GCF_006715575.1 - 23 region(s)

Identified secondary metabolite regions using strictness 'relaxed'

NZ_VFNO01000001.1 (Brevibacillus sp. AG162)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 1.1	transAT-PKS,cyclic-lactone-autoinducer,NRPS	89,907	201,325	Low	aurantinin B/aurantinin C/aurantinin D	PKS
Region 1.2	terpene	338,304	360,202
Region 1.3	T3PKS	465,222	506,286
Region 1.4	lanthipeptide-class-i	757,345	781,854
Region 1.5	NRPS,transAT-PKS-like	816,429	876,730
Region 1.6	NRPS,transAT-PKS	893,756	970,702
Region 1.7	NRPS,transAT-PKS	980,020	1,017,032

NZ_VFNO01000002.1 (Brevibacillus sp. AG162)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 2.1	NI-siderophore	24,076	55,787	High	petrobactin	other:other

NZ_VFNO01000003.1 (Brevibacillus sp. AG162)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 3.1	terpene-precursor	234,924	255,826
Region 3.2	azole-containing-RiPP	602,015	625,585
Region 3.3	NRPS	709,215	782,924	Medium	tyrocidine	NRPS:Type I
Region 3.4	opine-like-metallophore	785,703	807,844	High	bacillopaline	other:other
Region 3.5	NRPS	824,437	910,716	High	gramicidin	NRPS:Type I

NZ_VFNO01000005.1 (Brevibacillus sp. AG162)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 5.1	RiPP-like	62,298	73,146
Region 5.2	NRP-metallophore,NRPS	321,364	381,876	High	ulbactin F/ulbactin G	NRPS:Type I

NZ_VFNO01000006.1 (Brevibacillus sp. AG162)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 6.1	RRE-containing	155,160	176,314

NZ_VFNO01000008.1 (Brevibacillus sp. AG162)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 8.1	NRPS	138,781	203,187	Low	pacidamycin 1/pacidamycin 2/pacidamycin 3/pacidamycin 4/pacidamycin 5/pacidamycin 6/pacidamycin 7/pacidamycin D	NRPS:Type I

NZ_VFNO01000009.1 (Brevibacillus sp. AG162)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 9.1	azole-containing-RiPP	202,333	225,886

NZ_VFNO01000010.1 (Brevibacillus sp. AG162)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 10.1	NRPS	1	61,163	Low	scytocyclamide A/scytocyclamide B/scytocyclamide B3/scytocyclamide C/scytocyclamide A2/scytocyclamide B2	NRPS:Type I+PKS
Region 10.2	ectoine	70,117	80,500	High	ectoine	other:ectoine
Region 10.3	lanthipeptide-class-i,NRPS	164,107	201,887	Low	polymyxin	NRPS:Type I

NZ_VFNO01000018.1 (Brevibacillus sp. AG162)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 18.1	NRPS,transAT-PKS	1	48,216

NZ_VFNO01000020.1 (Brevibacillus sp. AG162)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 20.1	NRPS	1	6,867

No secondary metabolite regions were found in these records:: NZ_VFNO01000004.1 (Brevibacillus sp. AG162); NZ_VFNO01000007.1 (Brevibacillus sp. AG162); NZ_VFNO01000011.1 (Brevibacillus sp. AG162); NZ_VFNO01000012.1 (Brevibacillus sp. AG162); NZ_VFNO01000013.1 (Brevibacillus sp. AG162); NZ_VFNO01000014.1 (Brevibacillus sp. AG162); NZ_VFNO01000015.1 (Brevibacillus sp. AG162); NZ_VFNO01000016.1 (Brevibacillus sp. AG162); NZ_VFNO01000017.1 (Brevibacillus sp. AG162); NZ_VFNO01000019.1 (Brevibacillus sp. AG162); NZ_VFNO01000021.1 (Brevibacillus sp. AG162); NZ_VFNO01000022.1 (Brevibacillus sp. AG162); NZ_VFNO01000023.1 (Brevibacillus sp. AG162)

Compact view

NZ_VFNO01000001.1 - Region 1 - NRPS,cyclic-lactone-autoinducer,transAT-PKS

Download region GenBank file

Download region SVG

Location: 89,907 - 201,325 nt. (total: 111,419 nt) Show pHMM detection rules used

transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))
cyclic-lactone-autoinducer: (TIGR04223 or AgrB)
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: oxygenase

FB479_RS00740: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: acetyltransferase acylase methyltransferase

FB479_RS00610: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

FB479_RS00685: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

FB479_RS00695: methyltransferase

smcogs: SMCOG1089: methyltransferase

FB479_RS00720: methyltransferase

smcogs: SMCOG1089: methyltransferase

FB479_RS00790: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: hydrolase

FB479_RS00690: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

FB479_RS00730: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Ligases: ligase synthase

FB479_RS00700: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

FB479_RS00705: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

FB479_RS00710: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

FB479_RS00715: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

FB479_RS00725: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.84	NRPS	enniatin	Fusarium equiseti
BGC0002135.2	0.73	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.69	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
BGC0000307.4	0.65	NRPS	AbT1	Aureobasidium pullulans
BGC0001833.4	0.64	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.61	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	0.61	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.73	NRPS	enniatin	Fusarium equiseti
BGC0002135.2	0.69	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.68	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.66	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.66	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.66	NRPS	AbT1	Aureobasidium pullulans
BGC0001833.4	0.65	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001758.4	0.65	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.64	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	0.64	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:

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 26.53 out of 29.38

Confidence: strong

ToxT

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

Confidence: strong

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.71 out of 20.97

Confidence: medium

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.09 out of 26.33

Confidence: medium

ANR

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

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.60 out of 26.06

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 26.44 out of 28.19

Confidence: strong

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.05 out of 18.16

Confidence: strong

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.03 out of 28.19

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 24.03 out of 24.78

Confidence: strong

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 21.85 out of 25.31

Confidence: strong

Additional weak hits (14):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.73 out of 30.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.99 out of 29.38

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.46 out of 39.62

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.91 out of 26.06

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.69 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 24.66 out of 32.74

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.69 out of 27.55

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.14 out of 33.14

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.27 out of 20.01

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.83 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.88 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.16 out of 26.06

Confidence: weak

ClgR

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

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.12 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 89906 - 201325:

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

Polymer prediction:: (Me-mal - Me-ccmal) + (mal - ccmal - mal) + (Ala - ohmal - ccmal - ccmal - ohmal - mal) + (mal - ccmal) + (OMe-mal - mal) + (NMe-Ser)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

FB479_RS00685: mal - mal

PKS_AT (7..295): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 46.7
inactive: 30.4
Isobutyryl-CoA: 28.3
Methylmalonyl-CoA: 20.5
Methoxymalonyl-CoA: 17.3
Benzoyl-CoA: 9.3
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Propionyl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

PKS_AT (331..610): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 62.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 106.3
inactive: 36.4
Methoxymalonyl-CoA: 29.1
Methylmalonyl-CoA: 23.5
Propionyl-CoA: 17.5
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

FB479_RS00710: Ala

Search NORINE for peptide: strict or relaxed

AMP-binding (500..909): Ala

nrpys: Ala

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: TFLTFDVSLSEGNFMVAGEENIYGPTEASIYAAW
Nearest Stachelhaus code(s):: Ala DVSNMAIIYK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

FB479_RS00725: Ser

Search NORINE for peptide: strict or relaxed

AMP-binding (523..922): 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:: RWMTFDVSVWEWHFICSGEHNLYGPTEAAIDVTY
Nearest Stachelhaus code(s):: Ser DVWHISLIDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
AbrC3	Antibiotic production activator
CatR	H2O2-responsive repressor
CcpA	Catabolite control protein A
FuR variant 1	Ferric Uptake Regulator
LexA variant 2	Repressor of DNA damage response
MogR	Repressor of flagellar motility genes
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_VFNO01000001.1 - Region 2 - terpene

Download region GenBank file

Download region SVG

Location: 338,304 - 360,202 nt. (total: 21,899 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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

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: reductase

FB479_RS01570: alkyl hydroperoxide reductase subunit

smcogs: SMCOG1176: alkyl hydroperoxide reductase subunit

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002173.2	0.47	saccharide, terpene	fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol	Aspergillus fumigatus A1163
BGC0000663.5	0.30	terpene	hopene	Streptomyces coelicolor A3(2)
BGC0001791.4	0.30	NRPS	sunshinamide	Gynuella sunshinyii YC6258
BGC0002675.2	0.28	PKS	prodigiosin	Pseudoalteromonas rubra
BGC0000258.3	0.28	PKS	prodigiosin	Serratia sp.
BGC0002667.2	0.28	ribosomal	estericin A	Clostridium estertheticum
BGC0002386.2	0.27	NRPS, PKS	cyclo(n-Me-L-Leu-L-Val), cyclo(n-Me-L-Leu-L-Leu), cyclo(n-Me-L-Leu-L-Ile)	Sorangium cellulosum So0157-2
BGC0000969.5	0.26	NRPS, PKS	chondramide A	Chondromyces crocatus
BGC0000765.3	0.25	saccharide	exopolysaccharide	Lactobacillus johnsonii
BGC0001591.4	0.25	other (other)	fatty acid enol ester, N-tetradecanoyl tyrosine	uncultured bacterium CSLC2

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002173.2	0.47	saccharide, terpene	fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol	Aspergillus fumigatus A1163
BGC0000663.5	0.30	terpene	hopene	Streptomyces coelicolor A3(2)
BGC0001791.4	0.30	NRPS	sunshinamide	Gynuella sunshinyii YC6258
BGC0002675.2	0.28	PKS	prodigiosin	Pseudoalteromonas rubra
BGC0000258.3	0.28	PKS	prodigiosin	Serratia sp.
BGC0002667.2	0.28	ribosomal	estericin A	Clostridium estertheticum
BGC0002386.2	0.27	NRPS, PKS	cyclo(n-Me-L-Leu-L-Val), cyclo(n-Me-L-Leu-L-Leu), cyclo(n-Me-L-Leu-L-Ile)	Sorangium cellulosum So0157-2
BGC0000969.5	0.26	NRPS, PKS	chondramide A	Chondromyces crocatus
BGC0000765.3	0.25	saccharide	exopolysaccharide	Lactobacillus johnsonii
BGC0001591.4	0.25	other (other)	fatty acid enol ester, N-tetradecanoyl tyrosine	uncultured bacterium CSLC2

