Nonomuraea_NPDC050663 - 40 region(s)

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Location: 260,747 - 281,469 nt. (total: 20,723 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

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Gene overview

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ClusterBlast

KnownClusterBlast

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TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

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

Tailoring functions

Oxidoreductases: oxidoreductase

CDS_00304: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

Transferases: kinase

CDS_00300: PfkB domain protein

smcogs: SMCOG1276: PfkB domain protein

Lyases: dehydratase

CDS_00286: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001687.3	0.37	other (other)	N-tetradecanoyl tyrosine	uncultured bacterium CSL12
BGC0000879.5	0.37	other (other)	toyocamycin, sangivamycin	Streptomyces rimosus
BGC0001677.3	0.35	PKS	mycophenolic acid	Penicillium roqueforti
BGC0002616.2	0.35	PKS	mycophenolic acid	Penicillium roqueforti
BGC0001360.3	0.35	PKS	mycophenolic acid	Penicillium roqueforti FM164
BGC0000104.4	0.35	PKS	mycophenolic acid	Penicillium brevicompactum
BGC0002345.2	0.35	other (other)	hydrogen cyanide	Pseudomonas fluorescens
BGC0002619.2	0.34	PKS	mycophenolic acid	Penicillium brevicompactum
BGC0001937.4	0.34	other (other)	tubercidin	Streptomyces tubercidicus
BGC0000881.3	0.33	other (other)	toyocamycin	Streptomyces ahygroscopicus subsp. wuzhouensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001687.3	0.37	other (other)	N-tetradecanoyl tyrosine	uncultured bacterium CSL12
BGC0000879.5	0.37	other (other)	toyocamycin, sangivamycin	Streptomyces rimosus
BGC0001677.3	0.35	PKS	mycophenolic acid	Penicillium roqueforti
BGC0002616.2	0.35	PKS	mycophenolic acid	Penicillium roqueforti
BGC0001360.3	0.35	PKS	mycophenolic acid	Penicillium roqueforti FM164
BGC0000104.4	0.35	PKS	mycophenolic acid	Penicillium brevicompactum
BGC0002345.2	0.35	other (other)	hydrogen cyanide	Pseudomonas fluorescens
BGC0002619.2	0.34	PKS	mycophenolic acid	Penicillium brevicompactum
BGC0001937.4	0.34	other (other)	tubercidin	Streptomyces tubercidicus
BGC0000881.3	0.33	other (other)	toyocamycin	Streptomyces ahygroscopicus subsp. wuzhouensis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 23.75 out of 27.55

Confidence: medium

VqsM

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

Confidence: medium

Additional weak hits (9):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.36 out of 29.38

Confidence: weak

CopR

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

Confidence: weak

SypG

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

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.68 out of 29.38

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.04 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.84 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.58 out of 26.06

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.05 out of 21.55

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.21 out of 28.19

Confidence: weak

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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TFBS Finder

TFBS definitions

Regulator	Description
GnfM	Regulator of nitrogen-fixation genes
VqsM	Regulator of quorum-sensing signalling systems

NPDC050663.ctg-0001 - Region 2 - RiPP-like

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Location: 434,389 - 445,201 nt. (total: 10,813 nt) Show pHMM detection rules used

RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Ligases: ligase

CDS_00446: carboxylate-amine ligase

smcogs: SMCOG1165: carboxylate-amine ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001778.5	0.32	other (other)	showdomycin	Streptomyces showdoensis
BGC0001399.4	0.31	NRPS	fellutamide B	Aspergillus nidulans FGSC A4
BGC0001366.5	0.30	PKS	BE-24566B, zunyimycin A	Streptomyces sp. FJS31-2
BGC0001336.5	0.30	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0000420.5	0.29	NRPS	histidyltryptophanyldiketopiperazine, dehydrohistidyltryptophanyldiketopiperazine, roquefortine D, roquefortine C, glandicoline A, glandicoline B, meleagrine	Penicillium rubens Wisconsin 54-1255
BGC0001440.5	0.29	other (other)	cystargolide A, cystargolide B	Kitasatospora cystarginea
BGC0000821.5	0.27	other (other)	rebeccamycin	Lechevalieria aerocolonigenes
BGC0002412.2	0.27	NRPS	holomycin	Photobacterium galatheae
BGC0001895.4	0.27	PKS	huanglongmycin A, huanglongmycin B, huanglongmycin C	Streptomyces sp. CB09001
BGC0001882.3	0.27	PKS	chrysoxanthone A, chrysoxanthone B, chrysoxanthone C	Penicillium rubens Wisconsin 54-1255

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001778.5	0.32	other (other)	showdomycin	Streptomyces showdoensis
BGC0001399.4	0.31	NRPS	fellutamide B	Aspergillus nidulans FGSC A4
BGC0001366.5	0.30	PKS	BE-24566B, zunyimycin A	Streptomyces sp. FJS31-2
BGC0001336.5	0.30	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0000420.5	0.29	NRPS	histidyltryptophanyldiketopiperazine, dehydrohistidyltryptophanyldiketopiperazine, roquefortine D, roquefortine C, glandicoline A, glandicoline B, meleagrine	Penicillium rubens Wisconsin 54-1255
BGC0001440.5	0.29	other (other)	cystargolide A, cystargolide B	Kitasatospora cystarginea
BGC0000821.5	0.27	other (other)	rebeccamycin	Lechevalieria aerocolonigenes
BGC0002412.2	0.27	NRPS	holomycin	Photobacterium galatheae
BGC0001895.4	0.27	PKS	huanglongmycin A, huanglongmycin B, huanglongmycin C	Streptomyces sp. CB09001
BGC0001882.3	0.27	PKS	chrysoxanthone A, chrysoxanthone B, chrysoxanthone C	Penicillium rubens Wisconsin 54-1255

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: 18.50 out of 20.47

Confidence: medium

Additional weak hits (3):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.77 out of 21.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.74 out of 27.78

Confidence: weak

ZuR variant 1

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

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

NPDC050663.ctg-0002 - Region 1 - NRPS,azole-containing-RiPP

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Location: 49,648 - 110,194 nt. (total: 60,547 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)
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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zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Azole RiPPs

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: oxidoreductase

CDS_01000: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

Hydrolases: protease

CDS_00967: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

Ligases: ligase synthase

CDS_00985: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_00986: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_00988: 1-deoxy-D-xylulose-5-phosphate synthase

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

CDS_00990: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_00992: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_00994: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_00995: carboxylate-amine ligase

smcogs: SMCOG1165: carboxylate-amine ligase

Translocases: transporter

CDS_00981: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.64	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001833.4	0.60	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.60	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.59	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.59	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.57	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.57	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001166.5	0.56	NRPS	HC-toxin	Alternaria jesenskae
BGC0001135.5	0.56	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001641.4	0.56	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.73	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001833.4	0.71	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.70	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.70	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.70	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0001758.4	0.68	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.68	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2	0.68	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.67	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:

CcpA

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

Confidence: medium

CRP

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

Confidence: medium

Additional weak hits (32):

ArcA

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

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.54 out of 23.43

Confidence: weak

ClgR

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

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.62 out of 20.01

Confidence: weak

CcpA

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

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.10 out of 27.78

Confidence: weak

RutR

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

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.38 out of 27.78

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.51 out of 31.73

Confidence: weak

CodY

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.80 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.29 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.72 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.04 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.95 out of 26.06

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.12 out of 26.12

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: 17.18 out of 26.06

Confidence: weak

CodY

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.80 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.51 out of 31.73

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.44 out of 26.85

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.87 out of 31.73

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.22 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.14 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.62 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.30 out of 30.25

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.15 out of 35.63

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.65 out of 29.65

Confidence: weak

LexA variant 2

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.19 out of 26.06

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.65 out of 27.18

Confidence: weak

(Thi)azol(in)e containing peptide predictions

No core peptides found.

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Azole RiPPs

Predicted core structure(s)

For candidate cluster 1, location 49647 - 110194:

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

Polymer prediction:: (Gly) + (Asp)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 58946 - 110194:

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

Polymer prediction:: (Gly) + (Asp)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CDS_00985: X

AMP-binding (9..381): 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:: NATFGAYPAK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

CDS_00990: Asp

Search NORINE for peptide: strict or relaxed

AMP-binding (475..826): Asp

nrpys: Asp

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DFTKIGHVGK
Nearest Stachelhaus code(s):: Asp DLTKIGHVGK (71% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_00994: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (427..769): Gly

nrpys: Gly

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DILQLGMIWK
Nearest Stachelhaus code(s):: Gly DILQLGMIWK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

TFBS definitions

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

Core peptide predictions

No core peptides found.

NPDC050663.ctg-0002 - Region 2 - terpene

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Location: 580,556 - 601,506 nt. (total: 20,951 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: oxidoreductase

CDS_01495: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

Hydrolases: hydrolase

CDS_01499: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Lyases: cyclase hydratase

CDS_01485: Nitrilase/cyanide hydratase and apolipoprotein

smcogs: SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

CDS_01491: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthase

CDS_01500: carbamoyl phosphate synthase small subunit

smcogs: SMCOG1249: carbamoyl phosphate synthase small subunit

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002346.3	0.42	ribosomal	kyamicin	Saccharopolyspora sp.
BGC0001374.5	0.41	other (other)	thienodolin	Streptomyces albogriseolus
BGC0000583.5	0.41	ribosomal	grisemycin	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000528.5	0.40	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000903.3	0.39	other (other)	fluorometabolite	Streptomyces cattleya
BGC0000885.3	0.39	other (other)	4-hydroxy-3-nitrosobenzamide	Streptomyces murayamaensis
BGC0001810.3	0.39	PKS	trehangelin	Polymorphospora rubra
BGC0001513.3	0.38	PKS	anthrabenzoxocinone	Actinobacteria bacterium
BGC0001366.5	0.38	PKS	BE-24566B, zunyimycin A	Streptomyces sp. FJS31-2
BGC0002316.2	0.37	ribosomal	cebulantin	Saccharopolyspora cebuensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002346.3	0.42	ribosomal	kyamicin	Saccharopolyspora sp.
BGC0001374.5	0.41	other (other)	thienodolin	Streptomyces albogriseolus
BGC0000583.5	0.41	ribosomal	grisemycin	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000528.5	0.40	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000903.3	0.39	other (other)	fluorometabolite	Streptomyces cattleya
BGC0000885.3	0.39	other (other)	4-hydroxy-3-nitrosobenzamide	Streptomyces murayamaensis
BGC0001810.3	0.39	PKS	trehangelin	Polymorphospora rubra
BGC0001513.3	0.38	PKS	anthrabenzoxocinone	Actinobacteria bacterium
BGC0001366.5	0.38	PKS	BE-24566B, zunyimycin A	Streptomyces sp. FJS31-2
BGC0002316.2	0.37	ribosomal	cebulantin	Saccharopolyspora cebuensis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

No product predictions

Genes with terpene domains:

CDS_01491: T1TS

Domain 1 (36 - 315): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

CRP

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

Confidence: strong

CRP

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

Confidence: medium

Additional weak hits (6):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.38 out of 29.38

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.53 out of 20.97

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.03 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.69 out of 26.06

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.52 out of 18.57

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.29 out of 28.19

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein

NPDC050663.ctg-0002 - Region 3 - terpene

Download region SVG

Location: 716,282 - 740,821 nt. (total: 24,540 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Transferases: glycosyltransferase

CDS_01615: glycosyl transferase group 1

smcogs: SMCOG1045: glycosyl transferase group 1

Lyases: cyclase

CDS_01623: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: ligase synthase synthetase

CDS_01620: 1-deoxy-D-xylulose-5-phosphate synthase

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

CDS_01621: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

CDS_01628: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001181.4	0.80	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0001746.3	0.75	terpene	pristinol	Streptomyces pristinaespiralis ATCC 25486
BGC0000657.5	0.57	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0001240.4	0.56	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0002283.2	0.54	terpene	sodorifen	Serratia plymuthica
BGC0001361.3	0.54	terpene	sodorifen	Serratia plymuthica 4Rx13
BGC0000677.5	0.49	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002309.2	0.48	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001911.3	0.44	terpene	raimonol	Streptomyces anulatus
BGC0001910.4	0.44	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001181.4	0.80	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0001746.3	0.75	terpene	pristinol	Streptomyces pristinaespiralis ATCC 25486
BGC0000657.5	0.57	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0001240.4	0.56	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0002283.2	0.54	terpene	sodorifen	Serratia plymuthica
BGC0001361.3	0.54	terpene	sodorifen	Serratia plymuthica 4Rx13
BGC0000677.5	0.49	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002309.2	0.48	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001911.3	0.44	terpene	raimonol	Streptomyces anulatus
BGC0001910.4	0.44	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
sesquiterpene		germacradienol	C15	C1-C10	OH
sesquiterpene		geosmin	C12	C1-C10	OH

Genes with terpene domains:

CDS_01621: PT_FPPS_like

Domain 1 (43 - 337): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

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

CDS_01623: T1TS + T1TS

Domain 1 (5 - 317): Type 1 terpene synthase

Subtype: Geosmin synthase, N terminal domain

Reactions:: FPP → germacradienol

Domain 2 (333 - 668): Type 1 terpene synthase

Subtype: Geosmin synthase, C terminal domain

Reactions:: germacradienol → geosmin

Transcription Factor Binding Sites

Binding sites found:

CRP

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

Confidence: strong

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.36 out of 19.26

Confidence: medium

Additional weak hits (5):

ANR

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

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.72 out of 21.55

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.90 out of 33.73

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.34 out of 26.06

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.54 out of 29.65

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

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

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein

NPDC050663.ctg-0002 - Region 4 - terpene-precursor

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Location: 800,679 - 821,746 nt. (total: 21,068 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

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase

CDS_01698: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

CDS_01699: pyridine nucleotide-disulfide oxidoreductase

smcogs: SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

CDS_01709: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: phosphorylase

CDS_01701: thiamine-phosphate pyrophosphorylase

smcogs: SMCOG1280: thiamine-phosphate pyrophosphorylase

Ligases: synthetase

CDS_01702: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000677.5	0.43	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0001483.4	0.42	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8
BGC0001521.3	0.41	NRPS	auriculamide	Herpetosiphon aurantiacus DSM 785
BGC0000664.5	0.41	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3	0.41	terpene	isorenieratene	Streptomyces argillaceus
BGC0000867.3	0.40	other (other)	polyhydroxyalkanoic acids	Ectothiorhodospira shaposhnikovii
BGC0001928.2	0.40	other (other)	(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid	Streptomyces sp. MA37
BGC0000649.3	0.40	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001605.3	0.40	terpene	gibberellin	Sinorhizobium fredii NGR234
BGC0000633.3	0.40	terpene	carotenoid	Streptomyces avermitilis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000677.5	0.43	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0001483.4	0.42	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8
BGC0001521.3	0.41	NRPS	auriculamide	Herpetosiphon aurantiacus DSM 785
BGC0000664.5	0.41	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3	0.41	terpene	isorenieratene	Streptomyces argillaceus
BGC0000867.3	0.40	other (other)	polyhydroxyalkanoic acids	Ectothiorhodospira shaposhnikovii
BGC0001928.2	0.40	other (other)	(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid	Streptomyces sp. MA37
BGC0000649.3	0.40	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001605.3	0.40	terpene	gibberellin	Sinorhizobium fredii NGR234
BGC0000633.3	0.40	terpene	carotenoid	Streptomyces avermitilis

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

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

Genes with terpene domains:

CDS_01702: PT_FPPS_like

Domain 1 (47 - 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:

CRP

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

Confidence: medium

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 25.32 out of 29.65

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.64 out of 24.78

Confidence: medium

Additional weak hits (7):

ANR

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

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.35 out of 36.54

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.08 out of 21.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.84 out of 27.78

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.19 out of 29.65

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.07 out of 24.78

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.03 out of 23.43

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

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

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
LexA variant 1	Repressor of DNA damage response
LexA variant 2	Repressor of DNA damage response

NPDC050663.ctg-0002 - Region 5 - terpene-precursor

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Location: 835,384 - 856,415 nt. (total: 21,032 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

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Ligases: synthetase

CDS_01734: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000528.5	0.43	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002316.2	0.37	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0002309.2	0.37	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000903.3	0.33	other (other)	fluorometabolite	Streptomyces cattleya
BGC0002346.3	0.33	ribosomal	kyamicin	Saccharopolyspora sp.
BGC0000665.5	0.33	other (other), terpene	xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C	Streptomyces sp. HKI0576
BGC0000679.5	0.32	terpene	diazepinomicin	Micromonospora sp. M42
BGC0000503.5	0.32	ribosomal	cinnamycin	Streptomyces cinnamoneus
BGC0000643.3	0.32	terpene	carotenoid	Brevundimonas vesicularis
BGC0000634.3	0.32	terpene	carotenoid	Brevundimonas sp. SD212

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000528.5	0.43	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002316.2	0.37	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0002309.2	0.37	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000903.3	0.33	other (other)	fluorometabolite	Streptomyces cattleya
BGC0002346.3	0.33	ribosomal	kyamicin	Saccharopolyspora sp.
BGC0000665.5	0.33	other (other), terpene	xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C	Streptomyces sp. HKI0576
BGC0000679.5	0.32	terpene	diazepinomicin	Micromonospora sp. M42
BGC0000503.5	0.32	ribosomal	cinnamycin	Streptomyces cinnamoneus
BGC0000643.3	0.32	terpene	carotenoid	Brevundimonas vesicularis
BGC0000634.3	0.32	terpene	carotenoid	Brevundimonas sp. SD212

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

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

Genes with terpene domains:

CDS_01734: PT_FPPS_like

Domain 1 (47 - 337): 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: 19.19 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

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.21 out of 20.47

Confidence: medium

Additional weak hits (6):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.95 out of 30.97

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.64 out of 26.06

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.67 out of 21.55

Confidence: weak

LexA variant 1

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

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.98 out of 33.14

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

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
RpoN	Regulator of nitrogen assimilation and virulence
VqsM	Regulator of quorum-sensing signalling systems

NPDC050663.ctg-0003 - Region 1 - NRPS

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Location: 2,522 - 46,637 nt. (total: 44,116 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

