Select genomic region:
Overview
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### Identified secondary metabolite regions using strictness 'relaxed'

NZ_AP024135.1 (Streptomyces sp. EAS-AB2608)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | butyrolactone | 6,246 | 17,298 |
Region 2 | RRE-containing | 31,683 | 54,127 |
Region 3 | T1PKS,nucleoside,aminocoumarin,T3PKS,lassopeptide,terpene | 253,074 | 380,437 | Low | rubradirin | PKS
Region 4 | NRPS-like | 524,743 | 566,518 | Low | JBIR-126 | NRPS:Type I
Region 5 | atropopeptide | 567,201 | 588,445 |
Region 6 | terpene | 729,953 | 751,446 |
Region 7 | NRPS,RiPP-like | 824,878 | 903,788 | Medium | informatipeptin | ribosomal:RiPP:Lanthipeptide
Region 8 | terpene | 1,000,748 | 1,021,380 |  |
Region 9 | lanthipeptide-class-i | 1,148,269 | 1,173,410 |
Region 10 | ectoine | 1,499,990 | 1,510,394 | High | ectoine | other:other
Region 11 | T2PKS | 1,896,129 | 1,968,642 | High | spore pigment | PKS
Region 12 | NRPS | 2,055,901 | 2,103,169 | Low | cadaside A/cadaside B | NRPS:Type I
Region 13 | melanin | 2,582,311 | 2,592,838 |  |
Region 14 | NI-siderophore | 2,674,668 | 2,704,437 | High | desferrioxamin B/desferrioxamine E | other:other
Region 15 | NRPS-like,T1PKS,NRPS,amglyccycl,butyrolactone,terpene-precursor | 4,346,377 | 4,410,237 | Low | pyralomicin 1a | NRPS:Type I+PKS:Type I
Region 16 | terpene | 5,116,131 | 5,137,156 | High | albaflavenone | terpene
Region 17 | terpene-precursor | 5,140,686 | 5,161,816 | Low | pentalenolactone | terpene
Region 18 | aminopolycarboxylic-acid | 5,773,546 | 5,787,012 | High | Ethylenediaminesuccinic acid hydroxyarginine | other:other
Region 19 | NI-siderophore | 5,793,328 | 5,823,373 |  |
Region 20 | NRPS,NRPS-like | 5,899,488 | 6,014,089 | Low | friulimicin A/friulimicin B/friulimicin C/friulimicin D | NRPS:Type I
Region 21 | RiPP-like,t3nrps-iterative,NRPS,NAPAA | 6,020,217 | 6,086,407 |  |
Region 22 | RiPP-like | 6,132,417 | 6,143,736 |  |
Region 23 | terpene | 6,173,219 | 6,195,381 | High | geosmin | terpene:Sesquiterpene
Region 24 | NI-siderophore | 6,356,597 | 6,387,737 |  |
Region 25 | betalactone | 6,413,798 | 6,441,402 |
Region 26 | terpene | 6,957,639 | 6,984,410 | High | hopene | terpene
Region 27 | lassopeptide | 7,000,336 | 7,022,913 | High | citrulassin D | ribosomal:RiPP
Region 28 | hydrogen-cyanide | 7,061,525 | 7,074,374 | Low | aborycin | ribosomal:RiPP
Region 29 | T1PKS,NRPS-like | 7,110,118 | 7,220,655 | Medium | naphthomycin A | PKS
Region 30 | lassopeptide | 7,484,260 | 7,506,758 | High | ulleungdin | ribosomal:unmodified
Region 31 | t3nrps-iterative,hglE-KS,ectoine | 7,717,842 | 7,778,238 |  |
Region 32 | T3PKS,T2PKS,PKS-like | 7,837,781 | 7,920,218 | Low | rishirilide B/rishirilide A | PKS:Type II
Region 33 | T2PKS,azole-containing-RiPP,PKS-like,T1PKS | 8,160,384 | 8,233,455 | Low | LL-D49194α1 (LLD)/LL-D49194β2 | PKS
Region 34 | redox-cofactor | 8,245,341 | 8,267,534 | Low | isorenieratene | terpene
Region 35 | NRPS,T1PKS,hglE-KS,PKS-like | 8,381,711 | 8,507,432 | Low | sanglifehrin A | NRPS:Type I+PKS
Region 36 | melanin,terpene-precursor | 8,671,225 | 8,700,408 | Medium | melanin | other:other
Region 37 | CDPS | 8,789,757 | 8,810,467 | High | prunipeptin | ribosomal:RiPP
Region 38 | terpene | 8,836,434 | 8,861,023 | Medium | carotenoid | terpene
Region 39 | NRPS,cyanobactin,NRPS-like,T1PKS,t3nrps-iterative | 8,957,853 | 9,135,368 | High | tripartilactam/niizalactam C | PKS
Region 40 | RiPP-like | 9,175,623 | 9,187,527 |
Region 41 | lanthipeptide-class-i | 9,256,867 | 9,279,468 |

NZ_AP024135.1 - Region 1 - butyrolactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,246 - 17,298 nt. (total: 11,053 nt) Show pHMM detection rules used
Region on contig edge.
butyrolactone: AfsA

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
K6K39_RS00045: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.77 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.76 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.69 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002276.2 |  | 0.56 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002578.2 |  | 0.42 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002334.3 |  | 0.41 | other (other), ribosomal | heptyltyrazolone, nonyltyrazolone, undecyltyrazolone, (Z)-ω-6-undecenyltyrazolone | Pseudoalteromonas rubra
BGC0002493.3 |  | 0.40 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0000667.3 |  | 0.37 | terpene | PR-toxin | Penicillium roqueforti FM164
BGC0001364.3 |  | 0.35 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0002425.3 |  | 0.34 | ribosomal | stlassin | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.77 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.76 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.69 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002276.2 |  | 0.56 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002578.2 |  | 0.42 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002334.3 |  | 0.41 | other (other), ribosomal | heptyltyrazolone, nonyltyrazolone, undecyltyrazolone, (Z)-ω-6-undecenyltyrazolone | Pseudoalteromonas rubra
BGC0002493.3 |  | 0.40 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0000667.3 |  | 0.37 | terpene | PR-toxin | Penicillium roqueforti FM164
BGC0001364.3 |  | 0.35 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0002425.3 |  | 0.34 | ribosomal | stlassin | Streptomyces sp.

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (3):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.78 out of 26.85
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.18 out of 26.85
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_AP024135.1 - Region 2 - RRE-containing
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 31,683 - 54,127 nt. (total: 22,445 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
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
No tailoring functions detected.
Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001300.5 |  | 0.22 | PKS | anthracimycin | Streptomyces sp. CNH365

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001300.5 |  | 0.22 | PKS | anthracimycin | Streptomyces sp. CNH365

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (4):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.53 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.14 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.20 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (31682...54127)
K6K39_RS00190
  RRE type: Lanthipeptide_LanB_RRE
  Location: 184 - 262
  Score: 38.0

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_AP024135.1 - Region 3 - T1PKS,T3PKS,aminocoumarin,lassopeptide,nucleoside,terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 253,074 - 380,437 nt. (total: 127,364 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
nucleoside: (LipM or LipV or LipU or TunD or pur6 or pur10 or nikJ or nikO or truD)
aminocoumarin: (novK or novJ or novI or novH or SpcDK_cou)
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lasso peptides
Terpene
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
K6K39_RS01160: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

K6K39_RS01165: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

K6K39_RS01195: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

K6K39_RS01210: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

K6K39_RS01225: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

K6K39_RS01245: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

K6K39_RS01265: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

K6K39_RS01270: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

K6K39_RS01275: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

K6K39_RS01320: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

K6K39_RS01435: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

K6K39_RS01510: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

K6K39_RS01515: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acylase transferase
K6K39_RS01170: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

K6K39_RS01190: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase
K6K39_RS01250: HAD-superfamily hydrolase, subfamily IA, variant

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

K6K39_RS01400: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: dehydratase
K6K39_RS01240: L-carnitine dehydratase/bile acid-inducible

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

Ligases: ligase synthase synthetase
K6K39_RS01180: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

K6K39_RS01215: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

K6K39_RS01220: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS01290: hydroxymethylglutaryl-CoA synthase

smcogs
  SMCOG1043: hydroxymethylglutaryl-CoA synthase

K6K39_RS01335: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS01445: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

K6K39_RS01505: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Translocases: transporter
K6K39_RS01545: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T1PKS | nucleoside | aminocoumarin | T3PKS | lassopeptide | T3PKS | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002341.2 |  |  |  |  |  |  |  | 0.89 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0002127.3 |  |  |  |  |  |  |  | 0.88 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0002631.2 |  |  |  |  |  |  |  | 0.85 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001539.4 |  |  |  |  |  |  |  | 0.82 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000902.4 |  |  |  |  |  |  |  | 0.82 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0002053.3 |  |  |  |  |  |  |  | 0.82 | ribosomal | ulleungdin | Streptomyces sp.
BGC0002825.2 |  |  |  |  |  |  |  | 0.76 | ribosomal | nocapeptin A | Nocardia terpenica IFM 0406
BGC0002274.2 |  |  |  |  |  |  |  | 0.74 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0000285.5 |  |  |  |  |  |  |  | 0.72 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0002347.3 |  |  |  |  |  |  |  | 0.72 | other (other) | cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D | Actinoalloteichus caeruleus WH1-2216-6

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002341.2 |  | 0.75 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.73 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001539.4 |  | 0.73 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002053.3 |  | 0.72 | ribosomal | ulleungdin | Streptomyces sp.
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001507.3 |  | 0.68 | ribosomal | anantin C | Streptomyces olindensis
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.

#### Lassopeptide(s) for K6K39_RS01405

K6K39_RS01405
Leader:
MENRDEVYEAPMLSEAGDFTEVTL
Full core:
G W P W G D R Y D G G L P P Y W R F P Y G G
Putative macrolactam:
G W P W G D R Y D

#### antiSMASH-DB 4.0 matches for K6K39_RS01405

100.0%
NZ_AP024135.1 and 1 other:
NZ_CP011799.1 Lassopeptides: QR97_RS38205_lassopeptide
Lassopeptides: K6K39_RS01405_lassopeptide
1
G W P W G D R Y D G G L P P Y W R F P Y G G
22
G W P W G D R Y D G G L P P Y W R F P Y G G
1
G W P W G D R Y D G G L P P Y W R F P Y G G
22
90.9%
NZ_BNCB01000003.1:
Lassopeptides: IE323_RS06225_lassopeptide
1
G W P W G D R Y D G G L P P Y W R F P Y G
21
G W P W G+R Y D G G L P P Y W R F P Y G
1
G W P W G N R Y D G G L P P Y W R F P Y G
21
72.7%
NZ_BMSK01000006.1:
Lassopeptides: IE251_RS14140_lassopeptide
1
G W P W G D R Y D G G L P P Y W R F P Y G
21
G W P+G R D G G L P P Y W +P Y G
1
G W P F G Y R R D G G L P P Y W L Y P Y G
21
with 12 more sequence matches
Only the first 10 are displayed here.
63.6%
NZ_CP050504.1:
Lassopeptides: HB370_RS02875_lassopeptide
1
G W P W G D R Y D G G L P P Y W R F P Y
20
G W P+G R D G G L P P Y W +P+
1
G W P F G H R R D G G L P P Y W L Y P W
20
40.9%
NZ_BMNG01000001.1 and 1 other:
NZ_CP048641.1 Lassopeptides: G3H79_RS13380_lassopeptide
Lassopeptides: IEY91_RS02775_lassopeptide
1
G W P W G D R Y D G G L P P Y
15
G G R Y+G G P P Y
1
G E A L G A R Y E G G F P P Y
15
40.9%
NZ_CP023699.1:
Lassopeptides: CP970_RS03810_lassopeptide
1
G W P W G D R Y D G G L P P Y
15
G P G Y+G G P P Y
1
G E P L G A F Y E G G F P P Y
15
36.4%
NC_016582.1:
Lassopeptides: SBI_RS53910_lassopeptide
1
G W P W G D R Y D G G L P P Y W R F
18
G +G +Y D G G P Y ++
1
G S I F G F Q Y D G G F Y P Y S Q Y
18
36.4%
NZ_BMUM01000011.1 and 2 others:
NZ_CP022685.1 Lassopeptides: KY5_RS41585_lassopeptide NZ_CP066831.1 Lassopeptides: JEQ17_RS43720_lassopeptide
Lassopeptides: IE284_RS31510_lassopeptide
1
G W P W G D R Y D G G L P P Y
15
G G Y+G G P P Y
1
G E A L G A F Y E G G F P P Y
15
36.4%
NZ_BNBL01000011.1:
Lassopeptides: IE295_RS25550_lassopeptide
1
G W P W G D R Y D G G L P P Y
15
G G +Y+G G P P Y
1
G E A T G A Q Y E G G F P P Y
15
36.4%
NZ_CP040916.1:
Lassopeptides: FH965_RS40555_lassopeptide
1
G W P W G D R Y D G G L P P Y
15
G G Y+G G P P Y
1
G E A L G S Y Y E G G F P P Y
15
36.4%
NZ_JANFDE010000002.1 and 1 other:
NZ_WPBY01000032.1 Lassopeptides: GO001_RS30935_lassopeptide
Lassopeptides: FHS35_RS09150_lassopeptide
1
G W P W G D R Y D G G L P P Y
15
G G Y+G G P P Y
1
G E A L G A H Y E G G F P P Y
15
30.4%
NZ_AP018268.1:
Lanthipeptides: allorf_1172443_1172643_lanthipeptide
6
D R Y D G G L P P Y W R F P Y G
21
R Y G G P R G
1
Q R Y A G G F P D S R R L A C G
16
25.0%
NZ_PHJF01000008.1:
Lassopeptides: CV091_RS20315_lassopeptide
1
G W P W G D R Y D G G L P P
14
G G R D P P
1
G L S T G S R L D S S F P P
14

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

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

Genes with terpene domains:
K6K39_RS01500: PT_phytoene_like
Domain 1 (17 - 236): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

K6K39_RS01505: PT_FPPS_like
Domain 1 (41 - 308): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.38 out of 25.88
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.68 out of 20.47
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.59 out of 26.85
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 25.99 out of 29.51
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.74 out of 29.72
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.70 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.03 out of 28.19
Confidence: medium
Additional weak hits (35):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.12 out of 21.84
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.99 out of 36.54
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.25 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.08 out of 30.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.48 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.08 out of 29.38
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.12 out of 27.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.09 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.81 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.46 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.53 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.81 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.69 out of 36.54
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 19.26
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.87 out of 35.63
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.76 out of 32.93
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.80 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.32 out of 30.98
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.52 out of 36.53
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.55 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.77 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.21 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.29 out of 33.14
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 20.96 out of 36.53
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.62 out of 28.19
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.75 out of 27.04
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.69 out of 35.63
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.40 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.68 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Lasso peptides
NRPS/PKS products
NRPS/PKS substrates
RREFinder
Terpene
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

K6K39_RS01405 - Class II
  Cleavage pHMM score: 1.30
  RODEO score: 20
  Monoisotopic mass: 2580.2 Da
  Molecular weight: 2581.8 Da
  Number of bridges: 0

Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 3, location 253073 - 380437:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Tyr) + (Me-ccmal - ccmal - Me-ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 253073 - 309009:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Tyr) + (Me-ccmal - ccmal - Me-ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 295524 - 336700:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Tyr)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
K6K39_RS01190: mmal - mal - mmal
PKS_AT (570..865): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Malonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 220.2
  Ethylmalonyl-CoA: 214.5
  Methoxymalonyl-CoA: 180.6
  2-Methylbutyryl-CoA: 144.3
  trans-1,2-CPDA: 129.1
  Malonyl-CoA: 112.8
  Propionyl-CoA: 98.6
  CHC-CoA: 94.1
  Isobutyryl-CoA: 78.2
  Benzoyl-CoA: 62.2
  fatty_acid: 39.2
  Acetyl-CoA: 26.0
  inactive: 22.4
  3-Methylbutyryl-CoA: 15.2

PKS_AT (2322..2616): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 183.2
  inactive: 98.5
  Methoxymalonyl-CoA: 64.6
  Methylmalonyl-CoA: 45.0
  Propionyl-CoA: 31.9
  Ethylmalonyl-CoA: 25.2
  Acetyl-CoA: 23.8
  Isobutyryl-CoA: 19.7
  Benzoyl-CoA: 14.1
  trans-1,2-CPDA: 12.7
  CHC-CoA: 12.1
  2-Methylbutyryl-CoA: 9.0
  fatty_acid: 7.1
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4139..4439): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 83.3%
  Ethylmalonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 164.7
  Ethylmalonyl-CoA: 144.6
  Methoxymalonyl-CoA: 126.3
  trans-1,2-CPDA: 97.9
  2-Methylbutyryl-CoA: 84.1
  Propionyl-CoA: 82.0
  Malonyl-CoA: 68.8
  Isobutyryl-CoA: 59.1
  CHC-CoA: 44.9
  Benzoyl-CoA: 42.7
  inactive: 22.2
  fatty_acid: 17.2
  3-Methylbutyryl-CoA: 14.0
  Acetyl-CoA: 0.0

K6K39_RS01215: Tyr
Search NORINE for peptide: strict or relaxed
AMP-binding (402..793): Tyr
nrpys: Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LTMAFDAFIAEGLLMTAGEVNAYGPTETTVCATC
  Nearest Stachelhaus code(s):
    Tyr DAAIIAAVCK (76% 8Å match)
    dh-Trp DAALMGAVTK (59% 8Å match)
  Stachelhaus code match:
    80% (moderate)

K6K39_RS01220: X
AMP-binding (10..409): 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:
    MTSAHSSGATADVLFYTGSFQVYGTSETGLISLL
  Nearest Stachelhaus code(s):
    Pro DIAVITVLIK (29% 8Å match)
  Stachelhaus code match:
    60% (weak)

K6K39_RS01335: X
AMP-binding (17..410): 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:
    GLQGSAVMFEHLLTVVAGSHHAYGQTETGMLTVL
  Nearest Stachelhaus code(s):
    End DAEDVAAMIK (35% 8Å match)
  Stachelhaus code match:
    60% (weak)

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (333268...355933)
K6K39_RS01395
  RRE type: Stand_Alone_Lasso_RRE
  Location: 1 - 85
  Score: 77.9

Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
CelR | Cellobiose uptake repressor
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C
OsdR | Development and stress management regulator
PsrA | Oleic acid responsive regulator
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NZ_AP024135.1 - Region 4 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 524,743 - 566,518 nt. (total: 41,776 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
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
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase oxidoreductase oxygenase
K6K39_RS02185: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

K6K39_RS02230: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

K6K39_RS02240: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

K6K39_RS02260: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

K6K39_RS02270: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

K6K39_RS02275: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

K6K39_RS02325: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: Halogenation
K6K39_RS02235: flavin-dependent trp 6 7 halogenase

halogenases
  flavin-dependent trp 6 7 halogenase
MITE
  MITE0000130Halogenation (identity: 66.90%)