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

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

Genes with terpene domains:

FB479_RS01625: T2TS

Domain 1 (2 - 628): Type 2 terpene synthase

Subtype: Squalene substrate

Reactions:: squalene → hopanoid; squalene → polypodane

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

CatR

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

Confidence: medium

Additional weak hits (3):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.16 out of 31.73

Confidence: weak

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.86 out of 29.51

Confidence: weak

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.13 out of 29.72

Confidence: weak

Terpene

TFBS Finder

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
CatR	H2O2-responsive repressor
ToxT	Regulator of MSHA biosynthesis

NZ_VFNO01000001.1 - Region 3 - T3PKS

Download region GenBank file

Download region SVG

Location: 465,222 - 506,286 nt. (total: 41,065 nt) Show pHMM detection rules used

T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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 domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Transferases: glycosyltransferase methyltransferase

FB479_RS02195: glycosyl transferase group 1

smcogs: SMCOG1045: glycosyl transferase group 1

FB479_RS02295: isoprenylcysteine carboxyl methyltransferase

smcogs: SMCOG1150: isoprenylcysteine carboxyl methyltransferase

Hydrolases: peptidase

FB479_RS02250: gamma-glutamyltranspeptidase

smcogs: SMCOG1274: gamma-glutamyltranspeptidase

Lyases: cyclase dehydratase

FB479_RS02255: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

FB479_RS02305: diguanylate cyclase

smcogs: SMCOG1025: diguanylate cyclase

Ligases: synthase

FB479_RS02300: chalcone and stilbene synthase domain protein

smcogs: SMCOG1024: chalcone and stilbene synthase domain protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000282.3	0.68	PKS	2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001831.3	0.54	PKS	alkylpyrone-407, alkylpyrone-393	Myxococcus xanthus DK 1622
BGC0001962.3	0.50	PKS	hierridin B, hierridin C	Cyanobium sp. LEGE 06113
BGC0000779.3	0.47	saccharide	lipopolysaccharide	Aeromonas piscicola
BGC0002332.2	0.45	PKS	4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A	Candidatus Entotheonella sp.
BGC0001647.3	0.39	PKS	lagunapyrone A, lagunapyrone B, lagunapyrone C	Streptomyces sp. MP131-18
BGC0000249.5	0.39	PKS	nogalamycin	Streptomyces nogalater
BGC0001586.3	0.37	saccharide	EPS273	Pseudomonas stutzeri
BGC0001964.2	0.36	PKS	alkylpyrone-407, alkylpyrone-393	Cystobacterineae bacterium
BGC0000763.5	0.36	saccharide	stewartan	Pantoea stewartii subsp. stewartii DC283

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000282.3	0.68	PKS	2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001831.3	0.54	PKS	alkylpyrone-407, alkylpyrone-393	Myxococcus xanthus DK 1622
BGC0001962.3	0.50	PKS	hierridin B, hierridin C	Cyanobium sp. LEGE 06113
BGC0000779.3	0.47	saccharide	lipopolysaccharide	Aeromonas piscicola
BGC0002332.2	0.45	PKS	4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A	Candidatus Entotheonella sp.
BGC0001647.3	0.39	PKS	lagunapyrone A, lagunapyrone B, lagunapyrone C	Streptomyces sp. MP131-18
BGC0000249.5	0.39	PKS	nogalamycin	Streptomyces nogalater
BGC0001586.3	0.37	saccharide	EPS273	Pseudomonas stutzeri
BGC0001964.2	0.36	PKS	alkylpyrone-407, alkylpyrone-393	Cystobacterineae bacterium
BGC0000763.5	0.36	saccharide	stewartan	Pantoea stewartii subsp. stewartii DC283

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

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.86 out of 26.06

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: 23.52 out of 26.06

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.17 out of 27.78

Confidence: medium

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.94 out of 27.55

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.02 out of 23.79

Confidence: medium

Additional weak hits (6):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.18 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.46 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.49 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.61 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.12 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.48 out of 30.25

Confidence: weak

Detailed domain annotation

Selected features only

Show module domains

TFBS Finder

TFBS definitions

Regulator	Description
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
GnfM	Regulator of nitrogen-fixation genes
IolR	Regulator of the inositol catabolism
MogR	Repressor of flagellar motility genes
ToxT	Regulator of MSHA biosynthesis

NZ_VFNO01000001.1 - Region 4 - lanthipeptide-class-i

Download region GenBank file

Download region SVG

Location: 757,345 - 781,854 nt. (total: 24,510 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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

Lanthipeptides

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

Lyases: cyclase dehydratase

FB479_RS03790: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

FB479_RS03795: Lanthionine synthetase C family protein

smcogs: SMCOG1140: Lanthionine synthetase C family protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.76	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0000542.3	0.59	ribosomal	paenicidin B	Paenibacillus terrae
BGC0000541.5	0.59	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0001289.5	0.57	ribosomal	penisin	Paenibacillus ehimensis
BGC0002640.2	0.56	ribosomal	thalassomonasin A, thalassomonasin B	Thalassomonas actiniarum
BGC0000560.5	0.53	ribosomal	subtilomycin	Bacillus subtilis
BGC0002323.2	0.51	ribosomal	nisin J	Staphylococcus capitis
BGC0000515.4	0.50	ribosomal	geobacillin I	Geobacillus thermodenitrificans NG80-2
BGC0000556.5	0.49	ribosomal	streptin	Streptococcus pyogenes
BGC0000506.4	0.49	ribosomal	entianin	Bacillus subtilis subsp. spizizenii

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.76	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0000542.3	0.59	ribosomal	paenicidin B	Paenibacillus terrae
BGC0000541.5	0.59	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0001289.5	0.57	ribosomal	penisin	Paenibacillus ehimensis
BGC0002640.2	0.56	ribosomal	thalassomonasin A, thalassomonasin B	Thalassomonas actiniarum
BGC0000560.5	0.53	ribosomal	subtilomycin	Bacillus subtilis
BGC0002323.2	0.51	ribosomal	nisin J	Staphylococcus capitis
BGC0000515.4	0.50	ribosomal	geobacillin I	Geobacillus thermodenitrificans NG80-2
BGC0000556.5	0.49	ribosomal	streptin	Streptococcus pyogenes
BGC0000506.4	0.49	ribosomal	entianin	Bacillus subtilis subsp. spizizenii

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptides - No core peptides found.

Transcription Factor Binding Sites

Binding sites found:

FuR variant 1

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

Confidence: strong

ToxT

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

Confidence: strong

ToxT

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

Confidence: strong

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.68 out of 29.38

Confidence: medium

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.23 out of 29.38

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.70 out of 26.06

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.52 out of 26.06

Confidence: medium

CRP

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

Confidence: strong

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.95 out of 20.97

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 28.19

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.07 out of 18.16

Confidence: strong

Additional weak hits (8):

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.91 out of 32.74

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.69 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.25 out of 30.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.75 out of 26.06

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.13 out of 25.88

Confidence: weak

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 20.51 out of 29.51

Confidence: weak

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 18.76 out of 30.12

Confidence: weak

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 19.98 out of 30.12

Confidence: weak

Lanthipeptides

RREFinder

TFBS Finder

Core peptide predictions

No core peptides found.

RRE predictions

: RRE type: Lanthipeptide_LanB_RRE; Location: 159 - 252; Score: 50.6

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
CRP	Cyclic AMP receptor protein
CcpA	Catabolite control protein A
FuR variant 1	Ferric Uptake Regulator
MogR	Repressor of flagellar motility genes
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_VFNO01000001.1 - Region 5 - NRPS,transAT-PKS-like

Download region GenBank file

Download region SVG

Location: 816,429 - 876,730 nt. (total: 60,302 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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 oxidoreductase

FB479_RS04030: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

FB479_RS04105: dihydropteridine reductase

smcogs: SMCOG1159: dihydropteridine reductase

FB479_RS04140: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

FB479_RS04175: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

Transferases: aminotransferase sulfhydrylase

FB479_RS04045: O-succinylhomoserine sulfhydrylase

smcogs: SMCOG1168: O-succinylhomoserine sulfhydrylase

FB479_RS04180: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Hydrolases: protease

FB479_RS04165: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

Ligases: ligase synthase

FB479_RS04115: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

FB479_RS04120: 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	0.77	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.73	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.71	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001833.4	0.69	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.69	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.69	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001133.4	0.68	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001128.4	0.67	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.71	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.68	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.68	NRPS	HC-toxin	Alternaria jesenskae
BGC0001833.4	0.68	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.67	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001133.4	0.67	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001128.4	0.67	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters 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: 18.15 out of 20.97

Confidence: medium

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 24.25 out of 26.33

Confidence: strong

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.83 out of 27.78

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.05 out of 28.19

Confidence: medium

Additional weak hits (9):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.13 out of 30.22

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.34 out of 30.25

Confidence: weak

ClgR

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.51 out of 26.06

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.90 out of 25.88

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.12 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.83 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.18 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.42 out of 28.14

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 6, location 816428 - 876730:

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

Polymer prediction:: (fatty_acid - mal - Orn - D-X) + (Phe)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

FB479_RS04115: fatty_acid - Orn - X

Search NORINE for peptide: strict or relaxed

CAL_domain (34..480): fatty_acid

minowa: fatty_acid

Prediction, score:

fatty_acid: 245.8
NH2: 37.6
Acetyl-CoA: 8.1
shikimic_acid: 0.0
AHBA: 0.0

AMP-binding (3089..3490): 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:: VTWAFDVFAGDRESILGSDINSYGVTEAAIDSSY
Nearest Stachelhaus code(s):: Orn DVGEIGSIDK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4135..4535): X

nrpys: Asp, Asn, Glu, Gln, Aad

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: RWMTYDSAIWQWDFIIGGETNLYGPTEASIGCIA
Nearest Stachelhaus code(s):: Glu DVWHIGSIGK (62% 8Å match); Orn DVWNIGLIHK (56% 8Å match)
Stachelhaus code match:: 70% (weak)