Transferases: aminotransferase methyltransferase

CDS_01829: aminotransferase class V

smcogs: SMCOG1139: aminotransferase class V

CDS_01841: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

CDS_01851: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_01853: aminotransferase class V

smcogs: SMCOG1139: aminotransferase class V

Hydrolases: protease

CDS_01846: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

Lyases: dehydratase

CDS_01839: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase

CDS_01836: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.64	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000357.5	0.64	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
BGC0000307.4	0.63	NRPS	AbT1	Aureobasidium pullulans
BGC0001251.4	0.63	NRPS	epichloenin A	Epichloe festucae
BGC0000342.4	0.63	NRPS	enniatin	Fusarium equiseti
BGC0001249.5	0.63	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002164.2	0.63	NRPS	peramine	Epichloe festucae
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.63	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.64	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000357.5	0.64	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
BGC0000307.4	0.63	NRPS	AbT1	Aureobasidium pullulans
BGC0001251.4	0.63	NRPS	epichloenin A	Epichloe festucae
BGC0000342.4	0.63	NRPS	enniatin	Fusarium equiseti
BGC0001249.5	0.63	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002164.2	0.63	NRPS	peramine	Epichloe festucae
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.63	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.62 out of 29.72

Confidence: medium

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11

Confidence: strong

CelR

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

Confidence: strong

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11

Confidence: strong

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11

Confidence: strong

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.39 out of 30.11

Confidence: medium

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.19 out of 30.11

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.64 out of 23.79

Confidence: medium

Additional weak hits (13):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.32 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.66 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.47 out of 26.06

Confidence: weak

MatP

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

Confidence: weak

MexT

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

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.99 out of 21.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.86 out of 27.78

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.78 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.71 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.42 out of 32.74

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.61 out of 39.62

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.37 out of 29.38

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.94 out of 29.65

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 2521 - 46637:

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

NRPS/PKS substrate predictions

CDS_01839: X

AMP-binding (441..829): X

nrpys: Tyr, bOH-Tyr

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Polar aromatic ring (Tyr, bOH-Tyr)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DAGDMGHVCK
Nearest Stachelhaus code(s):: CysA DATKMGHVGK (56% 8Å match)
Stachelhaus code match:: 70% (weak)

TFBS definitions

Regulator	Description
CelR	Cellobiose uptake repressor
IolR	Regulator of the inositol catabolism
NtrC	Nitrogen regulatory protein C

NPDC050663.ctg-0003 - Region 2 - NRPS,NRPS-like,RRE-containing,T1PKS,azole-containing-RiPP

Download region SVG

Location: 482,750 - 598,539 nt. (total: 115,790 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)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Azole RiPPs

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_02303: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02328: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: sulfotransferase

CDS_02321: Sulfotransferase domain

extras: Sulfotransfer_1: Sulfotransferase domain

Hydrolases: esterase hydrolase

CDS_02281: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

CDS_02287: thioesterase

smcogs: SMCOG1004: thioesterase

CDS_02295: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

CDS_02325: thioesterase

smcogs: SMCOG1004: thioesterase

Lyases: dehydratase

CDS_02264: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_02273: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

Ligases: ligase synthase

CDS_02282: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_02283: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_02285: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_02286: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_02288: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_02291: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_02292: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_02323: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_02324: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Translocases: transport transporter

CDS_02267: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

CDS_02332: MMPL domain-containing transport protein

smcogs: SMCOG1035: MMPL domain-containing transport protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001132.4	1.65	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002075.3	1.64	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001128.4	1.61	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001249.5	1.61	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002286.3	1.59	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	1.58	NRPS	AM-toxin	Alternaria alternata
BGC0002164.2	1.58	NRPS	peramine	Epichloe festucae
BGC0001135.5	1.57	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001641.4	1.49	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	1.49	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001249.5	0.74	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001132.4	0.73	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.72	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.71	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001261.3	0.70	NRPS	AM-toxin	Alternaria alternata
BGC0001825.4	0.70	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001135.5	0.69	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.91 out of 27.18

Confidence: medium

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11

Confidence: strong

CelR

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

Confidence: strong

AfsR

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

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.21 out of 26.85

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.36 out of 23.79

Confidence: medium

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.49 out of 30.22

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

Additional weak hits (30):

RutR

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

Confidence: weak

ToxT

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

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.35 out of 21.55

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.76 out of 26.06

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.73 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: 15.43 out of 20.97

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.01 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.60 out of 28.14

Confidence: weak

MexT

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

Confidence: weak

MexT

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.05 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.98 out of 27.78

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.04 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.53 out of 29.38

Confidence: weak

CodY

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.46 out of 26.06

Confidence: weak

ANR

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

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.16 out of 29.25

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.98 out of 25.88

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.88 out of 19.26

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.26 out of 28.19

Confidence: weak

ZuR variant 1

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

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.11 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.88 out of 28.19

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.68 out of 24.78

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.34 out of 33.14

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.46 out of 35.63

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.29 out of 35.63

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.54 out of 35.63

Confidence: weak

(Thi)azol(in)e containing peptide predictions

No core peptides found.

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

RREFinder

TFBS Finder

Azole RiPPs

Predicted core structure(s)

For candidate cluster 2, location 482749 - 598539:

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

Polymer prediction:: (X) + (X - X) + (Asp) + (X) + (ccmal) + (Glu) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 490097 - 561457:

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

Polymer prediction:: (X - X) + (Asp) + (X) + (ccmal) + (Glu) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 556871 - 598539:

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

NRPS/PKS substrate predictions

CDS_02282: X

AMP-binding (27..409): 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:: DMTHVGGFAK
Nearest Stachelhaus code(s):: Glu DAMHVGGTAK (53% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_02283: Glu

Search NORINE for peptide: strict or relaxed

AMP-binding (469..864): Glu

nrpys: Glu

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: glu,gln (Glu, Gln)
Single AA prediction:: glu (Glu)

Stachelhaus prediction details:

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

CDS_02285: mal

PKS_AT (522..801): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 87.5%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 180.6
inactive: 97.6
Methoxymalonyl-CoA: 69.6
Methylmalonyl-CoA: 67.6
Propionyl-CoA: 53.1
Ethylmalonyl-CoA: 41.4
Isobutyryl-CoA: 31.9
Benzoyl-CoA: 31.8
Acetyl-CoA: 31.5
fatty_acid: 31.1
CHC-CoA: 25.4
2-Methylbutyryl-CoA: 21.4
trans-1,2-CPDA: 12.8
3-Methylbutyryl-CoA: 9.5

CDS_02286: X

AMP-binding (9..393): X

nrpys: (unknown)

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DVAIMGAVCK
Nearest Stachelhaus code(s):: Trp DVAMVGAVCK (53% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_02291: Asp

Search NORINE for peptide: strict or relaxed

AMP-binding (499..885): Asp

nrpys: Asp

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DLTKIAHVSK
Nearest Stachelhaus code(s):: Asp DLTKIGHVGK (59% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_02292: X - X

AMP-binding (8..389): 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:: DPSYVGVVTK
Nearest Stachelhaus code(s):: Gln DAWQVGVVDK (56% 8Å match); Trp DVALVGVVQK (53% 8Å match)
Stachelhaus code match:: 60% (weak)

AMP-binding (1052..1447): 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:: DVFTLMAIYK
Nearest Stachelhaus code(s):: Ser DVQTVMAIHK (50% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_02323: X

AMP-binding (16..391): 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:: DPRQCVCVLK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

RRE predictions

: RRE type: Thiopeptide_F_RRE; Location: 9 - 89; Score: 82.7; RRE type: Heterocycloanthracin_C_RRE; Location: 11 - 98; Score: 40.7
: RRE type: Thiopeptide_F_RRE; Location: 9 - 89; Score: 82.7; RRE type: Heterocycloanthracin_C_RRE; Location: 11 - 98; Score: 40.7

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR	Pleiotropic regulatory for antibiotic production
CelR	Cellobiose uptake repressor
ClgR	Caseinolytic protease gene regulator
IolR	Regulator of the inositol catabolism
NrdR	Represses ribonucleotide reductase encoding genes
RutR	Regulator of the pyrimidine and purine metabolism

Core peptide predictions

No core peptides found.

NPDC050663.ctg-0003 - Region 3 - NRPS,T1PKS

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Location: 601,848 - 665,786 nt. (total: 63,939 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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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

CDS_02348: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_02369: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

Transferases: acetyltransferase acylase transferase

CDS_02347: Chloramphenicol acetyltransferase

smcogs: SMCOG1156: Chloramphenicol acetyltransferase

CDS_02363: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_02372: glucose-1-phosphate adenylyl/thymidylyltransferase

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

Hydrolases: esterase

CDS_02361: thioesterase

smcogs: SMCOG1004: thioesterase

Ligases: ligase

CDS_02362: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_02365: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_02366: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_02367: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Translocases: permease

CDS_02378: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.90	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001135.5	0.89	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.89	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.89	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.87	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3	0.87	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0002135.2	0.86	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001249.5	0.84	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001758.4	0.83	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001261.3	0.83	NRPS	AM-toxin	Alternaria alternata

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001135.5	0.75	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.75	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.75	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.75	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001758.4	0.73	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001261.3	0.73	NRPS	AM-toxin	Alternaria alternata

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: medium

AbrC3

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

Confidence: strong

VqsM

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

Confidence: medium

Additional weak hits (21):

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.71 out of 27.55

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.75 out of 29.38

Confidence: weak

ANR

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

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.74 out of 29.25

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.13 out of 36.54

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.47 out of 27.55

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.14 out of 25.75

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.99 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.55 out of 27.78

Confidence: weak

MogR

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

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.07 out of 28.14

Confidence: weak

HipB

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

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.70 out of 30.25

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.86 out of 28.19

Confidence: weak

HypR

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

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.83 out of 29.65

Confidence: weak

LexA variant 1

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

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.64 out of 29.65

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.13 out of 36.53

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.22 out of 26.12

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 601847 - 665786:

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

Polymer prediction:: (X - X) + (ccmal) + (Gly) + (X - Ser) + (Ser)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CDS_02362: X - X

AMP-binding (16..403): 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:: DVLTLAWVCK
Nearest Stachelhaus code(s):: Pro DLLYLALVCK (68% 8Å match)
Stachelhaus code match:: 70% (weak)

AMP-binding (1045..1433): 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:: DPRHLGSAQK
Nearest Stachelhaus code(s):: Asp DPRHLALLAK (50% 8Å match); D-Asp DPRHVGIFIK (47% 8Å match); D-Glu DPRHSGVVGK (44% 8Å match)
Stachelhaus code match:: 60% (weak)

CDS_02363: mal

PKS_AT (532..819): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 79.2%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 158.6
inactive: 98.0
Methoxymalonyl-CoA: 63.7
Methylmalonyl-CoA: 51.3
Propionyl-CoA: 47.2
Isobutyryl-CoA: 26.5
Ethylmalonyl-CoA: 25.9
fatty_acid: 25.7
2-Methylbutyryl-CoA: 24.0
Benzoyl-CoA: 21.9
CHC-CoA: 18.7
Acetyl-CoA: 17.6
trans-1,2-CPDA: 9.2
3-Methylbutyryl-CoA: 0.0

CDS_02365: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (458..839): 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:: N/A
Single AA prediction:: gly (Gly)

Stachelhaus prediction details:

Stachelhaus sequence:: DILQIGFIWK
Nearest Stachelhaus code(s):: Gly DILQIGLIWK (74% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_02366: X - Ser

Search NORINE for peptide: strict or relaxed

AMP-binding (505..890): X

nrpys: Ala, 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:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DIAQITLIWK
Nearest Stachelhaus code(s):: Gly DILQIGLIWK (71% 8Å match); Ala DILQITLIYK (62% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1530..1920): 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:: DVWHISLVDK
Nearest Stachelhaus code(s):: Ser DVWHISLVDK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_02367: Ser

Search NORINE for peptide: strict or relaxed

AMP-binding (455..831): Ser

nrpys: Ser

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DVWHVSLVDK
Nearest Stachelhaus code(s):: Ser DVWHVSLVDK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
VqsM	Regulator of quorum-sensing signalling systems

NPDC050663.ctg-0003 - Region 4 - RiPP-like

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Location: 815,032 - 826,267 nt. (total: 11,236 nt) Show pHMM detection rules used

RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

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SubClusterBlast

TFBS Finder

Pfam domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

No tailoring functions detected.

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001849.4	0.37	ribosomal	thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D	Streptomyces varsoviensis
BGC0002152.2	0.34	other (other)	toxoflavin	Pseudomonas protegens Pf-5
BGC0001733.3	0.33	ribosomal	PcpA	Pleurocapsa sp. PCC 7327
BGC0002560.3	0.31	ribosomal	thiostreptamide S4	Streptomyces sp. NRRL S-4
BGC0002126.3	0.30	NRPS	hypeptin	Lysobacter sp. K5869
BGC0002669.2	0.30	ribosomal	TVA-YJ-2	Streptomyces sp. NRRL S-87
BGC0000385.5	0.30	NRPS	lysobactin	Lysobacter sp. ATCC 53042
BGC0000483.5	0.28	ribosomal	aeruginosamide B, aeruginosamide C	Microcystis aeruginosa PCC 9432
BGC0001895.4	0.28	PKS	huanglongmycin A, huanglongmycin B, huanglongmycin C	Streptomyces sp. CB09001
BGC0000367.5	0.27	NRPS	gramicidin	Brevibacillus brevis NBRC 100599

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001849.4	0.37	ribosomal	thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D	Streptomyces varsoviensis
BGC0002152.2	0.34	other (other)	toxoflavin	Pseudomonas protegens Pf-5
BGC0001733.3	0.33	ribosomal	PcpA	Pleurocapsa sp. PCC 7327
BGC0002560.3	0.31	ribosomal	thiostreptamide S4	Streptomyces sp. NRRL S-4
BGC0002126.3	0.30	NRPS	hypeptin	Lysobacter sp. K5869
BGC0002669.2	0.30	ribosomal	TVA-YJ-2	Streptomyces sp. NRRL S-87
BGC0000385.5	0.30	NRPS	lysobactin	Lysobacter sp. ATCC 53042
BGC0000483.5	0.28	ribosomal	aeruginosamide B, aeruginosamide C	Microcystis aeruginosa PCC 9432
BGC0001895.4	0.28	PKS	huanglongmycin A, huanglongmycin B, huanglongmycin C	Streptomyces sp. CB09001
BGC0000367.5	0.27	NRPS	gramicidin	Brevibacillus brevis NBRC 100599

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

AbrC3

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

Confidence: strong

Additional weak hits (3):

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.10 out of 39.62

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.09 out of 29.25

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.01 out of 36.53

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator

NPDC050663.ctg-0004 - Region 1 - lanthipeptide-class-iii

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Location: 14,922 - 37,798 nt. (total: 22,877 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Lanthipeptides

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_02658: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02659: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

Transferases: methyltransferase

CDS_02647: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: deformylase

CDS_02657: peptide deformylase

smcogs: SMCOG1275: peptide deformylase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002276.2	0.55	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0001928.2	0.47	other (other)	(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid	Streptomyces sp. MA37
BGC0000866.5	0.46	other (other)	polyhydroxyalkanoate	Burkholderia sp. DSM 9242
BGC0002700.2	0.45	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0000553.3	0.44	ribosomal	SRO15-2212	Streptomyces filamentosus NRRL 15998
BGC0000496.5	0.44	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3	0.43	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000551.5	0.43	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0002111.3	0.42	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000501.3	0.42	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002276.2	0.55	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0001928.2	0.47	other (other)	(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid	Streptomyces sp. MA37
BGC0000866.5	0.46	other (other)	polyhydroxyalkanoate	Burkholderia sp. DSM 9242
BGC0002700.2	0.45	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0000553.3	0.44	ribosomal	SRO15-2212	Streptomyces filamentosus NRRL 15998
BGC0000496.5	0.44	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3	0.43	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000551.5	0.43	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0002111.3	0.42	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000501.3	0.42	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for CDS_02652

allorf_024802_024918

Leader:

MTLLDLQGLEPETPGGGFD

Core:

SCHSRCCGGGASWLSLLLC

Core with dehydrations:

DhaCysHDhaRCysCysGGGADhaWLDhaLLLCys

antiSMASH-DB 4.0 matches for allorf_024802_024918

94.7%

NZ_JACDUR010000005.1:

Lanthipeptides: allorf_0025156_0025278_lanthipeptide

1

SCHSRCCGGGASWLSLLLC

19

SC+SRCCGGGASWLSLLLC

1

SCYSRCCGGGASWLSLLLC

19

73.7%

NZ_FNCN01000003.1:

Lanthipeptides: allorf_178077_178187_lanthipeptide

1

SCHSRCCGGGASWLSLLLC

19

S +SR CGGG SWLSLL+C

1

SHYSRGCGGG-SWLSLLIC

18

54.5%

NZ_RQJW01000008.1:

Lanthipeptides: EHO50_RS30030_lanthipeptide

4

SRCCGGGASWLSLLLC

19

S+ CGGG S LSLLLC

8

SKGCGGG-SRLSLLLC

22

with 30 more sequence matches

Only the first 10 are displayed here.