Hydrolases: esterase
K6K39_RS02255: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: lyase
K6K39_RS02285: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase
K6K39_RS02250: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.71 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002164.2 |  | 0.65 | NRPS | peramine | Epichloe festucae
BGC0002286.3 |  | 0.65 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.64 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002075.3 |  | 0.62 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.71 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002164.2 |  | 0.65 | NRPS | peramine | Epichloe festucae
BGC0002286.3 |  | 0.65 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.64 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002075.3 |  | 0.62 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (17):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.00 out of 27.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.76 out of 23.43
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.43 out of 27.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.31 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.45 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.53 out of 29.38
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.12 out of 32.93
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.88 out of 25.75
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.46 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.81 out of 21.84
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.40 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.10 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 11, location 524742 - 566518:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
K6K39_RS02250: X
AMP-binding (17..399): X
nrpys: 6-clTrp, Trp

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:
    FALVFDGWLWCLCLVLAGELNVYGPTETTIAATW
  Nearest Stachelhaus code(s):
    6-clTrp or Trp DGWCVAVIAK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_AP024135.1 - Region 5 - atropopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 567,201 - 588,445 nt. (total: 21,245 nt) Show pHMM detection rules used
atropopeptide: atropopeptide_p450

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase oxygenase
K6K39_RS02420: Biaryl bond formation

MITE
  MITE0000172Biaryl bond formation (identity: 77.30%)
smcogs
  SMCOG1034: cytochrome P450

K6K39_RS02465: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Hydrolases: hydrolase
K6K39_RS02395: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: hydratase
K6K39_RS02455: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

Ligases: oxygenase
K6K39_RS02420: Biaryl bond formation

MITE
  MITE0000172Biaryl bond formation (identity: 77.30%)
smcogs
  SMCOG1034: cytochrome P450

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | atropopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002751.2 |  | 0.61 | ribosomal | Amyxirubin B | Amycolatopsis xylanica
BGC0000908.3 |  | 0.39 | other (other) | melanin | Streptomyces avermitilis
BGC0000843.5 |  | 0.39 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0001650.4 |  | 0.38 | NRPS | Le-pyrrolopyrazines | Lysobacter enzymogenes
BGC0002594.2 |  | 0.38 | PKS | orcinol, orsellinic acid | Fusarium graminearum PH-1
BGC0001778.5 |  | 0.37 | other (other) | showdomycin | Streptomyces showdoensis
BGC0000821.5 |  | 0.37 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0002229.2 |  | 0.37 | PKS | 6-MSA, aculin A | Aspergillus aculeatus ATCC 16872
BGC0001441.5 |  | 0.37 | other (other) | belactosin A, belactosin C | Streptomyces sp.
BGC0001366.5 |  | 0.36 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002751.2 |  | 0.61 | ribosomal | Amyxirubin B | Amycolatopsis xylanica
BGC0000908.3 |  | 0.39 | other (other) | melanin | Streptomyces avermitilis
BGC0000843.5 |  | 0.39 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0001650.4 |  | 0.38 | NRPS | Le-pyrrolopyrazines | Lysobacter enzymogenes
BGC0002594.2 |  | 0.38 | PKS | orcinol, orsellinic acid | Fusarium graminearum PH-1
BGC0001778.5 |  | 0.37 | other (other) | showdomycin | Streptomyces showdoensis
BGC0000821.5 |  | 0.37 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0002229.2 |  | 0.37 | PKS | 6-MSA, aculin A | Aspergillus aculeatus ATCC 16872
BGC0001441.5 |  | 0.37 | other (other) | belactosin A, belactosin C | Streptomyces sp.
BGC0001366.5 |  | 0.36 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 27.18 out of 30.12
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.37 out of 30.12
Confidence: medium
Additional weak hits (12):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.80 out of 20.01
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.88 out of 25.75
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.02 out of 27.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 25.75
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.33 out of 26.85
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.60 out of 20.97
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.07 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.04 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.05 out of 33.14
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.67 out of 36.53
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
OsdR | Development and stress management regulator

NZ_AP024135.1 - Region 6 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 729,953 - 751,446 nt. (total: 21,494 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
K6K39_RS03130: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Transferases: methyltransferase
K6K39_RS03100: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0001605.3 |  | 0.42 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0002221.2 |  | 0.41 | terpene | ent-kauren-16alpha-ol | Serpula lacrymans var. lacrymans S7.9
BGC0001782.3 |  | 0.35 | other (other) | spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G | Streptomyces sp. SCSIO 03032
BGC0002036.4 |  | 0.34 | other (other) | dehydrofosmidomycin | Streptomyces lavendulae
BGC0000672.4 |  | 0.34 | terpene | phytocassane, oryzalides | Oryza sativa Japonica Group
BGC0002304.3 |  | 0.34 | NRPS, PKS | varicidin A | Talaromyces variabilis
BGC0002545.3 |  | 0.34 | PKS | sungeidine C, sungeidine B, sungeidine D, sungeidine H, sungeidine A, sungeidine E, sungeidine F, sungeidine G | Micromonospora sp.
BGC0001325.3 |  | 0.33 | other (other) | noscapine | Papaver somniferum
BGC0001595.3 |  | 0.31 | other (other) | fischerindole | Fischerella sp. SAG 46.79

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0001605.3 |  | 0.42 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0002221.2 |  | 0.41 | terpene | ent-kauren-16alpha-ol | Serpula lacrymans var. lacrymans S7.9
BGC0001782.3 |  | 0.35 | other (other) | spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G | Streptomyces sp. SCSIO 03032
BGC0002036.4 |  | 0.34 | other (other) | dehydrofosmidomycin | Streptomyces lavendulae
BGC0000672.4 |  | 0.34 | terpene | phytocassane, oryzalides | Oryza sativa Japonica Group
BGC0002304.3 |  | 0.34 | NRPS, PKS | varicidin A | Talaromyces variabilis
BGC0002545.3 |  | 0.34 | PKS | sungeidine C, sungeidine B, sungeidine D, sungeidine H, sungeidine A, sungeidine E, sungeidine F, sungeidine G | Micromonospora sp.
BGC0001325.3 |  | 0.33 | other (other) | noscapine | Papaver somniferum
BGC0001595.3 |  | 0.31 | other (other) | fischerindole | Fischerella sp. SAG 46.79

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene | drimane-type |  | C15 | C2-C7 + C6-C11 | PP

Genes with terpene domains:
K6K39_RS03120: T2TS
Domain 1 (9 - 490): Type 2 terpene synthase
Subtype: Sesquiterpene synthase, group b

Reactions:
  FPP → sesquiterpene_C2-C7/C6-C11_PP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.42 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.68 out of 20.47
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.00 out of 23.79
Confidence: medium
Additional weak hits (6):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.61 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.21 out of 30.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.25 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.66 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.09 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.21 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP024135.1 - Region 7 - NRPS,RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 824,878 - 903,788 nt. (total: 78,911 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
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
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
K6K39_RS03465: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

K6K39_RS03555: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acetyltransferase acyltransferase
K6K39_RS03455: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

K6K39_RS03525: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

K6K39_RS03545: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Hydrolases: hydrolase
K6K39_RS03485: isochorismatase

smcogs
  SMCOG1027: isochorismatase

K6K39_RS03550: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

K6K39_RS03600: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Isomerases: racemase
K6K39_RS03470: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase
K6K39_RS03535: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  | 0.44 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  | 0.42 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  |  | 0.41 | NRPS | AM-toxin | Alternaria alternata
BGC0000518.3 |  |  | 0.41 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0001128.4 |  |  | 0.40 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.39 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.39 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  |  | 0.38 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  |  | 0.37 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001133.4 |  |  | 0.37 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.72 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001133.4 |  | 0.69 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.68 out of 19.52
Confidence: medium
Additional weak hits (8):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.22 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.43 out of 30.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.38 out of 29.65
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 20.53 out of 36.53
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.75 out of 23.43
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 11.66 out of 26.06
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.03 out of 30.22
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 20.53 out of 36.53
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 14, location 824877 - 903788:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu - D-Ala - D-Val - D-Ala - Leu) + (D-Orn - Thr - D-X - Val - D-Leu)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
K6K39_RS03535: Orn - Thr - X - Val - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (519..906): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAHAFDTSLEGLDVMLGGEHNFYGPTECTVDALS
  Nearest Stachelhaus code(s):
    Orn DTEDMGFVDK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2016..2423): 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:
    LRTHFDFSVWEGNQIFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3078..3470): X
nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDHAFDTSWEGLNVLVGGEYNMYGPTECTVDAVY
  Nearest Stachelhaus code(s):
    Lys DTEDMGYVDK (76% 8Å match)
    Orn DTEDMGYVDK (76% 8Å match)
    Asp DMKDLGMVDK (65% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (4582..4963): 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:
    LDSSFDAATFEAWLWTGGDVDGYGPTETTTFATS
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (94% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (5615..5996): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAAAFDASVLEVLIVVGAEINSYGPTEATVVATW
  Nearest Stachelhaus code(s):
    Leu DALLVGAVVK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

K6K39_RS03545: Leu - Ala - Val - Ala - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (39..417): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAASFDASVLEVLIIVGAEINSYGPTEATIVATW
  Nearest Stachelhaus code(s):
    Leu or 3OH-Leu DALLIGAVVK (71% 8Å match)
    Leu DALLIGAVVK (71% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1113..1508): 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:
    LWATFDVSVFECSGVLAGEANIYGPTEATVYATA
  Nearest Stachelhaus code(s):
    Ala DVFSVAIVYK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2613..3009): 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:
    LDRSFDAATYEVWLWTGGEVDGYGPTETTTFATR
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4117..4513): 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:
    LWATFDVSVFESSAVLAGERNIYGPTEATVYATA
  Nearest Stachelhaus code(s):
    Ala DVFSVAIVYK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5724..6109): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAEAFDASVLEMLLIVGADVNSYGPTEATVVATW
  Nearest Stachelhaus code(s):
    Leu or 3OH-Leu DALLIGAVVK (76% 8Å match)
    Leu DALLIGAVVK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production

NZ_AP024135.1 - Region 8 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,000,748 - 1,021,380 nt. (total: 20,633 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
K6K39_RS04065: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: acetyltransferase
K6K39_RS04125: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001210.5 |  | 0.40 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002382.3 |  | 0.39 | ribosomal | grimoviridin | Grimontia marina
BGC0002285.2 |  | 0.38 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0002073.3 |  | 0.38 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0002222.2 |  | 0.37 | PKS | zopfiellin | Diffractella curvata
BGC0000518.3 |  | 0.36 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002568.2 |  | 0.36 | other (other) | Ethylenediaminesuccinic acid hydroxyarginine | Streptomyces scabiei 87.22
BGC0001792.5 |  | 0.35 | NRPS | surugamide A, surugamide D | Streptomyces albidoflavus
BGC0001964.2 |  | 0.34 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0001610.5 |  | 0.34 | other (other) | gougerotin | Streptomyces ahygroscopicus subsp. wuzhouensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001210.5 |  | 0.40 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002382.3 |  | 0.39 | ribosomal | grimoviridin | Grimontia marina
BGC0002285.2 |  | 0.38 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0002073.3 |  | 0.38 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0002222.2 |  | 0.37 | PKS | zopfiellin | Diffractella curvata
BGC0000518.3 |  | 0.36 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002568.2 |  | 0.36 | other (other) | Ethylenediaminesuccinic acid hydroxyarginine | Streptomyces scabiei 87.22
BGC0001792.5 |  | 0.35 | NRPS | surugamide A, surugamide D | Streptomyces albidoflavus
BGC0001964.2 |  | 0.34 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0001610.5 |  | 0.34 | other (other) | gougerotin | Streptomyces ahygroscopicus subsp. wuzhouensis

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
K6K39_RS04115: TS_Pyr4
Domain 1 (2 - 206): Pyr4 type terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (7):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.73 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.67 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.18 out of 20.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.25 out of 24.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.04 out of 29.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 14.97 out of 33.14
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_AP024135.1 - Region 9 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,148,269 - 1,173,410 nt. (total: 25,142 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lanthipeptides
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
K6K39_RS04745: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

K6K39_RS04850: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: cyclase dehydratase
K6K39_RS04815: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

K6K39_RS04820: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.52 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002609.2 |  | 0.51 | NRPS, PKS | ochratoxin A | Aspergillus welwitschiae
BGC0002316.2 |  | 0.47 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0001633.3 |  | 0.43 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000556.5 |  | 0.43 | ribosomal | streptin | Streptococcus pyogenes
BGC0000544.4 |  | 0.42 | ribosomal | planosporicin | Planomonospora alba
BGC0001727.3 |  | 0.42 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000866.5 |  | 0.42 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000603.5 |  | 0.41 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0000218.5 |  | 0.40 | PKS | doxorubicin | Streptomyces peucetius

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.52 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002609.2 |  | 0.51 | NRPS, PKS | ochratoxin A | Aspergillus welwitschiae
BGC0002316.2 |  | 0.47 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0001633.3 |  | 0.43 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000556.5 |  | 0.43 | ribosomal | streptin | Streptococcus pyogenes
BGC0000544.4 |  | 0.42 | ribosomal | planosporicin | Planomonospora alba
BGC0001727.3 |  | 0.42 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000866.5 |  | 0.42 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000603.5 |  | 0.41 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0000218.5 |  | 0.40 | PKS | doxorubicin | Streptomyces peucetius

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.

#### Lanthipeptide(s) for K6K39_RS04815

K6K39_RS04810
Leader:
MAPQNSTVPLKAATDFTGDGGSDFDLRVETVASVAVPG
Core:
A L L N D T G D G C G S T C Q S A C A N S T C I G G
Core with dehydrations:
A L L N D Dhb G D G Cys G Dha Dhb Cys Q Dha A Cys A N Dha Dhb Cys I G G

#### antiSMASH-DB 4.0 matches for K6K39_RS04810

100.0%
NZ_AP024135.1 and 3 others:
NZ_AP024135.1 Lanthipeptides: K6K39_RS04810_lanthipeptide NZ_CP084203.1 Lanthipeptides: KBP30_RS00925_lanthipeptide NZ_CP084203.1 Lanthipeptides: KBP30_RS00925_lanthipeptide
Lanthipeptides: K6K39_RS04810_lanthipeptide
1
A L L N D T G D G C G S T C Q S A C A N S T C I G G
26
A L L N D T G D G C G S T C Q S A C A N S T C I G G
1
A L L N D T G D G C G S T C Q S A C A N S T C I G G
26
96.2%
NZ_CP029188.1 and 1 other:
NZ_CP029188.1 Lanthipeptides: DDW44_RS30840_lanthipeptide
Lanthipeptides: DDW44_RS30840_lanthipeptide
1
A L L N D T G D G C G S T C Q S A C A N S T C I G G
26
A L L N D T G D G C G S T C Q S A C+N S T C I G G
1
A L L N D T G D G C G S T C Q S A C S N S T C I G G
26
88.5%
NZ_CP031264.1 and 1 other:
NZ_CP031264.1 Lanthipeptides: C7M71_RS17720_lanthipeptide
Lanthipeptides: C7M71_RS17720_lanthipeptide
2
L L N D T G D G C G S T C Q S A C A N S T C I G G
26
L L N D T G D G C G S T C Q S A C+N S T C I G
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
with 180 more sequence matches
Only the first 10 are displayed here.
88.5%
NZ_CP045096.1 and 1 other:
NZ_CP045096.1 Lanthipeptides: F9278_RS23695_lanthipeptide
Lanthipeptides: F9278_RS23695_lanthipeptide
2
L L N D T G D G C G S T C Q S A C A N S T C I G G
26
L L N D T G D G C G+T C Q S A C+N S T C I G G
1
L L N D T G D G C G A T C Q S A C S N S T C I G G
25
82.1%
NZ_CP084541.1 and 1 other:
NZ_CP084541.1 Lanthipeptides: LC193_RS13810_lanthipeptide
Lanthipeptides: LC193_RS13810_lanthipeptide
2
L L N D T G D G C G S T C Q S A C A N S T C I G G
26
L L N D T G D G C S T C Q S A C+N S T C I G G
4
L L N D T G D G C T S T C Q S A C S N S T C I G G
28
80.8%
NZ_CP045031.1 and 2 others:
NZ_JAGPXX010000003.1 Lanthipeptides: KBZ10_RS05935_lanthipeptide NZ_JAGPXX010000003.1 Lanthipeptides: KBZ10_RS05935_lanthipeptide
Lanthipeptides: F9V55_RS07565_lanthipeptide
3
L N D T G D G C G S T C Q S A C A N S T C I G G
26
L N D T D C G S T C Q S A C+N S T C I G G
1
L N D T S D N C G S T C Q S A C S N S T C I G G
24
80.8%
NZ_FOLM01000004.1 and 1 other:
NZ_FOLM01000004.1 Lanthipeptides: BM242_RS10130_lanthipeptide
Lanthipeptides: BM242_RS10130_lanthipeptide
2
L L N D T G D G C G S T C Q S A C A N S T C I G G
26
L L N D T D C S T C Q S A C+N S T C I G G
1
L L N D T D D N C T S T C Q S A C S N S T C I G G
25
76.9%
NZ_BMSX01000001.1 and 10 others:
NZ_BMSX01000001.1 Lanthipeptides: IE263_RS00615_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP102512.1 Lanthipeptides: JIX56_RS21495_lanthipeptide NZ_CP102512.1 Lanthipeptides: JIX56_RS21495_lanthipeptide NZ_CP119143.1 Lanthipeptides: PYR72_RS23045_lanthipeptide NZ_CP119143.1 Lanthipeptides: PYR72_RS23045_lanthipeptide NZ_KL997427.1 Lanthipeptides: IQ62_RS25015_lanthipeptide NZ_KL997427.1 Lanthipeptides: IQ62_RS25015_lanthipeptide
Lanthipeptides: IE263_RS00615_lanthipeptide
3
L N D T G D G C G S T C Q S A C A N S T C I G G
26
L N D T D C S T C Q S A C N S T C I G G
1
L N D T S D N C T S T C Q S A C T N S T C I G G
24
76.9%
NZ_VEHK01000015.1 and 1 other:
NZ_VEHK01000015.1 Lanthipeptides: FS984_RS32600_lanthipeptide
Lanthipeptides: FS984_RS32600_lanthipeptide
3
L N D T G D G C G S T C Q S A C A N S T C I G
25
L N D T D G C S T C Q S A C+N S T C I G
1
L N D T S D G C T S T C Q S A C S N S T C I G
23
73.1%
NZ_BBUZ01000023.1 and 5 others:
NZ_BBUZ01000023.1 Lanthipeptides: ASC60_RS09240_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS29940_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS29940_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS29795_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS29795_lanthipeptide
Lanthipeptides: ASC60_RS09240_lanthipeptide
2
L L N D T G D G C G S T C Q S A C A N S T C
23
L L N D T G D G C +T C Q S A C+N S T C
1
L L N D T G D G C T A T C Q S A C S N S T C
22
73.1%
NZ_BBYG01000008.1 and 3 others:
NZ_BBYG01000008.1 Lanthipeptides: AOQ37_RS04295_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS17875_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS17875_lanthipeptide
Lanthipeptides: AOQ37_RS04295_lanthipeptide
3
L N D T G D G C G S T C Q S A C A N S T C
23
L N D T G D G C S T C Q S A C+N S T C
1
L N D T G D G C T S T C Q S A C S N S T C
21
73.1%
NZ_CP030771.1 and 4 others:
NZ_CP030771.1 Lanthipeptides: C9F11_RS21100_lanthipeptide NZ_FNIE01000002.1 Lanthipeptides: BLR33_RS05585_lanthipeptide NZ_FNIE01000002.1 Lanthipeptides: BLR33_RS05585_lanthipeptide NZ_FNIE01000002.1 Lanthipeptides: BLR33_RS05585_lanthipeptide
Lanthipeptides: C9F11_RS21100_lanthipeptide
3
L N D T G D G C G S T C Q S A C A N S T C I G G
26
L N D T D C S T C S A C+N S T C I G G
1
L N D T S D N C T S T C A S A C S N S T C I G G
24
73.1%
NZ_KQ257877.1 and 1 other:
NZ_KQ257877.1 Lanthipeptides: IQ64_RS44800_lanthipeptide
Lanthipeptides: IQ64_RS44800_lanthipeptide
3
L N D T G D G C G S T C Q S A C A N S T C
23
L N D T G D G C G T C Q S A C+N S T C
1
L N D T G D G C G Q T C Q S A C S N S T C
21

