GCF_026768265.1 - 20 region(s)

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Location: 74,914 - 181,653 nt. (total: 106,740 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

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

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

OF778_RS21060: pyruvate oxidase/decarboxylase

smcogs: SMCOG1055: pyruvate oxidase/decarboxylase

Transferases: acetyltransferase aminotransferase methyltransferase

OF778_RS20885: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

OF778_RS20910: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

OF778_RS20995: aminotransferase

smcogs: SMCOG1019: aminotransferase

OF778_RS21010: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: esterase hydrolase

OF778_RS21015: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

OF778_RS21020: thioesterase

smcogs: SMCOG1004: thioesterase

Ligases: ligase synthase

OF778_RS20920: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

OF778_RS20925: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

OF778_RS20940: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

OF778_RS20975: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

OF778_RS20990: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

OF778_RS21000: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

OF778_RS21005: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

OF778_RS21025: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

OF778_RS21030: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001192.5	0.88	NRPS	colistin A, colistin B	Paenibacillus alvei
BGC0001153.5	0.88	NRPS	polymyxin B	Paenibacillus polymyxa
BGC0000408.5	0.87	NRPS	polymyxin	Paenibacillus polymyxa
BGC0002653.2	0.85	NRPS	macolacin	Paenibacillus xylanexedens
BGC0002135.2	0.78	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000426.5	0.77	NRPS	sevadicin	Paenibacillus larvae
BGC0001758.4	0.77	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.76	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001641.4	0.76	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.76	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001192.5	0.88	NRPS	colistin A, colistin B	Paenibacillus alvei
BGC0001153.5	0.88	NRPS	polymyxin B	Paenibacillus polymyxa
BGC0000408.5	0.87	NRPS	polymyxin	Paenibacillus polymyxa
BGC0002653.2	0.85	NRPS	macolacin	Paenibacillus xylanexedens
BGC0002135.2	0.78	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000426.5	0.77	NRPS	sevadicin	Paenibacillus larvae
BGC0001758.4	0.77	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.76	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001641.4	0.76	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.76	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.22 out of 18.57

Confidence: strong

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 24.11 out of 30.25

Confidence: medium

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.33 out of 30.25

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.41 out of 20.97

Confidence: medium

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.13 out of 18.57

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.07 out of 28.19

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.14 out of 18.16

Confidence: strong

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.26 out of 28.19

Confidence: medium

Additional weak hits (6):

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 22.79 out of 30.97

Confidence: weak

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.40 out of 20.47

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.80 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.92 out of 29.38

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 21.68 out of 33.14

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 21.78 out of 33.14

Confidence: weak

Module view

Legend

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 74913 - 181653:

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

Polymer prediction:: (D-Leu - Leu - Dab - Dab - Thr) + (Dab - Thr - Dab - Dab - Dab) + (D-Asn) + (X - ohmal) + (X - Glu) + (X - Leu)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

OF778_RS20920: Leu - Leu - Dab - Dab

Search NORINE for peptide: strict or relaxed

AMP-binding (278..668): Leu

nrpys: Leu

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: LMFAFDASCWEKILVTGGSFNAYGPTEASIVTTL
Nearest Stachelhaus code(s):: Leu DAWIVGAIVK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1785..2180): Leu

nrpys: Leu

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: VNTSFDGATFDGFILFGGENHVYGPTESTVYTTY
Nearest Stachelhaus code(s):: Leu DGFFLGVVYK (100% 8Å match); Ile DGFFLGVVYK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2822..3261): Dab

nrpys: Dab

SVM prediction details:

Predicted physicochemical class:: N/A
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:: TGYAFDVFVGDRESITSSDINAYGVTEAAIDSSF
Nearest Stachelhaus code(s):: Dab DVGEISAIDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3906..4345): Dab

nrpys: Dab

SVM prediction details:

Predicted physicochemical class:: N/A
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:: TGYAFDVFVGDRESITSSDINAYGVTEAAIDSSF
Nearest Stachelhaus code(s):: Dab DVGEISAIDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

OF778_RS20925: Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (269..676): 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:: LNDHFDFSVWEGNQIFGGEINMYGITETTVHVTY
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

OF778_RS20940: Dab - Thr - Dab - Dab - Dab

Search NORINE for peptide: strict or relaxed

AMP-binding (466..878): Dab

nrpys: Dab

SVM prediction details:

Predicted physicochemical class:: N/A
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:: TAYAFDVFVGDRESITSSDINSYGVTEAAIDSSF
Nearest Stachelhaus code(s):: Dab DVGEISSIDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1520..1927): 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:: LNDHFDFSVWEGNQIFGGEINMYGITETTVHVTY
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2585..3041): Dab

nrpys: Dab

SVM prediction details:

Predicted physicochemical class:: N/A
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:: TGYAFDVFVGDRESLTSSDINSYGVTEAAIDSSF
Nearest Stachelhaus code(s):: Dab DVGELSSIDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3683..4122): Dab

nrpys: Dab

SVM prediction details:

Predicted physicochemical class:: N/A
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:: TGYAFDVFVGDRESITSSDINAYGVTEAAIDSGF
Nearest Stachelhaus code(s):: Dab DVGEISAIDK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4765..5204): Dab

nrpys: Dab

SVM prediction details:

Predicted physicochemical class:: N/A
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:: TGYAFDVFVGDRESITSSDINAYGVTEAAIDSSF
Nearest Stachelhaus code(s):: Dab DVGEISAIDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

OF778_RS20990: Asn

Search NORINE for peptide: strict or relaxed

AMP-binding (465..859): Asn

nrpys: Asn

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: YWASFDLTVTSTKLIVGGEYNEYGPTEATVGCMI
Nearest Stachelhaus code(s):: Asn DLTKIGEVGK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

OF778_RS21000: X

AMP-binding (475..883): 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:: FWTNFDSSIQQSDESLGSEINGYGPAETTVETST
Nearest Stachelhaus code(s):: Lys or Arg DPEDIGGVEK (53% 8Å match); N6-ohLys DAQDAGCVEK (50% 8Å match); Lys DAQDAGCVEK (47% 8Å match)
Stachelhaus code match:: 70% (weak)

OF778_RS21005: X - Glu

Search NORINE for peptide: strict or relaxed

AMP-binding (483..915): X

nrpys: (unknown)

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: HAKAFDVSIWQIETIANGEINAYGPTECSDDVTQ
Nearest Stachelhaus code(s):: Dpr DVWEMNADDK (74% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1593..1998): Glu

nrpys: Glu

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:: glu (Glu)

Stachelhaus prediction details:

Stachelhaus sequence:: LGLTFDASLLEWQFISGGAYNHYGPTEVTVDATT
Nearest Stachelhaus code(s):: Gln DAWQVGVVDK (65% 8Å match); Glu DAKDIGVVDK (56% 8Å match); Val DALWIGGVFK (44% 8Å match)
Stachelhaus code match:: 70% (weak)

OF778_RS21025: X

AMP-binding (457..850): X

nrpys: Ala, Val

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:: LQTCFDVFTFEATPIVGGEKNGYGPAESTTYTTT
Nearest Stachelhaus code(s):: Ala or Val DVFWIGGTFK (59% 8Å match)
Stachelhaus code match:: 80% (moderate)

OF778_RS21030: Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (251..645): Leu

nrpys: Leu

SVM prediction details:

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

Stachelhaus prediction details:

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

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
CcpA	Catabolite control protein A
ColR	Phenol-responsive regulator
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_JAPDMW010000014.1 - Region 1 - RiPP-like

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Location: 140,052 - 152,226 nt. (total: 12,175 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

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

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 phosphotransferase

OF778_RS23090: Glucose-specific phosphotransferase enzyme IIA

smcogs: SMCOG1145: Glucose-specific phosphotransferase enzyme IIA

OF778_RS23110: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001862.4	0.57	ribosomal	pallidocin	Aeribacillus pallidus
BGC0002674.2	0.54	ribosomal	enterocin F4-9	Enterococcus faecalis
BGC0001864.3	0.53	ribosomal	listeriocytocin	Listeria monocytogenes SLCC2540
BGC0001863.4	0.52	ribosomal, terpene	bacillicn CER074	Bacillus mycoides
BGC0001861.4	0.51	ribosomal	bacillicin BAG2O	Bacillus cereus BAG2O-1
BGC0000558.5	0.49	ribosomal	sublancin 168	Bacillus subtilis subsp. subtilis str. 168
BGC0000484.5	0.48	ribosomal	glycocin F	Lactobacillus plantarum
BGC0002586.2	0.47	ribosomal	ASM1	Lactiplantibacillus plantarum
BGC0002005.2	0.46	ribosomal	RaxX	Xanthomonas oryzae pv. oryzae
BGC0000617.5	0.44	ribosomal	coagulin	Bacillus coagulans