50.0%

NZ_LWSF01000028.1:

Lanthipeptides: allorf_078284_078409_lanthipeptide

3

HSRCCGG-GASWLSLLLC

19

HS C G S LSLLLC

4

HSHCSTECGESTLSLLLC

21

47.4%

NZ_NBCN01000003.1:

Lanthipeptides: BKD26_RS38955_lanthipeptide

9

GGASWLSLLLC

19

GGAS LS+LLC

9

GGASRLSVLLC

19

43.5%

NZ_CP007155.1:

Lanthipeptides: KALB_RS46315_lanthipeptide

9

GGASWLSLLLC

19

GGAS LSLLLC

11

GGASGLSLLLC

21

42.9%

NZ_LIYH01000004.1:

Lanthipeptides: AMK26_RS36220_lanthipeptide

10

GASWLSLLLC

19

GAS LSLLLC

12

GASGLSLLLC

21

40.9%

NZ_CP031455.1:

Lanthipeptides: DXZ73_RS14610_lanthipeptide

8

GGGASWLSLLLC

19

GGGAS +SLL C

1

GGGASTVSLLSC

12

40.9%

NZ_CP097289.1:

Lanthipeptides: M4V62_RS29260_lanthipeptide

8

GGGASWLSLLLC

19

GGG S SLLLC

1

GGGQSTASLLLC

12

40.0%

NZ_BNBU01000005.1:

Lanthipeptides: IE303_RS19905_lanthipeptide

10

GASWLSLLLC

19

G S LSLLLC

1

GGSQLSLLLC

10

38.1%

NZ_BMVR01000001.1:

Lanthipeptides: IE274_RS00225_lanthipeptide

9

GGASWLSLLLC

19

GG S +SLLLC

1

GGGSQVSLLLC

11

37.5%

NZ_BMVE01000003.1and 14 others:

NZ_BMVL01000005.1 Lanthipeptides: IE257_RS16230_lanthipeptideNZ_CP011664.1 Lanthipeptides: M444_RS30240_lanthipeptideNZ_CP020039.1 Lanthipeptides: B4U39_RS34445_lanthipeptideNZ_CP020555.1 Lanthipeptides: B6R96_RS03515_lanthipeptideNZ_CP029189.1 Lanthipeptides: DEJ51_RS31910_lanthipeptideNZ_CP033581.1 Lanthipeptides: EES41_RS31595_lanthipeptideNZ_CP034350.1 Lanthipeptides: D1J60_RS32970_lanthipeptideNZ_CP115936.1 Lanthipeptides: PET44_RS28650_lanthipeptideNZ_JACHJG010000001.1 Lanthipeptides: FHS38_RS02665_lanthipeptideNZ_JAFLQY010000003.1 Lanthipeptides: J0X20_RS29030_lanthipeptideNZ_LIVP01000027.1 Lanthipeptides: AMK15_RS28680_lanthipeptideNZ_LWLD01000038.1 Lanthipeptides: A6A28_RS28600_lanthipeptideNZ_ML123038.1 Lanthipeptides: EES37_RS30340_lanthipeptideNZ_NNBM01000002.1 Lanthipeptides: CG724_RS07855_lanthipeptide

Lanthipeptides: IE248_RS10435_lanthipeptide

8

GGGASWLSLLLC

19

GGG S SLLLC

2

GGGGSRASLLLC

13

36.8%

NZ_CP022753.1and 1 other:

NZ_CP022753.1 Lanthipeptides: CDO52_RS14310_lanthipeptide

Lanthipeptides: CDO52_RS14310_lanthipeptide

10

GASWLSLLLC

19

S+LSLLLC

4

SVSYLSLLLC

13

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (10):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.21 out of 27.78

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.18 out of 28.14

Confidence: weak

CRP

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

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.91 out of 26.85

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.11 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.33 out of 28.14

Confidence: weak

ANR

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

Confidence: weak

NuR

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

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.30 out of 35.63

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.96 out of 29.25

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lanthipeptides

TFBS Finder

Core peptide predictions

allorf_024802_024918 - Class III: Cleavage pHMM score: 7.30; RODEO score: 0; Monoisotopic mass: 1881.9 Da; Molecular weight: 1883.2 Da; Number of bridges: 4; Additional modifications: Lac

TFBS definitions

Regulator	Description

NPDC050663.ctg-0004 - Region 2 - NRP-metallophore,NRPS

Download region SVG

Location: 205,989 - 253,918 nt. (total: 47,930 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_02856: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase glycosyltransferase

CDS_02847: glycosyl transferase group 1

smcogs: SMCOG1045: glycosyl transferase group 1

CDS_02864: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: hydrolase

CDS_02853: isochorismatase

smcogs: SMCOG1027: isochorismatase

Isomerases: isomerase

CDS_02855: isochorismate synthase

smcogs: SMCOG1018: isochorismate synthase

Ligases: ligase

CDS_02851: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_02854: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: permease

CDS_02833: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

CDS_02843: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000343.5	0.78	NRPS	enterobactin	Pseudomonas sp. J465
BGC0001268.4	0.64	NRPS, PKS	fusarin C	Fusarium fujikuroi
BGC0001135.5	0.60	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002164.2	0.60	NRPS	peramine	Epichloe festucae
BGC0000342.4	0.60	NRPS	enniatin	Fusarium equiseti
BGC0000307.4	0.59	NRPS	AbT1	Aureobasidium pullulans
BGC0002135.2	0.59	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001250.4	0.58	NRPS	epichloenin A	Epichloe festucae
BGC0001251.4	0.58	NRPS	epichloenin A	Epichloe festucae
BGC0001261.3	0.58	NRPS	AM-toxin	Alternaria alternata

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000343.5	0.71	NRPS	enterobactin	Pseudomonas sp. J465
BGC0001268.4	0.65	NRPS, PKS	fusarin C	Fusarium fujikuroi
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002164.2	0.64	NRPS	peramine	Epichloe festucae
BGC0000342.4	0.63	NRPS	enniatin	Fusarium equiseti
BGC0000307.4	0.63	NRPS	AbT1	Aureobasidium pullulans
BGC0002135.2	0.63	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001250.4	0.63	NRPS	epichloenin A	Epichloe festucae
BGC0001251.4	0.63	NRPS	epichloenin A	Epichloe festucae
BGC0001261.3	0.63	NRPS	AM-toxin	Alternaria alternata

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: medium

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 32.03 out of 36.53

Confidence: strong

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 32.03 out of 36.53

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47

Confidence: strong

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 31.03 out of 36.53

Confidence: medium

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.71 out of 36.53

Confidence: medium

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.03 out of 36.53

Confidence: medium

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.86 out of 21.84

Confidence: medium

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52

Confidence: medium

Additional weak hits (11):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.39 out of 27.78

Confidence: weak

SypG

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

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.27 out of 18.57

Confidence: weak

ANR

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

Confidence: weak

NuR

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

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.24 out of 36.53

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.85 out of 26.85

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.77 out of 39.62

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.88 out of 33.14

Confidence: weak

ZuR variant 1

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

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.05 out of 35.63

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 2, location 205988 - 253918:

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

Polymer prediction:: (Lys)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CDS_02851: Lys

Search NORINE for peptide: strict or relaxed

AMP-binding (401..744): Lys

nrpys: Lys

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 with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DAEDIGTVVK
Nearest Stachelhaus code(s):: Lys DAEDIGTVVK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_02854: diOH-Bz

Search NORINE for peptide: strict or relaxed

AMP-binding (30..408): 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:: PLPAQGVVNK
Nearest Stachelhaus code(s):: diOH-Bz PLPAQGVVNK (100% 8Å match); diOH-Bz or Sal PLPAQGVVNK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
DmdR1	Iron(II)-dependent repressor
MexT	Global virulence regulator
VqsM	Regulator of quorum-sensing signalling systems

NPDC050663.ctg-0004 - Region 3 - NRPS,T1PKS,betalactone

Download region SVG

Location: 414,396 - 590,063 nt. (total: 175,668 nt) Show pHMM detection rules used

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
betalactone: (HMGL-like and AMP-binding)
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 oxidase oxidoreductase

CDS_03028: FAD linked oxidase domain protein

smcogs: SMCOG1138: FAD linked oxidase domain protein

CDS_03076: flavin reductase domain protein FMN-binding

smcogs: SMCOG1160: flavin reductase domain protein FMN-binding

CDS_03083: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_03084: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_03085: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

Transferases: PPTase acetyltransferase acylase acyltransferase aminotransferase carboxylase methyltransferase transferase

CDS_03032: polyketide synthase associated protein papA3

smcogs: SMCOG1209: polyketide synthase associated protein papA3

CDS_03037: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

CDS_03039: acetyl-CoA carboxylase biotin carboxylase

smcogs: SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

CDS_03040: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1060: 4'-phosphopantetheinyl transferase

CDS_03054: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

CDS_03068: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_03069: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_03073: acetyl-CoA carboxylase, carboxyl transferase,

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

CDS_03086: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

CDS_03088: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

CDS_03090: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: esterase

CDS_03055: thioesterase

smcogs: SMCOG1004: thioesterase

CDS_03071: thioesterase

smcogs: SMCOG1004: thioesterase

Isomerases: isomerase

CDS_03066: isochorismate synthase

smcogs: SMCOG1018: isochorismate synthase

Ligases: ligase synthase

CDS_03027: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_03029: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_03031: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_03033: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_03034: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_03043: 2-isopropylmalate synthase

smcogs: SMCOG1271: 2-isopropylmalate synthase

CDS_03058: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_03059: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_03060: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_03062: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_03067: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_03070: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	1.53	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	1.48	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	1.44	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	1.43	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	1.43	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001261.3	1.42	NRPS	AM-toxin	Alternaria alternata
BGC0001825.4	1.42	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001135.5	1.41	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0000342.4	1.41	NRPS	enniatin	Fusarium equiseti
BGC0001166.5	1.39	NRPS	HC-toxin	Alternaria jesenskae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001128.4	0.74	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001276.3	0.73	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002286.3	0.73	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.73	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001273.3	0.73	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.73	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001758.4	0.73	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.87 out of 23.79

Confidence: medium

ToxT

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

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.34 out of 23.79

Confidence: medium

Additional weak hits (27):

CopR

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

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.14 out of 32.93

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.30 out of 26.85

Confidence: weak

ANR

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

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.51 out of 23.43

Confidence: weak

CRP

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

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.62 out of 32.74

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.77 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.35 out of 28.14

Confidence: weak

CopR

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

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.96 out of 30.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.26 out of 27.78

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.58 out of 31.73

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.61 out of 31.73

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.65 out of 27.55

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.50 out of 29.65

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.96 out of 24.78

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.75 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 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.13 out of 32.93

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.40 out of 28.19

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.73 out of 32.93

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.17 out of 39.62

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.08 out of 35.63

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.51 out of 26.85

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.11 out of 25.88

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 3, location 414395 - 509908:

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

Polymer prediction:: (mal - ohmal - ccmal - ccmal - ccmal - ccmal) + (Gly) + (Cys - Cys) + (Me-Cys) + (X) + (Aad) + (X) + (Ser)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 414395 - 468780:

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

Polymer prediction:: (X) + (Aad) + (X) + (Ser)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 455144 - 509908:

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

Polymer prediction:: (mal - ohmal - ccmal - ccmal - ccmal - ccmal) + (Gly) + (Cys - Cys) + (Me-Cys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 470746 - 590063:

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

Polymer prediction:: (ccmal - ccmal - ccmal - pk - ccmal) + (ohmal - pk) + (pk - mal) + (mal - ohmal - ccmal - ccmal - ccmal - ccmal) + (Gly) + (Cys - Cys) + (Me-Cys)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CDS_03027: Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (10..397): Thr

nrpys: Thr

SVM prediction details:

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

Stachelhaus prediction details:

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

CDS_03031: Ser

Search NORINE for peptide: strict or relaxed

AMP-binding (505..905): 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:: DVWHISLVDK
Nearest Stachelhaus code(s):: Ser DVWHISLVDK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_03032: X

AMP-binding (509..905): 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:: DLPKVAEVAK
Nearest Stachelhaus code(s):: D-Ala DLTKVNEVGK (59% 8Å match); Asn DLTKVGEVGK (56% 8Å match); Glu DLVKVASVNK (50% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_03033: Aad

Search NORINE for peptide: strict or relaxed

AMP-binding (462..855): Aad

nrpys: 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:: DPRHFTSRAK
Nearest Stachelhaus code(s):: Aad DPRHFVMRAK (71% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_03034: X

AMP-binding (539..932): 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:: DAIAVGVIDK
Nearest Stachelhaus code(s):: Gln DAWQVGVVDK (59% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_03058: Cys

Search NORINE for peptide: strict or relaxed

AMP-binding (525..911): 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 (97% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_03059: Cys - Cys

Search NORINE for peptide: strict or relaxed

AMP-binding (547..917): 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 (82% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1551..1919): 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 (82% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_03060: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (455..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 (97% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_03062: mal - mal - mal - mal - mal - mal

PKS_AT (529..816): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 83.3%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 197.6
inactive: 100.2
Methoxymalonyl-CoA: 60.2
Methylmalonyl-CoA: 49.5
Acetyl-CoA: 27.9
Benzoyl-CoA: 21.7
Propionyl-CoA: 20.2
Isobutyryl-CoA: 19.8
Ethylmalonyl-CoA: 15.4
CHC-CoA: 13.6
fatty_acid: 12.3
2-Methylbutyryl-CoA: 10.9
trans-1,2-CPDA: 8.8
3-Methylbutyryl-CoA: 0.0

PKS_AT (1543..1821): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 75.0%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 171.9
inactive: 82.3
Methoxymalonyl-CoA: 63.7
Methylmalonyl-CoA: 51.0
Acetyl-CoA: 28.5
Propionyl-CoA: 21.7
Isobutyryl-CoA: 18.1
Benzoyl-CoA: 15.7
Ethylmalonyl-CoA: 12.8
fatty_acid: 6.4
CHC-CoA: 5.9
2-Methylbutyryl-CoA: 3.3
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (2939..3204): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 183.3
inactive: 88.3
Methoxymalonyl-CoA: 64.7
Methylmalonyl-CoA: 54.1
Isobutyryl-CoA: 27.0
Ethylmalonyl-CoA: 22.8
Benzoyl-CoA: 19.3
Acetyl-CoA: 17.6
Propionyl-CoA: 15.6
2-Methylbutyryl-CoA: 13.1
CHC-CoA: 12.2
fatty_acid: 8.9
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (4608..4873): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 188.7
inactive: 91.8
Methoxymalonyl-CoA: 68.9
Methylmalonyl-CoA: 58.4
Isobutyryl-CoA: 29.3
Ethylmalonyl-CoA: 25.5
Benzoyl-CoA: 23.6
Propionyl-CoA: 20.4
CHC-CoA: 13.3
Acetyl-CoA: 13.0
2-Methylbutyryl-CoA: 12.4
fatty_acid: 10.8
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (6263..6531): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 182.5
inactive: 87.8
Methoxymalonyl-CoA: 63.3
Methylmalonyl-CoA: 52.6
Isobutyryl-CoA: 28.2
Ethylmalonyl-CoA: 21.2
Benzoyl-CoA: 18.5
Acetyl-CoA: 18.3
Propionyl-CoA: 15.6
CHC-CoA: 12.1
2-Methylbutyryl-CoA: 10.3
fatty_acid: 8.7
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (7927..8192): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 187.8
inactive: 89.6
Methoxymalonyl-CoA: 63.8
Methylmalonyl-CoA: 48.1
Isobutyryl-CoA: 25.1
Ethylmalonyl-CoA: 24.3
Benzoyl-CoA: 19.8
Acetyl-CoA: 17.6
2-Methylbutyryl-CoA: 16.4
Propionyl-CoA: 13.4
CHC-CoA: 11.8
fatty_acid: 9.0
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

CDS_03067: X

AMP-binding (31..435): X

nrpys: diOH-Bz, Sal

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: PLGGTGACGK
Nearest Stachelhaus code(s):: Hty DLGFTGAVCK (29% 8Å match)
Stachelhaus code match:: 60% (weak)

CDS_03068: pk - mal

PKS_AT (563..858): pk

ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:

Ethylmalonyl-CoA: 219.8
Methylmalonyl-CoA: 216.8
Methoxymalonyl-CoA: 180.3
2-Methylbutyryl-CoA: 129.7
trans-1,2-CPDA: 124.3
Propionyl-CoA: 112.1
Malonyl-CoA: 89.5
CHC-CoA: 81.8
Isobutyryl-CoA: 69.8
Benzoyl-CoA: 56.0
Acetyl-CoA: 39.1
inactive: 32.6
3-Methylbutyryl-CoA: 26.8
fatty_acid: 24.6

PKS_AT (2317..2610): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 217.4
inactive: 108.4
Methoxymalonyl-CoA: 59.2
Methylmalonyl-CoA: 51.2
Propionyl-CoA: 35.4
Isobutyryl-CoA: 30.8
Benzoyl-CoA: 19.8
Acetyl-CoA: 19.3
Ethylmalonyl-CoA: 19.2
2-Methylbutyryl-CoA: 10.3
CHC-CoA: 10.1
fatty_acid: 9.4
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

CDS_03069: mal - pk

PKS_AT (549..840): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 79.2%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 195.3
inactive: 97.9
Methoxymalonyl-CoA: 74.5
Methylmalonyl-CoA: 59.0
Isobutyryl-CoA: 30.2
Ethylmalonyl-CoA: 27.2
Acetyl-CoA: 21.9
Propionyl-CoA: 20.1
Benzoyl-CoA: 18.8
CHC-CoA: 13.9
fatty_acid: 11.1
trans-1,2-CPDA: 11.0
2-Methylbutyryl-CoA: 10.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (2114..2407): pk

ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:

Ethylmalonyl-CoA: 219.9
Methylmalonyl-CoA: 217.5
Methoxymalonyl-CoA: 186.2
2-Methylbutyryl-CoA: 157.0
trans-1,2-CPDA: 132.2
Propionyl-CoA: 119.1
Malonyl-CoA: 96.7
CHC-CoA: 93.4
Isobutyryl-CoA: 71.6
Benzoyl-CoA: 53.8
3-Methylbutyryl-CoA: 49.9
Acetyl-CoA: 46.4
inactive: 33.0
fatty_acid: 31.6

CDS_03070: mal - mal - mal - pk - mal

PKS_AT (551..816): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 186.4
inactive: 89.2
Methoxymalonyl-CoA: 67.0
Methylmalonyl-CoA: 55.0
Isobutyryl-CoA: 31.3
Ethylmalonyl-CoA: 24.8
Benzoyl-CoA: 19.6
Propionyl-CoA: 17.7
Acetyl-CoA: 16.6
2-Methylbutyryl-CoA: 14.0
CHC-CoA: 13.1
fatty_acid: 9.6
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (2214..2477): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 185.0
inactive: 90.0
Methoxymalonyl-CoA: 65.9
Methylmalonyl-CoA: 50.5
Isobutyryl-CoA: 29.3
Ethylmalonyl-CoA: 21.1
Benzoyl-CoA: 19.5
Propionyl-CoA: 18.5
Acetyl-CoA: 17.1
CHC-CoA: 14.4
2-Methylbutyryl-CoA: 11.6
fatty_acid: 9.1
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (3854..4124): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 182.2
inactive: 84.5
Methoxymalonyl-CoA: 60.7
Methylmalonyl-CoA: 47.8
Isobutyryl-CoA: 26.8
Ethylmalonyl-CoA: 21.3
Benzoyl-CoA: 18.9
Acetyl-CoA: 17.2
Propionyl-CoA: 14.7
2-Methylbutyryl-CoA: 13.0
CHC-CoA: 12.6
fatty_acid: 8.8
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (5537..5829): pk

ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:

Ethylmalonyl-CoA: 217.0
Methylmalonyl-CoA: 214.2
Methoxymalonyl-CoA: 178.9
2-Methylbutyryl-CoA: 139.1
trans-1,2-CPDA: 118.9
Propionyl-CoA: 110.7
Malonyl-CoA: 84.5
CHC-CoA: 81.8
Isobutyryl-CoA: 71.8
Benzoyl-CoA: 58.4
Acetyl-CoA: 43.4
3-Methylbutyryl-CoA: 33.4
inactive: 29.2
fatty_acid: 26.1