#### Lanthipeptide(s) for K6K39_RS04825

K6K39_RS04810
Leader:
MAPQNSTVPLKAATDFTGDGGSDFDLRVETVASVAVPG
Core:
A L L N D T G D G C G S T C Q S A C A N S T C I G G
Core with dehydrations:
A L L N D Dhb G D G Cys G Dha Dhb Cys Q Dha A Cys A N Dha Dhb Cys I G G

#### antiSMASH-DB 4.0 matches for K6K39_RS04810

100.0%
NZ_AP024135.1 and 3 others:
NZ_AP024135.1 Lanthipeptides: K6K39_RS04810_lanthipeptide NZ_CP084203.1 Lanthipeptides: KBP30_RS00925_lanthipeptide NZ_CP084203.1 Lanthipeptides: KBP30_RS00925_lanthipeptide
Lanthipeptides: K6K39_RS04810_lanthipeptide
1
A L L N D T G D G C G S T C Q S A C A N S T C I G G
26
A L L N D T G D G C G S T C Q S A C A N S T C I G G
1
A L L N D T G D G C G S T C Q S A C A N S T C I G G
26
96.2%
NZ_CP029188.1 and 1 other:
NZ_CP029188.1 Lanthipeptides: DDW44_RS30840_lanthipeptide
Lanthipeptides: DDW44_RS30840_lanthipeptide
1
A L L N D T G D G C G S T C Q S A C A N S T C I G G
26
A L L N D T G D G C G S T C Q S A C+N S T C I G G
1
A L L N D T G D G C G S T C Q S A C S N S T C I G G
26
88.5%
NZ_CP031264.1 and 1 other:
NZ_CP031264.1 Lanthipeptides: C7M71_RS17720_lanthipeptide
Lanthipeptides: C7M71_RS17720_lanthipeptide
2
L L N D T G D G C G S T C Q S A C A N S T C I G G
26
L L N D T G D G C G S T C Q S A C+N S T C I G
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
with 180 more sequence matches
Only the first 10 are displayed here.
88.5%
NZ_CP045096.1 and 1 other:
NZ_CP045096.1 Lanthipeptides: F9278_RS23695_lanthipeptide
Lanthipeptides: F9278_RS23695_lanthipeptide
2
L L N D T G D G C G S T C Q S A C A N S T C I G G
26
L L N D T G D G C G+T C Q S A C+N S T C I G G
1
L L N D T G D G C G A T C Q S A C S N S T C I G G
25
82.1%
NZ_CP084541.1 and 1 other:
NZ_CP084541.1 Lanthipeptides: LC193_RS13810_lanthipeptide
Lanthipeptides: LC193_RS13810_lanthipeptide
2
L L N D T G D G C G S T C Q S A C A N S T C I G G
26
L L N D T G D G C S T C Q S A C+N S T C I G G
4
L L N D T G D G C T S T C Q S A C S N S T C I G G
28
80.8%
NZ_CP045031.1 and 2 others:
NZ_JAGPXX010000003.1 Lanthipeptides: KBZ10_RS05935_lanthipeptide NZ_JAGPXX010000003.1 Lanthipeptides: KBZ10_RS05935_lanthipeptide
Lanthipeptides: F9V55_RS07565_lanthipeptide
3
L N D T G D G C G S T C Q S A C A N S T C I G G
26
L N D T D C G S T C Q S A C+N S T C I G G
1
L N D T S D N C G S T C Q S A C S N S T C I G G
24
80.8%
NZ_FOLM01000004.1 and 1 other:
NZ_FOLM01000004.1 Lanthipeptides: BM242_RS10130_lanthipeptide
Lanthipeptides: BM242_RS10130_lanthipeptide
2
L L N D T G D G C G S T C Q S A C A N S T C I G G
26
L L N D T D C S T C Q S A C+N S T C I G G
1
L L N D T D D N C T S T C Q S A C S N S T C I G G
25
76.9%
NZ_BMSX01000001.1 and 10 others:
NZ_BMSX01000001.1 Lanthipeptides: IE263_RS00615_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP102512.1 Lanthipeptides: JIX56_RS21495_lanthipeptide NZ_CP102512.1 Lanthipeptides: JIX56_RS21495_lanthipeptide NZ_CP119143.1 Lanthipeptides: PYR72_RS23045_lanthipeptide NZ_CP119143.1 Lanthipeptides: PYR72_RS23045_lanthipeptide NZ_KL997427.1 Lanthipeptides: IQ62_RS25015_lanthipeptide NZ_KL997427.1 Lanthipeptides: IQ62_RS25015_lanthipeptide
Lanthipeptides: IE263_RS00615_lanthipeptide
3
L N D T G D G C G S T C Q S A C A N S T C I G G
26
L N D T D C S T C Q S A C N S T C I G G
1
L N D T S D N C T S T C Q S A C T N S T C I G G
24
76.9%
NZ_VEHK01000015.1 and 1 other:
NZ_VEHK01000015.1 Lanthipeptides: FS984_RS32600_lanthipeptide
Lanthipeptides: FS984_RS32600_lanthipeptide
3
L N D T G D G C G S T C Q S A C A N S T C I G
25
L N D T D G C S T C Q S A C+N S T C I G
1
L N D T S D G C T S T C Q S A C S N S T C I G
23
73.1%
NZ_BBUZ01000023.1 and 5 others:
NZ_BBUZ01000023.1 Lanthipeptides: ASC60_RS09240_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS29940_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS29940_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS29795_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS29795_lanthipeptide
Lanthipeptides: ASC60_RS09240_lanthipeptide
2
L L N D T G D G C G S T C Q S A C A N S T C
23
L L N D T G D G C +T C Q S A C+N S T C
1
L L N D T G D G C T A T C Q S A C S N S T C
22
73.1%
NZ_BBYG01000008.1 and 3 others:
NZ_BBYG01000008.1 Lanthipeptides: AOQ37_RS04295_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS17875_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS17875_lanthipeptide
Lanthipeptides: AOQ37_RS04295_lanthipeptide
3
L N D T G D G C G S T C Q S A C A N S T C
23
L N D T G D G C S T C Q S A C+N S T C
1
L N D T G D G C T S T C Q S A C S N S T C
21
73.1%
NZ_CP030771.1 and 4 others:
NZ_CP030771.1 Lanthipeptides: C9F11_RS21100_lanthipeptide NZ_FNIE01000002.1 Lanthipeptides: BLR33_RS05585_lanthipeptide NZ_FNIE01000002.1 Lanthipeptides: BLR33_RS05585_lanthipeptide NZ_FNIE01000002.1 Lanthipeptides: BLR33_RS05585_lanthipeptide
Lanthipeptides: C9F11_RS21100_lanthipeptide
3
L N D T G D G C G S T C Q S A C A N S T C I G G
26
L N D T D C S T C S A C+N S T C I G G
1
L N D T S D N C T S T C A S A C S N S T C I G G
24
73.1%
NZ_KQ257877.1 and 1 other:
NZ_KQ257877.1 Lanthipeptides: IQ64_RS44800_lanthipeptide
Lanthipeptides: IQ64_RS44800_lanthipeptide
3
L N D T G D G C G S T C Q S A C A N S T C
23
L N D T G D G C G T C Q S A C+N S T C
1
L N D T G D G C G Q T C Q S A C S N S T C
21

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.61 out of 27.04
Confidence: medium
Additional weak hits (4):
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.88 out of 19.26
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.09 out of 21.55
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.11 out of 27.04
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.14 out of 26.06
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

K6K39_RS04810 - Class I
  Cleavage pHMM score: -2.50
  RODEO score: 22
  Monoisotopic mass: 2310.0 Da
  Molecular weight: 2311.5 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2329.5 Da N = 1
    2347.5 Da N = 2
K6K39_RS04810 - Class I
  Cleavage pHMM score: -2.50
  RODEO score: 22
  Monoisotopic mass: 2310.0 Da
  Molecular weight: 2311.5 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2329.5 Da N = 1
    2347.5 Da N = 2

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (1148268...1173410)
K6K39_RS04815
  RRE type: Lanthipeptide_LanB_RRE
  Location: 153 - 241
  Score: 76.9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor

NZ_AP024135.1 - Region 10 - ectoine
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,499,990 - 1,510,394 nt. (total: 10,405 nt) Show pHMM detection rules used
ectoine: ectoine_synt

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase
K6K39_RS06475: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

K6K39_RS06500: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.80 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.80 | other (other) | ectoine | Streptomyces anulatus
BGC0000859.3 |  | 0.60 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.59 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000854.3 |  | 0.58 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z
BGC0000857.3 |  | 0.58 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.53 | other (other) | ectoine | Methylarcula marina
BGC0000852.5 |  | 0.51 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.50 | other (other) | ectoine | Methylobacter marinus
BGC0000856.3 |  | 0.49 | other (other) | ectoine | Methylophaga thalassica

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.80 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.80 | other (other) | ectoine | Streptomyces anulatus
BGC0000859.3 |  | 0.60 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.59 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000854.3 |  | 0.58 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z
BGC0000857.3 |  | 0.58 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.53 | other (other) | ectoine | Methylarcula marina
BGC0000852.5 |  | 0.51 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.50 | other (other) | ectoine | Methylobacter marinus
BGC0000856.3 |  | 0.49 | other (other) | ectoine | Methylophaga thalassica

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.71 out of 20.47
Confidence: medium
Additional weak hits (6):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.27 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.10 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.21 out of 28.14
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.13 out of 26.33
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.00 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP024135.1 - Region 11 - T2PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,896,129 - 1,968,642 nt. (total: 72,514 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
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
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
K6K39_RS08285: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

K6K39_RS08375: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

K6K39_RS08450: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: methyltransferase transketolase
K6K39_RS08335: transketolase

smcogs
  SMCOG1204: transketolase

K6K39_RS08410: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: glucanase glucosidase hydrolase
K6K39_RS08505: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

K6K39_RS08570: Pullulanase, type I

smcogs
  SMCOG1297: Pullulanase, type I

K6K39_RS08575: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

K6K39_RS08580: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

Lyases: cyclase dehydratase
K6K39_RS08370: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

K6K39_RS08415: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

K6K39_RS08420: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

K6K39_RS08525: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
K6K39_RS08430: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

K6K39_RS08435: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000272.3 |  | 0.76 | PKS | spore pigment | Streptomyces collinus
BGC0000271.5 |  | 0.75 | PKS | spore pigment | Streptomyces avermitilis
BGC0000215.5 |  | 0.69 | PKS | curamycin | Streptomyces cyaneus
BGC0000231.5 |  | 0.61 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001513.3 |  | 0.59 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0001366.5 |  | 0.58 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2
BGC0000234.5 |  | 0.58 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001197.5 |  | 0.57 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001273.3 |  | 0.56 | PKS | asperlactone | Aspergillus ochraceus
BGC0002000.4 |  | 0.56 | PKS | setomimycin | Streptomyces aurantiacus JA 4570

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000272.3 |  | 0.76 | PKS | spore pigment | Streptomyces collinus
BGC0000271.5 |  | 0.75 | PKS | spore pigment | Streptomyces avermitilis
BGC0000215.5 |  | 0.69 | PKS | curamycin | Streptomyces cyaneus
BGC0000231.5 |  | 0.61 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001513.3 |  | 0.59 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0001366.5 |  | 0.58 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2
BGC0000234.5 |  | 0.58 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001197.5 |  | 0.57 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001273.3 |  | 0.56 | PKS | asperlactone | Aspergillus ochraceus
BGC0002000.4 |  | 0.56 | PKS | setomimycin | Streptomyces aurantiacus JA 4570

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.67 out of 19.26
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
Additional weak hits (21):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.09 out of 27.78
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.08 out of 30.22
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 26.85
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.00 out of 27.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.05 out of 21.55
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.09 out of 32.74
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.67 out of 26.85
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.00 out of 21.55
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.55 out of 29.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.37 out of 31.73
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.63 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.72 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.38 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.39 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.41 out of 21.55
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.08 out of 30.22
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.17 out of 29.65
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Type II PKS
TFBS Finder
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  1896128 to 1968642
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Product class(es):
  pentangular polyphenol
  tetracenomycin

K6K39_RS08410
  MET C6|C8 (Score: 507.9; E-value: 2.4e-155)
K6K39_RS08415
  CYC C4-C21/C2-C23|C2-C19 (Score: 163.0; E-value: 4.2e-51)
K6K39_RS08420
  CYC C9-C14 (Score: 252.1; E-value: 3.6e-78)
K6K39_RS08425
  ACP (Score: 71.0; E-value: 1.5e-22)
K6K39_RS08430
  CLF (Score: 553.2; E-value: 7.5e-169)
K6K39_RS08435
  KS (Score: 730.4; E-value: 1.3e-222)
K6K39_RS08440
  CYC C5-C18 (Score: 213.5; E-value: 1.8e-66)
K6K39_RS08450
  OXY (Score: 273.0; E-value: 1.2e-83)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_AP024135.1 - Region 12 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,055,901 - 2,103,169 nt. (total: 47,269 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
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
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
K6K39_RS09070: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

K6K39_RS09075: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

K6K39_RS09085: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

K6K39_RS09090: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

K6K39_RS09155: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

K6K39_RS09195: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

K6K39_RS09200: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Lyases: dehydratase
K6K39_RS09100: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Isomerases: mutase
K6K39_RS09025: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

K6K39_RS09170: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: ligase
K6K39_RS09095: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS09105: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001251.4 |  | 0.70 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.70 | NRPS | epichloenin A | Epichloe festucae
BGC0002276.2 |  | 0.67 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000357.5 |  | 0.66 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001261.3 |  | 0.65 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  | 0.65 | NRPS | enniatin | Fusarium equiseti
BGC0001166.5 |  | 0.65 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001251.4 |  | 0.70 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.70 | NRPS | epichloenin A | Epichloe festucae
BGC0002276.2 |  | 0.67 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000357.5 |  | 0.66 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001261.3 |  | 0.65 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  | 0.65 | NRPS | enniatin | Fusarium equiseti
BGC0001166.5 |  | 0.65 | NRPS | HC-toxin | Alternaria jesenskae

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.31 out of 27.18
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.21 out of 27.18
Confidence: medium
Additional weak hits (5):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.91 out of 36.54
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.12 out of 30.25
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.34 out of 20.01
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 20, location 2055900 - 2103169:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser - NMe-Gly)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
K6K39_RS09095: NH2
CAL_domain (154..480): NH2
minowa: NH2

Prediction, score:
  NH2: 142.1
  fatty_acid: 39.0
  Acetyl-CoA: 32.9
  AHBA: 17.5
  shikimic_acid: 0.0

K6K39_RS09105: Ser - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (467..867): 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:
    RWMTFDVSVWEWHFVCSGEYNLYGPTEAAIDVTH
  Nearest Stachelhaus code(s):
    Ser DVWHVSLIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1521..1921): 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:
    FAMTFDISVLEWQALVGGEYNMYGPTETTIWSTV
  Nearest Stachelhaus code(s):
    Gly DILQLGMIWK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NrdR | Represses ribonucleotide reductase encoding genes

NZ_AP024135.1 - Region 13 - melanin
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,582,311 - 2,592,838 nt. (total: 10,528 nt) Show pHMM detection rules used
melanin: melC

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
K6K39_RS11335: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | melanin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000910.3 |  | 0.81 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000911.3 |  | 0.79 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000909.3 |  | 0.68 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.47 | other (other) | melanin | Streptomyces avermitilis
BGC0000885.3 |  | 0.39 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000662.5 |  | 0.34 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000889.5 |  | 0.34 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.33 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001624.3 |  | 0.30 | other (other) | iso-A82775C | Pestalotiopsis fici

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000910.3 |  | 0.81 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000911.3 |  | 0.79 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000909.3 |  | 0.68 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.47 | other (other) | melanin | Streptomyces avermitilis
BGC0000885.3 |  | 0.39 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000662.5 |  | 0.34 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000889.5 |  | 0.34 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.33 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001624.3 |  | 0.30 | other (other) | iso-A82775C | Pestalotiopsis fici

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (5):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.40 out of 32.74
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.58 out of 27.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.96 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.18 out of 28.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 25.53 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_AP024135.1 - Region 14 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,674,668 - 2,704,437 nt. (total: 29,770 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
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
K6K39_RS11720: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

K6K39_RS11745: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

K6K39_RS11765: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Transferases: carboxylase transferase
K6K39_RS11730: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

K6K39_RS11735: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Lyases: decarboxylase
K6K39_RS11760: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: synthase
K6K39_RS11740: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

Translocases: transporter
K6K39_RS11840: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001453.5 |  | 0.85 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0000940.5 |  | 0.85 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0000941.3 |  | 0.83 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.82 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002690.2 |  | 0.63 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002464.3 |  | 0.61 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002620.2 |  | 0.60 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002284.3 |  | 0.60 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001453.5 |  | 0.85 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0000940.5 |  | 0.85 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0000941.3 |  | 0.83 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.82 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002690.2 |  | 0.63 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002464.3 |  | 0.61 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002620.2 |  | 0.60 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002284.3 |  | 0.60 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 34.36 out of 36.53
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.94 out of 36.53
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.00 out of 27.04
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.26 out of 23.43
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.49 out of 25.31
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (8):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.24 out of 20.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.32 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.45 out of 27.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.58 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.26 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.83 out of 21.55
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.99 out of 36.53
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.28 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
BldD | Development and antibiotic global regulator
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor
CelR | Cellobiose uptake repressor
DasR | N-acetylglucosamine dependent repressor
DmdR1 | Iron(II)-dependent repressor
RpoN | Regulator of nitrogen assimilation and virulence

