetylglucosamine dependent repressor
DmdR1	Iron(II)-dependent repressor
VqsM	Regulator of quorum-sensing signalling systems

JAMTCF010000021.1 - Region 2 - NRPS,T1PKS

Download region GenBank file

Download region SVG

Location: 65,780 - 113,446 nt. (total: 47,667 nt) Show pHMM detection rules used

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

LV78_006633: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

LV78_006635: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

LV78_006640: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

LV78_006649: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

Hydrolases: esterase hydrolase

LV78_006626: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

LV78_006634: thioesterase

smcogs: SMCOG1004: thioesterase

Ligases: ligase synthase

LV78_006637: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_006638: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

LV78_006639: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0001128.4	0.69	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001833.4	0.68	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001050.5	0.67	NRPS, PKS	thalassospiramide A	Tistrella bauzanensis
BGC0002135.2	0.67	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.65	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.68	NRPS	enniatin	Fusarium equiseti
BGC0001128.4	0.67	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.67	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001833.4	0.67	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.67	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001050.5	0.67	NRPS, PKS	thalassospiramide A	Tistrella bauzanensis
BGC0002135.2	0.67	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002286.3	0.66	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
BGC0001135.5	0.66	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:

ToxT

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

Confidence: strong

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.16 out of 20.97

Confidence: medium

CRP

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

Confidence: medium

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.63 out of 18.46

Confidence: medium

Additional weak hits (26):

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.83 out of 20.97

Confidence: weak

CcpA

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

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.07 out of 27.78

Confidence: weak

HipB

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

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.45 out of 32.74

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.86 out of 31.73

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.22 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.58 out of 27.78

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.44 out of 18.57

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.28 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.33 out of 30.25

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.66 out of 31.73

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.69 out of 28.14

Confidence: weak

MogR

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.69 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.78 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.38 out of 26.06

Confidence: weak

FuR variant 1

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

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.45 out of 29.65

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.32 out of 26.06

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.26 out of 28.19

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.40 out of 36.53

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.98 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.68 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.33 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.11 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 2, location 65779 - 113446:

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

Polymer prediction:: (Val) + (mal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

LV78_006637: mal

PKS_AT (672..939): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 16.3
Methoxymalonyl-CoA: 14.3
Methylmalonyl-CoA: 7.7
trans-1,2-CPDA: 0.0
inactive: 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

LV78_006638: Val

Search NORINE for peptide: strict or relaxed

AMP-binding (664..1060): 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:: DALWLGGTFK
Nearest Stachelhaus code(s):: Val DALWLGGTFK (88% 8Å match); bOH-Val DALWLGGTFK (79% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
CcpA	Catabolite control protein A
RpoN	Regulator of nitrogen assimilation and virulence
ToxT	Regulator of MSHA biosynthesis

JAMTCF010000023.1 - Region 1 - NRPS

Download region GenBank file

Download region SVG

Location: 21,685 - 66,052 nt. (total: 44,368 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 oxidoreductase oxygenase

LV78_006848: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

LV78_006849: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

LV78_006867: dioxygenase, TauD/TfdA

smcogs: SMCOG1121: dioxygenase, TauD/TfdA

LV78_006880: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: dehydratase

LV78_006871: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase

LV78_006865: 3-oxoacyl-(acyl carrier protein) synthase III

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

LV78_006869: 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	0.64	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002164.2	0.64	NRPS	peramine	Epichloe festucae
BGC0001135.5	0.63	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001249.5	0.63	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001166.5	0.63	NRPS	HC-toxin	Alternaria jesenskae
BGC0001240.4	0.63	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0002286.3	0.63	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.62	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0000307.4	0.62	NRPS	AbT1	Aureobasidium pullulans
BGC0002276.2	0.62	NRPS	choline	Aspergillus nidulans FGSC A4

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.64	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002164.2	0.64	NRPS	peramine	Epichloe festucae
BGC0001135.5	0.63	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001249.5	0.63	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001166.5	0.63	NRPS	HC-toxin	Alternaria jesenskae
BGC0001240.4	0.63	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0002286.3	0.63	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.62	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0000307.4	0.62	NRPS	AbT1	Aureobasidium pullulans
BGC0002276.2	0.62	NRPS	choline	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:

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.58 out of 26.85

Confidence: strong

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.44 out of 23.79

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.42 out of 23.79

Confidence: medium

AfsR

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

Confidence: medium

Additional weak hits (12):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.54 out of 30.25