PKS_AT (7234..7507): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 83.3%; Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 179.3
inactive: 80.5
Methoxymalonyl-CoA: 69.0
Methylmalonyl-CoA: 59.8
Isobutyryl-CoA: 36.2
Propionyl-CoA: 27.0
Ethylmalonyl-CoA: 21.1
Acetyl-CoA: 20.4
Benzoyl-CoA: 19.4
CHC-CoA: 18.7
2-Methylbutyryl-CoA: 11.4
fatty_acid: 9.4
trans-1,2-CPDA: 8.4
3-Methylbutyryl-CoA: 0.0

TFBS definitions

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

NPDC050663.ctg-0004 - Region 4 - betalactone

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Location: 812,627 - 838,004 nt. (total: 25,378 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

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase

CDS_03308: dihydropteridine reductase

smcogs: SMCOG1159: dihydropteridine reductase

CDS_03324: dehydrogenase

smcogs: SMCOG1072: dehydrogenase

Ligases: synthase

CDS_03314: 2-isopropylmalate synthase

smcogs: SMCOG1271: 2-isopropylmalate synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002706.2	0.41	NRPS	saframycin Mx1	Myxococcus xanthus
BGC0001294.5	0.40	other (other)	7-prenylisatin	Streptomyces sp. MBT28
BGC0000469.6	0.39	ribosomal	bottromycin A2	Streptomyces sp. BC16019
BGC0000470.6	0.38	ribosomal	bottromycin D	Streptomyces sp. WMMB272
BGC0000904.5	0.38	other (other)	FR-900098	Streptomyces rubellomurinus
BGC0000468.5	0.38	ribosomal	bottromycin A2	Streptomyces bottropensis DSM40262
BGC0001157.6	0.37	ribosomal	bottromycin A2	Streptomyces scabiei 87.22
BGC0001562.5	0.36	NRPS	curacomycin	Streptomyces curacoi
BGC0000275.4	0.36	PKS	tetracenomycin C	Streptomyces glaucescens
BGC0002081.3	0.36	PKS	streptoketide A, streptoketide B, streptoketide C, S2502, S2507, UWM5	Streptomyces sp. Tue6314

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002706.2	0.41	NRPS	saframycin Mx1	Myxococcus xanthus
BGC0001294.5	0.40	other (other)	7-prenylisatin	Streptomyces sp. MBT28
BGC0000469.6	0.39	ribosomal	bottromycin A2	Streptomyces sp. BC16019
BGC0000470.6	0.38	ribosomal	bottromycin D	Streptomyces sp. WMMB272
BGC0000904.5	0.38	other (other)	FR-900098	Streptomyces rubellomurinus
BGC0000468.5	0.38	ribosomal	bottromycin A2	Streptomyces bottropensis DSM40262
BGC0001157.6	0.37	ribosomal	bottromycin A2	Streptomyces scabiei 87.22
BGC0001562.5	0.36	NRPS	curacomycin	Streptomyces curacoi
BGC0000275.4	0.36	PKS	tetracenomycin C	Streptomyces glaucescens
BGC0002081.3	0.36	PKS	streptoketide A, streptoketide B, streptoketide C, S2502, S2507, UWM5	Streptomyces sp. Tue6314

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:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26

Confidence: strong

Additional weak hits (6):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.51 out of 30.22

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.47 out of 27.78

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.60 out of 29.25

Confidence: weak

ClgR

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

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.59 out of 35.63

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.34 out of 26.85

Confidence: weak

Detailed Pfam domain annotation

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Detailed TIGRFAM domain annotation

Selected features only

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TFBS Finder

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein

NPDC050663.ctg-0006 - Region 1 - PKS-like

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Location: 168,454 - 209,470 nt. (total: 41,017 nt) Show pHMM detection rules used

PKS-like: (t2pks2 or ksIII)

Legend:

core biosynthetic genes

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Gene details

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Gene overview

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MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

CDS_04193: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

CDS_04194: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_04195: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_04201: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase kinase methyltransferase

CDS_04192: PfkB domain protein

smcogs: SMCOG1276: PfkB domain protein

CDS_04199: glycerol kinase

smcogs: SMCOG1210: glycerol kinase

CDS_04214: methyltransferase

smcogs: SMCOG1248: methyltransferase

CDS_04226: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: phosphatase

CDS_04209: FkbH like protein

smcogs: SMCOG1256: FkbH like protein

Ligases: synthase

CDS_04208: 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
BGC0002276.2	0.58	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000221.5	0.48	PKS	erdacin	uncultured soil bacterium V167
BGC0001336.5	0.47	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0002127.3	0.47	PKS	flaviolin, 1,3,6,8-tetrahydroxynaphthalene	Streptomyces coelicolor A3(2)
BGC0000894.4	0.45	other (other)	citrinin	Monascus aurantiacus
BGC0000888.5	0.45	other (other)	bacilysin	Bacillus sp. CS93
BGC0000220.4	0.45	PKS	enterocin	Streptomyces maritimus
BGC0001986.3	0.44	other (other)	purincyclamide	Streptomyces chrestomyceticus
BGC0000248.5	0.44	PKS	α naphtocyclinoic acid, fogacin	Streptomyces arenae DSM 40737
BGC0001223.5	0.44	other (other)	hydroxysporine	uncultured bacterium

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002276.2	0.58	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000221.5	0.48	PKS	erdacin	uncultured soil bacterium V167
BGC0001336.5	0.47	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0002127.3	0.47	PKS	flaviolin, 1,3,6,8-tetrahydroxynaphthalene	Streptomyces coelicolor A3(2)
BGC0000894.4	0.45	other (other)	citrinin	Monascus aurantiacus
BGC0000888.5	0.45	other (other)	bacilysin	Bacillus sp. CS93
BGC0000220.4	0.45	PKS	enterocin	Streptomyces maritimus
BGC0001986.3	0.44	other (other)	purincyclamide	Streptomyces chrestomyceticus
BGC0000248.5	0.44	PKS	α naphtocyclinoic acid, fogacin	Streptomyces arenae DSM 40737
BGC0001223.5	0.44	other (other)	hydroxysporine	uncultured bacterium

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CRP

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

Confidence: strong

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52

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

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.10 out of 24.78

Confidence: medium

Additional weak hits (22):

ArcA

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

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.36 out of 32.93

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.12 out of 20.97

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.77 out of 28.14

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.55 out of 20.97

Confidence: weak

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.87 out of 32.38

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.93 out of 28.19

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.33 out of 27.04

Confidence: weak

CelR

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

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: 22.20 out of 30.11

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.25 out of 29.38

Confidence: weak

FuR variant 1

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.78 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.40 out of 27.78

Confidence: weak

OsdR

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

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.46 out of 29.65

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.51 out of 24.78

Confidence: weak

ZuR variant 2

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

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.08 out of 36.53

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.78 out of 20.01

Confidence: weak

ToxT

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

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

TFBS Finder

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
CRP	Cyclic AMP receptor protein
LexA variant 2	Repressor of DNA damage response

NPDC050663.ctg-0006 - Region 2 - azole-containing-RiPP,thioamitides

Download region SVG

Location: 281,997 - 310,437 nt. (total: 28,441 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)
thioamitides: ((YcaO or TIGR03604) and TfuA)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene overview

Tailoring

MIBiG comparison

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KnownClusterBlast

SubClusterBlast

TFBS Finder

Azole RiPPs

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: oxygenase

CDS_04310: monooxygenase FAD-binding

smcogs: SMCOG1246: monooxygenase FAD-binding

CDS_04313: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: methyltransferase

CDS_04312: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

Hydrolases: protease

CDS_04304: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

Lyases: hydratase

CDS_04301: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002084.4	0.48	ribosomal	biarylitide YYH	Planomonospora sp. ID82291
BGC0002099.3	0.48	ribosomal	biarylitide YFH	Planomonospora sp. ID107089
BGC0001849.4	0.33	ribosomal	thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D	Streptomyces varsoviensis
BGC0001224.5	0.32	other (other)	reductasporine	uncultured bacterium
BGC0001336.5	0.32	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0002825.2	0.32	ribosomal	nocapeptin A	Nocardia terpenica IFM 0406
BGC0001634.3	0.31	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0000575.5	0.31	ribosomal	lariatin	Rhodococcus jostii
BGC0000602.5	0.31	ribosomal	subtilosin A	Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0001485.4	0.31	other (other)	chuangxinmycin	Actinoplanes tsinanensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002084.4	0.57	ribosomal	biarylitide YYH	Planomonospora sp. ID82291
BGC0002099.3	0.57	ribosomal	biarylitide YFH	Planomonospora sp. ID107089
BGC0001849.4	0.48	ribosomal	thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D	Streptomyces varsoviensis
BGC0001224.5	0.47	other (other)	reductasporine	uncultured bacterium
BGC0001336.5	0.46	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0002825.2	0.46	ribosomal	nocapeptin A	Nocardia terpenica IFM 0406
BGC0001634.3	0.46	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0000575.5	0.46	ribosomal	lariatin	Rhodococcus jostii
BGC0000600.3	0.46	ribosomal	thurincin H	Bacillus thuringiensis
BGC0000602.5	0.46	ribosomal	subtilosin A	Bacillus subtilis subsp. spizizenii ATCC 6633

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: medium

AbrC3

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

Confidence: strong

Additional weak hits (7):

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.30 out of 28.19

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.42 out of 36.53

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.38 out of 29.25

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.73 out of 39.62

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.59 out of 28.19

Confidence: weak

HypR

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

Confidence: weak

HypR

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

Confidence: weak

(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: Stand_Alone_Lasso_RRE; Location: 1 - 89; Score: 40.8
: RRE type: Stand_Alone_Lasso_RRE; Location: 1 - 89; Score: 40.8

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
VqsM	Regulator of quorum-sensing signalling systems

Core peptide predictions

No core peptides found.

NPDC050663.ctg-0006 - Region 3 - lanthipeptide-class-iii

BGC0000553.3 (SSGG_RS09925):

Download region SVG

Location: 330,463 - 352,973 nt. (total: 22,511 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase

CDS_04344: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_04353: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: methyltransferase sulfotransferase

CDS_04345: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_04357: Sulfotransferase domain

extras: Sulfotransfer_3: Sulfotransferase domain

Lyases: decarboxylase

CDS_04343: putative carboxymuconolactone decarboxylase

smcogs: SMCOG1298: putative carboxymuconolactone decarboxylase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000551.5	0.65	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000496.5	0.65	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3	0.65	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000501.3	0.61	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0000519.4	0.60	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000518.3	0.52	ribosomal	informatipeptin	Streptomyces viridochromogenes DSM 40736
BGC0002700.2	0.52	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0000553.3	0.52	ribosomal	SRO15-2212	Streptomyces filamentosus NRRL 15998
BGC0002698.2	0.51	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0002111.3	0.48	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000551.5	0.65	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000496.5	0.65	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3	0.65	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000501.3	0.61	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0000519.4	0.60	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000518.3	0.52	ribosomal	informatipeptin	Streptomyces viridochromogenes DSM 40736
BGC0002700.2	0.52	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0000553.3	0.52	ribosomal	SRO15-2212	Streptomyces filamentosus NRRL 15998
BGC0002698.2	0.51	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0002111.3	0.48	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for CDS_04351

CDS_04350

Leader:

MVLLDLQGLEAPTSTDVAS

Core:

GGSTLTALTCNSGKPSNLSVALCH

Core with dehydrations:

GGDhaDhbLDhbALDhbCysNDhaGKPDhaNLDhaVALCysH

antiSMASH-DB 4.0 matches for CDS_04350

100.0%

NZ_JACDUR010000006.1and 2 others:

NZ_JPMW01000001.1 Lanthipeptides: EV45_RS41010_lanthipeptideNZ_JPMW01000001.1 Lanthipeptides: EV45_RS41005_lanthipeptide

Lanthipeptides: HNR30_RS31115_lanthipeptide

1

GGSTLTALTCNSGKPSNLSVALCH

24

GGSTLTALTCNSGKPSNLSVALCH

1

GGSTLTALTCNSGKPSNLSVALCH

24

91.7%

NZ_JACHIN010000017.1:

Lanthipeptides: HNR40_RS44190_lanthipeptide

1

GGSTLTALTCNSGKPSNLSVALCH

24

GGSTLT LTC+SGKPSNLSVALCH

1

GGSTLTVLTCHSGKPSNLSVALCH

24

91.7%

NZ_JAHFZZ010000011.1:

Lanthipeptides: KLK06_RS32640_lanthipeptide

1

GGSTLTALTCNSGKPSNLSVALCH

24

GGSTLTALTC SG PSNLSVALCH

1

GGSTLTALTCQSGHPSNLSVALCH

24

with 68 more sequence matches

Only the first 10 are displayed here.

87.5%

NZ_CP017717.1and 2 others:

NZ_FNDJ01000002.1 Lanthipeptides: BLS95_RS05705_lanthipeptideNZ_FNVT01000002.1 Lanthipeptides: C4V41_RS07345_lanthipeptide

Lanthipeptides: BKM31_RS59280_lanthipeptide

1

GGSTLTALTCNSGKPSNLSVALCH

24

GGSTLT L+C+SGKPSNLSVALCH

1

GGSTLTVLSCHSGKPSNLSVALCH

24

87.5%

NZ_JAIWLT010000005.1and 1 other:

NZ_JAIWLU010000020.1 Lanthipeptides: LDL05_RS29535_lanthipeptide

Lanthipeptides: LDL08_RS14700_lanthipeptide

1

GGSTLTALTCNSGKPSNLSVALCH

24

GGSTLT L C+SGKPSNLSVALCH

1

GGSTLTVLGCHSGKPSNLSVALCH

24

87.5%

NZ_WBMT01000033.1:

Lanthipeptides: F8566_RS47085_lanthipeptide

1

GGSTLTALTCNSGKPSNLSVALCH

24

GGSTLT LTC+SGKPSNLS ALCH

1

GGSTLTLLTCHSGKPSNLSAALCH

24

83.3%

NZ_CP084058.1:

Lanthipeptides: LCN96_RS39235_lanthipeptide

1

GGSTLTALTCNSGKPSNLSVALCH

24

GGSTLT L+C+SG PSNLSVALCH

1

GGSTLTVLSCHSGAPSNLSVALCH

24

83.3%

NZ_JACJIA010000018.1:

Lanthipeptides: HNR61_RS42145_lanthipeptide

1

GGSTLTALTCNSGKPSNLSVALCH

24

GGS+LTA TC S KPSNLSVALCH

1

GGSSLTAATCGSTKPSNLSVALCH

24

79.2%

NZ_JABWGN010000023.1:

Lanthipeptides: HTZ77_RS41305_lanthipeptide

1

GGSTLTALTCNSGKPSNLSVALCH

24

GGSTLT L C+SG PSNLSVA+CH

1

GGSTLTVLGCHSGAPSNLSVAVCH

24

79.2%

NZ_JABWGO010000017.1:

Lanthipeptides: HT134_RS41585_lanthipeptide

1

GGSTLTALTCNSGKPSNLSVALCH

24

GGSTLT L C+SG PSNLSVA+CH

1

GGSTLTVLGCHSGTPSNLSVAVCH

24

76.9%

NZ_BBYJ01000032.1and 1 other:

NZ_BBYM01000040.1 Lanthipeptides: AWQ70_RS39425_lanthipeptide

Lanthipeptides: AWQ71_RS42200_lanthipeptide

1

GGSTLTALTCNSGKPSNLSVALCH

24

GGSTLT LTC SG+PSNLS+ALCH

3

GGSTLTVLTCQSGRPSNLSIALCH

26

75.0%

NZ_JAKRKC020000001.1:

Lanthipeptides: MF672_RS25655_lanthipeptide

1

GGSTLTALTCNSGKPSNLSVALCH

24

GGS+LT TC S PSNLSVALCH

1

GGSSLTVATCGSHTPSNLSVALCH

24

75.0%

NZ_KI911782.1:

Lanthipeptides: JIAGA_RS34345_lanthipeptide

4

TLTALTCNSGKPSNLSVALCH

24

TLT LTC S KPSNLSVALCH

1

TLTVLTCGSVKPSNLSVALCH

21

MIBiG 4.0 matches for CDS_04350

41.7%

Lanthipeptide: SRO15-2212

2

GSTLTALTCNSGKPSNLSVALC

23

GS ++ L C S+LSV LC

2

GSQVSLLVCEY---SSLSVVLC

20

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.95 out of 27.78

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 (10):

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.72 out of 26.85

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.90 out of 29.38

Confidence: weak

PsrA

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

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.97 out of 32.74

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.38 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.72 out of 28.14

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.11 out of 27.55

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.50 out of 32.74

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 23.73 out of 35.63

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.12 out of 29.25

Confidence: weak

Detailed Pfam domain annotation

Selected features only

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Lanthipeptides

TFBS Finder

Core peptide predictions

CDS_04350 - Class III

Cleavage pHMM score: 9.50

RODEO score: 0

Monoisotopic mass: 2204.1 Da

Molecular weight: 2205.5 Da

Number of bridges: 2

Alternative weights: (assuming N unmodified Ser/Thr residues); 2223.5 Da N = 1; 2241.5 Da N = 2; 2259.5 Da N = 3; 2277.6 Da N = 4; 2295.6 Da N = 5

TFBS definitions

Regulator	Description
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC050663.ctg-0007 - Region 1 - betalactone

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Location: 208,200 - 237,789 nt. (total: 29,590 nt) Show pHMM detection rules used

betalactone: (HMGL-like and AMP-binding)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Pfam domains

Gene/CDS overview

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

Tailoring functions

Hydrolases: hydrolase

CDS_04713: isochorismatase

smcogs: SMCOG1027: isochorismatase

CDS_04719: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Lyases: dehydratase

CDS_04716: L-carnitine dehydratase/bile acid-inducible

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

Ligases: ligase synthase

CDS_04711: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_04718: 2-isopropylmalate synthase

smcogs: SMCOG1271: 2-isopropylmalate synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.56	NRPS	enniatin	Fusarium equiseti
BGC0002174.2	0.56	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0000307.4	0.56	NRPS	AbT1	Aureobasidium pullulans
BGC0001128.4	0.55	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	0.55	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3	0.55	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0002699.2	0.47	ribosomal	nostolysamide A, nostolysamide B	Nostoc punctiforme PCC 73102
BGC0002493.3	0.44	NRPS	parabactin	Paracoccus denitrificans PD1222
BGC0002020.3	0.44	NRPS, saccharide	photolose, oligosaccharide 1 (GlcNAc-β(1-4)-1,6-anhydro-β-GlcNAc), oligosaccharide 2 (GlcNAc-β(1-4)-GlcNAc-β(1-4)-1,6-anhydro-β-GlcNAc), oligosaccharide 3 (GlcNAc-β(1-4)-GlcNAc-β(1-4)-GlcNAc-β(1-4)-1,6-anhydro-β-GlcNAc), oligosaccharide 4 (GlcN-β(1-4)-GlcNAc-β(1-4)-1,6-anhydro-β-GlcNAc), oligosaccharide 5 (6-phosphoGlcN-β(1-4)-GlcNAc-β(1-4)-1,6-anhydro-β-GlcNAc)	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001137.5	0.43	other (other)	marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D	Marinactinospora thermotolerans