NZ_AP024135.1 - Region 15 - NRPS,NRPS-like,T1PKS,amglyccycl,butyrolactone,terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,346,377 - 4,410,237 nt. (total: 63,861 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
amglyccycl: (DOIS or ValA or salQ or strH or strK1 or strK2 or NeoL or SpcFG or SpcDK_glyc)
butyrolactone: AfsA
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
K6K39_RS19395: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

K6K39_RS19415: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

K6K39_RS19500: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

K6K39_RS19510: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

K6K39_RS19520: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

K6K39_RS19525: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: acylase acyltransferase
K6K39_RS19490: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

K6K39_RS19555: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

Hydrolases: esterase
K6K39_RS19480: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase
K6K39_RS19560: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase synthetase
K6K39_RS19485: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS19495: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

K6K39_RS19535: 3-dehydroquinate synthase

smcogs
  SMCOG1183: 3-dehydroquinate synthase

K6K39_RS19605: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS-like | T1PKS | NRPS | amglyccycl | butyrolactone | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000848.5 |  |  |  |  |  |  | 2.41 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  |  |  |  |  |  | 2.40 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  |  |  |  |  |  | 1.74 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0001249.5 |  |  |  |  |  |  | 1.24 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002286.3 |  |  |  |  |  |  | 1.03 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2 |  |  |  |  |  |  | 1.02 | NRPS | peramine | Epichloe festucae
BGC0001244.3 |  |  |  |  |  |  | 1.00 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001050.5 |  |  |  |  |  |  | 0.96 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0001273.3 |  |  |  |  |  |  | 0.95 | PKS | asperlactone | Aspergillus ochraceus
BGC0001833.4 |  |  |  |  |  |  | 0.95 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.77 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.77 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0000850.5 |  | 0.69 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0001244.3 |  | 0.67 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2 |  | 0.67 | NRPS | peramine | Epichloe festucae
BGC0001273.3 |  | 0.66 | PKS | asperlactone | Aspergillus ochraceus
BGC0001050.5 |  | 0.66 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

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

Genes with terpene domains:
K6K39_RS19605: PT_FPPS_like
Domain 1 (245 - 546): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.34 out of 25.88
Confidence: medium
Additional weak hits (21):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.51 out of 26.85
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.22 out of 26.12
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.87 out of 31.73
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.89 out of 27.55
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.86 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.66 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.14 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.00 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.06 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.62 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.28 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.85 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.19 out of 29.38
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.82 out of 27.55
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.93 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.03 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.13 out of 30.97
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.48 out of 35.63
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.78 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.81 out of 29.65
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.24 out of 36.53
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Terpene
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 23, location 4346376 - 4410237:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (mal) + (His)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 24, location 4346376 - 4388218:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (mal) + (His)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 25, location 4348411 - 4391552:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (mal) + (His)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 26, location 4351670 - 4394736:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (mal) + (His)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
K6K39_RS19485: His
Search NORINE for peptide: strict or relaxed
AMP-binding (3..401): His
nrpys: His

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    SARSFDSSVAGGLCIVAGEINEYGPTETTVWATY
  Nearest Stachelhaus code(s):
    His DSALIAEVWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

K6K39_RS19490: mal
PKS_AT (592..870): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 66.7%
  inactive: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 108.0
  Methoxymalonyl-CoA: 65.7
  Methylmalonyl-CoA: 57.3
  Ethylmalonyl-CoA: 21.0
  CHC-CoA: 18.7
  2-Methylbutyryl-CoA: 18.4
  inactive: 16.4
  Propionyl-CoA: 14.3
  Acetyl-CoA: 12.3
  trans-1,2-CPDA: 10.9
  Benzoyl-CoA: 10.5
  fatty_acid: 9.9
  Isobutyryl-CoA: 5.4
  3-Methylbutyryl-CoA: 0.0

K6K39_RS19495: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (24..417): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LPGAWDAFSLEGWLLTGGEINGYGPVESTVFATT
  Nearest Stachelhaus code(s):
    Val DALWLGGVFK (62% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
PsrA | Oleic acid responsive regulator

NZ_AP024135.1 - Region 16 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,116,131 - 5,137,156 nt. (total: 21,026 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
K6K39_RS22990: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Hydrolases: deformylase
K6K39_RS22980: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Lyases: cyclase
K6K39_RS22985: Terpene synthase/cyclase metal-binding domain protein

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

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000660.5 |  | 0.86 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0000675.5 |  | 0.49 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0000677.5 |  | 0.45 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000674.5 |  | 0.45 | terpene | (-)-δ-cadinene | Streptomyces clavuligerus ATCC 27064
BGC0001910.4 |  | 0.39 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0002339.3 |  | 0.38 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0000650.3 |  | 0.37 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000678.5 |  | 0.36 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000286.3 |  | 0.36 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0002012.4 |  | 0.35 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000660.5 |  | 0.86 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0000675.5 |  | 0.49 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0000677.5 |  | 0.45 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000674.5 |  | 0.45 | terpene | (-)-δ-cadinene | Streptomyces clavuligerus ATCC 27064
BGC0001910.4 |  | 0.39 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0002339.3 |  | 0.38 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0000650.3 |  | 0.37 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000678.5 |  | 0.36 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000286.3 |  | 0.36 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0002012.4 |  | 0.35 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
K6K39_RS22985: T1TS
Domain 1 (8 - 319): Type 1 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.75 out of 23.79
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 25.12 out of 27.18
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 23.40 out of 27.18
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.49 out of 27.04
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47
Confidence: medium
Additional weak hits (1):
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.20 out of 29.65
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
NrdR | Represses ribonucleotide reductase encoding genes
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP024135.1 - Region 17 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,140,686 - 5,161,816 nt. (total: 21,131 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: methyltransferase
K6K39_RS23155: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: synthetase
K6K39_RS23095: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0000948.5 |  | 0.45 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000678.5 |  | 0.43 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002400.2 |  | 0.43 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000664.5 |  | 0.38 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001911.3 |  | 0.37 | terpene | raimonol | Streptomyces anulatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0000948.5 |  | 0.45 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000678.5 |  | 0.43 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002400.2 |  | 0.43 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000664.5 |  | 0.38 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001911.3 |  | 0.37 | terpene | raimonol | Streptomyces anulatus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

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

Genes with terpene domains:
K6K39_RS23095: PT_FPPS_like
Domain 1 (82 - 374): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.86 out of 18.57
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.54 out of 23.79
Confidence: medium
Additional weak hits (6):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.16 out of 23.43
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.14 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.06 out of 29.65
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.48 out of 23.43
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism
ToxT | Regulator of MSHA biosynthesis

NZ_AP024135.1 - Region 18 - aminopolycarboxylic-acid
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,773,546 - 5,787,012 nt. (total: 13,467 nt) Show pHMM detection rules used
aminopolycarboxylic-acid: (AesA and AesB and AesC)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: deaminase
K6K39_RS25785: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Lyases: decarboxylase
K6K39_RS25780: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: synthase
K6K39_RS25775: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | aminopolycarboxylic-acid | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001587.5 |  | 0.83 | other (other) | ethylenediaminesuccinic acid hydroxyarginine (EDHA) | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002568.2 |  | 0.82 | other (other) | Ethylenediaminesuccinic acid hydroxyarginine | Streptomyces scabiei 87.22
BGC0002567.2 |  | 0.73 | other (other) | EDHA | Streptomyces sp. MA5143a
BGC0000943.5 |  | 0.40 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002487.3 |  | 0.37 | other (other) | staphylopine | Staphylococcus aureus subsp. aureus Mu50
BGC0000932.5 |  | 0.36 | other (other) | tropodithietic acid, hydroxytropodithietic acid | Phaeobacter inhibens DSM 17395
BGC0001429.4 |  | 0.35 | NRPS, PKS | myxochromide S1 | Stigmatella aurantiaca DW4/3-1
BGC0001431.4 |  | 0.35 | NRPS, PKS | myxochromide S | Stigmatella aurantiaca
BGC0000529.5 |  | 0.34 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0001079.5 |  | 0.34 | PKS, terpene | napyradiomycin A80915C, napyradiomycin 2, napyradiomycin 3, napyradiomycin 4 | Streptomyces aculeolatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001587.5 |  | 0.83 | other (other) | ethylenediaminesuccinic acid hydroxyarginine (EDHA) | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002568.2 |  | 0.82 | other (other) | Ethylenediaminesuccinic acid hydroxyarginine | Streptomyces scabiei 87.22
BGC0002567.2 |  | 0.73 | other (other) | EDHA | Streptomyces sp. MA5143a
BGC0000943.5 |  | 0.40 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002487.3 |  | 0.37 | other (other) | staphylopine | Staphylococcus aureus subsp. aureus Mu50
BGC0000932.5 |  | 0.36 | other (other) | tropodithietic acid, hydroxytropodithietic acid | Phaeobacter inhibens DSM 17395
BGC0001429.4 |  | 0.35 | NRPS, PKS | myxochromide S1 | Stigmatella aurantiaca DW4/3-1
BGC0001431.4 |  | 0.35 | NRPS, PKS | myxochromide S | Stigmatella aurantiaca
BGC0000529.5 |  | 0.34 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0001079.5 |  | 0.34 | PKS, terpene | napyradiomycin A80915C, napyradiomycin 2, napyradiomycin 3, napyradiomycin 4 | Streptomyces aculeolatus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.30 out of 36.53
Confidence: medium
Additional weak hits (2):
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.99 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.97 out of 36.53
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DmdR1 | Iron(II)-dependent repressor

NZ_AP024135.1 - Region 19 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,793,328 - 5,823,373 nt. (total: 30,046 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
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
K6K39_RS25940: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

Transferases: aminotransferase
K6K39_RS25895: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Isomerases: mutase
K6K39_RS25945: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002469.2 |  | 0.50 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002683.2 |  | 0.50 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000852.5 |  | 0.49 | other (other) | ectoine | Sporosarcina pasteurii
BGC0002633.2 |  | 0.49 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0000858.3 |  | 0.48 | other (other) | ectoine | Methylobacter marinus
BGC0000855.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000859.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000856.3 |  | 0.47 | other (other) | ectoine | Methylophaga thalassica
BGC0002052.3 |  | 0.46 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.46 | other (other) | ectoine | Streptomyces anulatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002469.2 |  | 0.50 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002683.2 |  | 0.50 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000852.5 |  | 0.49 | other (other) | ectoine | Sporosarcina pasteurii
BGC0002633.2 |  | 0.49 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0000858.3 |  | 0.48 | other (other) | ectoine | Methylobacter marinus
BGC0000855.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000859.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000856.3 |  | 0.47 | other (other) | ectoine | Methylophaga thalassica
BGC0002052.3 |  | 0.46 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.46 | other (other) | ectoine | Streptomyces anulatus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 26.06 out of 27.18
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.62 out of 27.18
Confidence: strong
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.93 out of 24.78
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.23 out of 23.43
Confidence: medium
Additional weak hits (10):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.65 out of 27.55
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.90 out of 33.73
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.03 out of 30.22
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.88 out of 29.65
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.77 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.90 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.09 out of 29.65
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.77 out of 25.88
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
CRP | Cyclic AMP receptor protein
LexA variant 2 | Repressor of DNA damage response
NrdR | Represses ribonucleotide reductase encoding genes

NZ_AP024135.1 - Region 20 - NRPS,NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,899,488 - 6,014,089 nt. (total: 114,602 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
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
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
K6K39_RS26315: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

K6K39_RS26320: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

K6K39_RS26395: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

K6K39_RS26425: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

Transferases: acyltransferase aminotransferase glycosyltransferase halogenase methyltransferase
K6K39_RS26350: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

K6K39_RS26415: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
MITE
  MITE0000030Halogenation (identity: 65.70%)
smcogs
  SMCOG1119: halogenase

K6K39_RS26430: aminotransferase

smcogs
  SMCOG1019: aminotransferase

K6K39_RS26445: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

K6K39_RS26475: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Hydrolases: amidase deaminase esterase hydrolase
K6K39_RS26310: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

K6K39_RS26390: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

K6K39_RS26460: amidase

smcogs
  SMCOG1105: amidase

K6K39_RS26485: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase synthase
K6K39_RS26325: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS26335: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS26385: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

K6K39_RS26400: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS26465: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS26470: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS26480: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Translocases: transporter
K6K39_RS26510: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001135.5 |  |  |  | 1.09 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  |  |  | 1.07 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  | 1.06 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  | 1.05 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  |  |  | 1.05 | NRPS | AM-toxin | Alternaria alternata
BGC0001758.4 |  |  |  | 1.02 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  |  |  | 1.02 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  |  | 1.02 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002164.2 |  |  |  | 0.99 | NRPS | peramine | Epichloe festucae
BGC0001641.4 |  |  |  | 0.99 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.77 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.76 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.76 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.76 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.76 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001641.4 |  | 0.73 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.65 out of 18.46
Confidence: strong
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.27 out of 29.51
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.43 out of 23.79
Confidence: medium
Additional weak hits (16):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.90 out of 30.22
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.29 out of 26.85
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.69 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.93 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.17 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.17 out of 29.38
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.50 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.06 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.42 out of 21.55
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.55 out of 35.63
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.35 out of 23.43
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.21 out of 26.85
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.10 out of 20.97
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.37 out of 35.63
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.00 out of 24.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 34, location 5899487 - 6014089:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly - Trp) + (X - X - Pro) + (Gly - D-Val) + (Gln - X - Tyr) + (X) + (Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 35, location 5899487 - 5943927:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 36, location 5919549 - 5961820:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (X) + (Gln - X - Tyr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 37, location 5937498 - 6014089:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly - Trp) + (X - X - Pro) + (Gly - D-Val) + (Gln - X - Tyr) + (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
K6K39_RS26325: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (54..446): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDPAWDAFSLEGWLFVGGEVNGYGPVESTVFATV
  Nearest Stachelhaus code(s):
    Val or aIle DALWWGGVFK (68% 8Å match)
    Val DALWIGGVFK (56% 8Å match)
  Stachelhaus code match:
    90% (moderate)

K6K39_RS26335: Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (18..398): 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:
    LWHAFDAFMWEPFLLTGGDVNHYGPTETTVVATS
  Nearest Stachelhaus code(s):
    Leu DAWFLGHVVK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

K6K39_RS26400: X
AMP-binding (171..573): X
nrpys: Dpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HAKAFDISLWQSQLSATGEVNAYGLTETSDDTNH
  Nearest Stachelhaus code(s):
    Dpr DIWQSTADDK (94% 8Å match)
    dnmeProp or Dab DIWQSTADDK (79% 8Å match)
    Asp DIWQSTADDK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

K6K39_RS26465: Gln - X - Tyr
Search NORINE for peptide: strict or relaxed
AMP-binding (463..869): Gln
nrpys: Gln

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HWMTFDASVWELQFFAGGEHNLYGPTECTVQATH
  Nearest Stachelhaus code(s):
    Gln DAWQFGLIQK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1532..1931): X
nrpys: OH-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:
    YWASFDLTVTGGKAVLGGEVNEYGPTETTVGCTY
  Nearest Stachelhaus code(s):
    OH-Asn DLTKVGEVGK (88% 8Å match)
    Asn DLTKVGEVGK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2588..2978): Tyr
nrpys: Tyr

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    tyr (Tyr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LHQVFDASVAEMHLMVGAEVNAYGPTEATVDSCF
  Nearest Stachelhaus code(s):
    dh-Trp DAALMGAVTK (53% 8Å match)
  Stachelhaus code match:
    80% (moderate)

K6K39_RS26470: Gly - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (470..868): 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:
    FAMTFDIAGLELQALVGGETNLYGPTETTIWSAS
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1530..1920): 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:
    FDKAFDASVLELPIAVGGDFNGYGPTEATVWVTS
  Nearest Stachelhaus code(s):
    Val DALWIGGVFK (44% 8Å match)
  Stachelhaus code match:
    70% (weak)

K6K39_RS26475: Trp - X - X - Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (42..444): Trp
nrpys: Trp

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:
    YWASFDLTVTGGKAVLGGEINEYGPTEATVGCVF
  Nearest Stachelhaus code(s):
    Trp DLTKVGEVGK (85% 8Å match)
    Asn DLTKVGEVGK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1100..1502): X
nrpys: OH-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:
    YWASFDLTVTGGKAVLGGEVNEYGPTETTVGCTY
  Nearest Stachelhaus code(s):
    OH-Asn DLTKVGEVGK (88% 8Å match)
    Asn DLTKVGEVGK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2783..3172): 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:
    FDVAFDPSVFEMQMVVGGEFNAYGPTEATVWVTV
  Nearest Stachelhaus code(s):
    Trp DVSQVGAVAK (65% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (4459..4869): 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:
    LWHTFDVSVQESYAAQAGEHNHYGPTETHAATSY
  Nearest Stachelhaus code(s):
    Pro DVQYAAHVVK (91% 8Å match)
  Stachelhaus code match:
    80% (moderate)

K6K39_RS26480: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (37..433): 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:
    FAMAFDIAGLDLQALVGAETNLYGPTETTVWSVL
  Nearest Stachelhaus code(s):
    Gly DILQLGLVWK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence

NZ_AP024135.1 - Region 21 - NAPAA,NRPS,RiPP-like,t3nrps-iterative
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,020,217 - 6,086,407 nt. (total: 66,191 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))
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NAPAA: (AMP-binding and TIGR02353)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
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
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
K6K39_RS26665: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

K6K39_RS26680: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

K6K39_RS26755: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

K6K39_RS26800: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: carbamoyltransferase
K6K39_RS26645: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

Hydrolases: deaminase esterase
K6K39_RS26750: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

K6K39_RS26760: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: decarboxylase hydratase
K6K39_RS26660: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

K6K39_RS26730: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase
K6K39_RS26675: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS26745: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

Translocases: permease transporter
K6K39_RS26650: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

K6K39_RS26700: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | RiPP-like | t3nrps-iterative | NRPS | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001132.4 |  |  |  |  | 0.94 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  |  |  | 0.94 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  |  |  |  | 0.93 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  |  |  | 0.92 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  |  |  |  | 0.92 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  |  |  | 0.92 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  |  |  |  | 0.91 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  |  |  |  | 0.90 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000307.4 |  |  |  |  | 0.90 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001166.5 |  |  |  |  | 0.89 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.65 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001166.5 |  | 0.63 | NRPS | HC-toxin | Alternaria jesenskae

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.29 out of 27.04
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.68 out of 19.52
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.98 out of 23.43
Confidence: medium
Additional weak hits (10):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.63 out of 29.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.74 out of 31.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.61 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.96 out of 30.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.17 out of 29.65
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.02 out of 27.04
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.28 out of 27.04
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.14 out of 18.57
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.40 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.50 out of 36.53
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 38, location 6020216 - 6086407:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 40, location 6021902 - 6086407:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
K6K39_RS26675: X
AMP-binding (48..433): 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:
    ITFPFGLGGLVPFTVSAGEINGIGATELLHIFIS
  Nearest Stachelhaus code(s):
    D-Hiv GALHVVGSIK (35% 8Å match)
  Stachelhaus code match:
    60% (weak)

K6K39_RS26760: X
AMP-binding (243..645): X
nrpys: Dpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HAKAFDISLWQSQLSVTGELNAYGLTETSDDTNH
  Nearest Stachelhaus code(s):
    Dpr DIWQSTADDK (94% 8Å match)
    dnmeProp or Dab DIWQSTADDK (79% 8Å match)
    Asp DIWQSTADDK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
BldD | Development and antibiotic global regulator
CRP | Cyclic AMP receptor protein
DasR | N-acetylglucosamine dependent repressor

NZ_AP024135.1 - Region 22 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,132,417 - 6,143,736 nt. (total: 11,320 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: deacetylase
K6K39_RS27065: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002150.2 |  | 0.43 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0002151.2 |  | 0.43 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0000541.5 |  | 0.33 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0002710.2 |  | 0.32 | NRPS | metachelin C, metachelin A, metachelin A-CE, metachelin B, dimerumic acid 11-mannoside, dimerumic acid | Metarhizium robertsii ARSEF 23
BGC0000306.5 |  | 0.31 | NRPS | arylomycin | Streptomyces filamentosus NRRL 11379
BGC0002303.3 |  | 0.30 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0002387.2 |  | 0.30 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0000410.5 |  | 0.29 | NRPS | pseudomonine | Pseudomonas fluorescens
BGC0000502.5 |  | 0.29 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001421.4 |  | 0.29 | NRPS, PKS | myxochromide B | Myxococcus sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002150.2 |  | 0.43 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0002151.2 |  | 0.43 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0000541.5 |  | 0.33 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0002710.2 |  | 0.32 | NRPS | metachelin C, metachelin A, metachelin A-CE, metachelin B, dimerumic acid 11-mannoside, dimerumic acid | Metarhizium robertsii ARSEF 23
BGC0000306.5 |  | 0.31 | NRPS | arylomycin | Streptomyces filamentosus NRRL 11379
BGC0002303.3 |  | 0.30 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0002387.2 |  | 0.30 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0000410.5 |  | 0.29 | NRPS | pseudomonine | Pseudomonas fluorescens
BGC0000502.5 |  | 0.29 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001421.4 |  | 0.29 | NRPS, PKS | myxochromide B | Myxococcus sp.