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001862.4	0.57	ribosomal	pallidocin	Aeribacillus pallidus
BGC0002674.2	0.54	ribosomal	enterocin F4-9	Enterococcus faecalis
BGC0001864.3	0.53	ribosomal	listeriocytocin	Listeria monocytogenes SLCC2540
BGC0001863.4	0.52	ribosomal, terpene	bacillicn CER074	Bacillus mycoides
BGC0001861.4	0.51	ribosomal	bacillicin BAG2O	Bacillus cereus BAG2O-1
BGC0000558.5	0.49	ribosomal	sublancin 168	Bacillus subtilis subsp. subtilis str. 168
BGC0000484.5	0.48	ribosomal	glycocin F	Lactobacillus plantarum
BGC0002586.2	0.47	ribosomal	ASM1	Lactiplantibacillus plantarum
BGC0002005.2	0.46	ribosomal	RaxX	Xanthomonas oryzae pv. oryzae
BGC0000617.5	0.44	ribosomal	coagulin	Bacillus coagulans

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.77 out of 20.97

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.25 out of 26.06

Confidence: medium

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.42 out of 19.52

Confidence: strong

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05

Confidence: medium

Additional weak hits (2):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.25 out of 31.73

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 24.95 out of 33.14

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR	Pleiotropic regulatory for antibiotic production
CcpA	Catabolite control protein A
MogR	Repressor of flagellar motility genes

NZ_JAPDMW010000015.1 - Region 1 - PKS-like,transAT-PKS

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Location: 43,135 - 148,803 nt. (total: 105,669 nt) Show pHMM detection rules used

Region on contig edge.

transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))
PKS-like: (t2pks2 or ksIII)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

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

OF778_RS23490: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

OF778_RS23495: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

OF778_RS23500: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

OF778_RS23505: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

OF778_RS23530: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase acylase glycosyltransferase methyltransferase

OF778_RS23445: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1012: 4'-phosphopantetheinyl transferase

OF778_RS23455: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

OF778_RS23520: methyltransferase

smcogs: SMCOG1089: methyltransferase

OF778_RS23540: glycosyltransferase

smcogs: SMCOG1102: glycosyltransferase

OF778_RS30090: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase

OF778_RS23385: hydrolase

smcogs: SMCOG1179: hydrolase

OF778_RS23450: metallo-beta-lactamase family protein

smcogs: SMCOG1170: metallo-beta-lactamase family protein

OF778_RS23535: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Lyases: dehydratase hydratase

OF778_RS23475: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

OF778_RS23545: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase

OF778_RS23465: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

OF778_RS23470: hydroxymethylglutaryl-CoA synthase

smcogs: SMCOG1043: hydroxymethylglutaryl-CoA synthase

OF778_RS23480: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

OF778_RS23485: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

OF778_RS23510: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

OF778_RS23515: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

OF778_RS23525: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001284.4	0.59	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001273.3	0.59	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.58	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002192.3	0.58	PKS	FR901512	fungal sp. No.14919
BGC0001164.3	0.58	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.57	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001254.3	0.56	PKS	ACT-Toxin II	Alternaria alternata
BGC0001258.3	0.54	PKS	1,3,6,8-tetrahydroxynaphthalene	Glarea lozoyensis
BGC0002175.3	0.54	PKS	YWA1	Aspergillus oryzae RIB40
BGC0002154.2	0.52	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002192.3	0.65	PKS	FR901512	fungal sp. No.14919
BGC0001164.3	0.65	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.64	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001160.5	0.64	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001276.3	0.64	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.64	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0000174.5	0.64	PKS	bryostatin	Candidatus Endobugula sertula
BGC0001284.4	0.63	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001254.3	0.63	PKS	ACT-Toxin II	Alternaria alternata

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ToxT

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

Confidence: strong

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 24.37 out of 27.78

Confidence: strong

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.17 out of 27.78

Confidence: medium

Additional weak hits (2):

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.45 out of 29.25

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.88 out of 33.14

Confidence: weak

Module view

Legend

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 43134 - 148803:

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

Polymer prediction:: (mal) + (ccmal) + (Me-ohmal - ohmal - ccmal) + (mal) + (Me-ohmal - ccmal) + (mal - mal) + (Me-ccmal) + (ccmal - mal) + (OMe-mal - ohmal) + (ccmal) + (mal)
Non-colinear ordering:: OF778_RS23480 + OF778_RS23485 + OF778_RS23490 + OF778_RS23495 + OF778_RS23500 + OF778_RS23505 + OF778_RS23510 + OF778_RS23515 + OF778_RS23520 + OF778_RS23525 + OF778_RS23530

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

OF778_RS30090: mal

PKS_AT (8..295): mal

ATSignature: (unknown)

No matches above 50%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 22.8
inactive: 14.4
Isobutyryl-CoA: 8.3
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Propionyl-CoA: 0.0
Methylmalonyl-CoA: 0.0
Methoxymalonyl-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

OF778_RS23455: mal

PKS_AT (4..284): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 128.2
inactive: 50.6
Methoxymalonyl-CoA: 50.3
Methylmalonyl-CoA: 47.6
Propionyl-CoA: 34.2
Isobutyryl-CoA: 16.7
CHC-CoA: 16.3
2-Methylbutyryl-CoA: 14.7
fatty_acid: 13.2
Ethylmalonyl-CoA: 11.1
trans-1,2-CPDA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

TFBS definitions

Regulator	Description
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
ToxT	Regulator of MSHA biosynthesis

NZ_JAPDMW010000001.1 - Region 1 - terpene-precursor

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Location: 180,346 - 201,287 nt. (total: 20,942 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

binding site

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Gene overview

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MIBiG comparison

KnownClusterBlast

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Terpene

TFBS Finder

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: carboxylase

OF778_RS00830: acetyl-CoA carboxylase biotin carboxylase

smcogs: SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Ligases: synthase synthetase

OF778_RS00870: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

OF778_RS00880: 1-deoxy-D-xylulose-5-phosphate synthase

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

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002283.2	0.49	terpene	sodorifen	Serratia plymuthica
BGC0001361.3	0.49	terpene	sodorifen	Serratia plymuthica 4Rx13
BGC0002397.2	0.47	terpene	astallatene	Arabidopsis thaliana
BGC0002400.2	0.44	terpene	boleracene	Brassica oleracea var. oleracea
BGC0002398.2	0.38	terpene	(-)-ent-quiannulatene	Arabidopsis thaliana
BGC0002284.3	0.38	other (other)	corynecin III, corynecin I, corynecin II	Rhodococcus sp. H-CA8f
BGC0000665.5	0.38	other (other), terpene	xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C	Streptomyces sp. HKI0576
BGC0000639.3	0.37	terpene	carotenoid	Enterobacteriaceae bacterium DC260
BGC0001594.3	0.37	other (other)	fischerindole L	Fischerella muscicola UTEX 1829
BGC0000642.3	0.37	terpene	carotenoid	Enterobacteriaceae bacterium DC413

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002283.2	0.49	terpene	sodorifen	Serratia plymuthica
BGC0001361.3	0.49	terpene	sodorifen	Serratia plymuthica 4Rx13
BGC0002397.2	0.47	terpene	astallatene	Arabidopsis thaliana
BGC0002400.2	0.44	terpene	boleracene	Brassica oleracea var. oleracea
BGC0002398.2	0.38	terpene	(-)-ent-quiannulatene	Arabidopsis thaliana
BGC0002284.3	0.38	other (other)	corynecin III, corynecin I, corynecin II	Rhodococcus sp. H-CA8f
BGC0000665.5	0.38	other (other), terpene	xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C	Streptomyces sp. HKI0576
BGC0000639.3	0.37	terpene	carotenoid	Enterobacteriaceae bacterium DC260
BGC0001594.3	0.37	other (other)	fischerindole L	Fischerella muscicola UTEX 1829
BGC0000642.3	0.37	terpene	carotenoid	Enterobacteriaceae bacterium DC413

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 precursor		FPP	C15	acyclic	PP

Genes with terpene domains:

OF778_RS00870: PT_FPPS_like

Domain 1 (48 - 313): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:: DMAPP, IPP → FPP

Transcription Factor Binding Sites

Binding sites found:

ToxT

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

Confidence: strong

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.95 out of 27.78

Confidence: medium

VqsM

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

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.25 out of 28.19

Confidence: medium

Additional weak hits (4):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.49 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.76 out of 26.06

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.18 out of 25.75

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.89 out of 36.54

Confidence: weak

Terpene

TFBS Finder

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
IPP	Isopentenyl diphosphate
PP	Diphosphate

TFBS definitions

Regulator	Description
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
ToxT	Regulator of MSHA biosynthesis
VqsM	Regulator of quorum-sensing signalling systems
ZuR variant 1	Zinc-responsive repressor

NZ_JAPDMW010000001.1 - Region 2 - NRPS,T1PKS

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Location: 653,826 - 717,853 nt. (total: 64,028 nt) Show pHMM detection rules used

Region on contig edge.