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.56	NRPS	enniatin	Fusarium equiseti
BGC0002174.2	0.56	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0000307.4	0.56	NRPS	AbT1	Aureobasidium pullulans
BGC0001128.4	0.55	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	0.55	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3	0.55	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0002699.2	0.47	ribosomal	nostolysamide A, nostolysamide B	Nostoc punctiforme PCC 73102
BGC0002493.3	0.44	NRPS	parabactin	Paracoccus denitrificans PD1222
BGC0002020.3	0.44	NRPS, saccharide	photolose, oligosaccharide 1 (GlcNAc-β(1-4)-1,6-anhydro-β-GlcNAc), oligosaccharide 2 (GlcNAc-β(1-4)-GlcNAc-β(1-4)-1,6-anhydro-β-GlcNAc), oligosaccharide 3 (GlcNAc-β(1-4)-GlcNAc-β(1-4)-GlcNAc-β(1-4)-1,6-anhydro-β-GlcNAc), oligosaccharide 4 (GlcN-β(1-4)-GlcNAc-β(1-4)-1,6-anhydro-β-GlcNAc), oligosaccharide 5 (6-phosphoGlcN-β(1-4)-GlcNAc-β(1-4)-1,6-anhydro-β-GlcNAc)	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001137.5	0.43	other (other)	marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D	Marinactinospora thermotolerans

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

AbrC3

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

Confidence: strong

Additional weak hits (12):

MexT

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

Confidence: weak

NtrC

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

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.69 out of 30.97

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.77 out of 36.54

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.88 out of 25.75

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.43 out of 36.54

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.76 out of 30.25

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.99 out of 30.97

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.33 out of 36.54

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.49 out of 21.55

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.87 out of 32.93

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.12 out of 28.19

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator

NPDC050663.ctg-0007 - Region 2 - NRPS,NRPS-like,T1PKS,terpene

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Location: 249,360 - 348,709 nt. (total: 99,350 nt) Show pHMM detection rules used

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

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Terpene

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

CDS_04753: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

CDS_04757: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

CDS_04795: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_04801: flavin reductase domain protein FMN-binding

smcogs: SMCOG1160: flavin reductase domain protein FMN-binding

CDS_04804: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_04819: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

CDS_04820: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_04823: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

Transferases: PPTase acylase aminotransferase halogenase kinase

CDS_04784: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1060: 4'-phosphopantetheinyl transferase

CDS_04787: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_04788: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_04802: flavin-dependent trp 5 halogenase

halogenases: flavin-dependent trp 5 halogenase
MITE: MITE0000030Halogenation (identity: 63.80%)
smcogs: SMCOG1119: halogenase

CDS_04803: aminotransferase

smcogs: SMCOG1019: aminotransferase

CDS_04808: flavin-dependent trp 6 7 halogenase

halogenases: flavin-dependent trp 6 7 halogenase
MITE: MITE0000030Halogenation (identity: 68.80%)
smcogs: SMCOG1119: halogenase

CDS_04827: PfkB domain protein

smcogs: SMCOG1276: PfkB domain protein

Hydrolases: esterase hydrolase

CDS_04775: alpha/beta hydrolase domain-containing protein

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

CDS_04782: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

CDS_04805: thioesterase

smcogs: SMCOG1004: thioesterase

CDS_04809: alpha/beta hydrolase domain-containing protein

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

CDS_04815: thioesterase

smcogs: SMCOG1004: thioesterase

CDS_04817: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: dehydratase

CDS_04789: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase synthetase

CDS_04752: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

CDS_04758: polyprenol-monophosphomannose synthase ppm1

smcogs: SMCOG1123: polyprenol-monophosphomannose synthase ppm1

CDS_04785: 3-oxoacyl-(acyl carrier protein) synthase III

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

CDS_04794: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_04806: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_04810: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_04811: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter

CDS_04744: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	1.19	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002164.2	1.01	NRPS	peramine	Epichloe festucae
BGC0001132.4	1.01	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.99	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.97	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.96	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001641.4	0.94	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.93	NRPS	AM-toxin	Alternaria alternata
BGC0001758.4	0.92	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.91	NRPS	icosalide A, icosalide B	Burkholderia gladioli

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002164.2	0.69	NRPS	peramine	Epichloe festucae
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.68	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.67	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.67	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001261.3	0.67	NRPS	AM-toxin	Alternaria alternata
BGC0001641.4	0.66	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.66	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.66	NRPS	icosalide A, icosalide B	Burkholderia gladioli

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Detailed terpene predictions

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
triterpene		squalene	C30	acyclic	none
triterpene		PSPP	C30	acyclic	PP
triterpene	C30 carotenoid	diapophytoene	C30	acyclic	none
tetraterpene	C40 carotenoid	phytoene	C40	acyclic	none
triterpene		hydroxysqualene	C30	acyclic	OH

Genes with terpene domains:

CDS_04752: PT_FPPS_like

Domain 1 (42 - 331): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

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

CDS_04754: PT_phytoene_like

Domain 1 (3 - 293): Prenyltransferase; Phytoene synthase like

Subtype: unknown

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

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: 20.89 out of 26.85

Confidence: medium

VqsM

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

Confidence: medium

IolR

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

Confidence: medium

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.64 out of 26.33

Confidence: medium

OsdR

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

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.70 out of 26.85

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 (38):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.63 out of 21.55

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 20.78 out of 31.73

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.98 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 24.15 out of 32.74

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.04 out of 27.78

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.90 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.19 out of 29.38

Confidence: weak

FuR variant 1

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

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.15 out of 28.14

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.91 out of 29.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.65 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

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.30 out of 20.97

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.78 out of 26.06

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.27 out of 21.55

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.95 out of 26.06

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.54 out of 39.62

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.80 out of 28.19

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

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.93 out of 31.73

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.30 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.47 out of 27.78

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.54 out of 32.93

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.77 out of 26.06

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.31 out of 29.65

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.39 out of 27.04

Confidence: weak

MatP

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

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.79 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.92 out of 28.14

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: 18.16 out of 29.38

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.40 out of 31.73

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.49 out of 29.38

Confidence: weak

PerR

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

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.85 out of 18.57

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.64 out of 33.14

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.08 out of 33.14

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.42 out of 35.63

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

Terpene

TFBS Finder

Predicted core structure(s)

For candidate cluster 2, location 249359 - 348709:

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

Polymer prediction:: (Me-mal) + (Me-redmal) + (Trp) + (Cys) + (Cys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 271145 - 317274:

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

Polymer prediction:: (Me-mal) + (Me-redmal) + (Trp)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 282129 - 323902:

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

Polymer prediction:: (Me-mal) + (Me-redmal) + (Trp) + (Cys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 300295 - 348709:

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

Polymer prediction:: (Trp) + (Cys) + (Cys)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CDS_04787: mmal

PKS_AT (94..369): mmal

ATSignature: (unknown)

No matches above 50%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 72.5
Methoxymalonyl-CoA: 64.7
Propionyl-CoA: 42.6
trans-1,2-CPDA: 38.9
CHC-CoA: 38.9
Ethylmalonyl-CoA: 37.7
Malonyl-CoA: 36.4
Acetyl-CoA: 25.7
2-Methylbutyryl-CoA: 23.8
Isobutyryl-CoA: 18.7
Benzoyl-CoA: 16.9
3-Methylbutyryl-CoA: 16.5
fatty_acid: 15.2
inactive: 0.0

CDS_04788: mmal

PKS_AT (565..855): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 79.2%; Ethylmalonyl-CoA: 70.8%; Malonyl-CoA: 70.8%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 143.3
Ethylmalonyl-CoA: 124.5
Methoxymalonyl-CoA: 110.5
Malonyl-CoA: 91.4
Isobutyryl-CoA: 73.3
Propionyl-CoA: 68.8
trans-1,2-CPDA: 67.6
2-Methylbutyryl-CoA: 67.5
Acetyl-CoA: 54.3
fatty_acid: 41.4
Benzoyl-CoA: 38.0
inactive: 32.8
CHC-CoA: 29.0
3-Methylbutyryl-CoA: 17.1

CDS_04794: Trp

Search NORINE for peptide: strict or relaxed

AMP-binding (7..403): Trp

nrpys: Trp

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DAWVTTAVGK
Nearest Stachelhaus code(s):: Trp DAWVMTGVGK (82% 8Å match); Kyn DAWTTTGVGK (71% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_04806: X

AMP-binding (33..432): 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:: Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: ALPTQGVITK
Nearest Stachelhaus code(s):: Hqa ALPTQGWLTK (71% 8Å match); COOH-Qui ALPTQGWLTK (68% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_04810: Cys

Search NORINE for peptide: strict or relaxed

AMP-binding (564..957): 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:: DLWNLSLIWK
Nearest Stachelhaus code(s):: Cys DLWNLSLIWK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_04811: Cys

Search NORINE for peptide: strict or relaxed

AMP-binding (538..933): 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:: DLYNMSLIWK
Nearest Stachelhaus code(s):: Cys DLYNMSLIWK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

Glossary

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

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
IolR	Regulator of the inositol catabolism
OsdR	Development and stress management regulator
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC050663.ctg-0008 - Region 1 - NRPS,RiPP-like

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Location: 3,271 - 63,526 nt. (total: 60,256 nt) Show pHMM detection rules used

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

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NRPS/PKS modules

Pfam domains

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NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: oxidoreductase oxygenase

CDS_04980: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_04990: flavin reductase domain protein FMN-binding

smcogs: SMCOG1160: flavin reductase domain protein FMN-binding

Transferases: glycosyltransferase halogenase methyltransferase sulfotransferase

CDS_04976: glycosyl transferase group 1

smcogs: SMCOG1045: glycosyl transferase group 1

CDS_04977: Sulfotransferase domain

extras: Sulfotransfer_3: Sulfotransferase domain

CDS_04989: conventional flavin-dependent halogenase

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

CDS_04999: methyltransferase

smcogs: SMCOG1248: methyltransferase

Ligases: ligase synthase

CDS_04969: polyprenol-monophosphomannose synthase ppm1

smcogs: SMCOG1123: polyprenol-monophosphomannose synthase ppm1

CDS_04983: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_04985: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_04986: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_04987: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.45	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	0.44	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.43	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002075.3	0.42	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001128.4	0.42	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.42	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.41	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.41	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.41	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002071.2	0.39	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.74	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001128.4	0.74	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.73	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.73	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.73	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002071.2	0.71	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027

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

Additional weak hits (11):

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.80 out of 36.54

Confidence: weak

ANR

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

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.48 out of 29.25

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.74 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.50 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.84 out of 26.06

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.53 out of 20.97

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.57 out of 27.04

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.85 out of 26.06

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.32 out of 29.38

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.07 out of 32.93

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 1, location 3270 - 63526:

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

Polymer prediction:: (Ile) + (Ser - X) + (Orn - X - X)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CDS_04983: Val

Search NORINE for peptide: strict or relaxed

AMP-binding (149..558): Val

nrpys: Val

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
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:: DMMQIGGIYK
Nearest Stachelhaus code(s):: Val DASQIGGIYK (56% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_04985: Ile

Search NORINE for peptide: strict or relaxed

AMP-binding (722..1113): Ile

nrpys: Ile

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DAFFYGITFK
Nearest Stachelhaus code(s):: Ile DAFFYGITFK (82% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_04986: Ser - X

Search NORINE for peptide: strict or relaxed

AMP-binding (476..871): 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:: DVWNVAMVHK
Nearest Stachelhaus code(s):: Ser DVWNVAMVHK (82% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1555..1942): 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:: DPFAYGISIK
Nearest Stachelhaus code(s):: Ile DAFFYGITFK (62% 8Å match); Ph-Gly DPFLWGILCK (53% 8Å match)
Stachelhaus code match:: 60% (weak)

CDS_04987: Orn - X - X

Search NORINE for peptide: strict or relaxed

AMP-binding (481..881): Orn

nrpys: 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:: DVGDIGAIDK
Nearest Stachelhaus code(s):: Lys DVGDVGSIDK (65% 8Å match); Orn DVGEIGSIDK (62% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1499..1876): X

nrpys: (unknown)

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:: DVSHVGAVDK
Nearest Stachelhaus code(s):: Ser DVSHVSAVDK (53% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (2511..2899): X

nrpys: (unknown)

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:: DTDDMGYNDK
Nearest Stachelhaus code(s):: Lys DTDDMGYVDK (68% 8Å match)
Stachelhaus code match:: 90% (moderate)

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

NPDC050663.ctg-0009 - Region 1 - NRPS-like,T1PKS

Download region SVG

Location: 106,639 - 153,611 nt. (total: 46,973 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

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other genes

resistance

TTA codons

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Select a gene to view the details available for it

Gene overview

Tailoring

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NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_05542: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

Transferases: acylase

CDS_05544: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: deacetylase esterase hydrolase

CDS_05535: acetylornithine deacetylase

smcogs: SMCOG1247: acetylornithine deacetylase

CDS_05543: thioesterase

smcogs: SMCOG1004: thioesterase

CDS_05556: alpha/beta hydrolase domain-containing protein

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

CDS_05557: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: decarboxylase

CDS_05553: putative carboxymuconolactone decarboxylase

smcogs: SMCOG1298: putative carboxymuconolactone decarboxylase

Ligases: ligase

CDS_05541: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter

CDS_05549: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001132.4	0.66	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.64	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2	0.64	NRPS	peramine	Epichloe festucae
BGC0001135.5	0.62	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001641.4	0.61	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.61	NRPS	AM-toxin	Alternaria alternata
BGC0002175.3	0.60	PKS	YWA1	Aspergillus oryzae RIB40
BGC0001758.4	0.60	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.60	NRPS	icosalide A, icosalide B	Burkholderia gladioli

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001132.4	0.66	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.66	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.65	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2	0.65	NRPS	peramine	Epichloe festucae
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001641.4	0.64	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000037.4	0.64	PKS	cichorine	Aspergillus nidulans FGSC A4
BGC0001261.3	0.64	NRPS	AM-toxin	Alternaria alternata
BGC0002175.3	0.63	PKS	YWA1	Aspergillus oryzae RIB40
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

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: 18.37 out of 20.47

Confidence: medium

Additional weak hits (7):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.12 out of 18.57

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.78 out of 26.06

Confidence: weak

MexT

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

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.89 out of 31.73

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.75 out of 28.19

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.69 out of 23.43

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 106638 - 153611:

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

Polymer prediction:: (mal) + (Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 106638 - 148366:

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

Polymer prediction:: (mal) + (Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 110686 - 153611:

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

Polymer prediction:: (mal) + (Val)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CDS_05541: Val

Search NORINE for peptide: strict or relaxed

AMP-binding (8..393): 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:: DAFFLGATFK
Nearest Stachelhaus code(s):: Val DAFWLGATFK (79% 8Å match); Ile DAFFLGVTFK (71% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_05544: mal

PKS_AT (519..810): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 66.7%; inactive: 58.3%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 133.8
Methoxymalonyl-CoA: 58.6
inactive: 57.9
Methylmalonyl-CoA: 53.7
Propionyl-CoA: 45.9
2-Methylbutyryl-CoA: 30.9
fatty_acid: 25.3
Ethylmalonyl-CoA: 24.5
Benzoyl-CoA: 18.9
CHC-CoA: 18.2
Acetyl-CoA: 17.9
Isobutyryl-CoA: 15.3
3-Methylbutyryl-CoA: 10.5
trans-1,2-CPDA: 0.0

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

NPDC050663.ctg-0009 - Region 2 - NRPS

Download region SVG

Location: 369,960 - 400,433 nt. (total: 30,474 nt) Show pHMM detection rules used

Region on contig edge.

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Ligases: ligase synthase

CDS_05756: 1-deoxy-D-xylulose-5-phosphate synthase

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

CDS_05758: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_05759: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_05762: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_05763: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_05764: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_05765: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.72	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001135.5	0.71	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.71	NRPS	HC-toxin	Alternaria jesenskae
BGC0001261.3	0.70	NRPS	AM-toxin	Alternaria alternata
BGC0002286.3	0.70	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.70	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.69	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001758.4	0.68	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.72	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001135.5	0.71	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.71	NRPS	HC-toxin	Alternaria jesenskae
BGC0001261.3	0.70	NRPS	AM-toxin	Alternaria alternata
BGC0002286.3	0.70	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.70	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.69	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001758.4	0.68	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 27.15 out of 30.11

Confidence: strong

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.62 out of 30.11

Confidence: strong

CelR

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

Confidence: strong

CelR

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

Confidence: strong

CelR

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

Confidence: strong

CelR

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

Confidence: strong

VqsM

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

Confidence: medium

MexT

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

Confidence: medium

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11

Confidence: strong

CelR

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

Confidence: strong

Additional weak hits (7):

HipB

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

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.13 out of 21.55

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.70 out of 21.55

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.28 out of 35.63

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.37 out of 28.14

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.26 out of 18.57

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 4, location 369959 - 400433:

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

Polymer prediction:: (Gly) + (X)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CDS_05758: X

AMP-binding (16..473): 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:: PINFGAYPAK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

CDS_05763: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (7..397): Gly

nrpys: Gly

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DILQLGVVWK
Nearest Stachelhaus code(s):: Gly DILQLGVVWK (82% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_05764: X

AMP-binding (440..814): 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:: DAEDIGTVIK
Nearest Stachelhaus code(s):: Lys DAEDIGSVIK (76% 8Å match)
Stachelhaus code match:: 90% (moderate)

TFBS definitions

Regulator	Description
CelR	Cellobiose uptake repressor
MexT	Global virulence regulator
VqsM	Regulator of quorum-sensing signalling systems

NPDC050663.ctg-0010 - Region 1 - NRPS

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Location: 8,141 - 52,274 nt. (total: 44,134 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_05805: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CDS_05806: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

Transferases: methyltransferase

CDS_05791: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

Ligases: ligase

CDS_05795: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_05796: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_05808: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: permease

CDS_05778: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.65	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.64	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.63	NRPS	AbT1	Aureobasidium pullulans
BGC0002164.2	0.63	NRPS	peramine	Epichloe festucae
BGC0000342.4	0.63	NRPS	enniatin	Fusarium equiseti
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.63	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.63	NRPS	AM-toxin	Alternaria alternata
BGC0001132.4	0.63	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.62	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.65	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.64	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.63	NRPS	AbT1	Aureobasidium pullulans
BGC0002164.2	0.63	NRPS	peramine	Epichloe festucae
BGC0000342.4	0.63	NRPS	enniatin	Fusarium equiseti
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.63	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.63	NRPS	AM-toxin	Alternaria alternata
BGC0001132.4	0.63	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.62	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:

AfsR

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

Confidence: medium

CRP

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

Confidence: medium

Additional weak hits (15):

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.07 out of 23.43

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.06 out of 39.62

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.68 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.00 out of 29.38

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.58 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.04 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.75 out of 29.38

Confidence: weak

MntR

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

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.61 out of 39.62

Confidence: weak

MexT

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

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.85 out of 35.63

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.05 out of 27.18

Confidence: weak

RutR

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

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.33 out of 24.78

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.09 out of 29.25

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 8140 - 52274:

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

NRPS/PKS substrate predictions

CDS_05795: X

AMP-binding (445..839): X

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

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DAGDMGHVCK
Nearest Stachelhaus code(s):: CysA DATKMGHVGK (53% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_05808: X

AMP-binding (63..261): 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:: GLGMLGI--K
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
CRP	Cyclic AMP receptor protein

NPDC050663.ctg-0010 - Region 2 - terpene

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Location: 132,202 - 153,200 nt. (total: 20,999 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: oxidoreductase

CDS_05904: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

Hydrolases: hydrolase

CDS_05895: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: cyclase

CDS_05902: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: ligase

CDS_05905: 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	0.56	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.55	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001201.3	0.51	terpene	eremophilene	Sorangium cellulosum So ce56
BGC0001844.4	0.42	NRPS	holrhizin A, holrhizin B, holrhizin C, holrhizin D	Paraburkholderia rhizoxinica HKI 454
BGC0001294.5	0.40	other (other)	7-prenylisatin	Streptomyces sp. MBT28
BGC0000393.5	0.38	NRPS, PKS	myxoprincomide-c506	Myxococcus xanthus DK 1622
BGC0002582.3	0.38	NRPS	guanipiperazine A, guanipiperazine B	Streptomyces chrestomyceticus
BGC0001149.5	0.38	NRPS, saccharide	brabantamide A	Pseudomonas sp. SHC52
BGC0001878.2	0.36	NRPS, PKS	detoxin N2, detoxin N3	Streptomyces sp. NRRL B-1347
BGC0002293.2	0.36	NRPS	ohmyungsamycin A, ohmyungsamycin B	Streptomyces sp.

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.56	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.55	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001201.3	0.51	terpene	eremophilene	Sorangium cellulosum So ce56
BGC0001844.4	0.42	NRPS	holrhizin A, holrhizin B, holrhizin C, holrhizin D	Paraburkholderia rhizoxinica HKI 454
BGC0001294.5	0.40	other (other)	7-prenylisatin	Streptomyces sp. MBT28
BGC0000393.5	0.38	NRPS, PKS	myxoprincomide-c506	Myxococcus xanthus DK 1622
BGC0002582.3	0.38	NRPS	guanipiperazine A, guanipiperazine B	Streptomyces chrestomyceticus
BGC0001149.5	0.38	NRPS, saccharide	brabantamide A	Pseudomonas sp. SHC52
BGC0001878.2	0.36	NRPS, PKS	detoxin N2, detoxin N3	Streptomyces sp. NRRL B-1347
BGC0002293.2	0.36	NRPS	ohmyungsamycin A, ohmyungsamycin B	Streptomyces sp.

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

No product predictions

Genes with terpene domains:

CDS_05902: T1TS

Domain 1 (4 - 318): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.77 out of 27.55

Confidence: medium

Additional weak hits (11):

ColR

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.48 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.70 out of 31.73

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.22 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.41 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.86 out of 28.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.39 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.93 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.56 out of 33.14

Confidence: weak

ZuR variant 1

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

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.92 out of 32.93

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
GnfM	Regulator of nitrogen-fixation genes

NPDC050663.ctg-0010 - Region 3 - NRPS,T1PKS

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Location: 205,352 - 256,959 nt. (total: 51,608 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

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_05970: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CDS_05972: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CDS_05995: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

Hydrolases: esterase hydrolase

CDS_05965: amidohydrolase

smcogs: SMCOG1244: amidohydrolase

CDS_05967: thioesterase

smcogs: SMCOG1004: thioesterase

Lyases: dehydratase lyase

CDS_05982: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

CDS_05985: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

CDS_05993: L-carnitine dehydratase/bile acid-inducible

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

Ligases: ligase synthase

CDS_05968: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_05971: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_05973: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_05974: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_05975: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_05976: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_05979: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_05983: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.89	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001132.4	0.79	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.78	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.76	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.76	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001641.4	0.74	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.74	NRPS	AbT1	Aureobasidium pullulans
BGC0001758.4	0.74	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002135.2	0.73	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.73	NRPS	AM-toxin	Alternaria alternata

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.75	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001132.4	0.71	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.70	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.70	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001641.4	0.70	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.70	NRPS	AbT1	Aureobasidium pullulans
BGC0001758.4	0.69	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002135.2	0.69	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata

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: 17.80 out of 20.47

Confidence: medium

VqsM

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

Confidence: medium

IolR

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

Confidence: medium

CatR

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

Confidence: medium

Additional weak hits (13):

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.67 out of 30.97

Confidence: weak

MogR

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

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.73 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.75 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.74 out of 28.14

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.57 out of 27.78

Confidence: weak

MexT

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

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.54 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.84 out of 33.14

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.96 out of 36.53

Confidence: weak

ZuR variant 1

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

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.67 out of 28.19

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.63 out of 23.43

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 205351 - 256959:

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

Polymer prediction:: (Me-redmal) + (X) + (Asn)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 205351 - 247955:

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

Polymer prediction:: (Me-redmal) + (X) + (Asn)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 209357 - 256959:

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

Polymer prediction:: (Me-redmal) + (X) + (Asn)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CDS_05971: Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (11..405): Thr

nrpys: Thr

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DFWCIGIVFK
Nearest Stachelhaus code(s):: Thr DFWNIGMVFK (76% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_05972: mmal

PKS_AT (10..288): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 83.3%; Ethylmalonyl-CoA: 75.0%; Malonyl-CoA: 70.8%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 157.9
Ethylmalonyl-CoA: 148.8
Methoxymalonyl-CoA: 131.3
Malonyl-CoA: 113.9
2-Methylbutyryl-CoA: 101.7
Propionyl-CoA: 90.9
Isobutyryl-CoA: 89.3
trans-1,2-CPDA: 84.6
CHC-CoA: 80.2
Benzoyl-CoA: 76.8
Acetyl-CoA: 67.8
fatty_acid: 56.8
inactive: 29.8
3-Methylbutyryl-CoA: 26.9

CDS_05973: NH2

CAL_domain (152..460): NH2

minowa: NH2

Prediction, score:

NH2: 118.6
Acetyl-CoA: 47.2
fatty_acid: 26.4
AHBA: 16.7
shikimic_acid: 0.0

CDS_05974: mal

PKS_AT (615..810): mal

ATSignature: (unknown)

No matches above 50%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 29.9
Methoxymalonyl-CoA: 29.4
Methylmalonyl-CoA: 27.0
Propionyl-CoA: 14.4
Isobutyryl-CoA: 10.1
Acetyl-CoA: 3.8
trans-1,2-CPDA: 0.0
inactive: 0.0
fatty_acid: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

CDS_05975: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (8..378): 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:: DILHVGFVWK
Nearest Stachelhaus code(s):: Gly DILQVGVIWK (71% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_05976: X

AMP-binding (17..424): 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:: DDVQISQIDK
Nearest Stachelhaus code(s):: Ser DVWHISLIDK (65% 8Å match)
Stachelhaus code match:: 60% (weak)

CDS_05979: Asn

Search NORINE for peptide: strict or relaxed

AMP-binding (447..829): Asn

nrpys: Asn

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:: asn (Asn)

Stachelhaus prediction details:

Stachelhaus sequence:: DMPKVGEVAK
Nearest Stachelhaus code(s):: Asn DMTKVGEVGK (50% 8Å match)
Stachelhaus code match:: 80% (moderate)

TFBS definitions

Regulator	Description
CatR	H2O2-responsive repressor
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC050663.ctg-0011 - Region 1 - T1PKS

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Location: 126,953 - 172,385 nt. (total: 45,433 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

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase

CDS_06187: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

CDS_06203: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CDS_06208: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: glycosyltransferase methyltransferase

CDS_06188: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

CDS_06194: glycosyltransferase

smcogs: SMCOG1102: glycosyltransferase

Hydrolases: dehalogenase esterase glucosidase

CDS_06199: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

CDS_06201: putative esterase

smcogs: SMCOG1104: putative esterase

CDS_06212: Alpha-glucosidase

smcogs: SMCOG1257: Alpha-glucosidase

Ligases: ligase synthase

CDS_06191: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_06202: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Translocases: transport

CDS_06192: MMPL domain-containing transport protein

smcogs: SMCOG1035: MMPL domain-containing transport protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001164.3	0.68	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.67	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002277.2	0.65	NRPS	atromentin	Suillus grevillei
BGC0001254.3	0.64	PKS	ACT-Toxin II	Alternaria alternata
BGC0001275.3	0.64	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001276.3	0.64	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.64	PKS	(-)-Mellein	Parastagonospora nodorum
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
BGC0000107.3	0.63	PKS	naphthopyrone	Aspergillus nidulans FGSC A4

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001164.3	0.68	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.67	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002277.2	0.65	NRPS	atromentin	Suillus grevillei
BGC0001254.3	0.64	PKS	ACT-Toxin II	Alternaria alternata
BGC0001275.3	0.64	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001276.3	0.64	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.64	PKS	(-)-Mellein	Parastagonospora nodorum
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
BGC0000107.3	0.63	PKS	naphthopyrone	Aspergillus nidulans FGSC A4

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (21):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.52 out of 31.73

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.67 out of 21.55

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.01 out of 29.38

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.75 out of 21.55

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 21.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.05 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.02 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.96 out of 29.38

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: 15.88 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

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.75 out of 28.19

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.76 out of 35.63

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.92 out of 29.65

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.26 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.87 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.58 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.87 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.57 out of 26.06

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.22 out of 33.14

Confidence: weak

AfsQ1

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

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 126952 - 172385:

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

Polymer prediction:: (pk)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CDS_06191: NH2

CAL_domain (155..467): NH2

minowa: NH2

Prediction, score:

NH2: 103.0
Acetyl-CoA: 56.1
fatty_acid: 37.8
shikimic_acid: 0.0
AHBA: 0.0

CDS_06202: pk

PKS_AT (590..849): pk

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 66.7%; Methylmalonyl-CoA: 62.5%; Ethylmalonyl-CoA: 54.2%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 104.8
Ethylmalonyl-CoA: 87.6
Methoxymalonyl-CoA: 85.2
Malonyl-CoA: 83.1
Propionyl-CoA: 74.2
2-Methylbutyryl-CoA: 74.0
fatty_acid: 70.2
trans-1,2-CPDA: 49.0
Acetyl-CoA: 42.9
Isobutyryl-CoA: 42.8
CHC-CoA: 38.4
inactive: 27.6
Benzoyl-CoA: 23.9
3-Methylbutyryl-CoA: 12.0

TFBS definitions

Regulator	Description

NPDC050663.ctg-0011 - Region 2 - NRPS,NRPS-like,PKS-like,azole-containing-RiPP,transAT-PKS

Download region SVG

Location: 201,987 - 296,670 nt. (total: 94,684 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)
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
PKS-like: (t2pks2 or ksIII)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Azole RiPPs

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

CDS_06260: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_06264: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_06279: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_06280: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_06292: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: PPTase acylase

CDS_06277: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_06286: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: esterase hydrolase

CDS_06278: thioesterase

smcogs: SMCOG1004: thioesterase

CDS_06300: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: dehydratase hydratase

CDS_06266: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

CDS_06276: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase

CDS_06275: hydroxymethylglutaryl-CoA synthase

smcogs: SMCOG1043: hydroxymethylglutaryl-CoA synthase

CDS_06283: hydroxymethylglutaryl-CoA synthase

smcogs: SMCOG1043: hydroxymethylglutaryl-CoA synthase

CDS_06285: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_06290: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_06294: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter

CDS_06303: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

CDS_06309: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000205.3	0.97	PKS	bryostatin	Candidatus Endobugula sertula
BGC0000255.5	0.88	PKS	pederin	Uncultured bacterium
BGC0001641.4	0.87	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.87	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002191.2	0.87	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001825.4	0.85	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001135.5	0.85	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.85	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000342.4	0.84	NRPS	enniatin	Fusarium equiseti
BGC0002631.2	0.84	ribosomal	Myxarylin	Pyxidicoccus fallax

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001641.4	0.66	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.66	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001825.4	0.65	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.65	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002286.3	0.65	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.65	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002075.3	0.64	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0002135.2	0.64	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (6):

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.39 out of 26.85

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.84 out of 25.88

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.19 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.96 out of 30.25

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.21 out of 20.97

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.39 out of 28.14

Confidence: weak

(Thi)azol(in)e containing peptide predictions

No core peptides found.

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

RREFinder

TFBS Finder

Azole RiPPs

Predicted core structure(s)

For candidate cluster 2, location 201986 - 296670:

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

Polymer prediction:: (Cys - mal - ohmal - ccmal) + (mal - Me-ccmal - ohmal - mal) + (Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 201986 - 283026:

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

Polymer prediction:: (Cys - mal - ohmal - ccmal) + (mal - Me-ccmal - ohmal - mal) + (Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 245630 - 286878:

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

Polymer prediction:: (mal - Me-ccmal - ohmal - mal) + (Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 254921 - 296670:

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

Polymer prediction:: (mal - Me-ccmal - ohmal - mal) + (Thr)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CDS_06277: mal

PKS_AT (5..273): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 112.9
Methoxymalonyl-CoA: 32.0
inactive: 31.1
Propionyl-CoA: 29.4
Methylmalonyl-CoA: 25.7
fatty_acid: 14.0
trans-1,2-CPDA: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

CDS_06279: Cys

Search NORINE for peptide: strict or relaxed

AMP-binding (899..1301): 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:: DLFNFSLVWK
Nearest Stachelhaus code(s):: Cys DLFNFSLVWK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_06290: X

AMP-binding (11..374): 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:: NASIMGGPAK
Nearest Stachelhaus code(s):: Phe DAPIMGGTCK (26% 8Å match)
Stachelhaus code match:: 60% (weak)

CDS_06294: Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (9..405): 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)

RRE predictions

: RRE type: Thiopeptide_F_RRE; Location: 0 - 79; Score: 63.4; RRE type: Heterocycloanthracin_C_RRE; Location: 5 - 74; Score: 33.5

TFBS definitions

Regulator	Description

Core peptide predictions

No core peptides found.

NPDC050663.ctg-0012 - Region 1 - NI-siderophore

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Location: 24,114 - 55,108 nt. (total: 30,995 nt) Show pHMM detection rules used

NI-siderophore: IucA_IucC

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core biosynthetic genes

additional biosynthetic genes

transport-related genes

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other genes

resistance

TTA codons

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TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Hydrolases: hydrolase protease

CDS_06348: alpha/beta hydrolase domain-containing protein

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

CDS_06363: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

Lyases: decarboxylase

CDS_06359: diaminopimelate decarboxylase

smcogs: SMCOG1264: diaminopimelate decarboxylase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002527.2	0.60	other (other)	vibrioferrin	Azotobacter vinelandii CA
BGC0001408.5	0.60	other (other)	xanthoferrin	Xanthomonas oryzae pv. oryzae KACC 10331
BGC0000946.5	0.59	other (other)	vibrioferrin	Vibrio parahaemolyticus
BGC0000947.5	0.49	other (other)	vibrioferrin	Vibrio alginolyticus
BGC0000943.5	0.45	other (other)	staphyloferrin B	Staphylococcus aureus subsp. aureus NCTC 8325
BGC0001880.3	0.42	ribosomal	scytodecamide	Scytonema sp. UIC 10036
BGC0000595.3	0.39	ribosomal	SCO-2138	Streptomyces coelicolor A3(2)
BGC0000477.3	0.38	ribosomal	patellin 2, patellin 3	uncultured Prochloron sp. 06037A
BGC0002571.2	0.37	NRPS	pyoverdine DC3000	Pseudomonas syringae pv. tomato str. DC3000
BGC0000597.4	0.37	ribosomal	SWA-2138	Streptomyces sp. e14

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002527.2	0.60	other (other)	vibrioferrin	Azotobacter vinelandii CA
BGC0001408.5	0.60	other (other)	xanthoferrin	Xanthomonas oryzae pv. oryzae KACC 10331
BGC0000946.5	0.59	other (other)	vibrioferrin	Vibrio parahaemolyticus
BGC0000947.5	0.49	other (other)	vibrioferrin	Vibrio alginolyticus
BGC0000943.5	0.45	other (other)	staphyloferrin B	Staphylococcus aureus subsp. aureus NCTC 8325
BGC0001880.3	0.42	ribosomal	scytodecamide	Scytonema sp. UIC 10036
BGC0000595.3	0.39	ribosomal	SCO-2138	Streptomyces coelicolor A3(2)
BGC0000477.3	0.38	ribosomal	patellin 2, patellin 3	uncultured Prochloron sp. 06037A
BGC0002571.2	0.37	NRPS	pyoverdine DC3000	Pseudomonas syringae pv. tomato str. DC3000
BGC0000597.4	0.37	ribosomal	SWA-2138	Streptomyces sp. e14

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.33 out of 24.78

Confidence: medium

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.62 out of 36.53

Confidence: medium

Additional weak hits (6):

ANR

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

Confidence: weak

CodY

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

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.18 out of 29.65

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.72 out of 26.85

Confidence: weak

MexT

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

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.60 out of 27.04

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
DmdR1	Iron(II)-dependent repressor
LexA variant 2	Repressor of DNA damage response
VqsM	Regulator of quorum-sensing signalling systems

NPDC050663.ctg-0013 - Region 1 - NI-siderophore

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Location: 50,423 - 80,147 nt. (total: 29,725 nt) Show pHMM detection rules used

NI-siderophore: IucA_IucC

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

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resistance

TTA codons

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Gene overview

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TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: oxidoreductase oxygenase