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (3):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 13.84 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.84 out of 27.78
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 20.57 out of 36.53
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_AP024135.1 - Region 23 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,173,219 - 6,195,381 nt. (total: 22,163 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
K6K39_RS27235: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Hydrolases: glucanase hydrolase peptidase
K6K39_RS27240: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

K6K39_RS27265: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

K6K39_RS27275: Pullulanase, type I

smcogs
  SMCOG1297: Pullulanase, type I

Lyases: cyclase
K6K39_RS27245: Terpene synthase/cyclase metal-binding domain protein

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

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.86 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001201.3 |  | 0.57 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.47 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002031.3 |  | 0.46 | other (other) | kitasetaline | Kitasatospora setae KM-6054
BGC0000849.4 |  | 0.45 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000844.5 |  | 0.45 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001986.3 |  | 0.44 | other (other) | purincyclamide | Streptomyces chrestomyceticus
BGC0001336.5 |  | 0.41 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001485.4 |  | 0.40 | other (other) | chuangxinmycin | Actinoplanes tsinanensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.86 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001201.3 |  | 0.57 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.47 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002031.3 |  | 0.46 | other (other) | kitasetaline | Kitasatospora setae KM-6054
BGC0000849.4 |  | 0.45 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000844.5 |  | 0.45 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001986.3 |  | 0.44 | other (other) | purincyclamide | Streptomyces chrestomyceticus
BGC0001336.5 |  | 0.41 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001485.4 |  | 0.40 | other (other) | chuangxinmycin | Actinoplanes tsinanensis

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

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

Genes with terpene domains:
K6K39_RS27245: T1TS + T1TS
Domain 1 (2 - 325): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (326 - 694): Type 1 terpene synthase
Subtype: Geosmin synthase, C terminal domain

Reactions:
  germacradienol → geosmin

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (7):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.09 out of 30.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.43 out of 26.06
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.96 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.82 out of 29.38
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.06 out of 27.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.00 out of 29.65
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_AP024135.1 - Region 24 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,356,597 - 6,387,737 nt. (total: 31,141 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
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase
K6K39_RS27980: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: hydrolase
K6K39_RS27965: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Isomerases: mutase
K6K39_RS27960: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
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
BGC0000946.5 |  | 0.46 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0000902.4 |  | 0.42 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0001206.5 |  | 0.42 | other (other) | indolmycin | Streptomyces griseus subsp. griseus
BGC0002584.2 |  | 0.42 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0000709.5 |  | 0.38 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0002681.3 |  | 0.38 | other (other) | rhizoferrin | Francisella tularensis subsp. tularensis SCHU S4
BGC0000229.5 |  | 0.38 | PKS, saccharide | grincamycin | Streptomyces lusitanus
BGC0002387.2 |  | 0.38 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0000285.5 |  | 0.37 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
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
BGC0000946.5 |  | 0.46 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0000902.4 |  | 0.42 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0001206.5 |  | 0.42 | other (other) | indolmycin | Streptomyces griseus subsp. griseus
BGC0002584.2 |  | 0.42 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0000709.5 |  | 0.38 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0002681.3 |  | 0.38 | other (other) | rhizoferrin | Francisella tularensis subsp. tularensis SCHU S4
BGC0000229.5 |  | 0.38 | PKS, saccharide | grincamycin | Streptomyces lusitanus
BGC0002387.2 |  | 0.38 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0000285.5 |  | 0.37 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.90 out of 23.79
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.57 out of 25.31
Confidence: medium
Additional weak hits (6):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.20 out of 26.06
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.37 out of 26.12
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.46 out of 31.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.43 out of 21.55
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.70 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
IolR | Regulator of the inositol catabolism

NZ_AP024135.1 - Region 25 - betalactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,413,798 - 6,441,402 nt. (total: 27,605 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase phosphate reductase
K6K39_RS28220: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

K6K39_RS28240: N-acetyl-gamma-glutamyl-phosphate reductase

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

K6K39_RS28295: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase halogenase kinase
K6K39_RS28245: acetylglutamate kinase

smcogs
  SMCOG1174: acetylglutamate kinase

K6K39_RS28280: aminotransferase

smcogs
  SMCOG1019: aminotransferase

K6K39_RS28305: ambiguous flavin-dependent halogenase

halogenases
  ambiguous flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

Ligases: ligase synthase
K6K39_RS28225: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

K6K39_RS28260: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.57 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000888.5 |  | 0.49 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001184.4 |  | 0.48 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0000234.5 |  | 0.45 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000231.5 |  | 0.45 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000895.5 |  | 0.44 | other (other) | citrulline | Lactobacillus plantarum subsp. plantarum
BGC0000883.5 |  | 0.44 | other (other) | arginomycin | Streptomyces arginensis
BGC0001137.5 |  | 0.44 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0002496.3 |  | 0.44 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0001374.5 |  | 0.44 | other (other) | thienodolin | Streptomyces albogriseolus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.57 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000888.5 |  | 0.49 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001184.4 |  | 0.48 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0000234.5 |  | 0.45 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000231.5 |  | 0.45 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000895.5 |  | 0.44 | other (other) | citrulline | Lactobacillus plantarum subsp. plantarum
BGC0000883.5 |  | 0.44 | other (other) | arginomycin | Streptomyces arginensis
BGC0001137.5 |  | 0.44 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0002496.3 |  | 0.44 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0001374.5 |  | 0.44 | other (other) | thienodolin | Streptomyces albogriseolus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.90 out of 26.85
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.88 out of 29.51
Confidence: medium
Additional weak hits (11):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.23 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.82 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.20 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.87 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.26 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.01 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.99 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.78 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.90 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DosR | Hypoxia stress response regulator
RutR | Regulator of the pyrimidine and purine metabolism

NZ_AP024135.1 - Region 26 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,957,639 - 6,984,410 nt. (total: 26,772 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
K6K39_RS30745: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

K6K39_RS30780: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: aminotransferase transferase
K6K39_RS30740: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

K6K39_RS30815: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Lyases: dehydratase
K6K39_RS30730: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase synthetase
K6K39_RS30785: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

K6K39_RS30810: 1-deoxy-D-xylulose-5-phosphate synthase

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

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.82 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000664.5 |  | 0.52 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000651.5 |  | 0.48 | terpene | KS-505a | Streptomyces argenteolus
BGC0002283.2 |  | 0.48 | terpene | sodorifen | Serratia plymuthica

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.82 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000664.5 |  | 0.52 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000651.5 |  | 0.48 | terpene | KS-505a | Streptomyces argenteolus
BGC0002283.2 |  | 0.48 | terpene | sodorifen | Serratia plymuthica

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
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:
K6K39_RS30770: PT_phytoene_like
Domain 1 (14 - 277): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  PSPP → hydroxysqualene

K6K39_RS30775: PT_phytoene_like
Domain 1 (17 - 309): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

K6K39_RS30785: PT_FPPS_like
Domain 1 (59 - 353): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

K6K39_RS30790: T2TS
Domain 1 (25 - 655): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.44 out of 23.79
Confidence: medium
Additional weak hits (3):
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.72 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.91 out of 29.65
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.10 out of 36.53
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism

NZ_AP024135.1 - Region 27 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,000,336 - 7,022,913 nt. (total: 22,578 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lasso peptides
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: transketolase
K6K39_RS30960: transketolase

smcogs
  SMCOG1204: transketolase

Hydrolases: hydrolase
K6K39_RS30985: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Ligases: synthase
K6K39_RS30925: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

K6K39_RS30955: 1-deoxy-D-xylulose-5-phosphate synthase

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

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001550.3 |  | 0.85 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001552.3 |  | 0.84 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001551.4 |  | 0.84 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001549.3 |  | 0.84 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001548.4 |  | 0.76 | ribosomal | citrulassin A | Streptomyces albulus
BGC0001781.4 |  | 0.71 | ribosomal | sphaericin | Planomonospora sphaerica
BGC0001645.3 |  | 0.70 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0001507.3 |  | 0.70 | ribosomal | anantin C | Streptomyces olindensis
BGC0001889.2 |  | 0.63 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0001634.3 |  | 0.62 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001550.3 |  | 0.85 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001552.3 |  | 0.84 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001551.4 |  | 0.84 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001549.3 |  | 0.84 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001548.4 |  | 0.76 | ribosomal | citrulassin A | Streptomyces albulus
BGC0001781.4 |  | 0.71 | ribosomal | sphaericin | Planomonospora sphaerica
BGC0001645.3 |  | 0.70 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0001507.3 |  | 0.70 | ribosomal | anantin C | Streptomyces olindensis
BGC0001889.2 |  | 0.63 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0001634.3 |  | 0.62 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (7):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.84 out of 27.78
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.42 out of 27.78
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.36 out of 27.55
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.21 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.40 out of 35.63
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (7000335...7022913)
K6K39_RS30980
  RRE type: Stand_Alone_Lasso_RRE
  Location: 2 - 83
  Score: 81.4
  RRE type: Lasso_Fused_RRE
  Location: 0 - 54
  Score: 25.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_AP024135.1 - Region 28 - hydrogen-cyanide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,061,525 - 7,074,374 nt. (total: 12,850 nt) Show pHMM detection rules used
hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase reductase
K6K39_RS31270: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

K6K39_RS31280: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Translocases: permease
K6K39_RS31250: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | hydrogen-cyanide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.63 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0002285.2 |  | 0.44 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0002116.3 |  | 0.41 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0000544.4 |  | 0.36 | ribosomal | planosporicin | Planomonospora alba
BGC0001657.4 |  | 0.35 | NRPS | lysocin | Lysobacter sp. RH2180-5
BGC0000916.5 |  | 0.35 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0000711.5 |  | 0.34 | saccharide | neomycin | Streptomyces fradiae
BGC0001561.4 |  | 0.33 | NRPS | curacomycin | Streptomyces curacoi
BGC0000709.5 |  | 0.33 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0002126.3 |  | 0.33 | NRPS | hypeptin | Lysobacter sp. K5869

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.63 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0002285.2 |  | 0.44 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0002116.3 |  | 0.41 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0000544.4 |  | 0.36 | ribosomal | planosporicin | Planomonospora alba
BGC0001657.4 |  | 0.35 | NRPS | lysocin | Lysobacter sp. RH2180-5
BGC0000916.5 |  | 0.35 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0000711.5 |  | 0.34 | saccharide | neomycin | Streptomyces fradiae
BGC0001561.4 |  | 0.33 | NRPS | curacomycin | Streptomyces curacoi
BGC0000709.5 |  | 0.33 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0002126.3 |  | 0.33 | NRPS | hypeptin | Lysobacter sp. K5869

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.05 out of 22.40
Confidence: strong
Additional weak hits (3):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.81 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.70 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 17.67 out of 22.40
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
HypR | L-hydroxyproline utilization repressor

NZ_AP024135.1 - Region 29 - NRPS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,110,118 - 7,220,655 nt. (total: 110,538 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
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
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
K6K39_RS31500: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

K6K39_RS31530: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

K6K39_RS31635: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

K6K39_RS31650: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: acetyltransferase acylase aminotransferase halogenase methyltransferase
K6K39_RS31535: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

K6K39_RS31610: flavin-dependent cycline orsellinic halogenase

halogenases
  flavin-dependent cycline orsellinic halogenase
smcogs
  SMCOG1119: halogenase

K6K39_RS31630: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

K6K39_RS41320: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

K6K39_RS41785: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Hydrolases: esterase hydrolase
K6K39_RS31640: HAD-superfamily hydrolase, subfamily IA, variant

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

K6K39_RS31655: thioesterase

smcogs
  SMCOG1004: thioesterase

K6K39_RS31670: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: hydratase
K6K39_RS31470: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: synthase
K6K39_RS31550: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

K6K39_RS31615: 3-dehydroquinate synthase

smcogs
  SMCOG1183: 3-dehydroquinate synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T1PKS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001276.3 |  |  | 0.85 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  |  | 0.83 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  |  | 0.70 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  | 0.70 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000041.3 |  |  | 0.66 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000106.5 |  |  | 0.65 | PKS | naphthomycin A | Streptomyces sp. CS
BGC0000067.5 |  |  | 0.57 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0000018.5 |  |  | 0.50 | PKS | angolamycin | Streptomyces eurythermus
BGC0001051.5 |  |  | 0.50 | NRPS, PKS | thuggacin A | Sorangium cellulosum
BGC0001012.3 |  |  | 0.48 | NRPS, PKS | meridamycin | Streptomyces violaceusniger

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002341.2 |  | 0.76 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0000106.5 |  | 0.75 | PKS | naphthomycin A | Streptomyces sp. CS
BGC0001273.3 |  | 0.75 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000018.5 |  | 0.70 | PKS | angolamycin | Streptomyces eurythermus
BGC0001160.5 |  | 0.70 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.70 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000041.3 |  | 0.67 | PKS | oronofacic acid | Pseudomonas syringae

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.12 out of 26.85
Confidence: medium
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 25.83 out of 30.22
Confidence: medium
Additional weak hits (10):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.77 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.17 out of 21.55
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.65 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.25 out of 27.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.83 out of 27.04
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.65 out of 24.78
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.60 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.10 out of 28.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 48, location 7110117 - 7220655:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (AHBA - Me-ccmal - mal - Me-ohmal) + (Me-ccmal - Me-ccmal - ccmal) + (ccmal) + (Me-ccmal) + (ccmal - Me-ccmal)
Non-colinear ordering:
  K6K39_RS31535 + K6K39_RS31540 + K6K39_RS31545 + K6K39_RS31550 + K6K39_RS42035 + K6K39_RS42040 + K6K39_RS41320

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
K6K39_RS31535: AHBA - mmal - mal - mmal
CAL_domain (149..467): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 349.2
  shikimic_acid: 174.3
  Acetyl-CoA: 17.1
  fatty_acid: 0.0
  NH2: 0.0

PKS_AT (1580..1876): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 207.5
  Ethylmalonyl-CoA: 200.9
  Methoxymalonyl-CoA: 165.3
  2-Methylbutyryl-CoA: 113.8
  trans-1,2-CPDA: 110.1
  Propionyl-CoA: 103.8
  Malonyl-CoA: 91.6
  CHC-CoA: 88.9
  Isobutyryl-CoA: 79.3
  Benzoyl-CoA: 57.6
  Acetyl-CoA: 39.9
  fatty_acid: 37.3
  3-Methylbutyryl-CoA: 24.2
  inactive: 12.4

PKS_AT (3280..3582): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  Propionyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 201.9
  inactive: 96.4
  Methoxymalonyl-CoA: 80.3
  Methylmalonyl-CoA: 69.2
  Isobutyryl-CoA: 47.6
  Propionyl-CoA: 45.4
  Benzoyl-CoA: 32.0
  CHC-CoA: 27.9
  Acetyl-CoA: 20.9
  2-Methylbutyryl-CoA: 16.8
  trans-1,2-CPDA: 14.0
  fatty_acid: 10.8
  3-Methylbutyryl-CoA: 0.0
  Ethylmalonyl-CoA: -2.4

PKS_AT (4581..4882): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Malonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 198.8
  Ethylmalonyl-CoA: 192.8
  Methoxymalonyl-CoA: 159.8
  2-Methylbutyryl-CoA: 110.0
  Propionyl-CoA: 102.0
  trans-1,2-CPDA: 99.7
  Malonyl-CoA: 93.7
  CHC-CoA: 83.4
  Isobutyryl-CoA: 80.6
  Benzoyl-CoA: 65.6
  Acetyl-CoA: 37.2
  3-Methylbutyryl-CoA: 32.0
  fatty_acid: 30.4
  inactive: 16.5

K6K39_RS31540: mmal - mmal - mal
PKS_AT (557..854): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Malonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 206.7
  Ethylmalonyl-CoA: 198.5
  Methoxymalonyl-CoA: 170.0
  trans-1,2-CPDA: 112.9
  2-Methylbutyryl-CoA: 110.9
  Propionyl-CoA: 101.3
  CHC-CoA: 93.8
  Malonyl-CoA: 92.7
  Isobutyryl-CoA: 73.1
  Benzoyl-CoA: 62.9
  Acetyl-CoA: 37.8
  fatty_acid: 32.1
  3-Methylbutyryl-CoA: 27.2
  inactive: 17.4

PKS_AT (2322..2618): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 205.1
  Ethylmalonyl-CoA: 200.4
  Methoxymalonyl-CoA: 165.3
  2-Methylbutyryl-CoA: 112.5
  trans-1,2-CPDA: 106.8
  Propionyl-CoA: 99.9
  Malonyl-CoA: 91.0
  CHC-CoA: 89.1
  Isobutyryl-CoA: 76.8
  Benzoyl-CoA: 57.6
  Acetyl-CoA: 40.5
  fatty_acid: 36.3
  3-Methylbutyryl-CoA: 27.1
  inactive: 12.1

PKS_AT (4067..4351): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 205.1
  inactive: 123.3
  Methoxymalonyl-CoA: 61.0
  Methylmalonyl-CoA: 51.5
  Acetyl-CoA: 27.0
  Propionyl-CoA: 24.9
  fatty_acid: 21.6
  Isobutyryl-CoA: 19.0
  Benzoyl-CoA: 11.4
  trans-1,2-CPDA: 9.6
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0
  Ethylmalonyl-CoA: -1.0

K6K39_RS31550: mal
PKS_AT (556..845): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 196.9
  inactive: 120.0
  Methoxymalonyl-CoA: 58.8
  Methylmalonyl-CoA: 47.2
  Acetyl-CoA: 26.8
  Propionyl-CoA: 20.6
  Isobutyryl-CoA: 19.9
  Ethylmalonyl-CoA: 19.5
  fatty_acid: 18.4
  Benzoyl-CoA: 12.3
  trans-1,2-CPDA: 11.8
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

K6K39_RS42035: mmal
PKS_AT (645..941): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 209.4
  Ethylmalonyl-CoA: 203.2
  Methoxymalonyl-CoA: 167.1
  2-Methylbutyryl-CoA: 114.0
  trans-1,2-CPDA: 110.1
  Propionyl-CoA: 103.8
  CHC-CoA: 93.3
  Malonyl-CoA: 92.7
  Isobutyryl-CoA: 84.4
  Benzoyl-CoA: 61.5
  Acetyl-CoA: 39.5
  fatty_acid: 37.3
  3-Methylbutyryl-CoA: 28.5
  inactive: 12.9

K6K39_RS42040: mal
PKS_AT (1069..1347): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 198.4
  inactive: 115.8
  Methoxymalonyl-CoA: 58.5
  Methylmalonyl-CoA: 49.0
  Acetyl-CoA: 26.9
  fatty_acid: 21.9
  Ethylmalonyl-CoA: 21.4
  Propionyl-CoA: 20.2
  Isobutyryl-CoA: 18.0
  Benzoyl-CoA: 11.9
  trans-1,2-CPDA: 10.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

K6K39_RS41320: mal - mmal
PKS_AT (554..843): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 194.2
  inactive: 121.0
  Methoxymalonyl-CoA: 55.4
  Methylmalonyl-CoA: 46.0
  Acetyl-CoA: 22.4
  Propionyl-CoA: 20.5
  fatty_acid: 19.0
  Ethylmalonyl-CoA: 19.0
  Isobutyryl-CoA: 17.6
  Benzoyl-CoA: 10.9
  trans-1,2-CPDA: 9.9
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

PKS_AT (2273..2570): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 83.3%
  Malonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 183.4
  Ethylmalonyl-CoA: 175.0
  Methoxymalonyl-CoA: 151.6
  2-Methylbutyryl-CoA: 97.2
  Propionyl-CoA: 93.2
  CHC-CoA: 90.2
  trans-1,2-CPDA: 81.9
  Malonyl-CoA: 75.5
  Isobutyryl-CoA: 70.7
  Benzoyl-CoA: 51.4
  Acetyl-CoA: 25.7
  fatty_acid: 21.6
  3-Methylbutyryl-CoA: 16.4
  inactive: 15.9

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ClgR | Caseinolytic protease gene regulator
RutR | Regulator of the pyrimidine and purine metabolism

NZ_AP024135.1 - Region 30 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,484,260 - 7,506,758 nt. (total: 22,499 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lasso peptides
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: glycosyltransferase
K6K39_RS32955: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: back translocase hydrolase
K6K39_RS32940: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

K6K39_RS32970: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002053.3 |  | 0.84 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001507.3 |  | 0.77 | ribosomal | anantin C | Streptomyces olindensis
BGC0001539.4 |  | 0.72 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002074.2 |  | 0.71 | ribosomal | huascopeptin | Streptomyces huasconensis
BGC0001552.3 |  | 0.69 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001307.3 |  | 0.69 | ribosomal | chaxapeptin | Streptomyces leeuwenhoekii
BGC0001493.5 |  | 0.66 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001549.3 |  | 0.65 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001550.3 |  | 0.65 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001551.4 |  | 0.63 | ribosomal | citrulassin E | Streptomyces glaucescens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002053.3 |  | 0.84 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001507.3 |  | 0.77 | ribosomal | anantin C | Streptomyces olindensis
BGC0001539.4 |  | 0.72 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002074.2 |  | 0.71 | ribosomal | huascopeptin | Streptomyces huasconensis
BGC0001552.3 |  | 0.69 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001307.3 |  | 0.69 | ribosomal | chaxapeptin | Streptomyces leeuwenhoekii
BGC0001493.5 |  | 0.66 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001549.3 |  | 0.65 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001550.3 |  | 0.65 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001551.4 |  | 0.63 | ribosomal | citrulassin E | Streptomyces glaucescens

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.

#### Lassopeptide(s) for K6K39_RS32965

K6K39_RS32965
Leader:
MNENIEISNSEPYEPPTVVEVGEFNEDTL
Full core:
G F I G W G K D I F G H Y S G G F
Putative macrolactam:
G F I G W G K D

#### antiSMASH-DB 4.0 matches for K6K39_RS32965

100.0%
NZ_AP024135.1 and 1 other:
NZ_CP011799.1 Lassopeptides: QR97_RS33380_lassopeptide
Lassopeptides: K6K39_RS32965_lassopeptide
1
G F I G W G K D I F G H Y S G G F
17
G F I G W G K D I F G H Y S G G F
1
G F I G W G K D I F G H Y S G G F
17
94.1%
NZ_BMSE01000003.1 and 2 others:
NZ_JACHGV010000006.1 Lassopeptides: HNR57_RS21035_lassopeptide NZ_KZ671966.1 Lassopeptides: BV882_RS06405_lassopeptide
Lassopeptides: IE153_RS10035_lassopeptide
1
G F I G W G K D I F G H Y S G G F
17
G F I G W G D I F G H Y S G G F
1
G F I G W G N D I F G H Y S G G F
17
94.1%
NZ_JACHJK010000012.1:
Lassopeptides: FHS34_RS30310_lassopeptide
1
G F I G W G K D I F G H Y S G G F
17
G F I G W G K D I F G H Y G G F
1
G F I G W G K D I F G H Y G G G F
17
with 6 more sequence matches
88.2%
NZ_CP026121.1 and 1 other:
NZ_CP075896.1 Lassopeptides: KJK29_RS31770_lassopeptide
Lassopeptides: C1703_RS06295_lassopeptide
1
G F I G W G K D I F G H Y S G G F
17
G F I G W G D I F G H Y S G F
1
G F I G W G N D I F G H Y S G D F
17
82.4%
NZ_AP026073.1 and 12 others:
NZ_BBNO01000002.1 Lassopeptides: TU31_RS37835_lassopeptide NZ_BNCA01000014.1 Lassopeptides: IE314_RS18405_lassopeptide NZ_CP007699.2 Lassopeptides: T261_RS42170_lassopeptide NZ_CP023691.1 Lassopeptides: CP981_RS21655_lassopeptide NZ_CP029042.1 Lassopeptides: DDE74_RS22295_lassopeptide NZ_CP029541.1 Lassopeptides: DKG71_RS23270_lassopeptide NZ_CP049782.1 Lassopeptides: G7Z12_RS16230_lassopeptide NZ_CP050976.1 Lassopeptides: HEP86_RS22775_lassopeptide NZ_CP102609.1 Lassopeptides: NUT86_RS23110_lassopeptide NZ_CP114202.1 Lassopeptides: STRLI_RS17465_lassopeptide NZ_CP114203.1 Lassopeptides: STRNI_RS19305_lassopeptide NZ_JAPKNL010000006.1 Lassopeptides: OSI21_RS10415_lassopeptide
Lassopeptides: HEK616_RS15635_lassopeptide
1
G F I G W G K D I F G H Y S G
15
G F I G W G K D I F G H Y G
1
G F I G W G K D I F G H Y G G
15
35.3%
NZ_CP086322.1:
Lassopeptides: K9S39_RS27710_lassopeptide
1
G F I G W G K D I F G
11
G +G W D F G
1
G L V G W H H D A F G
11
28.6%
NZ_CP092497.1:
Lassopeptides: allorf_4137077_4137205_lassopeptide
1
G F I G W G K D I F
10
G G W G+D F
2
G K C G W G R D R F
11
16.1%
NZ_CP035758.1:
Lanthipeptides: EPA93_RS48405_lanthipeptide
5
W G K D I F G H Y
13
W G G H Y
7
W G N T C T G H Y
15
10.6%
NZ_BNBI01000017.1:
Lanthipeptides: allorf_050255_050446_lanthipeptide
3
I G W G K D I F G H Y S G G
16
+ W + G H G G
25
V A W P V Q M P G H R R G G
38

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.34 out of 20.01
Confidence: medium
Additional weak hits (2):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.65 out of 24.78
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

K6K39_RS32965 - Class II
  Cleavage pHMM score: 1.80
  RODEO score: 20
  Monoisotopic mass: 1825.8 Da
  Molecular weight: 1827.0 Da
  Number of bridges: 0

RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (7484259...7506758)
K6K39_RS32975
  RRE type: Stand_Alone_Lasso_RRE
  Location: 1 - 76
  Score: 82.9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
ArgR | Regulator of arginine biosynthesis genes

NZ_AP024135.1 - Region 31 - ectoine,hglE-KS,t3nrps-iterative
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,717,842 - 7,778,238 nt. (total: 60,397 nt) Show pHMM detection rules used
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)
hglE-KS: (hglE or hglD)
ectoine: ectoine_synt

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
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
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase oxygenase
K6K39_RS33970: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

K6K39_RS34190: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: PPTase acetyltransferase acylase aminotransferase glycosyltransferase
K6K39_RS34005: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

K6K39_RS34080: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

K6K39_RS34115: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

K6K39_RS34140: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

K6K39_RS34165: Chloramphenicol acetyltransferase

smcogs
  SMCOG1156: Chloramphenicol acetyltransferase

K6K39_RS41365: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

K6K39_RS42075: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: back translocase hydrolase
K6K39_RS34025: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

K6K39_RS34135: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: decarboxylase hydratase
K6K39_RS33975: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

K6K39_RS34060: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase
K6K39_RS34070: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS42070: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | t3nrps-iterative | hglE-KS | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000852.5 |  |  |  | 1.15 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000859.3 |  |  |  | 1.06 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000856.3 |  |  |  | 1.05 | other (other) | ectoine | Methylophaga thalassica
BGC0002052.3 |  |  |  | 1.02 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  |  |  | 1.02 | other (other) | ectoine | Streptomyces anulatus
BGC0000858.3 |  |  |  | 1.00 | other (other) | ectoine | Methylobacter marinus
BGC0000855.3 |  |  |  | 0.97 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000857.3 |  |  |  | 0.95 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  |  |  | 0.95 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  |  |  | 0.76 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000852.5 |  | 0.71 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000859.3 |  | 0.68 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000856.3 |  | 0.68 | other (other) | ectoine | Methylophaga thalassica
BGC0002052.3 |  | 0.67 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.67 | other (other) | ectoine | Streptomyces anulatus
BGC0000858.3 |  | 0.67 | other (other) | ectoine | Methylobacter marinus
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000857.3 |  | 0.65 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.65 | other (other) | ectoine | Methylarcula marina
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.37 out of 30.12
Confidence: medium
Additional weak hits (15):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.33 out of 26.06
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.14 out of 26.12
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.64 out of 21.55
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.72 out of 30.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.48 out of 23.43
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.44 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.49 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.31 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.11 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.42 out of 28.14
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.03 out of 20.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.71 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 50, location 7717841 - 7778238:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
K6K39_RS34070: Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (12..409): Asp
nrpys: Asp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AAILFDYGLYQLPGTNTGAQVMYGLTECKRAAIM
  Nearest Stachelhaus code(s):
    Asp DYYPTTMRAK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

K6K39_RS34115: mal
PKS_AT (1360..1652): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 50.0
  Methoxymalonyl-CoA: 27.2
  inactive: 23.3
  Methylmalonyl-CoA: 19.1
  trans-1,2-CPDA: 14.7
  fatty_acid: 11.1
  Propionyl-CoA: 7.9
  Ethylmalonyl-CoA: 7.8
  Isobutyryl-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

K6K39_RS42075: mal
PKS_AT (261..437): mal
ATSignature: (unknown)
No matches above 50%
minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 4.6
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP024135.1 - Region 32 - PKS-like,T2PKS,T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,837,781 - 7,920,218 nt. (total: 82,438 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
T2PKS: (t2ks and t2clf)
PKS-like: (t2pks2 or ksIII)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
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
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase reductase
K6K39_RS34620: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

K6K39_RS34630: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

K6K39_RS34645: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

K6K39_RS34660: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

K6K39_RS34670: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

K6K39_RS34675: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

K6K39_RS34680: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

K6K39_RS34725: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

K6K39_RS34750: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

K6K39_RS34785: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

K6K39_RS34800: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

K6K39_RS34815: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase acyltransferase aminotransferase
K6K39_RS34540: acyltransferase

smcogs
  SMCOG1141: acyltransferase

K6K39_RS34570: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

K6K39_RS34805: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: deformylase
K6K39_RS34610: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Lyases: cyclase
K6K39_RS34745: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

Ligases: synthase
K6K39_RS34635: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

K6K39_RS34760: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

K6K39_RS34765: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

K6K39_RS34775: 3-oxoacyl-(acyl carrier protein) synthase III

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

K6K39_RS34780: 3-oxoacyl-(acyl carrier protein) synthase III

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

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T3PKS | T2PKS | PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002127.3 |  |  |  | 1.30 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  |  |  | 0.87 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000231.5 |  |  |  | 0.72 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000285.5 |  |  |  | 0.60 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0001310.5 |  |  |  | 0.59 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0001276.3 |  |  |  | 0.58 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  |  |  | 0.58 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  |  | 0.57 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  |  | 0.57 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000272.3 |  |  |  | 0.55 | PKS | spore pigment | Streptomyces collinus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002127.3 |  | 0.87 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.74 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000231.5 |  | 0.69 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000285.5 |  | 0.64 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0001310.5 |  | 0.63 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.62 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.62 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.62 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000272.3 |  | 0.61 | PKS | spore pigment | Streptomyces collinus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.51 out of 27.18
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 20.11 out of 23.05
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.85 out of 27.04
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.95 out of 23.79
Confidence: medium
Additional weak hits (21):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.03 out of 26.06
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.49 out of 39.62
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.35 out of 27.55
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.66 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.77 out of 32.74
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.48 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.45 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.37 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.74 out of 27.78
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.65 out of 26.12
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.81 out of 21.84
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.66 out of 27.18
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.02 out of 18.57
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.42 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.05 out of 35.63
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.41 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.73 out of 30.11
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
Type II PKS
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
K6K39_RS34805: pk
PKS_AT (7..286): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 54.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 44.0
  Methoxymalonyl-CoA: 43.7
  Malonyl-CoA: 36.2
  Ethylmalonyl-CoA: 25.8
  Propionyl-CoA: 25.1
  2-Methylbutyryl-CoA: 24.5
  CHC-CoA: 20.0
  fatty_acid: 18.2
  Isobutyryl-CoA: 15.4
  trans-1,2-CPDA: 14.6
  Acetyl-CoA: 12.8
  Benzoyl-CoA: 11.1
  3-Methylbutyryl-CoA: 7.7
  inactive: 0.0

Link to PARAS substrate predictor
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  7847738 to 7920218
Starter unit(s):
  propionyl-CoA (Score: 329.0; E-value: 2.25e-115)
Malonyl elongations:
  7 (Score: 639.6; E-value: 4e-195)
Product class(es):
  benzoisochromanequinone
Product molecular weight(s):
  propionyl-CoA_7: 355 Da

K6K39_RS34745
  CYC C7-C12 (Score: 360.9; E-value: 1e-110)
K6K39_RS34760
  KS (Score: 743.1; E-value: 1.9e-226)
K6K39_RS34765
  CLF 7 (Score: 639.6; E-value: 4e-195)
K6K39_RS34770
  ACP (Score: 97.1; E-value: 1.1e-30)
K6K39_RS34785
  KR (Score: 190.1; E-value: 1.3e-58)
K6K39_RS34790
  CYC C5-C14 (Score: 452.1; E-value: 1.8e-138)
K6K39_RS34805
  AT (Score: 408.3; E-value: 5.4e-125)
  AT BAB72049.1_Aklavinone_propionyl-CoA (Score: 329.0; E-value: 2.25e-115)
K6K39_RS34815
  KR C9 (Score: 441.6; E-value: 2e-135)
K6K39_RS34820
  OXY (Score: 36.5; E-value: 7e-12)
K6K39_RS34870
  OXY (Score: 80.5; E-value: 3e-25)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
NrdR | Represses ribonucleotide reductase encoding genes

NZ_AP024135.1 - Region 33 - PKS-like,T1PKS,T2PKS,azole-containing-RiPP
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,160,384 - 8,233,455 nt. (total: 73,072 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)
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)
PKS-like: (t2pks2 or ksIII)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
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Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Azole RiPPs
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
K6K39_RS36015: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

K6K39_RS36020: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

K6K39_RS36040: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

K6K39_RS36080: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

K6K39_RS36090: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

K6K39_RS36170: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: acylase glycosyltransferase kinase methyltransferase transferase
K6K39_RS36030: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

K6K39_RS36100: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

K6K39_RS36120: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

K6K39_RS36140: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

K6K39_RS36150: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

K6K39_RS36160: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

K6K39_RS36275: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

Hydrolases: hydrolase
K6K39_RS36130: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

Lyases: cyclase decarboxylase dehydratase
K6K39_RS35965: putative carboxymuconolactone decarboxylase

smcogs
  SMCOG1298: putative carboxymuconolactone decarboxylase

K6K39_RS35985: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

K6K39_RS36165: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

Ligases: synthase
K6K39_RS36110: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

K6K39_RS36115: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

K6K39_RS36145: 3-oxoacyl-(acyl carrier protein) synthase III

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

K6K39_RS36155: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T2PKS | azole-containing-RiPP | PKS-like | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000231.5 |  |  |  |  | 1.16 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000041.3 |  |  |  |  | 1.09 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001273.3 |  |  |  |  | 1.00 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  |  |  |  | 1.00 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000272.3 |  |  |  |  | 0.97 | PKS | spore pigment | Streptomyces collinus
BGC0001164.3 |  |  |  |  | 0.95 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  |  | 0.95 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000234.5 |  |  |  |  | 0.93 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001723.5 |  |  |  |  | 0.91 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001284.4 |  |  |  |  | 0.89 | PKS | alternariol | Parastagonospora nodorum SN15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000231.5 |  | 0.71 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000041.3 |  | 0.70 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001273.3 |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001284.4 |  | 0.63 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  | 0.63 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.63 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001268.4 |  | 0.61 | NRPS, PKS | fusarin C | Fusarium fujikuroi

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.19 out of 20.47
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 23.74 out of 27.18
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.99 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (9):
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.15 out of 27.78
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.37 out of 26.12
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.42 out of 31.73
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.33 out of 30.22
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.30 out of 18.57
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.60 out of 28.19
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
RREFinder
Type II PKS
TFBS Finder
Azole RiPPs
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 55, location 8160383 - 8233455:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-redmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 56, location 8160383 - 8232866:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-redmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 58, location 8182751 - 8223738:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-redmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 59, location 8187299 - 8233455:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-redmal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
K6K39_RS36150: mal
PKS_AT (14..297): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 56.5
  Methylmalonyl-CoA: 47.2
  Methoxymalonyl-CoA: 44.0
  Propionyl-CoA: 35.7
  inactive: 18.4
  Isobutyryl-CoA: 16.0
  2-Methylbutyryl-CoA: 13.8
  CHC-CoA: 10.8
  Ethylmalonyl-CoA: 10.2
  trans-1,2-CPDA: 10.1
  fatty_acid: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

K6K39_RS36160: mmal
PKS_AT (546..838): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 203.7
  Ethylmalonyl-CoA: 195.4
  Methoxymalonyl-CoA: 163.0
  2-Methylbutyryl-CoA: 137.8
  trans-1,2-CPDA: 115.3
  Propionyl-CoA: 106.4
  Malonyl-CoA: 101.1
  CHC-CoA: 99.7
  Isobutyryl-CoA: 75.2
  Benzoyl-CoA: 57.0
  3-Methylbutyryl-CoA: 45.1
  Acetyl-CoA: 43.4
  inactive: 22.6
  fatty_acid: 22.4

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (8173686...8197384)
K6K39_RS36060
  RRE type: Goadsporin_CD_RRE
  Location: 1 - 78
  Score: 36.9
  RRE type: Cyanobactin_D_RRE
  Location: 3 - 56
  Score: 29.7
  RRE type: NHLP_CD_RRE
  Location: 3 - 73
  Score: 25.3

Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  8160383 to 8232866
Starter unit(s):
  hexadienyl-CoA (Score: 487.0; E-value: 5.6e-137)
  2-methylbutyryl-CoA (Score: 361.0; E-value: 5.45e-128)
Malonyl elongations:
  8|9 (Score: 630.7; E-value: 2e-192)
Product molecular weight(s):
  2-methylbutyryl-CoA_8: 586 Da
  2-methylbutyryl-CoA_9: 628 Da
  hexadienyl-CoA_8: 596 Da
  hexadienyl-CoA_9: 638 Da

K6K39_RS36010
  ACP (Score: 98.3; E-value: 4.3e-31)
K6K39_RS36015
  KR C9 (Score: 443.4; E-value: 5.9e-136)
K6K39_RS36030
  GT (Score: 387.5; E-value: 2.1e-118)
K6K39_RS36100
  MET (Score: 254.3; E-value: 4e-78)
K6K39_RS36110
  KS (Score: 717.5; E-value: 1.1e-218)
K6K39_RS36115
  CLF 8|9 (Score: 630.7; E-value: 2e-192)
K6K39_RS36130
  CYC C5-C14 (Score: 436.7; E-value: 8.8e-134)
K6K39_RS36145
  KSIII (Score: 387.5; E-value: 1.2e-118)
  KSIII ADB23398.1_TLN-05220/TLN-05223_2-methylbutyryl-CoA (Score: 361.0; E-value: 5.45e-128)
K6K39_RS36150
  AT (Score: 400.6; E-value: 1.2e-122)
  AT AAP85359.1_Hedamycin_hexadienyl-CoA (Score: 384.0; E-value: 5.6e-137)
K6K39_RS36160
  AT (Score: 155.4; E-value: 4.4e-48)
  AT ADG86309.1_A-74528_hexadienyl-CoA (Score: 103.0; E-value: 1.26e-26)
K6K39_RS36165
  CYC C7-C12 (Score: 427.5; E-value: 5.5e-131)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NrdR | Represses ribonucleotide reductase encoding genes
VqsM | Regulator of quorum-sensing signalling systems

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
NZ_AP024135.1 - Region 34 - redox-cofactor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,245,341 - 8,267,534 nt. (total: 22,194 nt) Show pHMM detection rules used
redox-cofactor: (cds(PF04055 and (TIGR04085 or SPASM)) and (TIGR02111 or TIGR03966) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: esterase
K6K39_RS36430: putative esterase

smcogs
  SMCOG1104: putative esterase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | redox-cofactor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001227.3 |  | 0.47 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0001100.5 |  | 0.33 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0002300.2 |  | 0.30 | NRPS | albomycin delta2, albomycin delta1, albomycin epsilon | Streptomyces sp. ATCC 700974
BGC0000796.3 |  | 0.28 | saccharide | S-layer glycan | Paenibacillus alvei
BGC0000611.5 |  | 0.27 | ribosomal | siomycin A | Streptomyces sioyaensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001227.3 |  | 0.47 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0001100.5 |  | 0.33 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0002300.2 |  | 0.30 | NRPS | albomycin delta2, albomycin delta1, albomycin epsilon | Streptomyces sp. ATCC 700974
BGC0000796.3 |  | 0.28 | saccharide | S-layer glycan | Paenibacillus alvei
BGC0000611.5 |  | 0.27 | ribosomal | siomycin A | Streptomyces sioyaensis

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.34 out of 20.97
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.13 out of 23.79
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
Additional weak hits (6):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.42 out of 18.57
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.91 out of 29.38
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.29 out of 39.62
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.37 out of 28.19
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.71 out of 25.31
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (8245340...8267534)
K6K39_RS36380
  RRE type: PqqD_RRE
  Location: 1 - 73
  Score: 50.8

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP024135.1 - Region 35 - NRPS,PKS-like,T1PKS,hglE-KS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,381,711 - 8,507,432 nt. (total: 125,722 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
hglE-KS: (hglE or hglD)
PKS-like: (t2pks2 or ksIII)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
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
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
K6K39_RS36980: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

K6K39_RS37055: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

K6K39_RS37070: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

K6K39_RS37095: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: acylase
K6K39_RS37050: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

K6K39_RS37065: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: dehalogenase esterase hydrolase
K6K39_RS37085: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

K6K39_RS37090: thioesterase

smcogs
  SMCOG1004: thioesterase

K6K39_RS37115: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Ligases: ligase synthase
K6K39_RS36960: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

K6K39_RS36990: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS36995: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

K6K39_RS37060: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

K6K39_RS37075: 3-oxoacyl-(acyl carrier protein) synthase III

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

K6K39_RS41455: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

K6K39_RS42095: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

K6K39_RS42100: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS | T1PKS | hglE-KS | PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002192.3 |  |  |  |  | 1.16 | PKS | FR901512 | fungal sp. No.14919
BGC0001160.5 |  |  |  |  | 1.15 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001284.4 |  |  |  |  | 1.13 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  |  |  |  | 1.10 | PKS | ACT-Toxin II | Alternaria alternata
BGC0000041.3 |  |  |  |  | 1.07 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001268.4 |  |  |  |  | 1.06 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001164.3 |  |  |  |  | 0.87 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002135.2 |  |  |  |  | 0.85 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001276.3 |  |  |  |  | 0.85 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000067.5 |  |  |  |  | 0.85 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
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
BGC0001135.5 |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
Additional weak hits (22):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.41 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 14.96 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.92 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.58 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.38 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.00 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.97 out of 28.14
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 11.61 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.24 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.90 out of 36.54
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.10 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.14 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.25 out of 26.06
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.17 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.34 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.14 out of 28.19
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.46 out of 27.18
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.45 out of 29.65
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.59 out of 24.78
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 61, location 8381710 - 8507432:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val - X - X) + (Me-redmal) + (Me-mal - Me-ccmal) + (Me-ohmal - redmal) + (ccmal) + (ohmal) + (ccmal) + (Me-ohmal - ccemal) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 62, location 8381710 - 8432537:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val - X - X) + (Me-redmal) + (Me-mal - Me-ccmal) + (Me-ohmal - redmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 63, location 8392562 - 8498427:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val - X - X) + (Me-redmal) + (Me-mal - Me-ccmal) + (Me-ohmal - redmal) + (ccmal) + (ohmal) + (ccmal) + (Me-ohmal - ccemal) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 64, location 8459797 - 8504354:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (Me-ohmal - ccemal)
Non-colinear ordering:
  K6K39_RS37060 + K6K39_RS37050

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 65, location 8466409 - 8507432:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (Me-ohmal - ccemal)
Non-colinear ordering:
  K6K39_RS37060 + K6K39_RS37050

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
K6K39_RS36990: Val - X - X
Search NORINE for peptide: strict or relaxed
AMP-binding (498..892): 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:
    LQRSFDASTYESWLVVGGDVNGYGPTETTTFATL
  Nearest Stachelhaus code(s):
    Val DAYWVGGTFK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1537..1927): X
nrpys: mTyr

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:
    LDRYTDISTYEPCLLTGGEVDAYGPTEATAFTTL
  Nearest Stachelhaus code(s):
    mTyr DIYCLGAAFK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2578..2979): X
nrpys: Piz

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:
    MWQTFDVHVQESFVSQAGEHNHYGSTEIQVVTAL
  Nearest Stachelhaus code(s):
    Piz DVQFSAHVVK (94% 8Å match)
    Pro DVQFSAHVVK (68% 8Å match)
  Stachelhaus code match:
    100% (strong)

K6K39_RS36995: mmal
PKS_AT (641..938): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 220.4
  Ethylmalonyl-CoA: 211.2
  Methoxymalonyl-CoA: 184.9
  trans-1,2-CPDA: 139.6
  2-Methylbutyryl-CoA: 137.7
  CHC-CoA: 110.1
  Propionyl-CoA: 108.7
  Isobutyryl-CoA: 104.7
  Malonyl-CoA: 98.6
  Benzoyl-CoA: 82.2
  Acetyl-CoA: 56.9
  3-Methylbutyryl-CoA: 54.6
  fatty_acid: 35.7
  inactive: 25.6

K6K39_RS37000: mmal - mmal - mal
PKS_AT (556..853): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 226.0
  Ethylmalonyl-CoA: 215.1
  Methoxymalonyl-CoA: 187.1
  trans-1,2-CPDA: 143.0
  2-Methylbutyryl-CoA: 137.4
  Propionyl-CoA: 112.8
  Malonyl-CoA: 111.5
  CHC-CoA: 107.3
  Isobutyryl-CoA: 105.5
  Benzoyl-CoA: 88.5
  Acetyl-CoA: 58.6
  3-Methylbutyryl-CoA: 46.4
  inactive: 37.9
  fatty_acid: 26.4

PKS_AT (1571..1869): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 214.6
  Ethylmalonyl-CoA: 198.4
  Methoxymalonyl-CoA: 177.7
  2-Methylbutyryl-CoA: 152.1
  trans-1,2-CPDA: 125.5
  Propionyl-CoA: 112.8
  CHC-CoA: 107.2
  Malonyl-CoA: 105.7
  Isobutyryl-CoA: 95.7
  Benzoyl-CoA: 72.4
  Acetyl-CoA: 50.8
  3-Methylbutyryl-CoA: 38.6
  fatty_acid: 37.2
  inactive: 35.4

PKS_AT (3221..3462): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 170.6
  Methoxymalonyl-CoA: 74.6
  Methylmalonyl-CoA: 73.7
  inactive: 71.1
  Ethylmalonyl-CoA: 47.9
  Propionyl-CoA: 38.2
  Isobutyryl-CoA: 33.2
  trans-1,2-CPDA: 25.7
  2-Methylbutyryl-CoA: 24.9
  Acetyl-CoA: 24.6
  Benzoyl-CoA: 20.3
  CHC-CoA: 19.7
  fatty_acid: 19.4
  3-Methylbutyryl-CoA: 9.1

K6K39_RS41455: mmal - mal
PKS_AT (1082..1371): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 201.2
  Ethylmalonyl-CoA: 185.5
  Methoxymalonyl-CoA: 175.9
  2-Methylbutyryl-CoA: 130.5
  trans-1,2-CPDA: 106.8
  Propionyl-CoA: 105.7
  Malonyl-CoA: 102.9
  CHC-CoA: 93.6
  Benzoyl-CoA: 73.3
  Isobutyryl-CoA: 62.3
  Acetyl-CoA: 42.5
  3-Methylbutyryl-CoA: 37.3
  fatty_acid: 25.8
  inactive: 15.3

PKS_AT (2621..2915): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 188.4
  inactive: 84.3
  Methoxymalonyl-CoA: 73.7
  Methylmalonyl-CoA: 58.3
  Propionyl-CoA: 36.1
  Isobutyryl-CoA: 30.9
  Acetyl-CoA: 23.5
  Ethylmalonyl-CoA: 22.0
  Benzoyl-CoA: 21.7
  fatty_acid: 16.3
  2-Methylbutyryl-CoA: 14.3
  CHC-CoA: 13.4
  trans-1,2-CPDA: 6.9
  3-Methylbutyryl-CoA: 0.0

K6K39_RS37035: mal
PKS_AT (558..843): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 178.1
  inactive: 81.3
  Methoxymalonyl-CoA: 77.1
  Methylmalonyl-CoA: 64.2
  Isobutyryl-CoA: 50.5
  Ethylmalonyl-CoA: 49.0
  Propionyl-CoA: 40.2
  2-Methylbutyryl-CoA: 30.1
  Benzoyl-CoA: 19.7
  fatty_acid: 17.4
  trans-1,2-CPDA: 11.7
  Acetyl-CoA: 11.0
  3-Methylbutyryl-CoA: 7.2
  CHC-CoA: 5.0

K6K39_RS42095: mal
PKS_AT (508..749): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 170.6
  Methoxymalonyl-CoA: 74.6
  Methylmalonyl-CoA: 73.7
  inactive: 71.1
  Ethylmalonyl-CoA: 47.9
  Propionyl-CoA: 38.2
  Isobutyryl-CoA: 33.2
  trans-1,2-CPDA: 25.7
  2-Methylbutyryl-CoA: 24.9
  Acetyl-CoA: 24.6
  Benzoyl-CoA: 20.3
  CHC-CoA: 19.7
  fatty_acid: 19.4
  3-Methylbutyryl-CoA: 9.1

K6K39_RS42105: mal - mal
PKS_AT (252..522): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 183.6
  Methoxymalonyl-CoA: 80.8
  Methylmalonyl-CoA: 79.1
  inactive: 74.2
  Ethylmalonyl-CoA: 50.6
  Propionyl-CoA: 41.1
  Isobutyryl-CoA: 40.1
  trans-1,2-CPDA: 25.8
  2-Methylbutyryl-CoA: 24.5
  Acetyl-CoA: 24.4
  Benzoyl-CoA: 19.3
  fatty_acid: 19.0
  CHC-CoA: 17.1
  3-Methylbutyryl-CoA: 8.4

PKS_AT (1918..2205): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  Propionyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 195.8
  inactive: 104.0
  Methoxymalonyl-CoA: 60.7
  Methylmalonyl-CoA: 57.5
  Propionyl-CoA: 36.3
  Isobutyryl-CoA: 27.6
  Ethylmalonyl-CoA: 26.4
  fatty_acid: 20.1
  CHC-CoA: 18.8
  2-Methylbutyryl-CoA: 16.1
  Benzoyl-CoA: 14.3
  Acetyl-CoA: 10.3
  trans-1,2-CPDA: 3.6
  3-Methylbutyryl-CoA: 0.0

K6K39_RS37050: mmal - emal
PKS_AT (1260..1553): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 214.9
  Ethylmalonyl-CoA: 209.7
  Methoxymalonyl-CoA: 175.2
  2-Methylbutyryl-CoA: 149.8
  trans-1,2-CPDA: 127.4
  Malonyl-CoA: 112.7
  Propionyl-CoA: 112.5
  CHC-CoA: 112.2
  Isobutyryl-CoA: 78.0
  Benzoyl-CoA: 59.9
  3-Methylbutyryl-CoA: 43.9
  inactive: 40.1
  Acetyl-CoA: 36.0
  fatty_acid: 29.2

PKS_AT (2806..3104): emal
ATSignature: Ethylmalonyl-CoA, Methoxymalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 206.0
  Methylmalonyl-CoA: 184.7
  Methoxymalonyl-CoA: 159.5
  trans-1,2-CPDA: 119.3
  2-Methylbutyryl-CoA: 116.4
  Propionyl-CoA: 93.7
  Malonyl-CoA: 83.4
  Isobutyryl-CoA: 78.5
  CHC-CoA: 77.5
  Benzoyl-CoA: 74.0
  Acetyl-CoA: 40.4
  fatty_acid: 33.3
  3-Methylbutyryl-CoA: 21.2
  inactive: 14.8

K6K39_RS37060: mal
PKS_AT (542..828): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 63.1
  Methoxymalonyl-CoA: 21.6
  Methylmalonyl-CoA: 20.8
  inactive: 16.0
  CHC-CoA: 4.6
  Ethylmalonyl-CoA: 1.6
  Propionyl-CoA: 1.0
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

K6K39_RS37065: mal
PKS_AT (120..331): mal
ATSignature: (unknown)
No matches above 50%
minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 0.5
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
RpoN | Regulator of nitrogen assimilation and virulence

NZ_AP024135.1 - Region 36 - melanin,terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,671,225 - 8,700,408 nt. (total: 29,184 nt) Show pHMM detection rules used
melanin: melC
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
K6K39_RS37995: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

K6K39_RS38025: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Hydrolases: hydrolase
K6K39_RS38060: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: synthase synthetase
K6K39_RS38035: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

K6K39_RS38040: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | melanin | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000910.3 |  |  | 0.52 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000911.3 |  |  | 0.51 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000909.3 |  |  | 0.30 | other (other) | melanin | Streptomyces avermitilis
BGC0000908.3 |  |  | 0.28 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  |  | 0.28 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002397.2 |  |  | 0.16 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  |  | 0.14 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000677.5 |  |  | 0.13 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001605.3 |  |  | 0.12 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000633.3 |  |  | 0.12 | terpene | carotenoid | Streptomyces avermitilis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000910.3 |  | 0.80 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000911.3 |  | 0.79 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000909.3 |  | 0.64 | other (other) | melanin | Streptomyces avermitilis
BGC0000908.3 |  | 0.62 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.61 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002397.2 |  | 0.53 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.49 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000885.3 |  | 0.48 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000677.5 |  | 0.45 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002398.2 |  | 0.43 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