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

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

OF778_RS03070: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

OF778_RS03075: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

OF778_RS03090: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

OF778_RS03145: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

OF778_RS03230: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

Transferases: acylase

OF778_RS03135: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase

OF778_RS03130: thioesterase

smcogs: SMCOG1004: thioesterase

Ligases: ligase synthase

OF778_RS03105: 1-deoxy-D-xylulose-5-phosphate synthase

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

OF778_RS03125: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

OF778_RS03155: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

OF778_RS03160: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.68	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	0.67	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001825.4	0.67	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001132.4	0.67	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.65	NRPS	AM-toxin	Alternaria alternata
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.63	NRPS	HC-toxin	Alternaria jesenskae
BGC0001641.4	0.62	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.67	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	0.67	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001825.4	0.67	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001132.4	0.67	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.66	NRPS	AM-toxin	Alternaria alternata
BGC0001128.4	0.66	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.66	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.65	NRPS	HC-toxin	Alternaria jesenskae
BGC0001641.4	0.65	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57

Confidence: strong

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.31 out of 26.06

Confidence: medium

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.75 out of 27.55

Confidence: medium

Additional weak hits (4):

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.18 out of 29.25

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.22 out of 25.88

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.14 out of 29.38

Confidence: weak

Module view

Legend

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 653825 - 717853:

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

Polymer prediction:: (ccmal) + (mal) + (D-Val - Phe)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

OF778_RS03125: mal

PKS_AT (642..930): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 79.2%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 145.1
inactive: 117.3
Methylmalonyl-CoA: 53.6
Methoxymalonyl-CoA: 51.2
Isobutyryl-CoA: 33.0
Ethylmalonyl-CoA: 26.0
Benzoyl-CoA: 20.7
Propionyl-CoA: 16.5
fatty_acid: 11.8
trans-1,2-CPDA: 0.0
CHC-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

OF778_RS03135: mmal

PKS_AT (38..289): mmal

ATSignature: (unknown)

No matches above 50%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 10.0
trans-1,2-CPDA: 0.0
inactive: 0.0
fatty_acid: 0.0
Propionyl-CoA: 0.0
Methoxymalonyl-CoA: 0.0
Malonyl-CoA: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

OF778_RS03155: mal

PKS_AT (560..856): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 66.7%; inactive: 62.5%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: inactive

Prediction, score:

inactive: 92.1
Malonyl-CoA: 80.1
Methoxymalonyl-CoA: 39.4
Methylmalonyl-CoA: 27.0
Isobutyryl-CoA: 21.0
Benzoyl-CoA: 17.1
Propionyl-CoA: 15.3
2-Methylbutyryl-CoA: 10.1
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

OF778_RS03160: Val - Phe

Search NORINE for peptide: strict or relaxed

AMP-binding (713..1111): 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:: LNTGFDASTFEGWLIVGGDINGYGPTENTTFSTS
Nearest Stachelhaus code(s):: Val DAFWIGGTFK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2209..2596): Phe

nrpys: Phe

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: LWFAFDAFSWEMTLITAGSINAYGPTEDTVCTTA
Nearest Stachelhaus code(s):: Phe DAWTIAAVCK (71% 8Å match)
Stachelhaus code match:: 100% (strong)

TFBS definitions

Regulator	Description
GnfM	Regulator of nitrogen-fixation genes
MogR	Repressor of flagellar motility genes
ToxT	Regulator of MSHA biosynthesis

NZ_JAPDMW010000021.1 - Region 1 - NRP-metallophore,NRPS

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Location: 27,867 - 73,182 nt. (total: 45,316 nt) Show pHMM detection rules used

Region on contig edge.

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

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

OF778_RS26230: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase

OF778_RS26245: isochorismatase

smcogs: SMCOG1027: isochorismatase

Isomerases: isomerase

OF778_RS26235: isochorismate synthase

smcogs: SMCOG1018: isochorismate synthase

Ligases: ligase

OF778_RS26240: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

OF778_RS26250: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Translocases: transporter

OF778_RS26165: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000401.5	1.09	NRPS	paenibactin	Paenibacillus elgii B69
BGC0001185.5	1.03	NRPS	bacillibactin	Bacillus velezensis FZB42
BGC0000309.5	1.02	NRPS	bacillibactin	Bacillus subtilis subsp. subtilis str. 168
BGC0000343.5	0.86	NRPS	enterobactin	Pseudomonas sp. J465
BGC0001833.4	0.76	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002695.2	0.76	NRPS	bacillibactin, bacillibactin E, bacillibactin F	Bacillus sp. WMMC1349
BGC0001132.4	0.76	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.75	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.73	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.73	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000401.5	0.81	NRPS	paenibactin	Paenibacillus elgii B69
BGC0001185.5	0.79	NRPS	bacillibactin	Bacillus velezensis FZB42
BGC0000309.5	0.79	NRPS	bacillibactin	Bacillus subtilis subsp. subtilis str. 168
BGC0000343.5	0.74	NRPS	enterobactin	Pseudomonas sp. J465
BGC0001833.4	0.70	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002695.2	0.70	NRPS	bacillibactin, bacillibactin E, bacillibactin F	Bacillus sp. WMMC1349
BGC0001132.4	0.70	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.70	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.69	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.69	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.42 out of 27.78

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.06 out of 19.26

Confidence: strong

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 28.84 out of 29.38

Confidence: strong

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.17 out of 29.38

Confidence: medium

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.41 out of 29.38

Confidence: medium

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 27.42 out of 32.74

Confidence: medium

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.06 out of 29.38

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 25.23 out of 27.78

Confidence: strong

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 22.42 out of 25.88

Confidence: medium

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 22.49 out of 25.88

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 24.52 out of 28.19

Confidence: strong

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.70 out of 28.19

Confidence: medium

Additional weak hits (14):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.79 out of 30.22

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.15 out of 21.55

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.10 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.98 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 26.03 out of 32.74

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.47 out of 29.38

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.04 out of 31.73

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 25.00 out of 31.73

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 24.43 out of 31.73

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.62 out of 33.14

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.62 out of 35.63

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.72 out of 32.93

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 21.70 out of 30.11

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 21.70 out of 30.11

Confidence: weak

Module view

Legend

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 27866 - 73182:

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

Polymer prediction:: (Ala - Thr)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

OF778_RS26240: diOH-Bz

Search NORINE for peptide: strict or relaxed

AMP-binding (31..437): 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:: SMSLYPLSSPGGAVQVGGAQQVYGMAEGLVNYTR
Nearest Stachelhaus code(s):: diOH-Bz PLPAQGVVNK (91% 8Å match); diOH-Bz or Sal PLPAQGVVNK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

OF778_RS26250: Ala - Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (464..866): Ala

nrpys: Ala

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:: LDMTFDISVMELQAITGGENNQYGPTETTIYSTA
Nearest Stachelhaus code(s):: Ala DILQIGQIYK (91% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1531..1949): 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:: LATHFDFSVWEGNQVFGGEINMYGITETTVHVSF
Nearest Stachelhaus code(s):: Thr DFWNVGMVHK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1	Ferric Uptake Regulator
FuR variant 2	Ferric Uptake Regulator
PsrA	Oleic acid responsive regulator
ZuR variant 1	Zinc-responsive repressor

NZ_JAPDMW010000032.1 - Region 1 - NRPS

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Location: 1 - 27,510 nt. (total: 27,510 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

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

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KnownClusterBlast

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TFBS Finder

NRPS/PKS modules

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Hydrolases: dehalogenase

OF778_RS29220: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Ligases: ligase