FB479_RS04120: Phe

Search NORINE for peptide: strict or relaxed

AMP-binding (469..862): 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:: LFFAFDASVWEMTLITAGSINAYGPTETTICATT
Nearest Stachelhaus code(s):: Phe DAWTIAAICK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
CcpA	Catabolite control protein A
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
ZuR variant 1	Zinc-responsive repressor

NZ_VFNO01000001.1 - Region 6 - NRPS,transAT-PKS

Download region GenBank file

Download region SVG

Location: 893,756 - 970,702 nt. (total: 76,947 nt) Show pHMM detection rules used

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

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 oxidoreductase

FB479_RS04480: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

FB479_RS04495: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: acylase aminotransferase phosphorylase

FB479_RS04285: thiamine-phosphate pyrophosphorylase

smcogs: SMCOG1280: thiamine-phosphate pyrophosphorylase

FB479_RS04290: thiamine-phosphate pyrophosphorylase

smcogs: SMCOG1280: thiamine-phosphate pyrophosphorylase

FB479_RS04410: aminotransferase

smcogs: SMCOG1019: aminotransferase

FB479_RS04435: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: deaminase hydrolase

FB479_RS04460: ornithine cyclodeaminase

smcogs: SMCOG1158: ornithine cyclodeaminase

FB479_RS04470: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

FB479_RS04515: isochorismatase

smcogs: SMCOG1027: isochorismatase

FB479_RS04525: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: ligase synthase

FB479_RS04395: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS04405: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS04415: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS04420: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS04425: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

FB479_RS04430: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

FB479_RS04440: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

FB479_RS04455: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.88	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.87	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001249.5	0.83	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001261.3	0.82	NRPS	AM-toxin	Alternaria alternata
BGC0001758.4	0.80	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.79	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.79	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.77	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.77	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.76	NRPS	HC-toxin	Alternaria jesenskae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.75	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001261.3	0.73	NRPS	AM-toxin	Alternaria alternata
BGC0001758.4	0.72	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.71	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.71	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001133.4	0.70	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CcpA

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

Confidence: strong

ToxT

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

Confidence: strong

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.52 out of 27.78

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 19.78 out of 20.97

Confidence: strong

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.31 out of 28.19

Confidence: medium

Additional weak hits (8):

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.12 out of 20.47

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

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.49 out of 21.55

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.88 out of 39.62

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.40 out of 30.98

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 24.41 out of 35.63

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.06 out of 20.01

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.65 out of 29.25

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 7, location 893755 - 970702:

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

Polymer prediction:: (D-Asn) + (X) + (X - X) + (X) + (Me-ohmal - Gly) + (mal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

FB479_RS04395: Asn

Search NORINE for peptide: strict or relaxed

AMP-binding (466..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:: YWASFDLTVTSCKLIVGGELNEYGPTETVVGCMI
Nearest Stachelhaus code(s):: Asn DLTKIGEVGK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

FB479_RS04405: X

AMP-binding (470..865): X

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

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: AWHAFDASVVECLVLCTGEYNLYGPTENSISASG
Nearest Stachelhaus code(s):: Hpg DAVHLGLLCK (47% 8Å match)
Stachelhaus code match:: 60% (weak)

FB479_RS04415: X

AMP-binding (45..463): X

nrpys: Asp, Asn, Glu, Gln, Aad

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: TWLTFTDSVWEWQFFNGGEANIYGMTESAIYASV
Nearest Stachelhaus code(s):: Gln DAWQFGLIDK (59% 8Å match)
Stachelhaus code match:: 60% (weak)

FB479_RS04420: X

AMP-binding (275..693): 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:: HAKAFDISVWQSEVAVTGEVNMYGPTEASDDITH
Nearest Stachelhaus code(s):: Dpr DIWEVTADDK (91% 8Å match); Dab DIWELTADDK (65% 8Å match)
Stachelhaus code match:: 80% (moderate)

FB479_RS04425: X

AMP-binding (276..677): X

nrpys: Ser, Thr, Dhpg, Hpg

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: RWMTYDSSVWQWDFILGGETNLYGPTETSIGVIY
Nearest Stachelhaus code(s):: Glu DVWHIGSIGK (71% 8Å match); Orn DVWNIGLIHK (59% 8Å match)
Stachelhaus code match:: 70% (weak)

FB479_RS04430: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (2094..2487): 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:: FGITFDIFLLEVQLLIGGEYNLYGPTETTIWSTV
Nearest Stachelhaus code(s):: Gly DILQLGLIWK (79% 8Å match)
Stachelhaus code match:: 100% (strong)

FB479_RS04435: mal

PKS_AT (6..287): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 108.8
Methoxymalonyl-CoA: 46.1
Methylmalonyl-CoA: 38.6
inactive: 32.5
Propionyl-CoA: 26.1
2-Methylbutyryl-CoA: 9.1
Ethylmalonyl-CoA: 9.0
fatty_acid: 8.4
Acetyl-CoA: 8.2
trans-1,2-CPDA: 0.0
Isobutyryl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_VFNO01000001.1 - Region 7 - NRPS,transAT-PKS

Download region GenBank file

Download region SVG

Location: 980,020 - 1,017,032 nt. (total: 37,013 nt) Show pHMM detection rules used

Region on contig edge.

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

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 oxidoreductase

FB479_RS04610: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

FB479_RS04740: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

Transferases: acetyltransferase acylase

FB479_RS04615: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

FB479_RS04745: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase

FB479_RS04730: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: ligase synthase

FB479_RS04725: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS04750: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

FB479_RS04755: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.62	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001273.3	0.61	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.61	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.61	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002135.2	0.61	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.60	NRPS	AM-toxin	Alternaria alternata
BGC0000307.4	0.59	NRPS	AbT1	Aureobasidium pullulans
BGC0001250.4	0.59	NRPS	epichloenin A	Epichloe festucae
BGC0001251.4	0.59	NRPS	epichloenin A	Epichloe festucae
BGC0001268.4	0.59	NRPS, PKS	fusarin C	Fusarium fujikuroi

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.64	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.64	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.64	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002135.2	0.64	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.63	NRPS	AM-toxin	Alternaria alternata
BGC0000307.4	0.63	NRPS	AbT1	Aureobasidium pullulans
BGC0001250.4	0.63	NRPS	epichloenin A	Epichloe festucae
BGC0001251.4	0.63	NRPS	epichloenin A	Epichloe festucae
BGC0001268.4	0.63	NRPS, PKS	fusarin C	Fusarium fujikuroi

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: 20.95 out of 27.78

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 24.00 out of 24.78

Confidence: strong

Additional weak hits (7):

FuR variant 1

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

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.86 out of 31.73

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.10 out of 31.73

Confidence: weak

LuxO

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

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.69 out of 27.55

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.26 out of 35.63

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.08 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 8, location 980019 - 1017032:

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

Polymer prediction:: (D-Asn) + (ohmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

FB479_RS04725: Asn

Search NORINE for peptide: strict or relaxed

AMP-binding (462..853): 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:: YWATFDLTVTSPKTIVGGEFNEYGPTETVVGCMF
Nearest Stachelhaus code(s):: Asn DLTKIGEVGK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

FB479_RS04745: mal

PKS_AT (6..286): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 103.7
Methoxymalonyl-CoA: 39.8
Methylmalonyl-CoA: 33.8
inactive: 16.3
Isobutyryl-CoA: 12.6
Benzoyl-CoA: 12.5
Propionyl-CoA: 12.0
CHC-CoA: 8.7
Acetyl-CoA: 8.5
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Ethylmalonyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

FB479_RS04755: Ser

Search NORINE for peptide: strict or relaxed

AMP-binding (275..571): 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:: RWMTFDVSVWEWHFFTSGEVNLYGPTEATVDVSF
Nearest Stachelhaus code(s):: Ser DVWHFSLVDK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
LexA variant 2	Repressor of DNA damage response

NZ_VFNO01000002.1 - Region 1 - NI-siderophore

Download region GenBank file

Download region SVG

Location: 24,076 - 55,787 nt. (total: 31,712 nt) Show pHMM detection rules used

NI-siderophore: IucA_IucC

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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

Isomerases: mutase

FB479_RS04925: phosphoglycerate mutase

smcogs: SMCOG1101: phosphoglycerate mutase

Ligases: ligase

FB479_RS04950: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000942.4	0.80	other (other)	petrobactin	Bacillus anthracis str. Ames
BGC0002469.2	0.50	other (other)	woodybactin A, woodybactin B, woodybactin C, woodybactin D	Shewanella woodyi ATCC 51908
BGC0002692.2	0.50	other (other)	speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B	Kribbella speibonae
BGC0000295.5	0.50	NRPS	acinetoferrin	Acinetobacter haemolyticus
BGC0001572.3	0.49	other (other)	desferrioxamine E	Pantoea agglomerans
BGC0001499.5	0.48	other (other)	aerobactin	Pantoea ananatis
BGC0002694.2	0.48	other (other)	roseobactin	Phaeobacter inhibens 2.10
BGC0001713.5	0.47	other (other)	ochrobactin	Ochrobactrum anthropi
BGC0002683.2	0.47	NRPS	schizokinen	Nostoc sp. PCC 7120 = FACHB-418
BGC0002633.2	0.47	other (other)	schizokinen	Leptolyngbya sp. PCC 7376

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000942.4	0.80	other (other)	petrobactin	Bacillus anthracis str. Ames
BGC0002469.2	0.50	other (other)	woodybactin A, woodybactin B, woodybactin C, woodybactin D	Shewanella woodyi ATCC 51908
BGC0002692.2	0.50	other (other)	speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B	Kribbella speibonae
BGC0000295.5	0.50	NRPS	acinetoferrin	Acinetobacter haemolyticus
BGC0001572.3	0.49	other (other)	desferrioxamine E	Pantoea agglomerans
BGC0001499.5	0.48	other (other)	aerobactin	Pantoea ananatis
BGC0002694.2	0.48	other (other)	roseobactin	Phaeobacter inhibens 2.10
BGC0001713.5	0.47	other (other)	ochrobactin	Ochrobactrum anthropi
BGC0002683.2	0.47	NRPS	schizokinen	Nostoc sp. PCC 7120 = FACHB-418
BGC0002633.2	0.47	other (other)	schizokinen	Leptolyngbya sp. PCC 7376