CDS_06621: pyridine nucleotide-disulfide oxidoreductase

smcogs: SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

CDS_06632: lysine/ornithine N-monooxygenase

smcogs: SMCOG1080: lysine/ornithine N-monooxygenase

Transferases: aminotransferase methyltransferase

CDS_06635: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_06640: aminotransferase

smcogs: SMCOG1019: aminotransferase

Lyases: decarboxylase

CDS_06631: Decarboxylase, pyridoxal-dependent

smcogs: SMCOG1180: Decarboxylase, pyridoxal-dependent

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001478.5	0.82	other (other)	desferrioxamine E	Streptomyces sp. ID38640
BGC0000941.3	0.76	other (other)	desferrioxamin B	Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2	0.71	other (other)	legonoxamine A, desferrioxamine B, legonoxamine B	Streptomyces sp.
BGC0001453.5	0.70	other (other)	desferrioxamine	Streptomyces argillaceus
BGC0000940.5	0.70	other (other)	desferrioxamin B, desferrioxamine E	Streptomyces coelicolor A3(2)
BGC0001572.3	0.67	other (other)	desferrioxamine E	Pantoea agglomerans
BGC0002690.2	0.64	other (other)	FW0622	Verrucosispora sp. FIM060022
BGC0002620.2	0.63	other (other)	fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4	Fulvivirga marina
BGC0000244.4	0.61	PKS	nonactin, monactin, dinactin, trinactin, tetranactin	Streptomyces griseus subsp. griseus
BGC0002464.3	0.59	other (other)	alcaligin	Bordetella pertussis Tohama I

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001478.5	0.82	other (other)	desferrioxamine E	Streptomyces sp. ID38640
BGC0000941.3	0.76	other (other)	desferrioxamin B	Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2	0.71	other (other)	legonoxamine A, desferrioxamine B, legonoxamine B	Streptomyces sp.
BGC0001453.5	0.70	other (other)	desferrioxamine	Streptomyces argillaceus
BGC0000940.5	0.70	other (other)	desferrioxamin B, desferrioxamine E	Streptomyces coelicolor A3(2)
BGC0001572.3	0.67	other (other)	desferrioxamine E	Pantoea agglomerans
BGC0002690.2	0.64	other (other)	FW0622	Verrucosispora sp. FIM060022
BGC0002620.2	0.63	other (other)	fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4	Fulvivirga marina
BGC0000244.4	0.61	PKS	nonactin, monactin, dinactin, trinactin, tetranactin	Streptomyces griseus subsp. griseus
BGC0002464.3	0.59	other (other)	alcaligin	Bordetella pertussis Tohama I

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 (16):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22

Confidence: weak

ClgR

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

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.56 out of 30.22

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.99 out of 21.55

Confidence: weak

MogR

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

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.21 out of 21.55

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.02 out of 29.38

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.21 out of 29.25

Confidence: weak

MexT

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

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.12 out of 30.22

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.93 out of 28.19

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.36 out of 27.18

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.86 out of 29.65

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.59 out of 29.65

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.46 out of 24.78

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.50 out of 29.25

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

NPDC050663.ctg-0013 - Region 2 - CDPS

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Location: 157,244 - 177,927 nt. (total: 20,684 nt) Show pHMM detection rules used

CDPS: CDPS

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Gene overview

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Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: oxidase

CDS_06732: FAD linked oxidase domain protein

smcogs: SMCOG1138: FAD linked oxidase domain protein

Transferases: transferase

CDS_06734: acetyl-CoA carboxylase, carboxyl transferase,

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

Hydrolases: hydrolase

CDS_06731: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001948.3	0.49	other (other)	naseseazine C, C3-aryl pyrroloindolines	Streptomyces sp.
BGC0000885.3	0.43	other (other)	4-hydroxy-3-nitrosobenzamide	Streptomyces murayamaensis
BGC0000667.3	0.41	terpene	PR-toxin	Penicillium roqueforti FM164
BGC0002245.2	0.41	terpene	terpestacin, preterpestacin 3, preterpestacin 2, preterpestacin 1	Bipolaris maydis C5
BGC0000889.5	0.39	other (other)	bagremycin A, bagremycin B	Streptomyces sp. WK-5344
BGC0002211.3	0.38	PKS	HEx-pks1 polyketide	Paraphaeosphaeria sporulosa
BGC0002571.2	0.38	NRPS	pyoverdine DC3000	Pseudomonas syringae pv. tomato str. DC3000
BGC0001592.5	0.38	other (other)	ferroverdin, bagremycin	Streptomyces lunaelactis
BGC0002390.2	0.37	terpene	zealexin A1	Zea mays
BGC0001458.4	0.37	other (aminocoumarin)	salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K	Salinispora tropica CNB-440

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001948.3	0.49	other (other)	naseseazine C, C3-aryl pyrroloindolines	Streptomyces sp.
BGC0000885.3	0.43	other (other)	4-hydroxy-3-nitrosobenzamide	Streptomyces murayamaensis
BGC0000667.3	0.41	terpene	PR-toxin	Penicillium roqueforti FM164
BGC0002245.2	0.41	terpene	terpestacin, preterpestacin 3, preterpestacin 2, preterpestacin 1	Bipolaris maydis C5
BGC0000889.5	0.39	other (other)	bagremycin A, bagremycin B	Streptomyces sp. WK-5344
BGC0002211.3	0.38	PKS	HEx-pks1 polyketide	Paraphaeosphaeria sporulosa
BGC0002571.2	0.38	NRPS	pyoverdine DC3000	Pseudomonas syringae pv. tomato str. DC3000
BGC0001592.5	0.38	other (other)	ferroverdin, bagremycin	Streptomyces lunaelactis
BGC0002390.2	0.37	terpene	zealexin A1	Zea mays
BGC0001458.4	0.37	other (aminocoumarin)	salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K	Salinispora tropica CNB-440

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: 17.99 out of 20.97

Confidence: medium

Additional weak hits (12):

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.12 out of 26.85

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.64 out of 27.78

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.51 out of 31.73

Confidence: weak

CodY

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.80 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.29 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.72 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.04 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.38 out of 30.25

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.74 out of 27.18

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.56 out of 32.93

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.45 out of 33.14

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

TFBS Finder

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A

NPDC050663.ctg-0016 - Region 1 - NRPS

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Location: 167,420 - 216,766 nt. (total: 49,347 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_07459: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: esterase hydrolase

CDS_07448: isochorismatase

smcogs: SMCOG1027: isochorismatase

CDS_07465: thioesterase

smcogs: SMCOG1004: thioesterase

Ligases: ligase

CDS_07466: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter

CDS_07454: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001132.4	0.71	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.70	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.70	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.70	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0002286.3	0.69	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.69	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001050.5	0.68	NRPS, PKS	thalassospiramide A	Tistrella bauzanensis
BGC0002135.2	0.68	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001132.4	0.71	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.70	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.70	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.70	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0002286.3	0.69	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.69	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001050.5	0.68	NRPS, PKS	thalassospiramide A	Tistrella bauzanensis
BGC0002135.2	0.68	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (6):

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.67 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.37 out of 29.38

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.27 out of 27.78

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.73 out of 36.54

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.98 out of 36.54

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.25 out of 36.53

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 1, location 167419 - 216766:

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

Polymer prediction:: (Gly) + (Ser)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CDS_07465: Ser

Search NORINE for peptide: strict or relaxed

AMP-binding (494..870): Ser

nrpys: Ser

SVM prediction details:

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

Stachelhaus prediction details:

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

CDS_07466: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (453..829): Gly

nrpys: Gly

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: DILQLGMIWK
Nearest Stachelhaus code(s):: Gly DILQLGMIWK (79% 8Å match)
Stachelhaus code match:: 100% (strong)

TFBS definitions

Regulator	Description

NPDC050663.ctg-0017 - Region 1 - lanthipeptide-class-iii

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Location: 89,528 - 111,951 nt. (total: 22,424 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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

Hydrolases: hydrolase

CDS_07597: metallo-beta-lactamase family protein

smcogs: SMCOG1170: metallo-beta-lactamase family protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000551.5	0.65	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000496.5	0.63	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3	0.61	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000501.3	0.60	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0000519.4	0.60	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000546.3	0.52	ribosomal	SAL-2242	Streptomyces albidoflavus
BGC0000563.4	0.52	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0001226.4	0.52	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0000518.3	0.52	ribosomal	informatipeptin	Streptomyces viridochromogenes DSM 40736
BGC0002700.2	0.52	ribosomal	bacinapeptin	Bacillus nakamurai

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000551.5	0.65	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000496.5	0.63	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3	0.61	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000501.3	0.60	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0000519.4	0.60	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000546.3	0.52	ribosomal	SAL-2242	Streptomyces albidoflavus
BGC0000563.4	0.52	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0001226.4	0.52	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0000518.3	0.52	ribosomal	informatipeptin	Streptomyces viridochromogenes DSM 40736
BGC0002700.2	0.52	ribosomal	bacinapeptin	Bacillus nakamurai

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for CDS_07605

CDS_07606

Leader:

MTLLDLQTLEVPGGGH

Core:

GHGGGSTLTVLGCNSHTPSNLSLLICH

Core with dehydrations:

GHGGGDhaDhbLDhbVLGCysNDhaHDhbPDhaNLDhaLLICysH

antiSMASH-DB 4.0 matches for CDS_07606

92.6%

NZ_JACDUR010000003.1and 1 other:

NZ_JACDUR010000003.1 Lanthipeptides: HNR30_RS17930_lanthipeptide

Lanthipeptides: HNR30_RS17930_lanthipeptide

1

GHGGGSTLTVLGCNSHTPSNLSLLICH

27

GHGGGSTLTVLGCNS+TPSNLSLL+CH

1

GHGGGSTLTVLGCNSYTPSNLSLLLCH

27

88.9%

NZ_CP043661.1and 1 other:

NZ_SOCE01000001.1 Lanthipeptides: EV138_RS20105_lanthipeptide

Lanthipeptides: F1D05_RS17325_lanthipeptide

2

HGGGSTLTVLGCNSHTPSNLSLLICH

27

HGGGSTLTVLGC SHTPSNLSLL+CH

1

HGGGSTLTVLGCASHTPSNLSLLLCH

26

85.2%

NZ_JACHWA010000004.1:

Lanthipeptides: FHS43_RS13815_lanthipeptide

1

GHGGGSTLTVLGCNSHTPSNLSLLICH

27

GHGGGSTLTVLGC S PSNLSLL+CH

1

GHGGGSTLTVLGCASAKPSNLSLLLCH

27

with 89 more sequence matches

Only the first 10 are displayed here.

81.5%

NZ_SLWR01000003.1:

Lanthipeptides: EV646_RS09945_lanthipeptide

2

HGGGSTLTVLGCNSHTPSNLSLLICH

27

H GGSTLTVLGC S TPSNLSLL+CH

2

HPGGSTLTVLGCASQTPSNLSLLLCH

27

81.5%

NZ_SNWQ01000001.1:

Lanthipeptides: EV643_RS00390_lanthipeptide

2

HGGGSTLTVLGCNSHTPSNLSLLICH

27

H GGSTLTVLGC SH PSNLSLL+CH

1

HHGGSTLTVLGCGSHRPSNLSLLLCH

26

77.8%

NC_013595.1and 1 other:

NZ_FOQY01000005.1 Lanthipeptides: BM085_RS08660_lanthipeptide

Lanthipeptides: SROS_RS48825_lanthipeptide

3

GGGSTLTVLGCNSHTPSNLSLLICH

27

GGGSTLTVLGC S+ PSNLSLL+CH

2

GGGSTLTVLGCESYKPSNLSLLLCH

26

77.8%

NC_013729.1:

Lanthipeptides: KFLA_RS37060_lanthipeptide

3

GGGSTLTVLGCNSHTPSNLSLLICH

27

GGGSTLTVLGC S PSNLSLL+CH

2

GGGSTLTVLGCGSAKPSNLSLLLCH

26

77.8%

Lanthipeptides: DKM19_RS31645_lanthipeptide

3

GGGSTLTVLGCNSHTPSNLSLLICH

27

GGGSTLTVLGC S TPSNLSL++CH

2

GGGSTLTVLGCASVTPSNLSLILCH

26

77.8%

BGC0000553.3 (SSGG_RS09925):

Lanthipeptides: DKM19_RS31650_lanthipeptide

3

GGGSTLTVLGCNSHTPSNLSLLICH

27

GGGSTLTVLGC S TPSNLSL++CH

1

GGGSTLTVLGCASVTPSNLSLVLCH

25

77.8%

NZ_CP114065.1:

Lanthipeptides: OX958_RS04450_lanthipeptide

2

HGGGSTLTVLGCNSHTPSNLSLLICH

27

H GGSTLTVLGC S PSNLSLL+CH

1

HHGGSTLTVLGCGSQRPSNLSLLLCH

26

77.8%

NZ_PVZV01000008.1:

Lanthipeptides: C2865_RS30430_lanthipeptide

3

GGGSTLTVLGCNSHTPSNLSLLICH

27

GGGSTLTVLGC S PSNLSLL+CH

1

GGGSTLTVLGCASAKPSNLSLLLCH

25

77.8%

NZ_SHKR01000011.1and 6 others:

NZ_SNWS01000006.1 Lanthipeptides: EV651_RS15130_lanthipeptideNZ_SODF01000002.1 Lanthipeptides: EV650_RS20180_lanthipeptideNZ_SODP01000004.1 Lanthipeptides: EV653_RS35635_lanthipeptideNZ_SODT01000012.1 Lanthipeptides: EV647_RS27100_lanthipeptideNZ_SODU01000003.1 Lanthipeptides: EV137_RS31660_lanthipeptideNZ_SZPZ01000003.1 Lanthipeptides: FDA38_RS24670_lanthipeptide

Lanthipeptides: EV645_RS10765_lanthipeptide

4

GGSTLTVLGCNSHTPSNLSLLICH

27

GGSTLTVLGC S TPSNLSLL+CH

2

GGSTLTVLGCASQTPSNLSLLLCH

25

77.8%

NZ_SLWN01000005.1:

Lanthipeptides: EV652_RS16625_lanthipeptide

2

HGGGSTLTVLGCNSHTPSNLSLLICH

27

H GGSTLTVLGC S PSNLSLL+CH

1

HHGGSTLTVLGCASQRPSNLSLLLCH

26

MIBiG 4.0 matches for CDS_07606

18.5%

Lanthipeptide: SRO15-2212

19

SNLSLLICH

27

S +SLL+C

3

SQVSLLVCE

11

16.7%

BGC0002110.3 (QKV49893.1):

Lanthipeptide: birimositide

2

HGGGSTLT

9

+GG TLT

15

NGGWCTLT

22

Lanthipeptide(s) for CDS_07613

CDS_07606

Leader:

MTLLDLQTLEVPGGGH

Core:

GHGGGSTLTVLGCNSHTPSNLSLLICH

Core with dehydrations:

GHGGGDhaDhbLDhbVLGCysNDhaHDhbPDhaNLDhaLLICysH

antiSMASH-DB 4.0 matches for CDS_07606

92.6%

NZ_JACDUR010000003.1and 1 other:

NZ_JACDUR010000003.1 Lanthipeptides: HNR30_RS17930_lanthipeptide

Lanthipeptides: HNR30_RS17930_lanthipeptide

1

GHGGGSTLTVLGCNSHTPSNLSLLICH

27

GHGGGSTLTVLGCNS+TPSNLSLL+CH

1

GHGGGSTLTVLGCNSYTPSNLSLLLCH

27

88.9%

NZ_CP043661.1and 1 other:

NZ_SOCE01000001.1 Lanthipeptides: EV138_RS20105_lanthipeptide

Lanthipeptides: F1D05_RS17325_lanthipeptide

2

HGGGSTLTVLGCNSHTPSNLSLLICH

27

HGGGSTLTVLGC SHTPSNLSLL+CH

1

HGGGSTLTVLGCASHTPSNLSLLLCH

26

85.2%

NZ_JACHWA010000004.1:

Lanthipeptides: FHS43_RS13815_lanthipeptide

1

GHGGGSTLTVLGCNSHTPSNLSLLICH

27

GHGGGSTLTVLGC S PSNLSLL+CH

1

GHGGGSTLTVLGCASAKPSNLSLLLCH

27

with 89 more sequence matches

Only the first 10 are displayed here.