OF778_RS29185: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.70	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.70	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.69	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0002286.3	0.69	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001758.4	0.68	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.70	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.70	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.69	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0002286.3	0.69	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001758.4	0.68	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CcpA

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

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.79 out of 27.78

Confidence: medium

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 25.19 out of 30.25

Confidence: medium

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.67 out of 32.93

Confidence: medium

Additional weak hits (6):

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.58 out of 32.93

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.78 out of 28.14

Confidence: weak

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.21 out of 29.72

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.15 out of 36.54

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.28 out of 33.14

Confidence: weak

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 22.61 out of 30.12

Confidence: weak

Module view

Legend

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 27510:

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

Polymer prediction:: (Val - Val - Leu)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

OF778_RS29185: Val - Val - Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (486..883): 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:: LQAGFDASTFEGWLIIGGEWNGYGPTENTTFSTC
Nearest Stachelhaus code(s):: Val DAFWIGGTFK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1539..1938): 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:: LQAGFDASTFEGWLIIGGDWNGYGPTENTTFSTC
Nearest Stachelhaus code(s):: Val DAFWIGGTFK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2596..2991): Leu

nrpys: Leu

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: MWHAFDAAVAEPFMLTGGDINNYGPTECTVIATA
Nearest Stachelhaus code(s):: Leu DAWFLGNVVK (79% 8Å match)
Stachelhaus code match:: 80% (moderate)

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
ColR	Phenol-responsive regulator
LexA variant 3	Repressor of DNA damage response

NZ_JAPDMW010000034.1 - Region 1 - lassopeptide

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Location: 1 - 17,215 nt. (total: 17,215 nt) Show pHMM detection rules used

Region on contig edge.

lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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

KnownClusterBlast

SubClusterBlast

Lasso peptides

TFBS Finder

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

OF778_RS29460: FAD linked oxidase domain protein

smcogs: SMCOG1138: FAD linked oxidase domain protein

Hydrolases: hydrolase

OF778_RS29480: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001176.4	0.61	ribosomal	streptomonomicin	Streptomonospora alba
BGC0001645.3	0.59	ribosomal	lagmysin	Streptomyces sp. NRRL S-118
BGC0002825.2	0.54	ribosomal	nocapeptin A	Nocardia terpenica IFM 0406
BGC0001539.4	0.53	ribosomal	cattlecin	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001548.4	0.53	ribosomal	citrulassin A	Streptomyces albulus
BGC0002053.3	0.53	ribosomal	ulleungdin	Streptomyces sp.
BGC0001552.3	0.53	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001634.3	0.52	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0001549.3	0.51	ribosomal	citrulassin B	Streptomyces aurantiacus JA 4570
BGC0001550.3	0.51	ribosomal	citrulassin D	Streptomyces katrae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001176.4	0.61	ribosomal	streptomonomicin	Streptomonospora alba
BGC0001645.3	0.59	ribosomal	lagmysin	Streptomyces sp. NRRL S-118
BGC0002825.2	0.54	ribosomal	nocapeptin A	Nocardia terpenica IFM 0406
BGC0001539.4	0.53	ribosomal	cattlecin	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001548.4	0.53	ribosomal	citrulassin A	Streptomyces albulus
BGC0002053.3	0.53	ribosomal	ulleungdin	Streptomyces sp.
BGC0001552.3	0.53	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001634.3	0.52	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0001549.3	0.51	ribosomal	citrulassin B	Streptomyces aurantiacus JA 4570
BGC0001550.3	0.51	ribosomal	citrulassin D	Streptomyces katrae

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Lasso peptide predictions

Lassopeptides - No core peptides found.

Transcription Factor Binding Sites

Binding sites found:

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.21 out of 26.06

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.54 out of 27.78

Confidence: medium

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.79 out of 21.84

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.10 out of 23.79

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.08 out of 23.79

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.92 out of 24.78

Confidence: medium

Additional weak hits (3):

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.53 out of 33.73

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.72 out of 30.22

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.41 out of 29.65

Confidence: weak

Lasso peptides

RREFinder

TFBS Finder

Core peptide predictions

No core peptides found.

RRE predictions

: RRE type: Stand_Alone_Lasso_RRE; Location: 1 - 82; Score: 66.7

TFBS definitions

Regulator	Description
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
IolR	Regulator of the inositol catabolism
LexA variant 2	Repressor of DNA damage response
MexT	Global virulence regulator
MogR	Repressor of flagellar motility genes

NZ_JAPDMW010000003.1 - Region 1 - phosphonate

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Location: 434,434 - 451,975 nt. (total: 17,542 nt) Show pHMM detection rules used

phosphonate: (phosphonates and minimum(1, [2-Hacid_dh_C, Aldedh, Aminotran_1_2, Aminotran_5, AurF, CTP_transf_like, DUF4992, Fe-ADH, HMGL-like, Metallophos_2, NTP_transf_3, NTP_transf_5, PALP, PEP_mutase, TPP_enzyme_C, TPP_enzyme_N, phosphonates]) and not (phosphonatesHydrolase or phosphonatesMeIsocitrateLyase))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

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TFBS Finder

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Transferases: transferase

OF778_RS08300: glucose-1-phosphate adenylyl/thymidylyltransferase

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

Ligases: synthase

OF778_RS08270: 2-isopropylmalate synthase

smcogs: SMCOG1271: 2-isopropylmalate synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000904.5	0.51	other (other)	FR-900098	Streptomyces rubellomurinus
BGC0001859.4	0.50	other (phosphonate)	fosfomycin	Pseudomonas syringae
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0000563.4	0.42	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0001226.4	0.41	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0002116.3	0.41	ribosomal	darobactin A	Photorhabdus khanii HGB 1456
BGC0000501.3	0.40	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0000616.4	0.40	ribosomal	amylocyclicin	Bacillus velezensis FZB42
BGC0000626.3	0.40	ribosomal	thuricin	Bacillus thuringiensis
BGC0001579.4	0.40	ribosomal	duramycin	Streptomyces cinnamoneus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000904.5	0.51	other (other)	FR-900098	Streptomyces rubellomurinus
BGC0001859.4	0.50	other (phosphonate)	fosfomycin	Pseudomonas syringae
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0000563.4	0.42	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0001226.4	0.41	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0002116.3	0.41	ribosomal	darobactin A	Photorhabdus khanii HGB 1456
BGC0000501.3	0.40	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0000616.4	0.40	ribosomal	amylocyclicin	Bacillus velezensis FZB42
BGC0000626.3	0.40	ribosomal	thuricin	Bacillus thuringiensis
BGC0001579.4	0.40	ribosomal	duramycin	Streptomyces cinnamoneus

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

RpoN

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

Confidence: strong

AfsR

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

Confidence: medium

Additional weak hits (1):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 24.77 out of 31.73

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
RpoN	Regulator of nitrogen assimilation and virulence

NZ_JAPDMW010000004.1 - Region 1 - cyclic-lactone-autoinducer

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Location: 199,842 - 220,372 nt. (total: 20,531 nt) Show pHMM detection rules used

cyclic-lactone-autoinducer: (TIGR04223 or AgrB)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

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KnownClusterBlast

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TFBS Finder

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

OF778_RS10180: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000779.3	0.39	saccharide	lipopolysaccharide	Aeromonas piscicola
BGC0001768.4	0.35	NRPS	sansalvamide	[Nectria] haematococca mpVI 77-13-4
BGC0002161.2	0.35	PKS	scytalone, T3HN	Pestalotiopsis fici W106-1
BGC0002197.2	0.35	NRPS, PKS	terrestric acid	Penicillium crustosum
BGC0001605.3	0.34	terpene	gibberellin	Sinorhizobium fredii NGR234
BGC0001906.2	0.34	PKS	2-acetyl-1,3,6,8-tetrahydroxynaphthalene, 1,3,6,8-tetrahydroxynaphthalene	Daldinia eschscholzii IFB-TL01
BGC0002510.2	0.28	PKS	youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4	Streptomyces sp.
BGC0002547.2	0.27	PKS	youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4	Streptomyces youssoufiensis
BGC0002147.2	0.27	NRPS	bohemamine A, bohemamine B, bohemamine C	Streptomyces sp. CB02009
BGC0000298.5	0.27	NRPS	aeruginosin 98-A, aeruginosin 98-B, aeruginosin 98-C	Microcystis aeruginosa NIES-98