Similar known clusters from MIBiG 4.0

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: 23.85 out of 29.38

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.27 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.11 out of 28.19

Confidence: medium

Additional weak hits (6):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.25 out of 31.73

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.73 out of 30.25

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.90 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.80 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.57 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.70 out of 29.38

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
FuR variant 1	Ferric Uptake Regulator
ZuR variant 1	Zinc-responsive repressor

NZ_VFNO01000003.1 - Region 1 - terpene-precursor

Download region GenBank file

Download region SVG

Location: 234,924 - 255,826 nt. (total: 20,903 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

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

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

FB479_RS11035: acetyl-CoA carboxylase biotin carboxylase

smcogs: SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Ligases: synthase synthetase

FB479_RS11080: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

FB479_RS11090: 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
BGC0000639.3	0.38	terpene	carotenoid	Enterobacteriaceae bacterium DC260
BGC0000642.3	0.37	terpene	carotenoid	Enterobacteriaceae bacterium DC413
BGC0001911.3	0.37	terpene	raimonol	Streptomyces anulatus
BGC0000665.5	0.37	other (other), terpene	xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C	Streptomyces sp. HKI0576
BGC0000668.5	0.36	other (other), terpene	12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole	Hapalosiphon welwitschii UTEX B 1830

Reference	Similarity score	Type	Compound(s)	Organism
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
BGC0000639.3	0.38	terpene	carotenoid	Enterobacteriaceae bacterium DC260
BGC0000642.3	0.37	terpene	carotenoid	Enterobacteriaceae bacterium DC413
BGC0001911.3	0.37	terpene	raimonol	Streptomyces anulatus
BGC0000665.5	0.37	other (other), terpene	xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C	Streptomyces sp. HKI0576
BGC0000668.5	0.36	other (other), terpene	12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole	Hapalosiphon welwitschii UTEX B 1830

Similar known clusters 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:

FB479_RS11080: PT_FPPS_like

Domain 1 (35 - 300): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:: DMAPP, IPP → FPP

Transcription Factor Binding Sites

Binding sites found:

ZuR variant 1

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

Confidence: medium

Additional weak hits (2):

ANR

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

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.87 out of 29.65

Confidence: weak

Terpene

TFBS Finder

Glossary

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

TFBS definitions

Regulator	Description
ZuR variant 1	Zinc-responsive repressor

NZ_VFNO01000003.1 - Region 2 - azole-containing-RiPP

Download region GenBank file

Download region SVG

Location: 602,015 - 625,585 nt. (total: 23,571 nt) Show pHMM detection rules used

azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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

Azole RiPPs

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 aminotransferase

FB479_RS12910: aminotransferase class V

smcogs: SMCOG1139: aminotransferase class V

FB479_RS12915: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: dehalogenase

FB479_RS12850: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000849.4	0.47	other (butyrolactone)	SCB1, SCB2, SCB3	Streptomyces coelicolor A3(2)
BGC0001174.4	0.45	ribosomal	corynazolicin	Corynebacterium urealyticum DSM 7111
BGC0000569.5	0.43	ribosomal	plantazolicin	Bacillus velezensis FZB42
BGC0001146.5	0.43	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0000607.5	0.42	ribosomal	micrococcin P1	Macrococcus caseolyticus
BGC0001940.3	0.42	PKS	pyxidicycline A, pyxidicycline B	Pyxidicoccus fallax
BGC0000610.5	0.42	ribosomal	nosiheptide	Streptomyces actuosus
BGC0000925.5	0.42	other (other)	quinolobactin	Pseudomonas fluorescens
BGC0002285.2	0.41	ribosomal	aborycin	Streptomyces sp. ZS0098
BGC0002116.3	0.41	ribosomal	darobactin A	Photorhabdus khanii HGB 1456

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000849.4	0.47	other (butyrolactone)	SCB1, SCB2, SCB3	Streptomyces coelicolor A3(2)
BGC0001174.4	0.45	ribosomal	corynazolicin	Corynebacterium urealyticum DSM 7111
BGC0000569.5	0.43	ribosomal	plantazolicin	Bacillus velezensis FZB42
BGC0001146.5	0.43	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0000607.5	0.42	ribosomal	micrococcin P1	Macrococcus caseolyticus
BGC0001940.3	0.42	PKS	pyxidicycline A, pyxidicycline B	Pyxidicoccus fallax
BGC0000610.5	0.42	ribosomal	nosiheptide	Streptomyces actuosus
BGC0000925.5	0.42	other (other)	quinolobactin	Pseudomonas fluorescens
BGC0002285.2	0.41	ribosomal	aborycin	Streptomyces sp. ZS0098
BGC0002116.3	0.41	ribosomal	darobactin A	Photorhabdus khanii HGB 1456

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.54 out of 26.33

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16

Confidence: strong

Additional weak hits (3):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 26.36 out of 31.73

Confidence: weak

LexA variant 2

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

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.31 out of 25.88

Confidence: weak

(Thi)azol(in)e containing peptide predictions

No core peptides found.

RREFinder

TFBS Finder

Azole RiPPs

RRE predictions

: RRE type: Heterocycloanthracin_C_RRE; Location: 0 - 99; Score: 135.6; RRE type: Thiopeptide_F_RRE; Location: 7 - 88; Score: 43.0

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
AbrC3	Antibiotic production activator

Core peptide predictions

No core peptides found.

NZ_VFNO01000003.1 - Region 3 - NRPS

Download region GenBank file

Download region SVG

Location: 709,215 - 782,924 nt. (total: 73,710 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

Transferases: PPTase

FB479_RS13435: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: esterase hydrolase

FB479_RS13440: thioesterase

smcogs: SMCOG1004: thioesterase

FB479_RS13470: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

FB479_RS13505: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: ligase

FB479_RS13410: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS13415: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS13420: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000452.5	0.78	NRPS	tyrocidine	Brevibacillus brevis NBRC 100599
BGC0000426.5	0.76	NRPS	sevadicin	Paenibacillus larvae
BGC0001758.4	0.75	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001128.4	0.74	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.74	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001825.4	0.73	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001135.5	0.73	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000452.5	0.78	NRPS	tyrocidine	Brevibacillus brevis NBRC 100599
BGC0000426.5	0.76	NRPS	sevadicin	Paenibacillus larvae
BGC0001758.4	0.75	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001128.4	0.74	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.74	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001825.4	0.73	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001135.5	0.73	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis

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: 20.95 out of 27.78

Confidence: medium

NtrC

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

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.60 out of 26.06

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.25 out of 20.97

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.72 out of 20.97

Confidence: medium

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 23.01 out of 27.18

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.09 out of 20.47

Confidence: medium

Additional weak hits (9):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.00 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.74 out of 30.25

Confidence: weak

MogR

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.14 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.96 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.66 out of 26.06

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.31 out of 25.75

Confidence: weak

CopR

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

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.80 out of 31.73

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 3, location 709214 - 782924:

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

Polymer prediction:: (D-Phe) + (Pro - Phe - D-Leu) + (Asn - Gln - Tyr - Val - Orn - Leu)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

FB479_RS13410: Phe

Search NORINE for peptide: strict or relaxed

AMP-binding (37..430): 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:: LFFAFDASVWEMTLITAGSVNAYGPTETSICATI
Nearest Stachelhaus code(s):: Phe DAWTIAAICK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

FB479_RS13415: Pro - Phe - Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (472..870): 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:: LFTTFDVCYQESSLITAGEHNHYGPSETHVVTTY
Nearest Stachelhaus code(s):: Pro DVQSIAHVVK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1512..1906): Phe

nrpys: Phe

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: SWNLFDAFALTAVCMLGGEINAYGPTESSVIATY
Nearest Stachelhaus code(s):: Phe DALVMGAVIK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2550..2944): 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:: CWRFFDGFVASAYGSLGGENNEYGPTENSVVSTI
Nearest Stachelhaus code(s):: Leu DGAYTGEVVK (94% 8Å match)
Stachelhaus code match:: 90% (moderate)

FB479_RS13420: Asn - Gln - Tyr - Val - Orn - Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (477..870): 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:: YWASFDLTVTSTKLIVGGEFNEYGPTETVVGCMI
Nearest Stachelhaus code(s):: Asn DLTKIGEVGK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1512..1907): Gln

nrpys: Gln

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: HWMTFDASVWELQMLCGGEINLYGPTESTIDATY
Nearest Stachelhaus code(s):: Gln DAWQFGLIDK (97% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (2549..2945): 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:: SWKLFDGFVLSTTCTLGGEVNEYGPTESSVVATW
Nearest Stachelhaus code(s):: Tyr DGLTTGEVVK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3589..3982): 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:: LNTGFDAMTFEGWLIVGGEWNGYGPTENTTFSTC
Nearest Stachelhaus code(s):: Val DAFWIGGTFK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4624..5026): 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:: VAWAFDVSTGDREAILGADINSYGVTEACIDSSY
Nearest Stachelhaus code(s):: Orn DVGEIGSIDK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (5670..6067): 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:: CWRFFDGFVASAYGTLGGENNEYGPTENSVVTTI
Nearest Stachelhaus code(s):: Leu DGAYTGEVVK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
MogR	Repressor of flagellar motility genes
NrdR	Represses ribonucleotide reductase encoding genes
NtrC	Nitrogen regulatory protein C
VqsM	Regulator of quorum-sensing signalling systems

NZ_VFNO01000003.1 - Region 4 - opine-like-metallophore

Download region GenBank file

Download region SVG

Location: 785,703 - 807,844 nt. (total: 22,142 nt) Show pHMM detection rules used

opine-like-metallophore: (CntL and CntM)

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

No tailoring functions detected.