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

Genes with terpene domains:
K6K39_RS38040: PT_FPPS_like
Domain 1 (58 - 339): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.60 out of 19.26
Confidence: medium
Additional weak hits (10):
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.21 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.74 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.79 out of 36.54
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.87 out of 27.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.10 out of 26.06
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.65 out of 23.43
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.86 out of 29.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.08 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein

NZ_AP024135.1 - Region 37 - CDPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,789,757 - 8,810,467 nt. (total: 20,711 nt) Show pHMM detection rules used
CDPS: CDPS

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
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
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
K6K39_RS38525: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

K6K39_RS38550: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

K6K39_RS38580: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase
K6K39_RS38505: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: hydrolase
K6K39_RS38495: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | CDPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002725.3 |  | 0.79 | ribosomal | prunipeptin | Streptomyces prunicolor NBRC 13075
BGC0001986.3 |  | 0.51 | other (other) | purincyclamide | Streptomyces chrestomyceticus
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000858.3 |  | 0.47 | other (other) | ectoine | Methylobacter marinus
BGC0000853.3 |  | 0.45 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.45 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000919.5 |  | 0.44 | other (other) | phaseolotoxin | Pseudomonas syringae
BGC0002482.2 |  | 0.41 | other (other) | tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M | Symphyonema bifilamentata 97.28
BGC0001529.5 |  | 0.40 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0000905.5 |  | 0.40 | other (other) | heme D1 | Heliobacillus mobilis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002725.3 |  | 0.79 | ribosomal | prunipeptin | Streptomyces prunicolor NBRC 13075
BGC0001986.3 |  | 0.51 | other (other) | purincyclamide | Streptomyces chrestomyceticus
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000858.3 |  | 0.47 | other (other) | ectoine | Methylobacter marinus
BGC0000853.3 |  | 0.45 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.45 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000919.5 |  | 0.44 | other (other) | phaseolotoxin | Pseudomonas syringae
BGC0002482.2 |  | 0.41 | other (other) | tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M | Symphyonema bifilamentata 97.28
BGC0001529.5 |  | 0.40 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0000905.5 |  | 0.40 | other (other) | heme D1 | Heliobacillus mobilis

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (9):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.73 out of 28.14
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.20 out of 32.74
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.33 out of 30.25
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.75 out of 23.43
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.36 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.86 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.97 out of 35.63
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 26.85
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.19 out of 24.78
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production

NZ_AP024135.1 - Region 38 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,836,434 - 8,861,023 nt. (total: 24,590 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase electron transfer
K6K39_RS38725: flavodoxin

smcogs
  SMCOG1134: flavodoxin

K6K39_RS38735: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

K6K39_RS38755: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: methyltransferase
K6K39_RS38740: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: back translocase
K6K39_RS38710: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.72 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.68 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000649.3 |  | 0.67 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.65 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.64 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000645.3 |  | 0.48 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000650.3 |  | 0.47 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000648.3 |  | 0.47 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.47 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.45 | terpene | carotenoid | Enterobacteriaceae bacterium DC404

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.72 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.68 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000649.3 |  | 0.67 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.65 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.64 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000645.3 |  | 0.48 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000650.3 |  | 0.47 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000648.3 |  | 0.47 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.47 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.45 | terpene | carotenoid | Enterobacteriaceae bacterium DC404

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
tetraterpene | C40 carotenoid |  | C40 | unknown | unknown

Genes with terpene domains:
K6K39_RS38745: Lycopene_cycl
Domain 1 (6 - 382): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

K6K39_RS38760: PT_phytoene_like
Domain 1 (16 - 311): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (7):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.33 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.37 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.89 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.69 out of 26.06
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.66 out of 32.74
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 14.80 out of 33.14
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
PSPP | Presqualene diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_AP024135.1 - Region 39 - NRPS,NRPS-like,T1PKS,cyanobactin,t3nrps-iterative
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,957,853 - 9,135,368 nt. (total: 177,516 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
cyanobactin: (cyanobactin_synth or TIGR03678 or cyanobactin_precursor)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
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
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
K6K39_RS39325: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

K6K39_RS39500: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

K6K39_RS39510: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

K6K39_RS39515: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

K6K39_RS39575: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

K6K39_RS39605: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

K6K39_RS39640: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

K6K39_RS39650: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

K6K39_RS39745: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

K6K39_RS39755: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

K6K39_RS42135: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase acetyltransferase acylase acyltransferase aminotransferase glycosyltransferase methyltransferase
K6K39_RS39405: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

K6K39_RS39410: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

K6K39_RS39420: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

K6K39_RS39525: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

K6K39_RS39600: glycosyltransferase

smcogs
  SMCOG1102: glycosyltransferase

K6K39_RS39635: methyltransferase

smcogs
  SMCOG1089: methyltransferase

K6K39_RS39705: methyltransferase

smcogs
  SMCOG1089: methyltransferase

K6K39_RS39770: aminotransferase

smcogs
  SMCOG1019: aminotransferase

K6K39_RS39780: aminotransferase

smcogs
  SMCOG1019: aminotransferase

K6K39_RS39790: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

K6K39_RS41860: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: dehalogenase esterase hydrolase protease
K6K39_RS39310: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

K6K39_RS39385: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

K6K39_RS39400: amidohydrolase

smcogs
  SMCOG1244: amidohydrolase

K6K39_RS39495: thioesterase

smcogs
  SMCOG1004: thioesterase

K6K39_RS39520: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

K6K39_RS39695: thioesterase

smcogs
  SMCOG1004: thioesterase

K6K39_RS39740: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: decarboxylase
K6K39_RS39545: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase
K6K39_RS39440: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS39450: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

K6K39_RS39455: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

K6K39_RS39465: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

K6K39_RS39535: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS39540: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS39660: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

K6K39_RS39665: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS39670: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

K6K39_RS39685: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS39700: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

K6K39_RS39710: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS39720: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

K6K39_RS41545: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS | cyanobactin | NRPS-like | T1PKS | t3nrps-iterative | T1PKS | NRPS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002075.3 |  |  |  |  |  |  |  |  | 2.55 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001244.3 |  |  |  |  |  |  |  |  | 2.17 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  |  |  |  |  |  |  | 2.17 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001160.5 |  |  |  |  |  |  |  |  | 2.08 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  |  |  |  |  |  |  | 2.06 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001132.4 |  |  |  |  |  |  |  |  | 1.98 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  |  |  |  |  |  |  |  | 1.97 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  |  |  |  |  |  | 1.97 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  |  |  |  |  |  | 1.94 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  |  |  |  |  |  |  | 1.91 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002517.3 |  | 0.86 | PKS | tripartilactam, niizalactam C | Streptomyces sp.
BGC0001833.4 |  | 0.78 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.77 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.77 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.77 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  | 0.76 | NRPS | enniatin | Fusarium equiseti
BGC0001135.5 |  | 0.76 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002075.3 |  | 0.76 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.75 out of 26.85
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.47 out of 26.85
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.39 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 26.66 out of 30.11
Confidence: medium
Additional weak hits (27):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.74 out of 26.33
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.41 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.37 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.03 out of 29.38
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.67 out of 29.72
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.70 out of 26.33
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.43 out of 27.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.36 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.54 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.02 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.19 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.58 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.48 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.53 out of 21.55
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.60 out of 30.22
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.21 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.24 out of 21.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 14.88 out of 20.97
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.07 out of 32.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.71 out of 31.73
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.52 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.01 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.03 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.25 out of 24.78
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 71, location 8957852 - 9133051:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr) + (NH2 - Ser) + (NMe-Ser) + (X) + (X) + (Me-ccmal) + (ccmal) + (ccmal - Me-ccmal) + (ccmal) + (ohmal) + (ccmal) + (NH2) + (Ser)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 72, location 8957852 - 9003201:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - Me-ccmal) + (ohmal) + (ccmal) + (NH2) + (Ser)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 74, location 8965234 - 9007172:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - Me-ccmal) + (ohmal) + (ccmal) + (NH2) + (Ser)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 75, location 8968662 - 9079115:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-ccmal) + (ccmal) + (ccmal - Me-ccmal) + (ccmal) + (ohmal) + (ccmal) + (NH2) + (Ser)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 76, location 9073484 - 9133051:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (X) + (NMe-Ser) + (NH2 - Ser) + (Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 77, location 9093538 - 9135368:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (X) + (NMe-Ser) + (NH2 - Ser) + (Thr)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
K6K39_RS39420: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (926..1326): 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:
    RWMTFDVSVWEWHFIASGEHNLYGPTEASVDVSA
  Nearest Stachelhaus code(s):
    Ser DVWHISLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

K6K39_RS39440: NH2
CAL_domain (22..452): NH2
minowa: NH2

Prediction, score:
  NH2: 159.3
  fatty_acid: 54.8
  Acetyl-CoA: 45.1
  AHBA: 16.5
  shikimic_acid: 6.3

K6K39_RS39450: mal
PKS_AT (554..840): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 189.1
  inactive: 93.6
  Methoxymalonyl-CoA: 59.1
  Methylmalonyl-CoA: 56.8
  Isobutyryl-CoA: 26.8
  Ethylmalonyl-CoA: 26.5
  Propionyl-CoA: 25.7
  Acetyl-CoA: 17.0
  CHC-CoA: 15.9
  Benzoyl-CoA: 15.8
  fatty_acid: 13.1
  2-Methylbutyryl-CoA: 10.1
  trans-1,2-CPDA: 8.7
  3-Methylbutyryl-CoA: -0.8

K6K39_RS39455: mal
PKS_AT (549..825): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 213.2
  inactive: 113.7
  Methoxymalonyl-CoA: 59.1
  Methylmalonyl-CoA: 44.7
  Isobutyryl-CoA: 29.8
  Propionyl-CoA: 23.9
  Ethylmalonyl-CoA: 19.9
  Acetyl-CoA: 18.6
  Benzoyl-CoA: 18.1
  fatty_acid: 11.3
  2-Methylbutyryl-CoA: 3.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0
  CHC-CoA: -1.4

K6K39_RS41540: mal - mmal
PKS_AT (553..836): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 208.4
  inactive: 108.6
  Methoxymalonyl-CoA: 56.8
  Methylmalonyl-CoA: 51.2
  Isobutyryl-CoA: 22.2
  Benzoyl-CoA: 17.4
  Propionyl-CoA: 17.2
  Acetyl-CoA: 17.2
  Ethylmalonyl-CoA: 13.5
  CHC-CoA: 10.5
  2-Methylbutyryl-CoA: 0.9
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2222..2511): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 217.3
  Ethylmalonyl-CoA: 211.4
  Methoxymalonyl-CoA: 177.1
  trans-1,2-CPDA: 138.1
  2-Methylbutyryl-CoA: 136.1
  Propionyl-CoA: 113.3
  Malonyl-CoA: 104.5
  CHC-CoA: 93.2
  Isobutyryl-CoA: 76.4
  Benzoyl-CoA: 70.4
  Acetyl-CoA: 44.8
  fatty_acid: 33.3
  inactive: 28.4
  3-Methylbutyryl-CoA: 26.3

K6K39_RS41545: mal
PKS_AT (1102..1386): mal
ATSignature: Malonyl-CoA, inactive

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 91.7%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 188.4
  inactive: 96.4
  Methoxymalonyl-CoA: 53.2
  Methylmalonyl-CoA: 44.4
  Acetyl-CoA: 28.0
  Propionyl-CoA: 19.7
  Isobutyryl-CoA: 15.3
  Benzoyl-CoA: 14.2
  fatty_acid: 13.1
  Ethylmalonyl-CoA: 11.1
  trans-1,2-CPDA: 10.2
  CHC-CoA: 10.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

K6K39_RS39525: pk
PKS_AT (26..279): pk
ATSignature: (unknown)
No matches above 50%
minowa: CHC-CoA

Prediction, score:
  CHC-CoA: 11.5
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Malonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

K6K39_RS39535: Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (16..414): 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:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    YLLFFDCAMFDCFSFFAGEENLYGPTELTITITA
  Nearest Stachelhaus code(s):
    Ala DCFFFALITK (94% 8Å match)
    bMe-Asp DCFFFALITK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

K6K39_RS39540: X
AMP-binding (38..433): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AAIFWDYGLYKLPITNTGAIIQFGQTECKRVSVL
  Nearest Stachelhaus code(s):
    3S-Abu DYYPTTQRIK (94% 8Å match)
    Asp DYYPTTMRVK (65% 8Å match)
  Stachelhaus code match:
    90% (moderate)

K6K39_RS42135: mal
PKS_AT (673..967): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 204.4
  inactive: 101.7
  Methoxymalonyl-CoA: 68.9
  Methylmalonyl-CoA: 59.7
  Isobutyryl-CoA: 32.3
  Propionyl-CoA: 25.8
  CHC-CoA: 18.4
  Ethylmalonyl-CoA: 17.0
  Benzoyl-CoA: 15.2
  Acetyl-CoA: 14.2
  fatty_acid: 11.8
  2-Methylbutyryl-CoA: 8.9
  3-Methylbutyryl-CoA: 6.7
  trans-1,2-CPDA: 3.0

K6K39_RS41860: mmal
PKS_AT (564..858): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 225.5
  Ethylmalonyl-CoA: 213.6
  Methoxymalonyl-CoA: 187.8
  2-Methylbutyryl-CoA: 143.8
  trans-1,2-CPDA: 140.2
  Malonyl-CoA: 107.9
  CHC-CoA: 107.6
  Propionyl-CoA: 107.0
  Isobutyryl-CoA: 96.8
  Benzoyl-CoA: 79.5
  3-Methylbutyryl-CoA: 63.3
  Acetyl-CoA: 53.8
  fatty_acid: 34.6
  inactive: 33.3

K6K39_RS39665: X
AMP-binding (252..651): 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:
    ADVSFDLSVYDGLAIQAGDYNGGGPAESCVLSVM
  Nearest Stachelhaus code(s):
    Pro DVLLVAGVLK (38% 8Å match)
  Stachelhaus code match:
    70% (weak)

K6K39_RS39685: X
AMP-binding (497..926): 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:
    YAMAFDVLLEEPELAMGGELHVYGLTEVTCTSTV
  Nearest Stachelhaus code(s):
    Ahp DVENAGVVTK (50% 8Å match)
  Stachelhaus code match:
    80% (moderate)

K6K39_RS39700: X
AMP-binding (520..926): X
nrpys: Ser, Thr, Dhpg, Hpg

SVM prediction details:
  Predicted physicochemical class:
    N/A
  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:
    TGLSYDMSVYEGSSVLGGDYNLAGMTETSYCTLY
  Nearest Stachelhaus code(s):
    Pro DMYFAGLICK (38% 8Å match)
  Stachelhaus code match:
    70% (weak)

K6K39_RS39705: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (504..913): 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:
    RWMTFDVSVWEWHFVCSGEHNLYGPTEAAIDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHVSLIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

K6K39_RS39710: NH2 - Ser
Search NORINE for peptide: strict or relaxed
CAL_domain (35..480): NH2
minowa: NH2

Prediction, score:
  NH2: 40.6
  AHBA: 24.8
  fatty_acid: 12.9
  Acetyl-CoA: 7.5
  shikimic_acid: 3.6

AMP-binding (1205..1610): 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:
    RWMTFDVAGWEAHFVCSGEHNLYGPAETAIEVTA
  Nearest Stachelhaus code(s):
    Ser DVWHVSLIDK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

K6K39_RS39720: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (12..420): 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:
    LVVHFDFSVWEGSQILGGEVNMYGITEATVHASY
  Nearest Stachelhaus code(s):
    Thr DFWSIGMVHK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
CelR | Cellobiose uptake repressor
RutR | Regulator of the pyrimidine and purine metabolism

NZ_AP024135.1 - Region 40 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 9,175,623 - 9,187,527 nt. (total: 11,905 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
K6K39_RS39960: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001485.4 |  | 0.44 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001157.6 |  | 0.40 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000468.5 |  | 0.40 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0000470.6 |  | 0.39 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000469.6 |  | 0.37 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0000598.5 |  | 0.36 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0001940.3 |  | 0.34 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0001753.3 |  | 0.34 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus
BGC0000188.5 |  | 0.33 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0000243.4 |  | 0.32 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001485.4 |  | 0.44 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001157.6 |  | 0.40 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000468.5 |  | 0.40 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0000470.6 |  | 0.39 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000469.6 |  | 0.37 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0000598.5 |  | 0.36 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0001940.3 |  | 0.34 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0001753.3 |  | 0.34 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus
BGC0000188.5 |  | 0.33 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0000243.4 |  | 0.32 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.87 out of 29.72
Confidence: medium
Additional weak hits (6):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.44 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.17 out of 27.78
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.74 out of 26.33
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.07 out of 28.14
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.61 out of 25.31
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NtrC | Nitrogen regulatory protein C

NZ_AP024135.1 - Region 41 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 9,256,867 - 9,279,468 nt. (total: 22,602 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lanthipeptides
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
K6K39_RS40310: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase
K6K39_RS40405: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Hydrolases: hydrolase
K6K39_RS41605: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

K6K39_RS41610: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: cyclase
K6K39_RS40360: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002316.2 |  | 0.48 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0001364.3 |  | 0.41 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0001727.3 |  | 0.38 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0001137.5 |  | 0.37 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0000679.5 |  | 0.33 | terpene | diazepinomicin | Micromonospora sp. M42
BGC0001940.3 |  | 0.33 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0002002.3 |  | 0.33 | NRPS | 1,6-phenazinedimethanol, fontizine A | Serratia fonticola
BGC0002448.2 |  | 0.33 | NRPS | Q6402A | Streptomyces violaceusniger
BGC0000914.5 |  | 0.32 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0000335.4 |  | 0.32 | NRPS, PKS | cystomanamide A, cystomanamide B, cystomanamide C, cystomanamide D | Cystobacter fuscus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002316.2 |  | 0.48 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0001364.3 |  | 0.41 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0001727.3 |  | 0.38 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0001137.5 |  | 0.37 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0000679.5 |  | 0.33 | terpene | diazepinomicin | Micromonospora sp. M42
BGC0001940.3 |  | 0.33 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0002002.3 |  | 0.33 | NRPS | 1,6-phenazinedimethanol, fontizine A | Serratia fonticola
BGC0002448.2 |  | 0.33 | NRPS | Q6402A | Streptomyces violaceusniger
BGC0000914.5 |  | 0.32 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0000335.4 |  | 0.32 | NRPS, PKS | cystomanamide A, cystomanamide B, cystomanamide C, cystomanamide D | Cystobacter fuscus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
Additional weak hits (6):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.65 out of 26.85
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.70 out of 29.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 26.33
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.37 out of 28.19
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
VqsM | Regulator of quorum-sensing signalling systems