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000779.3	0.39	saccharide	lipopolysaccharide	Aeromonas piscicola
BGC0001768.4	0.35	NRPS	sansalvamide	[Nectria] haematococca mpVI 77-13-4
BGC0002161.2	0.35	PKS	scytalone, T3HN	Pestalotiopsis fici W106-1
BGC0002197.2	0.35	NRPS, PKS	terrestric acid	Penicillium crustosum
BGC0001605.3	0.34	terpene	gibberellin	Sinorhizobium fredii NGR234
BGC0001906.2	0.34	PKS	2-acetyl-1,3,6,8-tetrahydroxynaphthalene, 1,3,6,8-tetrahydroxynaphthalene	Daldinia eschscholzii IFB-TL01
BGC0002510.2	0.28	PKS	youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4	Streptomyces sp.
BGC0002547.2	0.27	PKS	youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4	Streptomyces youssoufiensis
BGC0002147.2	0.27	NRPS	bohemamine A, bohemamine B, bohemamine C	Streptomyces sp. CB02009
BGC0000298.5	0.27	NRPS	aeruginosin 98-A, aeruginosin 98-B, aeruginosin 98-C	Microcystis aeruginosa NIES-98

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.75 out of 18.57

Confidence: strong

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.02 out of 21.84

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.79 out of 28.19

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.41 out of 27.04

Confidence: medium

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.76 out of 29.25

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.96 out of 24.78

Confidence: medium

Additional weak hits (1):

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.04 out of 29.65

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
DasR	N-acetylglucosamine dependent repressor
LexA variant 2	Repressor of DNA damage response
MexT	Global virulence regulator
SypG	Regulator of biofilm formation and host colonization
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_JAPDMW010000005.1 - Region 1 - NRPS-like

Download region SVG

Location: 1 - 23,056 nt. (total: 23,056 nt) Show pHMM detection rules used

Region on contig edge.

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

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

Lyases: dehydratase

OF778_RS11540: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.62	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.62	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001758.4	0.61	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001128.4	0.60	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.60	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002164.2	0.60	NRPS	peramine	Epichloe festucae
BGC0002286.3	0.60	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	0.60	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000357.5	0.60	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0001240.4	0.60	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.62	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.62	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001758.4	0.61	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001128.4	0.60	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.60	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002164.2	0.60	NRPS	peramine	Epichloe festucae
BGC0002286.3	0.60	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	0.60	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000357.5	0.60	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0001240.4	0.60	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.07 out of 18.46

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.60 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.28 out of 28.19

Confidence: medium

Additional weak hits (2):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.34 out of 29.38

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.36 out of 27.18

Confidence: weak

Module view

Legend

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 23056:

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

Polymer prediction:: (Leu)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

OF778_RS11540: Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (36..431): Leu

nrpys: Leu

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: MWHAFDAAVAEPFMLTAGDINNYGPTECTVVATA
Nearest Stachelhaus code(s):: Leu DAWFLGNVVK (79% 8Å match)
Stachelhaus code match:: 80% (moderate)

TFBS definitions

Regulator	Description
RpoN	Regulator of nitrogen assimilation and virulence
ZuR variant 1	Zinc-responsive repressor

NZ_JAPDMW010000005.1 - Region 2 - NRPS,terpene

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Location: 77,468 - 185,406 nt. (total: 107,939 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)
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

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

NRPS/PKS modules

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

OF778_RS12170: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

Transferases: kinase

OF778_RS12120: PfkB domain protein

smcogs: SMCOG1276: PfkB domain protein

OF778_RS12165: glycerol kinase

smcogs: SMCOG1210: glycerol kinase

Hydrolases: hydrolase

OF778_RS11950: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

OF778_RS12020: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: ligase synthase

OF778_RS12080: Pseudouridine synthase

smcogs: SMCOG1154: Pseudouridine synthase

OF778_RS12130: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

OF778_RS12135: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

OF778_RS12140: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000400.5	0.53	NRPS	paenibacterin	Paenibacillus sp. OSY-SE
BGC0001758.4	0.44	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.44	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	0.44	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001153.5	0.42	NRPS	polymyxin B	Paenibacillus polymyxa
BGC0001192.5	0.42	NRPS	colistin A, colistin B	Paenibacillus alvei
BGC0002653.2	0.42	NRPS	macolacin	Paenibacillus xylanexedens
BGC0001128.4	0.42	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.41	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.41	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000400.5	0.80	NRPS	paenibacterin	Paenibacillus sp. OSY-SE
BGC0001758.4	0.75	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.74	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001153.5	0.74	NRPS	polymyxin B	Paenibacillus polymyxa
BGC0001192.5	0.74	NRPS	colistin A, colistin B	Paenibacillus alvei
BGC0002653.2	0.74	NRPS	macolacin	Paenibacillus xylanexedens
BGC0001128.4	0.73	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

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
triterpene	hopanoid		C30	hopanoid skeleton	unknown
triterpene	polypodane		C30	polypodane skeleton	unknown

Genes with terpene domains:

OF778_RS11970: T2TS

Domain 1 (5 - 626): Type 2 terpene synthase

Subtype: Squalene substrate

Reactions:: squalene → hopanoid; squalene → polypodane

Transcription Factor Binding Sites

Binding sites found:

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.97 out of 21.55

Confidence: medium

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 23.41 out of 27.55

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.98 out of 28.19

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 23.46 out of 24.78

Confidence: strong

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.75 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.87 out of 28.19

Confidence: medium

Additional weak hits (15):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.13 out of 21.55

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 21.43 out of 30.11

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 21.93 out of 30.11

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.53 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.65 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.29 out of 26.06

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.37 out of 32.74

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 24.03 out of 32.74

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.29 out of 36.54

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.25 out of 30.97

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.79 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.32 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.45 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.75 out of 26.06

Confidence: weak

LuxO

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

Confidence: weak

Module view

Legend

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 77467 - 185406:

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

Polymer prediction:: (D-Orn - Val - Thr - D-Orn - Ser - Tyr) + (D-X - D-Ser - Ile - Pro - X) + (Pro - Ile)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 96227 - 185406:

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

Polymer prediction:: (D-Orn - Val - Thr - D-Orn - Ser - Tyr) + (D-X - D-Ser - Ile - Pro - X) + (Pro - Ile)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

OF778_RS12130: Orn - Val - Thr - Orn - Ser

Search NORINE for peptide: strict or relaxed

AMP-binding (468..868): 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:: LAWAFDVFTGDRESVVGSDLNSYGVTEACVDACY
Nearest Stachelhaus code(s):: Orn DVGEIGSVDK (91% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1993..2393): 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:: LGASFDAATFEGWMLVGGDINGYGPTENTTFTCC
Nearest Stachelhaus code(s):: Val DAFWLGGTFK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3035..3434): 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:: LNSHFDFSVWEGNQIFGGEINMYGITETTVHVTY
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4077..4477): 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:: MAWAFDVFSGDRESIIGSDINSYGVTEACVDSSY
Nearest Stachelhaus code(s):: Orn DVGEIGSVDK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (5616..6021): 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:: RWMTFDVSVWEWHFFTSGEINLYGPTEATVDVTY
Nearest Stachelhaus code(s):: Ser DVWHFSLVDK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

OF778_RS12135: Tyr - X - Ser - Ile - Pro

Search NORINE for peptide: strict or relaxed

AMP-binding (261..655): Tyr

nrpys: Tyr

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: AWRFFDGFVMSGICTLAGEFNEYGPTENSVVATC
Nearest Stachelhaus code(s):: Tyr DGTITAEVAK (76% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1297..1697): 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:: MAWAFDVFSGDRDCAVGSDINSYGVTETCIDASY
Nearest Stachelhaus code(s):: Lys DVGDVGSIDK (76% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (2830..3234): 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:: RWMTFDVSVWEWHFFTSGEINLYGPTEATVDVTY
Nearest Stachelhaus code(s):: Ser DVWHFSLVDK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4355..4757): 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:: VETSFDGSTFDGFILFGGEKHVYGPTESTVFATC
Nearest Stachelhaus code(s):: Ile DGFFLGVVFK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (5398..5796): Pro

nrpys: Pro

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: LYQAFDVCYQESFIITAGEHNHYGPSETHVVTTY
Nearest Stachelhaus code(s):: Pro DVQFIAHVVK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

OF778_RS12140: X - Pro - Ile

Search NORINE for peptide: strict or relaxed

AMP-binding (269..666): X

nrpys: (unknown)

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: INTSFDGSAFDGLILFGGEKHAYGPSESTVYATW
Nearest Stachelhaus code(s):: Leu DGFLLGLVYK (82% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1309..1707): Pro

nrpys: Pro

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: LYQAFDVCYQESFIITAGEHNHYGPSETHVVTTY
Nearest Stachelhaus code(s):: Pro DVQFIAHVVK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2349..2745): 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:: VDASFDGSTFDGFILFGGEKHVYGPTESTVFATS
Nearest Stachelhaus code(s):: Ile DGFFLGVVFK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
ArcA	Repressor of carbon oxidation
GnfM	Regulator of nitrogen-fixation genes
LexA variant 2	Repressor of DNA damage response
ZuR variant 1	Zinc-responsive repressor

NZ_JAPDMW010000005.1 - Region 3 - RiPP-like

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Location: 215,368 - 227,323 nt. (total: 11,956 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

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

KnownClusterBlast

SubClusterBlast

TFBS Finder

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Transferases: acetyltransferase

OF778_RS12405: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001174.4	0.37	ribosomal	corynazolicin	Corynebacterium urealyticum DSM 7111
BGC0000607.5	0.36	ribosomal	micrococcin P1	Macrococcus caseolyticus
BGC0000569.5	0.36	ribosomal	plantazolicin	Bacillus velezensis FZB42
BGC0001173.5	0.36	ribosomal	plantazolicin	Bacillus pumilus ATCC 7061
BGC0001146.5	0.34	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0000606.5	0.33	ribosomal	lactazole	Streptomyces lactacystinaeus
BGC0000603.5	0.33	ribosomal	cyclothiazomycin	Streptomyces hygroscopicus
BGC0000480.5	0.32	ribosomal	tenuecyclamide A, tenuecyclamide C	Nostoc spongiaeforme var. tenue str. Carmeli
BGC0000471.4	0.32	ribosomal	viridisamide A	Oscillatoria nigro-viridis PCC 7112
BGC0000477.3	0.32	ribosomal	patellin 2, patellin 3	uncultured Prochloron sp. 06037A

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001174.4	0.37	ribosomal	corynazolicin	Corynebacterium urealyticum DSM 7111
BGC0000607.5	0.36	ribosomal	micrococcin P1	Macrococcus caseolyticus
BGC0000569.5	0.36	ribosomal	plantazolicin	Bacillus velezensis FZB42
BGC0001173.5	0.36	ribosomal	plantazolicin	Bacillus pumilus ATCC 7061
BGC0001146.5	0.34	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0000606.5	0.33	ribosomal	lactazole	Streptomyces lactacystinaeus
BGC0000603.5	0.33	ribosomal	cyclothiazomycin	Streptomyces hygroscopicus
BGC0000480.5	0.32	ribosomal	tenuecyclamide A, tenuecyclamide C	Nostoc spongiaeforme var. tenue str. Carmeli
BGC0000471.4	0.32	ribosomal	viridisamide A	Oscillatoria nigro-viridis PCC 7112
BGC0000477.3	0.32	ribosomal	patellin 2, patellin 3	uncultured Prochloron sp. 06037A

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: 17.40 out of 19.26

Confidence: medium

Additional weak hits (2):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.93 out of 26.06

Confidence: weak

CsoR

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

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein

NZ_JAPDMW010000005.1 - Region 4 - NRPS,NRPS-like,T1PKS,transAT-PKS

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Location: 339,762 - 403,258 nt. (total: 63,497 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))
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

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

OF778_RS13105: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

OF778_RS13120: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

OF778_RS13150: dehydrogenase

smcogs: SMCOG1181: dehydrogenase

Transferases: PPTase acylase aminotransferase

OF778_RS13110: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

OF778_RS13115: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

OF778_RS13140: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: phosphatase

OF778_RS13125: FkbH like protein

smcogs: SMCOG1256: FkbH like protein

Ligases: ligase synthase

OF778_RS13090: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

OF778_RS13095: 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	1.62	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001132.4	1.31	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001758.4	1.29	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	1.18	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001275.3	1.07	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001164.3	1.06	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	1.06	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001276.3	1.06	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001876.2	0.96	NRPS	thalassospiramide A	Thalassospira sp. CNJ-328
BGC0001748.4	0.90	NRPS, PKS	pseudospumigin A, pseudospumigin B, pseudospumigin C, pseudospumigin D, pseudospumigin E, pseudospumigin F	Nostoc sp. CENA543

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.72	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001132.4	0.66	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001758.4	0.66	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.63	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001275.3	0.60	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001164.3	0.60	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.60	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001276.3	0.60	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001876.2	0.57	NRPS	thalassospiramide A	Thalassospira sp. CNJ-328
BGC0001748.4	0.55	NRPS, PKS	pseudospumigin A, pseudospumigin B, pseudospumigin C, pseudospumigin D, pseudospumigin E, pseudospumigin F	Nostoc sp. CENA543

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.21 out of 27.78

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.30 out of 27.78

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.28 out of 27.78

Confidence: medium

Additional weak hits (2):

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 25.79 out of 32.74

Confidence: weak

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.31 out of 20.47

Confidence: weak

Module view

Legend

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 339761 - 403258:

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

Polymer prediction:: (X - mal - Gly - Ile) + (fatty_acid - mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 339761 - 396363:

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

Polymer prediction:: (X - mal - Gly - Ile) + (fatty_acid - mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 8, location 356484 - 403258:

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

Polymer prediction:: (X - mal - Gly - Ile) + (fatty_acid - mal)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

OF778_RS13090: X - mal - Gly - Ile

Search NORINE for peptide: strict or relaxed

AMP-binding (462..868): X

nrpys: Gly, Ala

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: TDLTFDVSGTEGNFCIGGEENVYGPTECTIWASH
Nearest Stachelhaus code(s):: Arg DVENVGVISK (44% 8Å match)
Stachelhaus code match:: 70% (weak)

PKS_AT (1589..1881): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 83.3%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 98.0
Methoxymalonyl-CoA: 52.2
inactive: 50.0
Methylmalonyl-CoA: 43.1
Propionyl-CoA: 28.0
Isobutyryl-CoA: 14.9
fatty_acid: 13.6
Ethylmalonyl-CoA: 13.2
Acetyl-CoA: 11.9
2-Methylbutyryl-CoA: 9.6
trans-1,2-CPDA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

AMP-binding (2528..2928): 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:: FDITFDIFAFEVLSLSGGEFNMYGPTETTIWSVA
Nearest Stachelhaus code(s):: Gly DILQLGMIWK (65% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (4485..4892): 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:: VNASFDGSVFDGFILIGGEINGYGPTETTVFAAY
Nearest Stachelhaus code(s):: Ile DGFFLGVVFK (74% 8Å match)
Stachelhaus code match:: 90% (moderate)

OF778_RS13095: fatty_acid

CAL_domain (170..482): fatty_acid

minowa: fatty_acid

Prediction, score:

fatty_acid: 61.6
NH2: 38.2
shikimic_acid: 0.0
Acetyl-CoA: 0.0
AHBA: 0.0

OF778_RS13110: mal

PKS_AT (6..293): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 72.2
Methoxymalonyl-CoA: 58.7
Methylmalonyl-CoA: 54.8
Ethylmalonyl-CoA: 43.7
inactive: 38.4
Propionyl-CoA: 30.2
2-Methylbutyryl-CoA: 27.3
Isobutyryl-CoA: 22.9
trans-1,2-CPDA: 22.3
Acetyl-CoA: 20.1
fatty_acid: 15.7
CHC-CoA: 15.4
Benzoyl-CoA: 11.0
3-Methylbutyryl-CoA: 0.0

TFBS definitions

Regulator	Description
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria

NZ_JAPDMW010000006.1 - Region 1 - ranthipeptide,resorcinol

Download region SVG

Location: 105,426 - 155,548 nt. (total: 50,123 nt) Show pHMM detection rules used

ranthipeptide: (TIGR03973 or SCIFF or (cds(PF04055 and (TIGR04085 or SPASM)) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]) and not (TIGR01716 or subtilosin or TIGR02111 or TIGR03966 or TIGR04103 or (YcaO or TIGR03604))))
resorcinol: DarB