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002488.3	0.84	other (other)	bacillopaline	Paenibacillus mucilaginosus KNP414
BGC0002487.3	0.79	other (other)	staphylopine	Staphylococcus aureus subsp. aureus Mu50
BGC0002489.2	0.52	other (other)	pseudopaline	Pseudomonas aeruginosa PAO1
BGC0002490.2	0.50	other (other)	yersinopine	Yersinia pestis CO92
BGC0002698.2	0.45	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0000513.3	0.41	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000501.3	0.40	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0000504.5	0.40	ribosomal	cytolysin ClyLl, cytolysin ClyLs	Plasmid pAD1
BGC0000528.5	0.40	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000552.3	0.39	ribosomal	SmbA, SmbB	Streptococcus mutans

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002488.3	0.84	other (other)	bacillopaline	Paenibacillus mucilaginosus KNP414
BGC0002487.3	0.79	other (other)	staphylopine	Staphylococcus aureus subsp. aureus Mu50
BGC0002489.2	0.52	other (other)	pseudopaline	Pseudomonas aeruginosa PAO1
BGC0002490.2	0.50	other (other)	yersinopine	Yersinia pestis CO92
BGC0002698.2	0.45	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0000513.3	0.41	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000501.3	0.40	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0000504.5	0.40	ribosomal	cytolysin ClyLl, cytolysin ClyLs	Plasmid pAD1
BGC0000528.5	0.40	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000552.3	0.39	ribosomal	SmbA, SmbB	Streptococcus mutans

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ANR

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

Confidence: medium

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.45 out of 26.33

Confidence: medium

Additional weak hits (3):

AfsQ1

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

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.32 out of 23.43

Confidence: weak

HipB

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

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator

NZ_VFNO01000003.1 - Region 5 - NRPS

Download region GenBank file

Download region SVG

Location: 824,437 - 910,716 nt. (total: 86,280 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

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: electron transfer oxygenase

FB479_RS13745: flavodoxin

smcogs: SMCOG1134: flavodoxin

FB479_RS13800: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

Hydrolases: deacetylase esterase hydrolase

FB479_RS13720: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

FB479_RS13725: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

FB479_RS13805: acetylornithine deacetylase

smcogs: SMCOG1247: acetylornithine deacetylase

FB479_RS13830: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

FB479_RS13925: thioesterase

smcogs: SMCOG1004: thioesterase

Ligases: ligase

FB479_RS13795: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

FB479_RS13945: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS13950: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000342.4	0.71	NRPS	enniatin	Fusarium equiseti
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0001825.4	0.69	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001135.5	0.68	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.68	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.66	NRPS	HC-toxin	Alternaria jesenskae
BGC0001128.4	0.66	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.65	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.72	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0000367.5	0.71	NRPS	gramicidin	Brevibacillus brevis NBRC 100599
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4	0.71	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001132.4	0.70	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001135.5	0.70	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001825.4	0.70	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:

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.87 out of 26.85

Confidence: medium

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.93 out of 27.55

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.28 out of 27.78

Confidence: medium

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 24.10 out of 29.25

Confidence: medium

Additional weak hits (8):

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.93 out of 33.73

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.18 out of 29.38

Confidence: weak

HipB

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

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.48 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.50 out of 28.14

Confidence: weak

HipB

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

Confidence: weak

ANR

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

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.74 out of 28.14

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 5, location 824436 - 910716:

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

Polymer prediction:: (Ala - D-Leu - Ala) + (X - D-Gly) + (Pro - D-Lys - Phe)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 824436 - 876457:

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

Polymer prediction:: (Pro - D-Lys - Phe)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 871300 - 910716:

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

Polymer prediction:: (X - D-Gly) + (Ala - D-Leu - Ala)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

FB479_RS13795: Pro - Lys - Phe

Search NORINE for peptide: strict or relaxed

AMP-binding (467..870): 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:: LWQAFDVCYQESYFIVAGEHNHYGPSETHVVTAL
Nearest Stachelhaus code(s):: Pro DVQYIAHVVK (85% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1512..1911): Lys

nrpys: Lys

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:: MAWAFDVFTGDRDTVIGADLNSYGVTETCIDACY
Nearest Stachelhaus code(s):: Lys DVGDVGSIDK (79% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3027..3417): 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:: LLFAFDAAVWEQTLITAGSFNAYGPTEDSIATTI
Nearest Stachelhaus code(s):: Phe DAWTIAAIAK (76% 8Å match)
Stachelhaus code match:: 100% (strong)

FB479_RS13945: X - Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (207..593): X

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

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: FWHSFDGSVLEPFFLTGGDYNLYGPTECTIAATI
Nearest Stachelhaus code(s):: Gly DILQLGLIWK (53% 8Å match)
Stachelhaus code match:: 70% (weak)

AMP-binding (1228..1625): 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:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: VAMTFDISVAEGNFLACGEENIYGPTEATIYTSR
Nearest Stachelhaus code(s):: Gly DIANLCIIYK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

FB479_RS13950: Ala - Leu - Ala

Search NORINE for peptide: strict or relaxed

AMP-binding (450..847): Ala

nrpys: Ala

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: QALTFDVSVAEGNFMAAGEENIYGPTEATIYASC
Nearest Stachelhaus code(s):: Ala DVANFAIIYK (85% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1513..1907): 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:: LWHAFDASVWEPFLLTGGDVNQYGPTENTVVATA
Nearest Stachelhaus code(s):: Leu DAWFLGQVVK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3030..3423): Ala

nrpys: Ala

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: FWATFDLSVYEVNTNLAGEFNLYGPSEDTTYSTY
Nearest Stachelhaus code(s):: Ala DLYNNALTYK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
GnfM	Regulator of nitrogen-fixation genes
RutR	Regulator of the pyrimidine and purine metabolism
SypG	Regulator of biofilm formation and host colonization

NZ_VFNO01000005.1 - Region 1 - RiPP-like

Download region GenBank file

Download region SVG

Location: 62,298 - 73,146 nt. (total: 10,849 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

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

Transferases: aminotransferase

FB479_RS16625: aminotransferase

smcogs: SMCOG1019: aminotransferase

FB479_RS16635: aminotransferase

smcogs: SMCOG1019: aminotransferase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000902.4	0.42	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0001184.4	0.39	other (other)	bacilysin	Bacillus velezensis FZB42
BGC0000285.5	0.34	PKS, saccharide	flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin	Saccharopolyspora erythraea
BGC0000306.5	0.31	NRPS	arylomycin	Streptomyces filamentosus NRRL 11379
BGC0000721.4	0.29	saccharide	tobramycin	Streptoalloteichus tenebrarius
BGC0000395.5	0.29	NRPS	nocardicin A	Nocardia uniformis subsp. tsuyamanensis
BGC0001964.2	0.28	PKS	alkylpyrone-407, alkylpyrone-393	Cystobacterineae bacterium
BGC0000993.4	0.26	NRPS, PKS	FR901228	Chromobacterium violaceum
BGC0001230.5	0.26	NRPS, PKS	salinamide A, salinamide B, salinamide C, salinamide D, salinamide E, salinamide F, desmethylsalinamide C, desmethylsalinamide E	Streptomyces sp. CNB091
BGC0000388.5	0.26	NRPS	mannopeptimycin	Streptomyces hygroscopicus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000902.4	0.42	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0001184.4	0.39	other (other)	bacilysin	Bacillus velezensis FZB42
BGC0000285.5	0.34	PKS, saccharide	flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin	Saccharopolyspora erythraea
BGC0000306.5	0.31	NRPS	arylomycin	Streptomyces filamentosus NRRL 11379
BGC0000721.4	0.29	saccharide	tobramycin	Streptoalloteichus tenebrarius
BGC0000395.5	0.29	NRPS	nocardicin A	Nocardia uniformis subsp. tsuyamanensis
BGC0001964.2	0.28	PKS	alkylpyrone-407, alkylpyrone-393	Cystobacterineae bacterium
BGC0000993.4	0.26	NRPS, PKS	FR901228	Chromobacterium violaceum
BGC0001230.5	0.26	NRPS, PKS	salinamide A, salinamide B, salinamide C, salinamide D, salinamide E, salinamide F, desmethylsalinamide C, desmethylsalinamide E	Streptomyces sp. CNB091
BGC0000388.5	0.26	NRPS	mannopeptimycin	Streptomyces hygroscopicus

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: 18.57 out of 18.57

Confidence: strong

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 28.43 out of 29.38

Confidence: strong

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.47 out of 29.38

Confidence: medium

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.03 out of 29.38

Confidence: medium

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.26 out of 29.38

Confidence: medium

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.13 out of 29.38

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.87 out of 27.78

Confidence: medium

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.25 out of 29.38

Confidence: medium

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.34 out of 29.38

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.53 out of 28.19

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.74 out of 24.78

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.75 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.27 out of 28.19

Confidence: medium

Additional weak hits (8):

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.98 out of 29.25

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.73 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.64 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

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.38 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.39 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.88 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.38 out of 32.74

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1	Ferric Uptake Regulator
LexA variant 2	Repressor of DNA damage response
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_VFNO01000005.1 - Region 2 - NRP-metallophore,NRPS

Download region GenBank file

Download region SVG

Location: 321,364 - 381,876 nt. (total: 60,513 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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

Transferases: PPTase aminotransferase kinase

FB479_RS17825: aminotransferase

smcogs: SMCOG1019: aminotransferase

FB479_RS17855: PfkB domain protein

smcogs: SMCOG1276: PfkB domain protein

FB479_RS17900: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: esterase hydrolase

FB479_RS17870: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

FB479_RS17905: thioesterase

smcogs: SMCOG1004: thioesterase

Ligases: ligase

FB479_RS17875: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

FB479_RS17890: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

FB479_RS17895: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter

FB479_RS17800: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002472.2	1.36	NRPS	ulbactin F, ulbactin G	Brevibacillus brevis
BGC0001641.4	0.61	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.60	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.60	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.60	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.60	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.60	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.60	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001135.5	0.59	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.59	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002472.2	0.88	NRPS	ulbactin F, ulbactin G	Brevibacillus brevis
BGC0001641.4	0.64	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.64	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.64	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.64	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.64	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.64	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.63	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001135.5	0.63	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.63	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 22.17 out of 25.88

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.29 out of 27.78

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.19 out of 19.26

Confidence: medium

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.83 out of 29.38

Confidence: medium

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.81 out of 29.38

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.48 out of 20.97

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.46 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.06 out of 28.19

Confidence: medium

ZuR variant 1

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

Confidence: medium

ZuR variant 1

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

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.95 out of 28.19

Confidence: medium

Additional weak hits (12):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.16 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.73 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.12 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 25.85 out of 32.74