Confidence: weak

CcpA

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

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.47 out of 30.25

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.97 out of 26.85

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.43 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.12 out of 28.14

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.89 out of 21.55

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.34 out of 28.19

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.28 out of 27.04

Confidence: weak

CatR

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

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.43 out of 28.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.75 out of 28.19

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 21684 - 66052:

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

Polymer prediction:: (Orn)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

LV78_006869: X

AMP-binding (18..418): 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:: GFGCVGINTK
Nearest Stachelhaus code(s):: Val DFFCVGIVHK (38% 8Å match)
Stachelhaus code match:: 60% (weak)

LV78_006871: Orn

Search NORINE for peptide: strict or relaxed

AMP-binding (462..887): Orn

nrpys: Orn

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:: DTEDAGLVDK
Nearest Stachelhaus code(s):: Orn DTEDMGLVDK (79% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
IolR	Regulator of the inositol catabolism
RutR	Regulator of the pyrimidine and purine metabolism

JAMTCF010000026.1 - Region 1 - terpene

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Location: 1 - 13,129 nt. (total: 13,129 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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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

Transferases: aminotransferase

LV78_007179: aminotransferase class V

smcogs: SMCOG1139: aminotransferase class V

Ligases: ligase

LV78_007175: carboxylate-amine ligase

smcogs: SMCOG1165: carboxylate-amine ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001639.3	0.40	ribosomal	klebsidin	Klebsiella pneumoniae
BGC0000572.5	0.36	ribosomal	capistruin	Burkholderia thailandensis E444
BGC0002382.3	0.36	ribosomal	grimoviridin	Grimontia marina
BGC0001229.4	0.36	ribosomal	SBI-06990 A1, SBI-06989 A2	Streptomyces bingchenggensis BCW-1
BGC0001407.5	0.36	ribosomal	bicereucin	Bacillus cereus SJ1
BGC0000497.3	0.34	ribosomal	BHT-Aα, BHT-Aβ	Streptococcus ratti
BGC0002442.3	0.34	ribosomal	toyoncin	Bacillus toyonensis
BGC0000569.5	0.32	ribosomal	plantazolicin	Bacillus velezensis FZB42
BGC0001173.5	0.32	ribosomal	plantazolicin	Bacillus pumilus ATCC 7061
BGC0000496.5	0.32	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001639.3	0.40	ribosomal	klebsidin	Klebsiella pneumoniae
BGC0000572.5	0.36	ribosomal	capistruin	Burkholderia thailandensis E444
BGC0002382.3	0.36	ribosomal	grimoviridin	Grimontia marina
BGC0001229.4	0.36	ribosomal	SBI-06990 A1, SBI-06989 A2	Streptomyces bingchenggensis BCW-1
BGC0001407.5	0.36	ribosomal	bicereucin	Bacillus cereus SJ1
BGC0000497.3	0.34	ribosomal	BHT-Aα, BHT-Aβ	Streptococcus ratti
BGC0002442.3	0.34	ribosomal	toyoncin	Bacillus toyonensis
BGC0000569.5	0.32	ribosomal	plantazolicin	Bacillus velezensis FZB42
BGC0001173.5	0.32	ribosomal	plantazolicin	Bacillus pumilus ATCC 7061
BGC0000496.5	0.32	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350

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
tetraterpene	C40 carotenoid		C40	unknown	unknown

Genes with terpene domains:

LV78_007173: Lycopene_cycl

Domain 1 (2 - 310): Lycopene cyclase

Reactions:: C40_carotenoid → C40_carotenoid

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (5):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.38 out of 21.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.98 out of 27.78

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.19 out of 30.98

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.27 out of 18.57

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.48 out of 35.63

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

No acronyms to display

TFBS definitions

Regulator	Description

JAMTCF010000028.1 - Region 1 - terpene-precursor

Download region GenBank file

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Location: 34,697 - 55,737 nt. (total: 21,041 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

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KnownClusterBlast

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Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