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

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

OF778_RS14315: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase

OF778_RS14225: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: synthase

OF778_RS14335: 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
BGC0002306.2	0.40	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0001928.2	0.25	other (other)	(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid	Streptomyces sp. MA37
BGC0000622.5	0.24	ribosomal	megacin	Bacillus megaterium
BGC0000486.4	0.24	ribosomal	butyrivibriocin AR10	Butyrivibrio fibrisolvens
BGC0000513.3	0.23	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000515.4	0.22	ribosomal	geobacillin I	Geobacillus thermodenitrificans NG80-2
BGC0000552.3	0.22	ribosomal	SmbA, SmbB	Streptococcus mutans
BGC0000506.4	0.22	ribosomal	entianin	Bacillus subtilis subsp. spizizenii
BGC0000527.5	0.22	ribosomal	mersacidin	Bacillus sp. HIL-Y85/54728
BGC0000521.3	0.22	ribosomal	lacticin 481	Lactococcus lactis subsp. lactis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.52	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0002425.3	0.45	ribosomal	stlassin	Streptomyces sp.
BGC0001928.2	0.45	other (other)	(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid	Streptomyces sp. MA37
BGC0000888.5	0.45	other (other)	bacilysin	Bacillus sp. CS93
BGC0001526.4	0.44	other (other)	bartoloside E, bartoloside F, bartoloside G, bartoloside H, bartoloside I, bartoloside J, bartoloside K	Synechocystis salina LEGE 06099
BGC0002150.2	0.42	ribosomal	triculamin	Streptomyces triculaminicus
BGC0002151.2	0.42	ribosomal	alboverticillin	Streptomyces griseocarneus
BGC0001525.3	0.41	other (other)	bartoloside B, bartoloside C, bartoloside D	Synechocystis salina LEGE 06155
BGC0000231.5	0.41	PKS	griseusin A, griseusin B	Streptomyces griseus
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 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: 17.85 out of 20.97

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.06 out of 19.26

Confidence: strong

ToxT

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

Confidence: strong

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.04 out of 26.06

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.38 out of 26.06

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 24.69 out of 27.78

Confidence: strong

ToxT

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

Confidence: strong

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.96 out of 20.97

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.70 out of 28.19

Confidence: medium

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.52 out of 32.93

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.31 out of 24.78

Confidence: medium

Additional weak hits (8):

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.85 out of 39.62

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 26.15 out of 39.62

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.76 out of 30.25

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.98 out of 29.25

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 24.88 out of 31.73

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.50 out of 26.12

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 22.66 out of 26.12

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.88 out of 26.06

Confidence: weak

RREFinder

TFBS Finder

RRE predictions

: RRE type: Ranthipeptide_rSAM_RRE; Location: 0 - 99; Score: 100.2

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
CcpA	Catabolite control protein A
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
LexA variant 2	Repressor of DNA damage response
LexA variant 3	Repressor of DNA damage response
MogR	Repressor of flagellar motility genes
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_JAPDMW010000006.1 - Region 2 - proteusin

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Location: 315,476 - 335,718 nt. (total: 20,243 nt) Show pHMM detection rules used

proteusin: (PoyD or TIGR03793)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

No tailoring functions detected.

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0000513.3	0.42	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000551.5	0.42	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000519.4	0.41	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0001639.3	0.40	ribosomal	klebsidin	Klebsiella pneumoniae
BGC0002698.2	0.40	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0002005.2	0.40	ribosomal	RaxX	Xanthomonas oryzae pv. oryzae
BGC0001887.3	0.39	ribosomal	huazacin	Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0000516.4	0.38	ribosomal	geobacillin II	Geobacillus thermodenitrificans
BGC0002699.2	0.37	ribosomal	nostolysamide A, nostolysamide B	Nostoc punctiforme PCC 73102

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0000513.3	0.42	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000551.5	0.42	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000519.4	0.41	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0001639.3	0.40	ribosomal	klebsidin	Klebsiella pneumoniae
BGC0002698.2	0.40	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0002005.2	0.40	ribosomal	RaxX	Xanthomonas oryzae pv. oryzae
BGC0001887.3	0.39	ribosomal	huazacin	Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0000516.4	0.38	ribosomal	geobacillin II	Geobacillus thermodenitrificans
BGC0002699.2	0.37	ribosomal	nostolysamide A, nostolysamide B	Nostoc punctiforme PCC 73102

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.75 out of 18.57

Confidence: strong

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.28 out of 29.38

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.91 out of 19.26

Confidence: medium

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.63 out of 18.46

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.25 out of 28.19

Confidence: medium

Additional weak hits (16):

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.23 out of 33.73

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.35 out of 25.75

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.74 out of 27.55

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 26.29 out of 32.74

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.16 out of 29.38

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.34 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.43 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.18 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.28 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.55 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.48 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.03 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.78 out of 28.14

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.10 out of 33.14

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 35.63

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.78 out of 28.14

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
FuR variant 1	Ferric Uptake Regulator
RpoN	Regulator of nitrogen assimilation and virulence
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_JAPDMW010000007.1 - Region 1 - NRPS,T1PKS,azole-containing-RiPP,terpene-precursor

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Location: 137,495 - 206,172 nt. (total: 68,678 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))
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)
terpene-precursor: (PT_FPPS_like and not PT_HPP)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Azole RiPPs

NRPS/PKS modules

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

OF778_RS16355: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

Hydrolases: hydrolase

OF778_RS16365: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: ligase synthase synthetase

OF778_RS16240: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

OF778_RS16245: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

OF778_RS16335: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.73	NRPS	enniatin	Fusarium equiseti
BGC0001833.4	0.71	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0000426.5	0.70	NRPS	sevadicin	Paenibacillus larvae
BGC0002135.2	0.70	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001132.4	0.69	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001164.3	0.69	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001825.4	0.69	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001160.5	0.69	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001135.5	0.69	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001133.4	0.68	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0001833.4	0.69	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0000426.5	0.68	NRPS	sevadicin	Paenibacillus larvae
BGC0002135.2	0.68	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001164.3	0.68	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001825.4	0.67	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001160.5	0.67	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001135.5	0.67	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001133.4	0.67	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004

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:

OF778_RS16335: PT_FPPS_like

Domain 1 (535 - 758): 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:

ToxT

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

Confidence: strong

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.94 out of 20.97

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.07 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.38 out of 28.19

Confidence: medium

Additional weak hits (9):

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.71 out of 30.97

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.34 out of 29.25

Confidence: weak

AfsQ1

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

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 25.29 out of 36.54

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.91 out of 30.97

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.65 out of 29.38

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 25.75

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.98 out of 28.14

Confidence: weak

(Thi)azol(in)e containing peptide predictions

No core peptides found.

Module view

Legend

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

RREFinder

Terpene

TFBS Finder

Azole RiPPs

Predicted core structure(s)

For candidate cluster 1, location 137494 - 206172:

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

Polymer prediction:: (fatty_acid - mal - X) + (D-Leu)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 137494 - 192892:

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

Polymer prediction:: (fatty_acid - mal - X) + (D-Leu)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

OF778_RS16240: fatty_acid - mal - X

CAL_domain (35..483): fatty_acid

minowa: fatty_acid

Prediction, score:

fatty_acid: 255.3
NH2: 31.5
shikimic_acid: 0.0
Acetyl-CoA: 0.0
AHBA: 0.0

PKS_AT (1191..1483): mal

ATSignature: Malonyl-CoA, inactive

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 154.4
inactive: 105.2
Methylmalonyl-CoA: 70.1
Methoxymalonyl-CoA: 68.4
Isobutyryl-CoA: 46.8
Propionyl-CoA: 38.9
Ethylmalonyl-CoA: 35.2
CHC-CoA: 31.8
2-Methylbutyryl-CoA: 30.5
Acetyl-CoA: 29.1
trans-1,2-CPDA: 24.4
Benzoyl-CoA: 23.0
3-Methylbutyryl-CoA: 16.7
fatty_acid: 0.0

AMP-binding (2687..3094): 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:: 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:: LSTHFDFSVWEGNQNFGGEINMYGITETTVVSTY
Nearest Stachelhaus code(s):: Val DFWNIGMVVK (76% 8Å match)
Stachelhaus code match:: 90% (moderate)

OF778_RS16245: Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (512..908): Leu

nrpys: Leu

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: LWHAFDASVWEPFLLTGGDFNHYGPSEGTVVSTA
Nearest Stachelhaus code(s):: Leu DAWFLGHVVK (74% 8Å match)
Stachelhaus code match:: 100% (strong)

RRE predictions

: RRE type: Heterocycloanthracin_C_RRE; Location: 1 - 96; Score: 154.8; RRE type: Thiopeptide_F_RRE; Location: 4 - 86; Score: 43.7

Glossary

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

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

Core peptide predictions

No core peptides found.