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.42 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.47 out of 32.74

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.02 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.96 out of 29.38

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.83 out of 31.73

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.00 out of 31.73

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.69 out of 27.55

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.56 out of 36.54

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 321363 - 381876:

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

Polymer prediction:: (Me-Cys - Me-Cys) + (Cys)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

FB479_RS17875: Cys

Search NORINE for peptide: strict or relaxed

AMP-binding (539..933): Cys

nrpys: Cys

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: TDMAFDLSVYDANSLLSGDVSLGGATEASIWSNY
Nearest Stachelhaus code(s):: Cys DLYNLSLIWK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

FB479_RS17890: Cys - Cys

Search NORINE for peptide: strict or relaxed

AMP-binding (567..965): Cys

nrpys: Cys

SVM prediction details:

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

Stachelhaus prediction details:

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

AMP-binding (2029..2433): Cys

nrpys: Cys

SVM prediction details:

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

Stachelhaus prediction details:

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

FB479_RS17895: diOH-Bz

Search NORINE for peptide: strict or relaxed

AMP-binding (30..435): 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:: NATLFPLCCPGGGLQVGGSQQVFGMAEGLICCTS
Nearest Stachelhaus code(s):: Sal TLPAQGVICK (82% 8Å match)
Stachelhaus code match:: 80% (moderate)

Link to PARAS substrate predictor

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
FuR variant 1	Ferric Uptake Regulator
PsrA	Oleic acid responsive regulator
ZuR variant 1	Zinc-responsive repressor

NZ_VFNO01000006.1 - Region 1 - RRE-containing

Download region GenBank file

Download region SVG

Location: 155,160 - 176,314 nt. (total: 21,155 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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

No tailoring functions detected.

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002317.2	0.48	ribosomal	herbicolin O, mcceh252, pantocin A	Pantoea agglomerans
BGC0000585.5	0.39	ribosomal	microcin C7	Escherichia coli
BGC0000546.3	0.37	ribosomal	SAL-2242	Streptomyces albidoflavus
BGC0000547.5	0.36	ribosomal	salivaricin 9	Streptococcus salivarius
BGC0001787.3	0.36	ribosomal	suicin 3908	Streptococcus suis
BGC0001210.5	0.36	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0000626.3	0.36	ribosomal	thuricin	Bacillus thuringiensis
BGC0000845.5	0.36	other (non-nrp beta-lactam)	clavulanic acid	Streptomyces clavuligerus ATCC 27064
BGC0000498.5	0.35	ribosomal	bovicin HJ50	Streptococcus equinus
BGC0000561.5	0.35	ribosomal	thermophilin 1277	Streptococcus thermophilus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002317.2	0.48	ribosomal	herbicolin O, mcceh252, pantocin A	Pantoea agglomerans
BGC0000585.5	0.39	ribosomal	microcin C7	Escherichia coli
BGC0000546.3	0.37	ribosomal	SAL-2242	Streptomyces albidoflavus
BGC0000547.5	0.36	ribosomal	salivaricin 9	Streptococcus salivarius
BGC0001787.3	0.36	ribosomal	suicin 3908	Streptococcus suis
BGC0001210.5	0.36	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0000626.3	0.36	ribosomal	thuricin	Bacillus thuringiensis
BGC0000845.5	0.36	other (non-nrp beta-lactam)	clavulanic acid	Streptomyces clavuligerus ATCC 27064
BGC0000498.5	0.35	ribosomal	bovicin HJ50	Streptococcus equinus
BGC0000561.5	0.35	ribosomal	thermophilin 1277	Streptococcus thermophilus

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.41 out of 23.79

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 19.12 out of 20.97

Confidence: strong

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.48 out of 18.57

Confidence: strong

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.44 out of 26.06

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.69 out of 26.06

Confidence: medium

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.82 out of 27.55

Confidence: medium

Additional weak hits (4):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.31 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.38 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.68 out of 26.06

Confidence: weak

NrdR

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

Confidence: weak

RREFinder

TFBS Finder

RRE predictions

: RRE type: Pantocin_Microcin_RRE; Location: 2 - 90; Score: 51.8

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
GnfM	Regulator of nitrogen-fixation genes
IolR	Regulator of the inositol catabolism
MogR	Repressor of flagellar motility genes
ToxT	Regulator of MSHA biosynthesis

NZ_VFNO01000008.1 - Region 1 - NRPS

Download region GenBank file

Download region SVG

Location: 138,781 - 203,187 nt. (total: 64,407 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

Lyases: cyclase hydratase lyase

FB479_RS22370: Nitrilase/cyanide hydratase and apolipoprotein

smcogs: SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

FB479_RS22430: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

FB479_RS22440: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

FB479_RS22525: diguanylate cyclase

smcogs: SMCOG1025: diguanylate cyclase

Ligases: ligase synthase

FB479_RS22435: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

FB479_RS22455: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS22460: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

FB479_RS22465: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS22470: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.75	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001128.4	0.72	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.71	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001133.4	0.71	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.71	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.70	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001240.4	0.70	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.75	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001128.4	0.72	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.71	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001133.4	0.71	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.71	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.70	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001240.4	0.70	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

RpoN

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

Confidence: strong

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.51 out of 30.25

Confidence: medium

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.87 out of 21.55

Confidence: medium

NtrC

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

Confidence: medium

Additional weak hits (11):

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.76 out of 36.54

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.55 out of 32.93

Confidence: weak

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.77 out of 32.38

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.82 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.43 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.93 out of 26.06

Confidence: weak

NuR

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

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.13 out of 20.01

Confidence: weak

CopR

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

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.25 out of 32.93

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.04 out of 29.65

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 138780 - 203187:

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

Polymer prediction:: (Glu - Ser - X) + (X) + (Phe - D-Orn)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

FB479_RS22455: Phe - Orn

Search NORINE for peptide: strict or relaxed

AMP-binding (448..868): Phe

nrpys: Phe

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: N/A
Single AA prediction:: phe (Phe)

Stachelhaus prediction details:

Stachelhaus sequence:: HAKAFDISVWQAQMISTGEVNTYGATECSDDTMH
Nearest Stachelhaus code(s):: L-Dbu DIWQGTADDK (79% 8Å match); dnmeProp or Dab DIWQSTADDK (79% 8Å match); Asp DIWQSTADDK (74% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1534..1934): 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:: LAWAFDVFTGDRESILGSDINSYGVTEATIDASY
Nearest Stachelhaus code(s):: Orn DVGEIGSIDK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

FB479_RS22465: X - X

AMP-binding (8..406): 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:: LHVAFDASTFEGLLLVGGDINCYGPTETTTFATF
Nearest Stachelhaus code(s):: Val DAFWLGCTFK (79% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1063..1467): X

nrpys: (unknown)

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: RWMTFDDAAVEWQFISSGEHNTWGATEVSIDSTI
Nearest Stachelhaus code(s):: Ser DVWHISLIDK (62% 8Å match)
Stachelhaus code match:: 60% (weak)

FB479_RS22470: Glu - Ser

Search NORINE for peptide: strict or relaxed

AMP-binding (245..652): 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:: glu,gln (Glu, Gln)
Single AA prediction:: glu (Glu)

Stachelhaus prediction details:

Stachelhaus sequence:: FTLTFDASVWEWEFTAGGEYNTYGPTETTVEVAS
Nearest Stachelhaus code(s):: Gln DAWHFGSVEK (74% 8Å match); Glu DAWHFGSVEK (71% 8Å match)
Stachelhaus code match:: 70% (weak)

AMP-binding (1324..1728): 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:: RWMTFDVSVTELHFYTTGEHNLYGPTETTIEVTY
Nearest Stachelhaus code(s):: Ser DVWHFSLIEK (76% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
ArcA	Repressor of carbon oxidation
ColR	Phenol-responsive regulator
NtrC	Nitrogen regulatory protein C
RpoN	Regulator of nitrogen assimilation and virulence

NZ_VFNO01000009.1 - Region 1 - azole-containing-RiPP

Download region GenBank file

Download region SVG

Location: 202,333 - 225,886 nt. (total: 23,554 nt) Show pHMM detection rules used

azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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

Azole RiPPs

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

FB479_RS23965: aminotransferase

smcogs: SMCOG1019: aminotransferase

Ligases: synthase

FB479_RS23925: Pseudouridine synthase

smcogs: SMCOG1154: Pseudouridine synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000851.5	0.46	other (other)	albonoursin	Streptomyces noursei ATCC 11455
BGC0001145.5	0.44	ribosomal	cyclothiazomycin b1	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001146.5	0.43	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0000607.5	0.43	ribosomal	micrococcin P1	Macrococcus caseolyticus
BGC0000603.5	0.40	ribosomal	cyclothiazomycin	Streptomyces hygroscopicus
BGC0001640.3	0.40	ribosomal	kocurin	Kocuria rosea
BGC0000605.5	0.39	ribosomal	GE37468	Streptomyces sp. ATCC 55365
BGC0001860.4	0.39	ribosomal	thiomuracin	Thermobispora bispora DSM 43833
BGC0000628.4	0.39	ribosomal	lactocillin	Lactobacillus paragasseri JV-V03
BGC0000613.5	0.39	ribosomal	thiomuracin A	Nonomuraea sp. Bp3714-39

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000851.5	0.46	other (other)	albonoursin	Streptomyces noursei ATCC 11455
BGC0001145.5	0.44	ribosomal	cyclothiazomycin b1	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001146.5	0.43	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0000607.5	0.43	ribosomal	micrococcin P1	Macrococcus caseolyticus
BGC0000603.5	0.40	ribosomal	cyclothiazomycin	Streptomyces hygroscopicus
BGC0001640.3	0.40	ribosomal	kocurin	Kocuria rosea
BGC0000605.5	0.39	ribosomal	GE37468	Streptomyces sp. ATCC 55365
BGC0001860.4	0.39	ribosomal	thiomuracin	Thermobispora bispora DSM 43833
BGC0000628.4	0.39	ribosomal	lactocillin	Lactobacillus paragasseri JV-V03
BGC0000613.5	0.39	ribosomal	thiomuracin A	Nonomuraea sp. Bp3714-39

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.53 out of 27.04

Confidence: medium

Additional weak hits (2):

HipB

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

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 25.46 out of 30.98

Confidence: weak

(Thi)azol(in)e containing peptide predictions

No core peptides found.