81.5%

NZ_SLWR01000003.1:

Lanthipeptides: EV646_RS09945_lanthipeptide

2

HGGGSTLTVLGCNSHTPSNLSLLICH

27

H GGSTLTVLGC S TPSNLSLL+CH

2

HPGGSTLTVLGCASQTPSNLSLLLCH

27

81.5%

NZ_SNWQ01000001.1:

Lanthipeptides: EV643_RS00390_lanthipeptide

2

HGGGSTLTVLGCNSHTPSNLSLLICH

27

H GGSTLTVLGC SH PSNLSLL+CH

1

HHGGSTLTVLGCGSHRPSNLSLLLCH

26

77.8%

NC_013595.1and 1 other:

NZ_FOQY01000005.1 Lanthipeptides: BM085_RS08660_lanthipeptide

Lanthipeptides: SROS_RS48825_lanthipeptide

3

GGGSTLTVLGCNSHTPSNLSLLICH

27

GGGSTLTVLGC S+ PSNLSLL+CH

2

GGGSTLTVLGCESYKPSNLSLLLCH

26

77.8%

NC_013729.1:

Lanthipeptides: KFLA_RS37060_lanthipeptide

3

GGGSTLTVLGCNSHTPSNLSLLICH

27

GGGSTLTVLGC S PSNLSLL+CH

2

GGGSTLTVLGCGSAKPSNLSLLLCH

26

77.8%

Lanthipeptides: DKM19_RS31645_lanthipeptide

3

GGGSTLTVLGCNSHTPSNLSLLICH

27

GGGSTLTVLGC S TPSNLSL++CH

2

GGGSTLTVLGCASVTPSNLSLILCH

26

77.8%

BGC0000553.3 (SSGG_RS09925):

Lanthipeptides: DKM19_RS31650_lanthipeptide

3

GGGSTLTVLGCNSHTPSNLSLLICH

27

GGGSTLTVLGC S TPSNLSL++CH

1

GGGSTLTVLGCASVTPSNLSLVLCH

25

77.8%

NZ_CP114065.1:

Lanthipeptides: OX958_RS04450_lanthipeptide

2

HGGGSTLTVLGCNSHTPSNLSLLICH

27

H GGSTLTVLGC S PSNLSLL+CH

1

HHGGSTLTVLGCGSQRPSNLSLLLCH

26

77.8%

NZ_PVZV01000008.1:

Lanthipeptides: C2865_RS30430_lanthipeptide

3

GGGSTLTVLGCNSHTPSNLSLLICH

27

GGGSTLTVLGC S PSNLSLL+CH

1

GGGSTLTVLGCASAKPSNLSLLLCH

25

77.8%

NZ_SHKR01000011.1and 6 others:

NZ_SNWS01000006.1 Lanthipeptides: EV651_RS15130_lanthipeptideNZ_SODF01000002.1 Lanthipeptides: EV650_RS20180_lanthipeptideNZ_SODP01000004.1 Lanthipeptides: EV653_RS35635_lanthipeptideNZ_SODT01000012.1 Lanthipeptides: EV647_RS27100_lanthipeptideNZ_SODU01000003.1 Lanthipeptides: EV137_RS31660_lanthipeptideNZ_SZPZ01000003.1 Lanthipeptides: FDA38_RS24670_lanthipeptide

Lanthipeptides: EV645_RS10765_lanthipeptide

4

GGSTLTVLGCNSHTPSNLSLLICH

27

GGSTLTVLGC S TPSNLSLL+CH

2

GGSTLTVLGCASQTPSNLSLLLCH

25

77.8%

NZ_SLWN01000005.1:

Lanthipeptides: EV652_RS16625_lanthipeptide

2

HGGGSTLTVLGCNSHTPSNLSLLICH

27

H GGSTLTVLGC S PSNLSLL+CH

1

HHGGSTLTVLGCASQRPSNLSLLLCH

26

MIBiG 4.0 matches for CDS_07606

18.5%

Lanthipeptide: SRO15-2212

19

SNLSLLICH

27

S +SLL+C

3

SQVSLLVCE

11

16.7%

BGC0002110.3 (QKV49893.1):

Lanthipeptide: birimositide

2

HGGGSTLT

9

+GG TLT

15

NGGWCTLT

22

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: medium

Additional weak hits (11):

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: 16.94 out of 27.78

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.88 out of 25.75

Confidence: weak

CopR

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

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.09 out of 31.73

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.00 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.47 out of 29.38

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.32 out of 26.85

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.53 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.36 out of 28.19

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.21 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

CDS_07606 - Class III

Cleavage pHMM score: 8.40

RODEO score: 0

Monoisotopic mass: 2548.3 Da

Molecular weight: 2549.9 Da

Number of bridges: 2

Alternative weights: (assuming N unmodified Ser/Thr residues); 2567.9 Da N = 1; 2585.9 Da N = 2; 2603.9 Da N = 3; 2621.9 Da N = 4; 2640.0 Da N = 5

CDS_07606 - Class III

Cleavage pHMM score: 8.40

RODEO score: 0

Monoisotopic mass: 2548.3 Da

Molecular weight: 2549.9 Da

Number of bridges: 2

Alternative weights: (assuming N unmodified Ser/Thr residues); 2567.9 Da N = 1; 2585.9 Da N = 2; 2603.9 Da N = 3; 2621.9 Da N = 4; 2640.0 Da N = 5

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

NPDC050663.ctg-0021 - Region 1 - lanthipeptide-class-i

Download region SVG

Location: 41,573 - 67,108 nt. (total: 25,536 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Lanthipeptides

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_08306: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Hydrolases: protease

CDS_08326: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

Lyases: cyclase

CDS_08313: Lanthionine synthetase C family protein

smcogs: SMCOG1140: Lanthionine synthetase C family protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002640.2	0.56	ribosomal	thalassomonasin A, thalassomonasin B	Thalassomonas actiniarum
BGC0000528.5	0.55	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000519.4	0.53	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0002316.2	0.52	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0002698.2	0.51	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0000503.5	0.50	ribosomal	cinnamycin	Streptomyces cinnamoneus
BGC0002346.3	0.50	ribosomal	kyamicin	Saccharopolyspora sp.
BGC0000556.5	0.50	ribosomal	streptin	Streptococcus pyogenes
BGC0000560.5	0.48	ribosomal	subtilomycin	Bacillus subtilis
BGC0002323.2	0.48	ribosomal	nisin J	Staphylococcus capitis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002640.2	0.56	ribosomal	thalassomonasin A, thalassomonasin B	Thalassomonas actiniarum
BGC0000528.5	0.55	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000519.4	0.53	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0002316.2	0.52	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0002698.2	0.51	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0000503.5	0.50	ribosomal	cinnamycin	Streptomyces cinnamoneus
BGC0002346.3	0.50	ribosomal	kyamicin	Saccharopolyspora sp.
BGC0000556.5	0.50	ribosomal	streptin	Streptococcus pyogenes
BGC0000560.5	0.48	ribosomal	subtilomycin	Bacillus subtilis
BGC0002323.2	0.48	ribosomal	nisin J	Staphylococcus capitis

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptides - No core peptides found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: medium

Additional weak hits (3):

MexT

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

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.78 out of 29.38

Confidence: weak

ANR

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

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lanthipeptides

TFBS Finder

Core peptide predictions

No core peptides found.

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

NPDC050663.ctg-0022 - Region 1 - RiPP-like

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Location: 135,135 - 146,304 nt. (total: 11,170 nt) Show pHMM detection rules used

Region on contig edge.

RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: oxidoreductase

CDS_08560: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002115.3	0.54	ribosomal	streptamidine	Streptomyces albidoflavus J1074
BGC0002531.3	0.45	NRPS	cepaciachelin	Burkholderia ambifaria AMMD
BGC0002073.3	0.45	NRPS	dehydroxynocardamine	Corynebacterium propinquum
BGC0002150.2	0.43	ribosomal	triculamin	Streptomyces triculaminicus
BGC0002151.2	0.43	ribosomal	alboverticillin	Streptomyces griseocarneus
BGC0000563.4	0.42	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0001226.4	0.42	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0001870.3	0.41	other (other)	putrebactin, avaroferrin	Xenorhabdus budapestensis
BGC0000551.5	0.41	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000513.3	0.41	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002115.3	0.54	ribosomal	streptamidine	Streptomyces albidoflavus J1074
BGC0002531.3	0.45	NRPS	cepaciachelin	Burkholderia ambifaria AMMD
BGC0002073.3	0.45	NRPS	dehydroxynocardamine	Corynebacterium propinquum
BGC0002150.2	0.43	ribosomal	triculamin	Streptomyces triculaminicus
BGC0002151.2	0.43	ribosomal	alboverticillin	Streptomyces griseocarneus
BGC0000563.4	0.42	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0001226.4	0.42	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0001870.3	0.41	other (other)	putrebactin, avaroferrin	Xenorhabdus budapestensis
BGC0000551.5	0.41	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000513.3	0.41	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

AbrC3

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

Confidence: strong

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 27.11 out of 30.98

Confidence: medium

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.90 out of 36.53

Confidence: medium

Additional weak hits (8):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.24 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 25.90 out of 32.74

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.77 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.55 out of 32.74

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.88 out of 28.19

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.22 out of 30.98

Confidence: weak

CsoR

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

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.57 out of 36.53

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
DmdR1	Iron(II)-dependent repressor
NuR	Nickel-responsive regulator

NPDC050663.ctg-0027 - Region 1 - terpene

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Location: 9,099 - 31,030 nt. (total: 21,932 nt) Show pHMM detection rules used

Region on contig edge.

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_09120: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Hydrolases: hydrolase

CDS_09122: hydrolase

smcogs: SMCOG1179: hydrolase

Lyases: cyclase

CDS_09113: Terpene synthase/cyclase metal-binding domain protein

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

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001181.4	0.77	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0000657.5	0.57	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0002194.3	0.34	PKS	epipyrone A	Epicoccum nigrum
BGC0001954.2	0.33	NRPS, PKS	wortmanamide A, wortmanamide B	Talaromyces wortmannii
BGC0002186.2	0.33	NRPS, PKS	fusaristatin A	Fusarium graminearum PH-1
BGC0002187.3	0.31	PKS	monorden D, monocillin IV, monocillin VI, monocillin VII, pochonin M, monocillin V, monocillin II	Pochonia chlamydosporia 170
BGC0000134.3	0.31	PKS	radicicol	Pochonia chlamydosporia
BGC0001305.4	0.31	PKS	fujikurin A, fujikurin B, fujikurin C, fujikurin D	Fusarium fujikuroi IMI 58289
BGC0002266.3	0.31	PKS, terpene	calidoustene A, calidoustene B, calidoustene C	Aspergillus calidoustus
BGC0000983.5	0.31	NRPS, PKS	cytochalasin E, cytochalasin K	Aspergillus clavatus NRRL 1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001181.4	0.77	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0000657.5	0.57	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0002194.3	0.34	PKS	epipyrone A	Epicoccum nigrum
BGC0001954.2	0.33	NRPS, PKS	wortmanamide A, wortmanamide B	Talaromyces wortmannii
BGC0002186.2	0.33	NRPS, PKS	fusaristatin A	Fusarium graminearum PH-1
BGC0002187.3	0.31	PKS	monorden D, monocillin IV, monocillin VI, monocillin VII, pochonin M, monocillin V, monocillin II	Pochonia chlamydosporia 170
BGC0000134.3	0.31	PKS	radicicol	Pochonia chlamydosporia
BGC0001305.4	0.31	PKS	fujikurin A, fujikurin B, fujikurin C, fujikurin D	Fusarium fujikuroi IMI 58289
BGC0002266.3	0.31	PKS, terpene	calidoustene A, calidoustene B, calidoustene C	Aspergillus calidoustus
BGC0000983.5	0.31	NRPS, PKS	cytochalasin E, cytochalasin K	Aspergillus clavatus NRRL 1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

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

Genes with terpene domains:

CDS_09113: T1TS + T1TS

Domain 1 (1 - 316): Type 1 terpene synthase

Subtype: Geosmin synthase, N terminal domain

Reactions:: FPP → germacradienol

Domain 2 (342 - 622): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.07 out of 26.85

Confidence: medium

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.82 out of 21.84

Confidence: medium

VqsM

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

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 24.01 out of 28.19

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16

Confidence: strong

Additional weak hits (10):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 20.30 out of 31.73

Confidence: weak

MatP

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

Confidence: weak

MexT

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

Confidence: weak

MexT

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

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.37 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.71 out of 29.38

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.06 out of 29.65

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.00 out of 29.65

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.60 out of 35.63

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.81 out of 26.85

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
FPP	Farnesyl diphosphate

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
MexT	Global virulence regulator
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems
ZuR variant 1	Zinc-responsive repressor

NPDC050663.ctg-0028 - Region 1 - hydrogen-cyanide

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Location: 763 - 13,637 nt. (total: 12,875 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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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

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 reductase

CDS_09189: alkyl hydroperoxide reductase subunit

smcogs: SMCOG1176: alkyl hydroperoxide reductase subunit

CDS_09191: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

Hydrolases: deaminase

CDS_09185: ornithine cyclodeaminase

smcogs: SMCOG1158: ornithine cyclodeaminase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002285.2	0.34	ribosomal	aborycin	Streptomyces sp. ZS0098
BGC0000709.5	0.31	saccharide	neomycin	Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000595.3	0.29	ribosomal	SCO-2138	Streptomyces coelicolor A3(2)
BGC0001148.5	0.28	NRPS, ribosomal	pheganomycin	Streptomyces cirratus
BGC0002496.3	0.28	NRPS	serratiochelin A, serratiochelin C, serratiochelin B	Serratia plymuthica
BGC0000935.5	0.28	PKS, other (aminocoumarin)	esmeraldin	Streptomyces antibioticus
BGC0002010.4	0.26	NRPS, PKS	streptophenazine B, streptophenazine C, streptophenazine F, streptophenazine G, streptophenazine H	Streptomyces sp. CNB091
BGC0000135.5	0.22	PKS	reveromycin A	Streptomyces sp. SN-593
BGC0000279.5	0.21	PKS	xantholipin	Streptomyces flavogriseus
BGC0002430.3	0.19	NRPS, saccharide	gausemycin A, gausemycin B	Streptomyces kanamyceticus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002285.2	0.34	ribosomal	aborycin	Streptomyces sp. ZS0098
BGC0000709.5	0.31	saccharide	neomycin	Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000595.3	0.29	ribosomal	SCO-2138	Streptomyces coelicolor A3(2)
BGC0001148.5	0.28	NRPS, ribosomal	pheganomycin	Streptomyces cirratus
BGC0002496.3	0.28	NRPS	serratiochelin A, serratiochelin C, serratiochelin B	Serratia plymuthica
BGC0000935.5	0.28	PKS, other (aminocoumarin)	esmeraldin	Streptomyces antibioticus
BGC0002010.4	0.26	NRPS, PKS	streptophenazine B, streptophenazine C, streptophenazine F, streptophenazine G, streptophenazine H	Streptomyces sp. CNB091
BGC0000135.5	0.22	PKS	reveromycin A	Streptomyces sp. SN-593
BGC0000279.5	0.21	PKS	xantholipin	Streptomyces flavogriseus
BGC0002430.3	0.19	NRPS, saccharide	gausemycin A, gausemycin B	Streptomyces kanamyceticus

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: medium

IolR

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

Confidence: medium

Additional weak hits (8):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.03 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.38 out of 27.78

Confidence: weak

ToxT

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.01 out of 26.06

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.32 out of 26.85

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.49 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.76 out of 28.19

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.11 out of 24.78

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

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

NPDC050663.ctg-0031 - Region 1 - NRPS

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Location: 16,967 - 60,745 nt. (total: 43,779 nt) Show pHMM detection rules used

Region on contig edge.

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

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TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_09437: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: acetyltransferase methyltransferase

CDS_09439: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

CDS_09440: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

Hydrolases: glucosidase

CDS_09458: Alpha-glucosidase

smcogs: SMCOG1257: Alpha-glucosidase

Ligases: ligase synthase

CDS_09442: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_09447: 1-deoxy-D-xylulose-5-phosphate synthase

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

CDS_09449: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_09450: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_09451: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Translocases: transporter

CDS_09425: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

CDS_09429: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

CDS_09461: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.63	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.63	NRPS	AbT1	Aureobasidium pullulans
BGC0002164.2	0.63	NRPS	peramine	Epichloe festucae
BGC0000357.5	0.63	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0001251.4	0.63	NRPS	epichloenin A	Epichloe festucae
BGC0001250.4	0.63	NRPS	epichloenin A	Epichloe festucae
BGC0000342.4	0.63	NRPS	enniatin	Fusarium equiseti
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001166.5	0.63	NRPS	HC-toxin	Alternaria jesenskae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.63	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.63	NRPS	AbT1	Aureobasidium pullulans
BGC0002164.2	0.63	NRPS	peramine	Epichloe festucae
BGC0000357.5	0.63	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0001251.4	0.63	NRPS	epichloenin A	Epichloe festucae
BGC0001250.4	0.63	NRPS	epichloenin A	Epichloe festucae
BGC0000342.4	0.63	NRPS	enniatin	Fusarium equiseti
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001166.5	0.63	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:

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.79 out of 30.11

Confidence: medium

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.79 out of 21.84

Confidence: medium

Additional weak hits (12):

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.07 out of 26.85

Confidence: weak

MatP

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

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.15 out of 21.55

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.08 out of 21.55

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.53 out of 30.25

Confidence: weak

CodY

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

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.69 out of 21.55

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.19 out of 30.11

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.51 out of 31.73

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.98 out of 31.73

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.19 out of 26.06

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.39 out of 28.19

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 16966 - 60745:

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

NRPS/PKS substrate predictions

CDS_09442: X

AMP-binding (436..816): X

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

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DAGDMGHVCK
Nearest Stachelhaus code(s):: CysA DATKMGHVGK (53% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_09450: X

AMP-binding (9..389): 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:: PINFGAYPAK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

TFBS definitions

Regulator	Description
CelR	Cellobiose uptake repressor
MexT	Global virulence regulator

NPDC050663.ctg-0035 - Region 1 - T3PKS

Download region SVG

Location: 1 - 30,745 nt. (total: 30,745 nt) Show pHMM detection rules used

Region on contig edge.

T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

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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

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

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Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: oxidoreductase

CDS_09570: oxidoreductase

smcogs: SMCOG1161: oxidoreductase

CDS_09573: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: methyltransferase

CDS_09569: Methylation

MITE: MITE0000155Methylation (identity: 72.70%)
smcogs: SMCOG1150: isoprenylcysteine carboxyl methyltransferase

Ligases: synthase

CDS_09568: chalcone and stilbene synthase domain protein

smcogs: SMCOG1024: chalcone and stilbene synthase domain protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000282.3	0.75	PKS	2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001831.3	0.51	PKS	alkylpyrone-407, alkylpyrone-393	Myxococcus xanthus DK 1622
BGC0000902.4	0.47	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0001077.4	0.45	PKS	6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone	Actinoplanes missouriensis 431
BGC0000285.5	0.45	PKS, saccharide	flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin	Saccharopolyspora erythraea
BGC0001647.3	0.42	PKS	lagunapyrone A, lagunapyrone B, lagunapyrone C	Streptomyces sp. MP131-18
BGC0002362.3	0.38	PKS	loseolamycin A1, loseolamycin A2	Micromonospora endolithica
BGC0000843.5	0.37	other (non-nrp beta-lactam)	alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate	Streptomyces clavuligerus ATCC 27064
BGC0001909.3	0.37	PKS	strobilurin A	Strobilurus tenacellus
BGC0002621.2	0.37	other (other)	angustmycin A, angustmycin B, angustmycin C, aristeromycin, arabinofuranosyladenine	Streptomyces angustmyceticus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000282.3	0.75	PKS	2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001831.3	0.51	PKS	alkylpyrone-407, alkylpyrone-393	Myxococcus xanthus DK 1622
BGC0000902.4	0.47	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0001077.4	0.45	PKS	6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone	Actinoplanes missouriensis 431
BGC0000285.5	0.45	PKS, saccharide	flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin	Saccharopolyspora erythraea
BGC0001647.3	0.42	PKS	lagunapyrone A, lagunapyrone B, lagunapyrone C	Streptomyces sp. MP131-18
BGC0002362.3	0.38	PKS	loseolamycin A1, loseolamycin A2	Micromonospora endolithica
BGC0000843.5	0.37	other (non-nrp beta-lactam)	alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate	Streptomyces clavuligerus ATCC 27064
BGC0001909.3	0.37	PKS	strobilurin A	Strobilurus tenacellus
BGC0002621.2	0.37	other (other)	angustmycin A, angustmycin B, angustmycin C, aristeromycin, arabinofuranosyladenine	Streptomyces angustmyceticus

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.07 out of 20.47

Confidence: medium

VqsM

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

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.50 out of 20.47

Confidence: medium

Additional weak hits (4):

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.37 out of 29.25

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.79 out of 25.88

Confidence: weak

MexT

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

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.88 out of 26.12

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

TFBS Finder

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

NPDC050663.ctg-0036 - Region 1 - RiPP-like