NZ_JAPDMW010000007.1 - Region 2 - NRPS,T1PKS

Download region SVG

Location: 230,541 - 287,562 nt. (total: 57,022 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

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

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 reductase

OF778_RS16555: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

OF778_RS16595: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

OF778_RS16625: alkyl hydroperoxide reductase subunit

smcogs: SMCOG1176: alkyl hydroperoxide reductase subunit

OF778_RS16650: Halogenation

MITE: MITE0000005Halogenation (identity: 61.30%)
smcogs: SMCOG1103: FAD dependent oxidoreductase

Transferases: methyltransferase oxidoreductase

OF778_RS16545: methyltransferase

smcogs: SMCOG1248: methyltransferase

OF778_RS16650: Halogenation

MITE: MITE0000005Halogenation (identity: 61.30%)
smcogs: SMCOG1103: FAD dependent oxidoreductase

Hydrolases: dehalogenase

OF778_RS16685: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Ligases: ligase synthase

OF778_RS16605: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

OF778_RS16610: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

OF778_RS16615: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.87	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.82	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.78	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.75	NRPS	HC-toxin	Alternaria jesenskae
BGC0001261.3	0.73	NRPS	AM-toxin	Alternaria alternata
BGC0001758.4	0.72	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001128.4	0.72	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.71	NRPS	AbT1	Aureobasidium pullulans
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.69	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.72	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.71	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0001758.4	0.69	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001128.4	0.69	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.68	NRPS	AbT1	Aureobasidium pullulans
BGC0002286.3	0.68	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.26 out of 27.78

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.65 out of 27.78

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.97 out of 27.78

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.22 out of 28.19

Confidence: medium

Additional weak hits (10):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.85 out of 30.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.17 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.22 out of 28.14

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 24.07 out of 30.97

Confidence: weak

CopR

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

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.16 out of 27.55

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.71 out of 33.73

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.78 out of 30.98

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.14 out of 22.40

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.10 out of 30.98

Confidence: weak

Module view

Legend

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 5, location 230540 - 287562:

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

Polymer prediction:: (Dab - Ile - Gly) + (X)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

OF778_RS16605: X

AMP-binding (516..913): X

nrpys: Val, Leu, Ile, Abu, Ival

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: FWYVFDMSVAEGFLLTGGDYEAYGPTECTIASTY
Nearest Stachelhaus code(s):: Leu DIHFVGAIAK (47% 8Å match)
Stachelhaus code match:: 70% (weak)

OF778_RS16615: Dab - Ile - Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (463..871): Dab

nrpys: Dab

SVM prediction details:

Predicted physicochemical class:: N/A
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:: TANAFDVFVGDREAIVSSDINSYGVTEAAIDSSY
Nearest Stachelhaus code(s):: Dab DVGEISSIDK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1512..1907): 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:: N/A
Single AA prediction:: ile (Ile)

Stachelhaus prediction details:

Stachelhaus sequence:: FASSFDGSIFDGVILVGGEKNIYGPTEATVFATY
Nearest Stachelhaus code(s):: Ile DGFFLGVVFK (71% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (2551..2950): 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:: LGITFDIFVLELQTLIGGEFNMYGPTETTVWSTV
Nearest Stachelhaus code(s):: Gly DILQLGMVWK (76% 8Å match)
Stachelhaus code match:: 100% (strong)

TFBS definitions

Regulator	Description
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
ZuR variant 1	Zinc-responsive repressor

NZ_JAPDMW010000007.1 - Region 3 - NRPS

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Location: 299,748 - 344,303 nt. (total: 44,556 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

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

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

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

OF778_RS16805: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase aminotransferase

OF778_RS16790: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

OF778_RS16810: aminotransferase

smcogs: SMCOG1019: aminotransferase

Hydrolases: esterase

OF778_RS16875: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

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

Ligases: ligase

OF778_RS16860: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

OF778_RS16865: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000426.5	0.65	NRPS	sevadicin	Paenibacillus larvae
BGC0001135.5	0.65	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.63	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.63	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2	0.63	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001240.4	0.63	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0000357.5	0.63	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0001825.4	0.62	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001758.4	0.62	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.62	NRPS	icosalide A, icosalide B	Burkholderia gladioli

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000426.5	0.65	NRPS	sevadicin	Paenibacillus larvae
BGC0001135.5	0.65	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.63	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.63	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2	0.63	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001240.4	0.63	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0000357.5	0.63	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0001825.4	0.62	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001758.4	0.62	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.62	NRPS	icosalide A, icosalide B	Burkholderia gladioli

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 26.61 out of 29.38

Confidence: strong

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.49 out of 29.38

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.60 out of 20.97

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.54 out of 27.78

Confidence: medium

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.48 out of 27.55

Confidence: medium

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.63 out of 18.46

Confidence: medium

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.62 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.87 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.21 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.18 out of 28.19

Confidence: medium

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 19.13 out of 20.01

Confidence: strong

AfsR

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

Confidence: medium

Additional weak hits (10):

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.16 out of 36.54

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.86 out of 30.25

Confidence: weak

LuxO

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

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.47 out of 36.54

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.50 out of 26.12

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 22.59 out of 30.97

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.07 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.12 out of 29.38

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.75 out of 33.73

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 21.73 out of 30.97

Confidence: weak

Module view

Legend

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 299747 - 344303:

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

Polymer prediction:: (D-Tyr)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

OF778_RS16865: Tyr

Search NORINE for peptide: strict or relaxed

AMP-binding (466..778): Tyr

nrpys: Tyr

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: TYRIFDGFVATSISTLAGEVIEYGPSENSVVTSI
Nearest Stachelhaus code(s):: Tyr DGTITAEVAK (65% 8Å match); Leu DGAYTGEVVK (65% 8Å match)
Stachelhaus code match:: 80% (moderate)

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
AfsR	Pleiotropic regulatory for antibiotic production
ArgR	Regulator of arginine biosynthesis genes
CcpA	Catabolite control protein A
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1	Ferric Uptake Regulator
GnfM	Regulator of nitrogen-fixation genes
RpoN	Regulator of nitrogen assimilation and virulence
ZuR variant 1	Zinc-responsive repressor

NZ_JAPDMW010000008.1 - Region 1 - NRPS

Download region SVG

Location: 97,623 - 144,357 nt. (total: 46,735 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

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

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

OF778_RS17495: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

OF778_RS17585: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

Transferases: PPTase kinase methyltransferase

OF778_RS17510: glycerol kinase

smcogs: SMCOG1210: glycerol kinase

OF778_RS17520: methyltransferase

smcogs: SMCOG1089: methyltransferase

OF778_RS17565: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1012: 4'-phosphopantetheinyl transferase

Ligases: ligase synthase

OF778_RS17515: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

OF778_RS17560: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Translocases: transporter

OF778_RS17610: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002164.2	0.68	NRPS	peramine	Epichloe festucae
BGC0001135.5	0.67	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.65	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.65	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2	0.64	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001240.4	0.64	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001641.4	0.64	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.62	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.62	NRPS	icosalide A, icosalide B	Burkholderia gladioli

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002164.2	0.68	NRPS	peramine	Epichloe festucae
BGC0001135.5	0.67	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.65	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.65	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2	0.64	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001240.4	0.64	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001641.4	0.64	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.62	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.62	NRPS	icosalide A, icosalide B	Burkholderia gladioli

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

ToxT

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

Confidence: strong

LexA variant 2

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

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.70 out of 26.06

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.08 out of 26.06

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.86 out of 28.19

Confidence: medium

AfsQ1

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

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.03 out of 28.19

Confidence: medium

Additional weak hits (5):

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.64 out of 23.43

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.41 out of 30.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.49 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.86 out of 26.06

Confidence: weak

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.16 out of 29.51

Confidence: weak

Module view

Legend

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 97622 - 144357:

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

Polymer prediction:: (Ile - Val)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

OF778_RS17560: Ile - Val

Search NORINE for peptide: strict or relaxed

AMP-binding (221..614): 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:: LRTGFDASTFEGFLLVGGESNIYGPTENTTFSTS
Nearest Stachelhaus code(s):: Ile DAFFLGITFK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1254..1647): 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:: LNTGFDASTFEGWLLVGGDVNGYGPTENTTFSCC
Nearest Stachelhaus code(s):: Val DAFWLGGTFK (91% 8Å match)
Stachelhaus code match:: 100% (strong)