RREFinder

TFBS Finder

Azole RiPPs

RRE predictions

: RRE type: Heterocycloanthracin_C_RRE; Location: 0 - 99; Score: 130.0; RRE type: Thiopeptide_F_RRE; Location: 7 - 88; Score: 55.0

TFBS definitions

Regulator	Description
DasR	N-acetylglucosamine dependent repressor

Core peptide predictions

No core peptides found.

NZ_VFNO01000010.1 - Region 1 - NRPS

Download region GenBank file

Download region SVG

Location: 1 - 61,163 nt. (total: 61,163 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

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

FB479_RS24195: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

Hydrolases: back translocase

FB479_RS24160: GTP-binding protein LepA

smcogs: SMCOG1190: GTP-binding protein LepA

Ligases: ligase

FB479_RS24085: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS24090: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS24095: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.72	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.72	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.71	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001133.4	0.71	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0000426.5	0.71	NRPS	sevadicin	Paenibacillus larvae
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0002071.2	0.69	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.72	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.72	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.71	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001133.4	0.71	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0000426.5	0.71	NRPS	sevadicin	Paenibacillus larvae
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0002071.2	0.69	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027

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: 21.75 out of 27.78

Confidence: medium

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.09 out of 26.33

Confidence: medium

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.52 out of 25.88

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.89 out of 20.97

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.70 out of 27.78

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.73 out of 27.78

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.57 out of 28.19

Confidence: medium

Additional weak hits (4):

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.39 out of 28.14

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.84 out of 29.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.09 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.55 out of 30.25

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 - 61163:

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

Polymer prediction:: (D-Val) + (Val - D-Val - X - D-Leu - X - D-Leu) + (Trp - D-Leu - Trp - Gly)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

FB479_RS24085: Val

Search NORINE for peptide: strict or relaxed

AMP-binding (1..212): 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:: ----FDAATFEGWLLVGGDINGYGPTENTTFTCC
Nearest Stachelhaus code(s):: Val DAFWLGGTFK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

FB479_RS24090: Val - Val - X - Leu - X - Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (467..865): 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:: LNTSFDAATFEGWLLVGGDINGYGPTENTTFTCC
Nearest Stachelhaus code(s):: Val DAFWLGGTFK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1530..1928): 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:: LNTSFDAATFEGWLLVGGDINGYGPTENTTFTCC
Nearest Stachelhaus code(s):: Val DAFWLGGTFK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3057..3446): X

nrpys: (unknown)

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: MYLCFDVSVAEMMTVIGGEFNCYGPTEATVCTTL
Nearest Stachelhaus code(s):: Trp DVAMVGAVCK (71% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (4108..4502): 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:: LWHAFDASVWEPFLLTGGDVNQYGPTENAVVATA
Nearest Stachelhaus code(s):: Leu DAWFLGQVVK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (5631..6020): X

nrpys: (unknown)

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: LALTFDVSVSEMTMIVGGEFNCYGPTETTVTATL
Nearest Stachelhaus code(s):: Trp DVSAIGCVTK (88% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (6688..7081): 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:: LWHAFDAAVWEPFLLTGGDVNQYGPTENAVVATA
Nearest Stachelhaus code(s):: Leu DAWFLGQVVK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

FB479_RS24095: Trp - Leu - Trp - Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (470..859): Trp

nrpys: Trp

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:: MALTFDVSVSEMSMIVGGEFNCYGPTEATVCSTM
Nearest Stachelhaus code(s):: Trp DVSSIGCVCK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1524..1918): 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:: LWHSFDASVWEPFLLTGGDVNQYGPTENAVVATA
Nearest Stachelhaus code(s):: Leu DAWFLGQVVK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3050..3440): Trp

nrpys: Trp

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: MAYTFDVSISEQSMEVGGDYNCYGPTEATVGTVI
Nearest Stachelhaus code(s):: Trp DVSSEGCVGK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4104..4495): 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:: ala (Ala)

Stachelhaus prediction details:

Stachelhaus sequence:: FWATFDLSVYEANTNLCGEFNLYGPTEDTVYSTH
Nearest Stachelhaus code(s):: Gly DLYNNCLVYK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
CcpA	Catabolite control protein A
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
PsrA	Oleic acid responsive regulator
ZuR variant 1	Zinc-responsive repressor

NZ_VFNO01000010.1 - Region 2 - ectoine

Download region GenBank file

Download region SVG

Location: 70,117 - 80,500 nt. (total: 10,384 nt) Show pHMM detection rules used

ectoine: ectoine_synt

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

Transferases: aminotransferase

FB479_RS24280: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000852.5	0.80	other (other)	ectoine	Sporosarcina pasteurii
BGC0002052.3	0.80	other (ectoine)	ectoine	Streptomyces sp.
BGC0000858.3	0.73	other (other)	ectoine	Methylobacter marinus
BGC0000853.3	0.73	other (other)	ectoine	Streptomyces anulatus
BGC0000855.3	0.72	other (other)	ectoine	Methylomicrobium kenyense
BGC0000859.3	0.66	other (other)	ectoine	Methylomicrobium alcaliphilum
BGC0000856.3	0.66	other (other)	ectoine	Methylophaga thalassica
BGC0000857.3	0.60	other (other)	ectoine	Methylophaga alcalica
BGC0000854.3	0.60	other (other)	ectoine	Methylomicrobium alcaliphilum 20Z
BGC0000860.3	0.60	other (other)	ectoine	Methylarcula marina

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000852.5	0.80	other (other)	ectoine	Sporosarcina pasteurii
BGC0002052.3	0.80	other (ectoine)	ectoine	Streptomyces sp.
BGC0000858.3	0.73	other (other)	ectoine	Methylobacter marinus
BGC0000853.3	0.73	other (other)	ectoine	Streptomyces anulatus
BGC0000855.3	0.72	other (other)	ectoine	Methylomicrobium kenyense
BGC0000859.3	0.66	other (other)	ectoine	Methylomicrobium alcaliphilum
BGC0000856.3	0.66	other (other)	ectoine	Methylophaga thalassica
BGC0000857.3	0.60	other (other)	ectoine	Methylophaga alcalica
BGC0000854.3	0.60	other (other)	ectoine	Methylomicrobium alcaliphilum 20Z
BGC0000860.3	0.60	other (other)	ectoine	Methylarcula marina

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

RpoN

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

Confidence: medium

MexT

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

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.91 out of 28.19

Confidence: medium

Additional weak hits (4):

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.90 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.82 out of 29.38

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.94 out of 26.06

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.12 out of 30.98

Confidence: weak

TFBS Finder

TFBS definitions

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

NZ_VFNO01000010.1 - Region 3 - NRPS,lanthipeptide-class-i

Download region GenBank file

Download region SVG

Location: 164,107 - 201,887 nt. (total: 37,781 nt) Show pHMM detection rules used

Region on contig edge.

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

Lanthipeptides

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

FB479_RS24850: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Transferases: PPTase

FB479_RS24835: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: esterase hydrolase phosphatase

FB479_RS24765: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

FB479_RS24840: thioesterase

smcogs: SMCOG1004: thioesterase

FB479_RS24845: FkbH like protein

smcogs: SMCOG1256: FkbH like protein

FB479_RS24855: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: cyclase dehydratase

FB479_RS24800: Lanthionine synthetase C family protein

smcogs: SMCOG1140: Lanthionine synthetase C family protein

FB479_RS24805: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

Ligases: ligase

FB479_RS24810: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS24860: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS24870: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.93	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0001132.4	0.58	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.58	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	0.56	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002274.2	0.55	NRPS	aspulvinone H, aspulvinone B1	Aspergillus terreus NIH2624
BGC0002193.2	0.54	other (other)	phenguignardic acid	Aspergillus terreus NIH2624
BGC0001289.5	0.45	ribosomal	penisin	Paenibacillus ehimensis
BGC0002635.2	0.44	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0001160.5	0.41	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0000542.3	0.40	ribosomal	paenicidin B	Paenibacillus terrae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.76	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0000342.4	0.68	NRPS	enniatin	Fusarium equiseti
BGC0002135.2	0.67	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.67	NRPS	icosalide A, icosalide B	Burkholderia gladioli
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
BGC0001135.5	0.66	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001133.4	0.66	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for FB479_RS24805

allorf_179113_179274

Leader:

MDRTHDLFDLDIQEFEVTSNQPN

Core:

LATFWCTSRIACSTGDCPTFSGNTCHICET

Core with dehydrations:

LADhbFWCysDhbDhaRIACysDhaDhbGDCysPDhbFDhaGNDhbCysHICysEDhb

antiSMASH-DB 4.0 matches for allorf_179113_179274

100.0%

NZ_VFNO01000010.1:

Lanthipeptides: allorf_179113_179274_lanthipeptide

1

LATFWCTSRIACSTGDCPTFSGNTCHICET

30

LATFWCTSRIACSTGDCPTFSGNTCHICET

1

LATFWCTSRIACSTGDCPTFSGNTCHICET

30

30.0%

NZ_FNET01000034.1and 3 others:

NZ_FNET01000034.1 Lanthipeptides: BLR21_RS39400_lanthipeptideNZ_FWYC01000020.1 Lanthipeptides: B9C42_RS36845_lanthipeptideNZ_FWYC01000020.1 Lanthipeptides: B9C42_RS36845_lanthipeptide

Lanthipeptides: BLR21_RS39400_lanthipeptide

15

GDCPTFS--GNTCH

26

GDCPT GNTC

2

GDCPTDDGCGNTCE

15

25.7%

NZ_LT985747.1:

Lanthipeptides: C8268_RS22865_lanthipeptide

8

SRIACSTGDCPTFSGNTCHI

27

SR+ C+ G C SGN C +

4

SRLICTPGSC---SGNNCVL

20

with 6 more sequence matches

25.0%

NZ_CP047419.1and 3 others:

NZ_CP047419.1 Lanthipeptides: GTU71_RS12785_lanthipeptideNZ_PSTO01000045.1 Lanthipeptides: C5C10_RS15570_lanthipeptideNZ_PSTO01000045.1 Lanthipeptides: C5C10_RS15570_lanthipeptide