LV78_007414: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

LV78_007426: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

LV78_007433: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

Ligases: synthase synthetase

LV78_007420: 1-deoxy-D-xylulose-5-phosphate synthase

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

LV78_007422: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002162.3	0.49	terpene	sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8	Aspergillus fischeri NRRL 181
BGC0002283.2	0.49	terpene	sodorifen	Serratia plymuthica
BGC0001361.3	0.48	terpene	sodorifen	Serratia plymuthica 4Rx13
BGC0000666.5	0.47	terpene	xiamycin A	Streptomyces sp. SCSIO 02999
BGC0000665.5	0.46	other (other), terpene	xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C	Streptomyces sp. HKI0576
BGC0000657.5	0.46	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0000189.4	0.46	PKS	3-(2'-hydroxy-3'-oxo-4'-methylpentyl)-indole, 3-(2'-hydroxy-3'-oxo-4'-methylhexyl)-indole, 3-(2'-acetoxy-3'-oxo-4'-methylpentyl)-indole, 3-(2'-acetoxy-3'-oxo-4'-methylhexyl)-indole	Xenorhabdus bovienii SS-2004
BGC0001529.5	0.42	other (other)	benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K	Streptomyces sp. RI18
BGC0001156.5	0.42	terpene	platencin	Streptomyces platensis
BGC0000668.5	0.41	other (other), terpene	12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole	Hapalosiphon welwitschii UTEX B 1830

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002162.3	0.49	terpene	sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8	Aspergillus fischeri NRRL 181
BGC0002283.2	0.49	terpene	sodorifen	Serratia plymuthica
BGC0001361.3	0.48	terpene	sodorifen	Serratia plymuthica 4Rx13
BGC0000666.5	0.47	terpene	xiamycin A	Streptomyces sp. SCSIO 02999
BGC0000665.5	0.46	other (other), terpene	xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C	Streptomyces sp. HKI0576
BGC0000657.5	0.46	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0000189.4	0.46	PKS	3-(2'-hydroxy-3'-oxo-4'-methylpentyl)-indole, 3-(2'-hydroxy-3'-oxo-4'-methylhexyl)-indole, 3-(2'-acetoxy-3'-oxo-4'-methylpentyl)-indole, 3-(2'-acetoxy-3'-oxo-4'-methylhexyl)-indole	Xenorhabdus bovienii SS-2004
BGC0001529.5	0.42	other (other)	benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K	Streptomyces sp. RI18
BGC0001156.5	0.42	terpene	platencin	Streptomyces platensis
BGC0000668.5	0.41	other (other), terpene	12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole	Hapalosiphon welwitschii UTEX B 1830

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:

LV78_007422: PT_FPPS_like

Domain 1 (61 - 341): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

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

Transcription Factor Binding Sites

Binding sites found:

AfsQ1

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

Confidence: strong

CRP

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

Confidence: strong

Additional weak hits (12):

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.14 out of 25.88

Confidence: weak

MogR

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.82 out of 26.06

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.38 out of 33.14

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.49 out of 23.43

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.62 out of 29.38

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.20 out of 30.11

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.30 out of 30.11

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.69 out of 27.78

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.44 out of 30.25

Confidence: weak

HexR

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

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.92 out of 25.88

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

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

TFBS definitions

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

JAMTCF010000034.1 - Region 1 - NRPS,T1PKS

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Location: 3,784 - 51,981 nt. (total: 48,198 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

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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

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

LV78_007791: pyridine nucleotide-disulfide oxidoreductase

smcogs: SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

LV78_007792: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

LV78_007793: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

LV78_007811: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

Transferases: aminotransferase glycosyltransferase

LV78_007794: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

LV78_007805: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Hydrolases: esterase

LV78_007810: thioesterase

smcogs: SMCOG1004: thioesterase

Ligases: ligase synthase

LV78_007799: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_007800: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_007802: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

LV78_007807: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

LV78_007809: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0000342.4	0.72	NRPS	enniatin	Fusarium equiseti
BGC0001132.4	0.72	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.70	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001825.4	0.70	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002135.2	0.70	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001641.4	0.69	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.68	NRPS	AM-toxin	Alternaria alternata
BGC0002286.3	0.68	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.70	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0001132.4	0.69	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.68	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.68	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002135.2	0.68	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001641.4	0.67	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.67	NRPS	AM-toxin	Alternaria alternata
BGC0002286.3	0.67	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.86 out of 25.31

Confidence: medium

Additional weak hits (20):

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.65 out of 26.12

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.68 out of 35.63

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

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.17 out of 21.55

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.52 out of 26.06

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.37 out of 20.97

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.76 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.24 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.66 out of 27.78

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.48 out of 26.85

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 18.77 out of 33.73

Confidence: weak

MatP

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

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.35 out of 27.78

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.62 out of 32.93

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.29 out of 26.85

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.84 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.47 out of 26.06

Confidence: weak

MexT

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

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.03 out of 26.85

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.28 out of 28.19

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 3783 - 51981:

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

Polymer prediction:: (Arg) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 3783 - 47020:

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

Polymer prediction:: (Arg) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 8387 - 51981:

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

Polymer prediction:: (Arg) + (mal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

LV78_007799: X

AMP-binding (17..414): 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:: DVQFLTQVSK
Nearest Stachelhaus code(s):: Pro DVQFMAQVVK (68% 8Å match)
Stachelhaus code match:: 70% (weak)

LV78_007800: X

AMP-binding (41..376): 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:: GLQSTGTVAK
Nearest Stachelhaus code(s):: Suc ALQSTGTPRK (79% 8Å match)
Stachelhaus code match:: 70% (weak)

LV78_007807: Arg

Search NORINE for peptide: strict or relaxed

AMP-binding (478..870): Arg

nrpys: Arg

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DVENVGAVTK
Nearest Stachelhaus code(s):: Arg DVENVGAVTK (62% 8Å match)
Stachelhaus code match:: 100% (strong)

LV78_007809: mal

PKS_AT (502..786): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 62.5%; inactive: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 102.9
Methoxymalonyl-CoA: 72.2
Methylmalonyl-CoA: 52.4
Propionyl-CoA: 51.0
inactive: 46.2
2-Methylbutyryl-CoA: 36.4
CHC-CoA: 30.8
Ethylmalonyl-CoA: 25.3
Acetyl-CoA: 23.6
fatty_acid: 21.7
trans-1,2-CPDA: 20.5
Isobutyryl-CoA: 16.7
Benzoyl-CoA: 16.6
3-Methylbutyryl-CoA: 10.4

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CatR	H2O2-responsive repressor

JAMTCF010000041.1 - Region 1 - lassopeptide

Download region GenBank file

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Location: 1 - 9,793 nt. (total: 9,793 nt) Show pHMM detection rules used

Region on contig edge.

lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

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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

Lasso peptides

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

Hydrolases: hydrolase

LV78_008008: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001645.3	0.56	ribosomal	lagmysin	Streptomyces sp. NRRL S-118
BGC0001781.4	0.52	ribosomal	sphaericin	Planomonospora sphaerica
BGC0001550.3	0.49	ribosomal	citrulassin D	Streptomyces katrae
BGC0001634.3	0.48	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0000578.3	0.40	ribosomal	SRO15-2005	Streptomyces filamentosus NRRL 15998
BGC0000444.5	0.34	NRPS	thaxtomin A	Streptomyces turgidiscabies Car8
BGC0001435.4	0.28	NRPS, PKS	ikarugamycin	Streptomyces sp. ZJ306
BGC0000001.5	0.22	PKS	abyssomicin C, atrop-abyssomicin C	Verrucosispora maris AB-18-032
BGC0000119.5	0.20	PKS, saccharide	7-deoxypactamycin	Streptomyces pactum
BGC0000445.5	0.20	NRPS	thiocoraline	Micromonospora sp. ML1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001645.3	0.56	ribosomal	lagmysin	Streptomyces sp. NRRL S-118
BGC0001781.4	0.52	ribosomal	sphaericin	Planomonospora sphaerica
BGC0001550.3	0.49	ribosomal	citrulassin D	Streptomyces katrae
BGC0001634.3	0.48	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0000578.3	0.40	ribosomal	SRO15-2005	Streptomyces filamentosus NRRL 15998
BGC0000444.5	0.34	NRPS	thaxtomin A	Streptomyces turgidiscabies Car8
BGC0001435.4	0.28	NRPS, PKS	ikarugamycin	Streptomyces sp. ZJ306
BGC0000001.5	0.22	PKS	abyssomicin C, atrop-abyssomicin C	Verrucosispora maris AB-18-032
BGC0000119.5	0.20	PKS, saccharide	7-deoxypactamycin	Streptomyces pactum
BGC0000445.5	0.20	NRPS	thiocoraline	Micromonospora sp. ML1

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Lasso peptide predictions

Lassopeptides - No core peptides found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (3):

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.98 out of 39.62

Confidence: weak

FuR variant 1

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

Confidence: weak

LexA variant 1

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

Confidence: weak

Detailed Pfam 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 - 82; Score: 42.8

TFBS definitions

Regulator	Description