Lanthipeptides: GTU71_RS12785_lanthipeptide

1

LATFWCTSRIACSTGDCPTFS

21

+A+ S + S+G CPTFS

11

VASATAVSALVTSSGLCPTFS

31

21.2%

NC_017621.1and 16 others:

NZ_CP039462.1 Lanthipeptides: E8M06_RS05390_lanthipeptideNZ_JABTZM010000032.1 Lanthipeptides: HRQ47_RS09675_lanthipeptideNZ_JAEVFQ010000010.1 Lanthipeptides: JNO64_RS06375_lanthipeptideNZ_JAFFHD010000003.1 Lanthipeptides: JN532_RS02075_lanthipeptideNZ_JAGFVG010000007.1 Lanthipeptides: J5581_RS04225_lanthipeptideNZ_JAIJZO010000001.1 Lanthipeptides: K5Q34_RS00965_lanthipeptideNZ_JAIMDS010000024.1 Lanthipeptides: K6V32_RS10650_lanthipeptideNZ_JAJUWV010000001.1 Lanthipeptides: LZF89_RS05505_lanthipeptideNZ_JAMDIS010000017.1 Lanthipeptides: M5P45_RS08180_lanthipeptideNZ_JAMYIU010000001.1 Lanthipeptides: NKE44_RS01780_lanthipeptideNZ_JAMYIX010000001.1 Lanthipeptides: NKE54_RS02675_lanthipeptideNZ_JAMYIY010000001.1 Lanthipeptides: NKE64_RS02785_lanthipeptideNZ_JAMYJP010000014.1 Lanthipeptides: NKE68_RS07350_lanthipeptideNZ_LR738722.1 Lanthipeptides: STREPSUIS_RS03955_lanthipeptideNZ_VZMP01000023.1 Lanthipeptides: F6P50_RS09295_lanthipeptideNZ_VZNS01000007.1 Lanthipeptides: F6P79_RS05700_lanthipeptide

Lanthipeptides: SSUD12_RS06540_lanthipeptide

14

TGDCPTFSGNTC

25

T DCP F N C

10

TKDCPGFLSNVC

21

21.2%

NZ_AQQB01000068.1and 6 others:

NZ_BCEY01000024.1 Lanthipeptides: GOZ53_RS05100_lanthipeptideNZ_BCEZ01000067.1 Lanthipeptides: GOZ55_RS11230_lanthipeptideNZ_BCFC01000053.1 Lanthipeptides: GOZ35_RS07920_lanthipeptideNZ_BCFG01000017.1 Lanthipeptides: GOZ50_RS03220_lanthipeptideNZ_BCFI01000009.1 Lanthipeptides: GOZ54_RS02495_lanthipeptideNZ_CP019557.1 Lanthipeptides: BZG42_RS05725_lanthipeptide

Lanthipeptides: K738_RS01000000110290_lanthipeptide

14

TGDCPTFSGNTC

25

T DCP F N C

10

TKDCPGFLSNIC

21

20.8%

NZ_KZ859514.1:

Lanthipeptides: DPQ64_RS19160_lanthipeptide

3

TFWCTSRIACSTGDCPT

19

+F CT CSTGDC T

28

SFSCTGSCLCSTGDCDT

44

20.0%

NZ_BBQG01000021.1and 4 others:

NZ_CP048875.1 Lassopeptides: G3260_RS22950_lassopeptideNZ_CP050693.1 Lassopeptides: HC362_RS11085_lassopeptideNZ_CP103060.1 Lassopeptides: NR995_RS11105_lassopeptideNZ_KE150472.1 Lassopeptides: HMPREF1486_RS35370_lassopeptide

Lassopeptides: TU22_RS34200_lassopeptide

13

STGDCPTFSG

22

+GDCP F G

3

PSGDCPDFLG

12

14.0%

NZ_KN234784.1:

Lanthipeptides: allorf_44132_44347_lanthipeptide

5

WCTSRIACSTGDCPTFSGNT

24

CT+R A TG P+

11

HCTARHALPTGSSPSHDAQQ

30

MIBiG 4.0 matches for allorf_179113_179274

8.8%

BGC0000535.4 (ADJ56352.1):

Lanthipeptide: nisin A

24

TCH

26

TCH

25

TCH

27

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.07 out of 18.16

Confidence: strong

ToxT

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

Confidence: strong

ToxT

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

Confidence: strong

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.24 out of 30.25

Confidence: medium

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 23.04 out of 29.25

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.64 out of 26.06

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.66 out of 27.78

Confidence: medium

Additional weak hits (3):

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.09 out of 20.01

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 24.62 out of 32.74

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.28 out of 26.06

Confidence: weak

Module view

Legend

Detailed domain annotation

Selected features only

Show module domains

Lanthipeptides

NRPS/PKS products

NRPS/PKS substrates

RREFinder

TFBS Finder

Core peptide predictions

allorf_179113_179274 - Class I

Cleavage pHMM score: 3.20

RODEO score: 24

Monoisotopic mass: 3062.3 Da

Molecular weight: 3064.4 Da

Number of bridges: 5

Alternative weights: (assuming N unmodified Ser/Thr residues); 3082.5 Da N = 1; 3100.5 Da N = 2; 3118.5 Da N = 3; 3136.5 Da N = 4

Predicted core structure(s)

For candidate cluster 3, location 164106 - 201887:

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

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 170684 - 201887:

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

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

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

FB479_RS24810: X

AMP-binding (9..409): X

nrpys: (unknown)

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: NAMLFCMTVC-GAGCSGGALEGYGLSEAAPATTF
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

FB479_RS24860: Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (470..869): 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:: LHEHFDFSVWEGNQIFGGEINMYGITETTVHVTY
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

FB479_RS24865: X

A-OX (493..1247): X

No predictions made

Link to PARAS substrate predictor

RRE predictions

: RRE type: Lanthipeptide_LanB_RRE; Location: 158 - 255; Score: 54.4

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
ColR	Phenol-responsive regulator
MogR	Repressor of flagellar motility genes
SypG	Regulator of biofilm formation and host colonization
ToxT	Regulator of MSHA biosynthesis

NZ_VFNO01000018.1 - Region 1 - NRPS,transAT-PKS

Download region GenBank file

Download region SVG

Location: 1 - 48,216 nt. (total: 48,216 nt) Show pHMM detection rules used

Region on contig edge.

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

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

FB479_RS30150: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

Transferases: acylase

FB479_RS30125: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: ligase synthase

FB479_RS30120: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS30130: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

FB479_RS30135: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

FB479_RS30140: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

FB479_RS30145: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

FB479_RS30180: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

FB479_RS30185: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

FB479_RS30190: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.85	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.76	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001261.3	0.74	NRPS	AM-toxin	Alternaria alternata
BGC0001128.4	0.72	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.72	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4	0.71	NRPS	enniatin	Fusarium equiseti
BGC0001244.3	0.69	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001132.4	0.69	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001273.3	0.69	PKS	asperlactone	Aspergillus ochraceus

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
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
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
BGC0000342.4	0.68	NRPS	enniatin	Fusarium equiseti
BGC0001244.3	0.68	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001273.3	0.67	PKS	asperlactone	Aspergillus ochraceus

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ToxT

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

Confidence: medium

Additional weak hits (11):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.21 out of 26.06

Confidence: weak

CodY

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.60 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.42 out of 31.73

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.55 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.22 out of 28.14

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.91 out of 31.73

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.76 out of 27.78

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.13 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 21.59 out of 33.14

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 20.80 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 0 - 48216:

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

Polymer prediction:: (Gly) + (ohmal) + (ccmal - Gly) + (ccmal) + (ccmal) + (Phe) + (ohmal) + (mal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

FB479_RS30120: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (620..1013): 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:: LGMTFDIFVLELQTLIGGEHNMYGPTETTVWSMT
Nearest Stachelhaus code(s):: Gly DILQLGMVWK (79% 8Å match)
Stachelhaus code match:: 100% (strong)

FB479_RS30125: mal

PKS_AT (6..292): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 89.8
inactive: 35.4
Methoxymalonyl-CoA: 34.5
Methylmalonyl-CoA: 24.5
Propionyl-CoA: 14.9
2-Methylbutyryl-CoA: 11.3
CHC-CoA: 9.1
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

FB479_RS30135: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (1940..2365): 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:: N/A

Stachelhaus prediction details:

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

FB479_RS30180: Phe

Search NORINE for peptide: strict or relaxed

AMP-binding (478..868): Phe

nrpys: Phe

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: QYVAFNATIWEMTMITAGSLNAYGSTETTNSALV
Nearest Stachelhaus code(s):: Phe DAWTIAAICK (62% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
ToxT	Regulator of MSHA biosynthesis

NZ_VFNO01000020.1 - Region 1 - NRPS

Download region GenBank file

Download region SVG

Location: 1 - 6,867 nt. (total: 6,867 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

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

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

Ligases: ligase

FB479_RS30220: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.69	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000342.4	0.68	NRPS	enniatin	Fusarium equiseti
BGC0001135.5	0.67	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001261.3	0.66	NRPS	AM-toxin	Alternaria alternata
BGC0001132.4	0.66	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.65	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5	0.65	NRPS	HC-toxin	Alternaria jesenskae
BGC0001758.4	0.65	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.65	NRPS	icosalide A, icosalide B	Burkholderia gladioli

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.69	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000342.4	0.68	NRPS	enniatin	Fusarium equiseti
BGC0001135.5	0.67	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001261.3	0.66	NRPS	AM-toxin	Alternaria alternata
BGC0001132.4	0.66	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.65	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5	0.65	NRPS	HC-toxin	Alternaria jesenskae
BGC0001758.4	0.65	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.65	NRPS	icosalide A, icosalide B	Burkholderia gladioli

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Module view

Legend

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

Predicted core structure(s)

For candidate cluster 1, location 0 - 6867:

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

Polymer prediction:: (Ala)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

FB479_RS30220: Ala

Search NORINE for peptide: strict or relaxed

AMP-binding (1148..1541): Ala

nrpys: Ala

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: FWATFDLSVYEVNTNLAGEFNLYGPSEDTTYSTY
Nearest Stachelhaus code(s):: Ala DLYNNALTYK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor