Select genomic region:
Overview
1.1
1.2
1.3
1.4
1.5
1.6
1.7
1.8
1.9
1.10
1.11
1.12
1.13
1.14
1.15
1.16
1.17
1.18
1.19
1.20
1.21
1.22
1.23
1.24
1.25
1.26
2.1
2.2
2.3
2.4
2.5
2.6
2.7
2.8
2.9
2.10
2.11
2.12
2.13
2.14
2.15
2.16
2.17
2.18
2.19
2.20
2.21
2.22
2.23
2.24

### Identified secondary metabolite regions using strictness 'relaxed'

NZ_LJIW01000001.1 (Streptomyces malaysiensis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | T3PKS,T1PKS,nucleoside | 133,122 | 338,697 | High | bafilomycin B1 | PKS:Type I
Region 1.2 | NAPAA | 563,322 | 597,509 |  |
Region 1.3 | NRPS-like | 878,743 | 921,481 |  |
Region 1.4 | lanthipeptide-class-ii,NRPS,T1PKS,terpene | 957,131 | 1,031,110 |  |
Region 1.5 | terpene | 1,138,870 | 1,162,662 | Low | brasilicardin A | terpene+saccharide
Region 1.6 | NRPS | 1,185,337 | 1,264,086 |  |
Region 1.7 | RiPP-like,T1PKS,hglE-KS | 1,272,584 | 1,398,754 | High | hexacosalactone A | other:other
Region 1.8 | terpene-precursor | 1,480,101 | 1,501,183 |  |
Region 1.9 | T1PKS,NRPS-like | 1,533,386 | 1,613,403 | High | hygrocin A/hygrocin B | PKS
Region 1.10 | T1PKS,NRPS | 1,617,407 | 1,734,797 | Medium | meridamycin | NRPS:Type I+PKS
Region 1.11 | terpene | 1,930,927 | 1,952,114 | High | pristinol | terpene
Region 1.12 | terpene | 1,961,063 | 1,983,062 | High | cyclooctatin | terpene:Diterpene
Region 1.13 | betalactone,T1PKS,NRPS-like | 2,046,477 | 2,143,525 | Medium | geldanamycin | PKS
Region 1.14 | terpene,PKS-like | 2,462,922 | 2,507,049 | Low | rustmicin | PKS:Iterative type I
Region 1.15 | T1PKS,NRPS-like | 2,581,817 | 2,658,607 | Low | macbecin/macbecin II | PKS
Region 1.16 | 2dos,T1PKS,NRPS-like | 2,703,603 | 2,786,829 | Low | divergolide A/divergolide B/divergolide C/divergolide D | PKS:Type I
Region 1.17 | terpene | 2,973,705 | 3,002,770 | Low | aurachin C/aurachin D/aurachin SS | PKS+terpene
Region 1.18 | NI-siderophore | 3,036,382 | 3,068,159 | Low | peucechelin | NRPS:Type I
Region 1.19 | ectoine | 3,223,361 | 3,233,765 | High | ectoine | other:other
Region 1.20 | lanthipeptide-class-i | 3,976,215 | 4,002,677 |
Region 1.21 | T1PKS | 4,340,792 | 4,523,551 | Medium | desulfoclethramycin/clethramycin | other:other
Region 1.22 | RiPP-like | 4,661,194 | 4,673,590 |  |
Region 1.23 | HR-T2PKS | 4,680,361 | 4,730,634 | Medium | cinnapeptin | NRPS:Type I
Region 1.24 | NRPS | 4,780,519 | 4,824,529 | Medium | ochronotic pigment | other:other
Region 1.25 | indole | 5,023,833 | 5,044,981 | Medium | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | other:other
Region 1.26 | terpene | 5,664,428 | 5,686,824 | High | geosmin | terpene:Sesquiterpene

NZ_LJIW01000002.1 (Streptomyces malaysiensis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | NRPS,terpene-precursor | 5,774 | 66,037 |  |
Region 2.2 | NRPS,T1PKS,NRPS-like | 362,619 | 468,577 | Low | rapamycin | NRPS:Type I+PKS
Region 2.3 | T1PKS | 552,127 | 599,383 |  |
Region 2.4 | arylpolyene,NRPS | 658,964 | 731,781 | High | coprisamide C/coprisamide D | NRPS:Type I
Region 2.5 | NRP-metallophore,NRPS | 962,332 | 1,020,665 | High | coelichelin | NRPS:Type I
Region 2.6 | NRPS-like,NRPS,betalactone,T1PKS,T3PKS | 1,044,703 | 1,165,355 | Medium | totopotensamide A/totopotensamide B | NRPS:Type I+PKS
Region 2.7 | butyrolactone | 1,280,067 | 1,291,062 |  |
Region 2.8 | NRPS,NRPS-like | 1,321,466 | 1,409,740 | Medium | glycinocin A | NRPS:Type I
Region 2.9 | T1PKS | 1,435,569 | 1,573,992 | High | azalomycin F3a | PKS
Region 2.10 | T1PKS | 1,786,623 | 1,961,609 | High | nigericin | PKS:Type I
Region 2.11 | T1PKS | 2,053,609 | 2,133,513 | High | efomycin K/efomycin L | PKS
Region 2.12 | redox-cofactor | 2,160,780 | 2,182,871 |  |
Region 2.13 | hserlactone | 2,295,766 | 2,316,524 |  |
Region 2.14 | butyrolactone | 2,327,642 | 2,338,577 |
Region 2.15 | T1PKS | 2,509,112 | 2,557,505 |
Region 2.16 | terpene | 2,887,638 | 2,914,091 | High | hopene | terpene
Region 2.17 | triceptide | 2,940,510 | 2,961,670 |
Region 2.18 | T2PKS | 3,107,092 | 3,179,607 | High | spore pigment | PKS
Region 2.19 | T1PKS | 3,290,528 | 3,353,153 |  |
Region 2.20 | RiPP-like | 3,410,713 | 3,422,215 |  |
Region 2.21 | NRPS,aminocoumarin,arylpolyene,terpene-precursor | 3,539,445 | 3,620,587 | High | cinnapeptin | NRPS:Type I
Region 2.22 | NI-siderophore | 3,689,075 | 3,719,258 |  |
Region 2.23 | NRPS-like | 4,255,263 | 4,298,109 | High | echoside A/echoside B/echoside C/echoside D/echoside E | NRPS:Type I
Region 2.24 | NI-siderophore,lanthipeptide-class-i | 4,807,378 | 4,858,226 | High | legonoxamine A/desferrioxamine B/legonoxamine B | other:other

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | T3PKS,T1PKS,nucleoside | 133,122 | 338,697 | High | bafilomycin B1 | PKS:Type I
Region 1.2 | NAPAA | 563,322 | 597,509 |  |
Region 1.3 | NRPS-like | 878,743 | 921,481 |  |
Region 1.4 | lanthipeptide-class-ii,NRPS,T1PKS,terpene | 957,131 | 1,031,110 |  |
Region 1.5 | terpene | 1,138,870 | 1,162,662 | Low | brasilicardin A | terpene+saccharide
Region 1.6 | NRPS | 1,185,337 | 1,264,086 |  |
Region 1.7 | RiPP-like,T1PKS,hglE-KS | 1,272,584 | 1,398,754 | High | hexacosalactone A | other:other
Region 1.8 | terpene-precursor | 1,480,101 | 1,501,183 |  |
Region 1.9 | T1PKS,NRPS-like | 1,533,386 | 1,613,403 | High | hygrocin A/hygrocin B | PKS
Region 1.10 | T1PKS,NRPS | 1,617,407 | 1,734,797 | Medium | meridamycin | NRPS:Type I+PKS
Region 1.11 | terpene | 1,930,927 | 1,952,114 | High | pristinol | terpene
Region 1.12 | terpene | 1,961,063 | 1,983,062 | High | cyclooctatin | terpene:Diterpene
Region 1.13 | betalactone,T1PKS,NRPS-like | 2,046,477 | 2,143,525 | Medium | geldanamycin | PKS
Region 1.14 | terpene,PKS-like | 2,462,922 | 2,507,049 | Low | rustmicin | PKS:Iterative type I
Region 1.15 | T1PKS,NRPS-like | 2,581,817 | 2,658,607 | Low | macbecin/macbecin II | PKS
Region 1.16 | 2dos,T1PKS,NRPS-like | 2,703,603 | 2,786,829 | Low | divergolide A/divergolide B/divergolide C/divergolide D | PKS:Type I
Region 1.17 | terpene | 2,973,705 | 3,002,770 | Low | aurachin C/aurachin D/aurachin SS | PKS+terpene
Region 1.18 | NI-siderophore | 3,036,382 | 3,068,159 | Low | peucechelin | NRPS:Type I
Region 1.19 | ectoine | 3,223,361 | 3,233,765 | High | ectoine | other:other
Region 1.20 | lanthipeptide-class-i | 3,976,215 | 4,002,677 |
Region 1.21 | T1PKS | 4,340,792 | 4,523,551 | Medium | desulfoclethramycin/clethramycin | other:other
Region 1.22 | RiPP-like | 4,661,194 | 4,673,590 |  |
Region 1.23 | HR-T2PKS | 4,680,361 | 4,730,634 | Medium | cinnapeptin | NRPS:Type I
Region 1.24 | NRPS | 4,780,519 | 4,824,529 | Medium | ochronotic pigment | other:other
Region 1.25 | indole | 5,023,833 | 5,044,981 | Medium | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | other:other
Region 1.26 | terpene | 5,664,428 | 5,686,824 | High | geosmin | terpene:Sesquiterpene
Region 2.1 | NRPS,terpene-precursor | 5,774 | 66,037 |  |
Region 2.2 | NRPS,T1PKS,NRPS-like | 362,619 | 468,577 | Low | rapamycin | NRPS:Type I+PKS
Region 2.3 | T1PKS | 552,127 | 599,383 |  |
Region 2.4 | arylpolyene,NRPS | 658,964 | 731,781 | High | coprisamide C/coprisamide D | NRPS:Type I
Region 2.5 | NRP-metallophore,NRPS | 962,332 | 1,020,665 | High | coelichelin | NRPS:Type I
Region 2.6 | NRPS-like,NRPS,betalactone,T1PKS,T3PKS | 1,044,703 | 1,165,355 | Medium | totopotensamide A/totopotensamide B | NRPS:Type I+PKS
Region 2.7 | butyrolactone | 1,280,067 | 1,291,062 |  |
Region 2.8 | NRPS,NRPS-like | 1,321,466 | 1,409,740 | Medium | glycinocin A | NRPS:Type I
Region 2.9 | T1PKS | 1,435,569 | 1,573,992 | High | azalomycin F3a | PKS
Region 2.10 | T1PKS | 1,786,623 | 1,961,609 | High | nigericin | PKS:Type I
Region 2.11 | T1PKS | 2,053,609 | 2,133,513 | High | efomycin K/efomycin L | PKS
Region 2.12 | redox-cofactor | 2,160,780 | 2,182,871 |  |
Region 2.13 | hserlactone | 2,295,766 | 2,316,524 |  |
Region 2.14 | butyrolactone | 2,327,642 | 2,338,577 |
Region 2.15 | T1PKS | 2,509,112 | 2,557,505 |
Region 2.16 | terpene | 2,887,638 | 2,914,091 | High | hopene | terpene
Region 2.17 | triceptide | 2,940,510 | 2,961,670 |
Region 2.18 | T2PKS | 3,107,092 | 3,179,607 | High | spore pigment | PKS
Region 2.19 | T1PKS | 3,290,528 | 3,353,153 |  |
Region 2.20 | RiPP-like | 3,410,713 | 3,422,215 |  |
Region 2.21 | NRPS,aminocoumarin,arylpolyene,terpene-precursor | 3,539,445 | 3,620,587 | High | cinnapeptin | NRPS:Type I
Region 2.22 | NI-siderophore | 3,689,075 | 3,719,258 |  |
Region 2.23 | NRPS-like | 4,255,263 | 4,298,109 | High | echoside A/echoside B/echoside C/echoside D/echoside E | NRPS:Type I
Region 2.24 | NI-siderophore,lanthipeptide-class-i | 4,807,378 | 4,858,226 | High | legonoxamine A/desferrioxamine B/legonoxamine B | other:other

No secondary metabolite regions were found in these records:
  NZ_LJIW01000003.1 (Streptomyces malaysiensis)
  NZ_LJIW01000004.1 (Streptomyces malaysiensis)

Compact view
NZ_LJIW01000001.1 - Region 1 - T1PKS,T3PKS,nucleoside
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
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Location: 133,122 - 338,697 nt. (total: 205,576 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
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)

#### 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.
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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.
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Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
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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
SMF913_RS00795: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

SMF913_RS00905: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

SMF913_RS00945: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

SMF913_RS00970: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS01050: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS01055: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS01100: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

SMF913_RS01110: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

SMF913_RS49785: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase aminotransferase methyltransferase
SMF913_RS00990: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

SMF913_RS01165: aminotransferase

smcogs
  SMCOG1019: aminotransferase

SMF913_RS01175: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: deacetylase peptidase phosphatase
SMF913_RS00925: gamma-glutamyltranspeptidase

smcogs
  SMCOG1274: gamma-glutamyltranspeptidase

SMF913_RS01095: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

SMF913_RS01185: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

Lyases: decarboxylase dehydratase
SMF913_RS01065: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

SMF913_RS01085: putative carboxymuconolactone decarboxylase

smcogs
  SMCOG1298: putative carboxymuconolactone decarboxylase

Ligases: ligase synthase
SMF913_RS00880: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

SMF913_RS00975: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

SMF913_RS00980: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS00985: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS01035: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS01060: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS01070: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS01075: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

SMF913_RS01080: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS49790: 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 | T3PKS | T1PKS | nucleoside | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001454.5 |  |  |  | 0.64 | other (other) | germicidin | Streptomyces argillaceus
BGC0001276.3 |  |  |  | 0.47 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  |  |  | 0.47 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  |  | 0.47 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  |  | 0.46 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  |  |  | 0.40 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001665.3 |  |  |  | 0.38 | PKS | methylated alkyl-resorcinol, methylated acyl-phloroglucinol | Mycobacterium marinum M
BGC0001537.5 |  |  |  | 0.36 | PKS | butyrolactol A | Streptomyces sp. NBRC 110030
BGC0000068.5 |  |  |  | 0.35 | PKS | geldanamycin | Streptomyces hygroscopicus
BGC0000847.4 |  |  |  | 0.35 | other (non-nrp beta-lactam) | thienamycin | Streptomyces cattleya

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001454.5 |  | 0.86 | other (other) | germicidin | Streptomyces argillaceus
BGC0001276.3 |  | 0.77 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.77 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.72 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000067.5 |  | 0.66 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0001160.5 |  | 0.66 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.66 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001012.3 |  | 0.65 | NRPS, PKS | meridamycin | Streptomyces violaceusniger

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.
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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: 17.13 out of 19.26
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.03 out of 26.85
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.00 out of 23.79
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.84 out of 30.12
Confidence: medium
Additional weak hits (25):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.92 out of 36.54
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.32 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.17 out of 29.38
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.18 out of 25.75
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.29 out of 33.73
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.29 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.27 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.61 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.63 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.04 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.84 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.61 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.52 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.03 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.11 out of 31.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.94 out of 31.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 26.33
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.68 out of 32.93
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.56 out of 29.65
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.39 out of 25.88
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.18 out of 18.57
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.07 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.72 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.78 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 1, location 133121 - 338697:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (emal - Me-ohmal) + (ohmal) + (ohmal) + (Me-ccmal - Me-ccmal) + (Me-mal - ccmal - pk) + (Me-mal - Me-ohmal - ohmal - Me-mal) + (Me-ohmal - pk - ccmal) + (Me-ccmal - Me-redmal - Me-ohmal - Me-ccmal) + (pk) + (Me-ccmal - ohmal) + (Me-redmal - ccmal) + (pk)
Non-colinear ordering:
  SMF913_RS00990 + SMF913_RS00985 + SMF913_RS00980 + SMF913_RS00975 + SMF913_RS01080 + SMF913_RS01065 + SMF913_RS01060 + SMF913_RS01055 + SMF913_RS01050 + SMF913_RS01035 + SMF913_RS49790 + SMF913_RS49785

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 157557 - 330682:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (emal - Me-ohmal) + (ohmal) + (ohmal) + (Me-ccmal - Me-ccmal) + (Me-mal - ccmal - pk) + (Me-mal - Me-ohmal - ohmal - Me-mal) + (Me-ohmal - pk - ccmal) + (Me-ccmal - Me-redmal - Me-ohmal - Me-ccmal) + (pk) + (Me-ccmal - ohmal) + (Me-redmal - ccmal) + (pk)
Non-colinear ordering:
  SMF913_RS00990 + SMF913_RS00985 + SMF913_RS00980 + SMF913_RS00975 + SMF913_RS01080 + SMF913_RS01065 + SMF913_RS01060 + SMF913_RS01055 + SMF913_RS01050 + SMF913_RS01035 + SMF913_RS49790 + SMF913_RS49785

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).
SMF913_RS00975: mmal - mmal
PKS_AT (555..837): 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: 210.7
  Ethylmalonyl-CoA: 202.8
  Methoxymalonyl-CoA: 176.5
  2-Methylbutyryl-CoA: 137.2
  trans-1,2-CPDA: 123.2
  Propionyl-CoA: 104.7
  Malonyl-CoA: 98.0
  CHC-CoA: 86.5
  Isobutyryl-CoA: 68.2
  Benzoyl-CoA: 52.7
  3-Methylbutyryl-CoA: 36.0
  inactive: 35.0
  Acetyl-CoA: 34.9
  fatty_acid: 16.2

PKS_AT (2241..2530): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 201.0
  Ethylmalonyl-CoA: 186.7
  Methoxymalonyl-CoA: 170.7
  2-Methylbutyryl-CoA: 146.0
  trans-1,2-CPDA: 121.4
  Propionyl-CoA: 108.4
  CHC-CoA: 99.4
  Malonyl-CoA: 93.5
  Isobutyryl-CoA: 66.4
  Benzoyl-CoA: 59.9
  3-Methylbutyryl-CoA: 40.2
  Acetyl-CoA: 39.4
  fatty_acid: 24.9
  inactive: 21.4

SMF913_RS00980: mal
PKS_AT (827..1099): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 70.8%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 164.8
  inactive: 81.7
  Methoxymalonyl-CoA: 78.9
  Methylmalonyl-CoA: 68.4
  Propionyl-CoA: 38.3
  Ethylmalonyl-CoA: 33.4
  CHC-CoA: 30.9
  fatty_acid: 28.8
  Isobutyryl-CoA: 27.5
  Acetyl-CoA: 21.3
  2-Methylbutyryl-CoA: 21.3
  trans-1,2-CPDA: 19.9
  Benzoyl-CoA: 19.0
  3-Methylbutyryl-CoA: 16.1

SMF913_RS00985: mal
PKS_AT (908..1198): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 201.1
  inactive: 92.7
  Methoxymalonyl-CoA: 69.9
  Methylmalonyl-CoA: 60.4
  Isobutyryl-CoA: 35.7
  Ethylmalonyl-CoA: 23.7
  Propionyl-CoA: 22.2
  Acetyl-CoA: 18.5
  Benzoyl-CoA: 16.5
  fatty_acid: 15.5
  CHC-CoA: 14.2
  2-Methylbutyryl-CoA: 9.5
  trans-1,2-CPDA: 8.6
  3-Methylbutyryl-CoA: 4.3

SMF913_RS00990: emal - mmal
PKS_AT (97..394): emal
ATSignature: Isobutyryl-CoA

Top 3 matches:
  Isobutyryl-CoA: 83.3%
  2-Methylbutyryl-CoA: 79.2%
  Malonyl-CoA: 75.0%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 157.8
  Methylmalonyl-CoA: 156.8
  2-Methylbutyryl-CoA: 156.4
  Methoxymalonyl-CoA: 124.7
  Propionyl-CoA: 116.0
  CHC-CoA: 96.6
  trans-1,2-CPDA: 90.2
  Malonyl-CoA: 70.5
  Isobutyryl-CoA: 66.6
  3-Methylbutyryl-CoA: 37.3
  Benzoyl-CoA: 34.0
  Acetyl-CoA: 27.7
  inactive: 25.5
  fatty_acid: 19.5

PKS_AT (1097..1395): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 211.3
  Ethylmalonyl-CoA: 200.0
  Methoxymalonyl-CoA: 167.7
  2-Methylbutyryl-CoA: 145.4
  trans-1,2-CPDA: 121.7
  CHC-CoA: 111.4
  Propionyl-CoA: 103.0
  Malonyl-CoA: 96.8
  Isobutyryl-CoA: 70.3
  Benzoyl-CoA: 65.4
  Acetyl-CoA: 45.5
  3-Methylbutyryl-CoA: 37.7
  inactive: 31.9
  fatty_acid: 25.9

SMF913_RS49785: pk
PKS_AT (557..852): pk
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 189.2
  Methylmalonyl-CoA: 183.8
  Methoxymalonyl-CoA: 160.1
  2-Methylbutyryl-CoA: 119.1
  trans-1,2-CPDA: 98.0
  Propionyl-CoA: 93.2
  CHC-CoA: 89.8
  Malonyl-CoA: 77.4
  Isobutyryl-CoA: 70.0
  3-Methylbutyryl-CoA: 49.3
  Acetyl-CoA: 48.9
  Benzoyl-CoA: 45.0
  inactive: 21.3
  fatty_acid: 10.8

SMF913_RS49790: mmal - mal
PKS_AT (571..857): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 206.7
  Ethylmalonyl-CoA: 195.6
  Methoxymalonyl-CoA: 172.0
  2-Methylbutyryl-CoA: 139.7
  trans-1,2-CPDA: 126.4
  CHC-CoA: 113.3
  Propionyl-CoA: 110.4
  Malonyl-CoA: 87.9
  Isobutyryl-CoA: 70.5
  Benzoyl-CoA: 55.4
  Acetyl-CoA: 26.2
  inactive: 25.0
  fatty_acid: 19.3
  3-Methylbutyryl-CoA: 19.3

PKS_AT (2560..2825): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 175.9
  inactive: 83.7
  Methoxymalonyl-CoA: 78.5
  Methylmalonyl-CoA: 59.9
  CHC-CoA: 22.6
  Ethylmalonyl-CoA: 22.2
  Isobutyryl-CoA: 18.6
  Benzoyl-CoA: 16.8
  trans-1,2-CPDA: 16.4
  fatty_acid: 16.2
  Acetyl-CoA: 16.0
  Propionyl-CoA: 15.8
  2-Methylbutyryl-CoA: 10.4
  3-Methylbutyryl-CoA: 0.0

SMF913_RS01035: mmal - mal
PKS_AT (560..840): 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: 206.6
  Ethylmalonyl-CoA: 195.7
  Methoxymalonyl-CoA: 173.2
  2-Methylbutyryl-CoA: 139.0
  trans-1,2-CPDA: 131.6
  Propionyl-CoA: 107.0
  Malonyl-CoA: 99.5
  CHC-CoA: 81.3
  Isobutyryl-CoA: 63.6
  Benzoyl-CoA: 51.3
  3-Methylbutyryl-CoA: 47.8
  Acetyl-CoA: 39.9
  inactive: 38.6
  fatty_acid: 19.0

PKS_AT (2241..2501): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 164.3
  inactive: 76.2
  Methoxymalonyl-CoA: 64.1
  Methylmalonyl-CoA: 46.3
  Isobutyryl-CoA: 24.1
  Acetyl-CoA: 21.2
  fatty_acid: 19.9
  Propionyl-CoA: 19.6
  CHC-CoA: 16.2
  Benzoyl-CoA: 15.4
  Ethylmalonyl-CoA: 14.7
  2-Methylbutyryl-CoA: 7.6
  trans-1,2-CPDA: 2.8
  3-Methylbutyryl-CoA: 0.0

SMF913_RS01045: pk
PKS_AT (26..248): pk
ATSignature: (unknown)
No matches above 50%
minowa: trans-1,2-CPDA

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

SMF913_RS01050: pk
PKS_AT (565..845): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 226.2
  Methylmalonyl-CoA: 220.1
  Methoxymalonyl-CoA: 181.4
  2-Methylbutyryl-CoA: 144.9
  trans-1,2-CPDA: 138.9
  Propionyl-CoA: 114.3
  CHC-CoA: 109.8
  Malonyl-CoA: 105.8
  Isobutyryl-CoA: 75.3
  Benzoyl-CoA: 65.7
  Acetyl-CoA: 44.0
  inactive: 28.6
  3-Methylbutyryl-CoA: 27.9
  fatty_acid: 23.8

SMF913_RS01055: mmal - mmal - mmal - mmal
PKS_AT (574..855): 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: 218.3
  Ethylmalonyl-CoA: 216.0
  Methoxymalonyl-CoA: 183.3
  2-Methylbutyryl-CoA: 146.2
  trans-1,2-CPDA: 128.7
  Malonyl-CoA: 105.3
  CHC-CoA: 102.9
  Propionyl-CoA: 102.8
  Isobutyryl-CoA: 83.4
  Benzoyl-CoA: 65.3
  Acetyl-CoA: 34.7
  3-Methylbutyryl-CoA: 26.1
  inactive: 23.5
  fatty_acid: 23.5

PKS_AT (2230..2513): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 207.5
  Ethylmalonyl-CoA: 202.1
  Methoxymalonyl-CoA: 166.5
  2-Methylbutyryl-CoA: 140.1
  trans-1,2-CPDA: 124.3
  Propionyl-CoA: 107.3
  Malonyl-CoA: 90.6
  CHC-CoA: 90.4
  Isobutyryl-CoA: 65.1
  Benzoyl-CoA: 60.2
  Acetyl-CoA: 37.0
  3-Methylbutyryl-CoA: 31.6
  fatty_acid: 27.6
  inactive: 20.6

PKS_AT (4195..4483): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 212.8
  Ethylmalonyl-CoA: 210.1
  Methoxymalonyl-CoA: 164.8
  2-Methylbutyryl-CoA: 133.5
  trans-1,2-CPDA: 129.0
  Propionyl-CoA: 101.4
  CHC-CoA: 94.8
  Malonyl-CoA: 87.1
  Isobutyryl-CoA: 62.3
  Benzoyl-CoA: 53.6
  Acetyl-CoA: 33.9
  3-Methylbutyryl-CoA: 26.2
  inactive: 25.1
  fatty_acid: 18.6

PKS_AT (5646..5928): 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: 219.2
  Ethylmalonyl-CoA: 217.4
  Methoxymalonyl-CoA: 180.1
  trans-1,2-CPDA: 137.8
  2-Methylbutyryl-CoA: 137.2
  Propionyl-CoA: 111.1
  CHC-CoA: 98.3
  Malonyl-CoA: 94.4
  Isobutyryl-CoA: 67.7
  Benzoyl-CoA: 56.4
  Acetyl-CoA: 36.7
  fatty_acid: 32.6
  3-Methylbutyryl-CoA: 28.7
  inactive: 25.7

SMF913_RS01060: mmal - pk - mal
PKS_AT (560..842): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 205.8
  Ethylmalonyl-CoA: 202.2
  Methoxymalonyl-CoA: 165.5
  2-Methylbutyryl-CoA: 130.0
  trans-1,2-CPDA: 128.1
  Propionyl-CoA: 99.1
  CHC-CoA: 87.6
  Malonyl-CoA: 71.5
  Isobutyryl-CoA: 51.1
  Benzoyl-CoA: 45.3
  Acetyl-CoA: 29.0
  inactive: 23.8
  3-Methylbutyryl-CoA: 22.8
  fatty_acid: 17.3

PKS_AT (2066..2358): pk
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 180.8
  Methylmalonyl-CoA: 180.5
  Methoxymalonyl-CoA: 163.0
  2-Methylbutyryl-CoA: 137.8
  trans-1,2-CPDA: 108.9
  Propionyl-CoA: 99.6
  CHC-CoA: 87.5
  Malonyl-CoA: 83.1
  Isobutyryl-CoA: 48.6
  Acetyl-CoA: 35.4
  Benzoyl-CoA: 33.0
  3-Methylbutyryl-CoA: 29.4
  inactive: 18.7
  fatty_acid: 13.1

PKS_AT (3523..3820): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 91.7%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 208.4
  inactive: 106.7
  Methoxymalonyl-CoA: 66.0
  Methylmalonyl-CoA: 56.0
  Propionyl-CoA: 32.4
  Ethylmalonyl-CoA: 24.5
  Acetyl-CoA: 23.5
  Isobutyryl-CoA: 20.8
  2-Methylbutyryl-CoA: 20.7
  CHC-CoA: 11.8
  Benzoyl-CoA: 11.4
  fatty_acid: 9.5
  trans-1,2-CPDA: 9.1
  3-Methylbutyryl-CoA: 0.0

SMF913_RS01065: mmal - mmal - mal - mmal
PKS_AT (532..810): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 87.5%
  Malonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 198.4
  Ethylmalonyl-CoA: 186.3
  Methoxymalonyl-CoA: 167.6
  2-Methylbutyryl-CoA: 140.4
  Malonyl-CoA: 104.7
  Propionyl-CoA: 97.7
  trans-1,2-CPDA: 91.7
  CHC-CoA: 82.4
  Isobutyryl-CoA: 81.3
  Benzoyl-CoA: 53.0
  Acetyl-CoA: 45.6
  inactive: 34.9
  fatty_acid: 26.5
  3-Methylbutyryl-CoA: 14.6

PKS_AT (1508..1805): 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: 208.3
  Ethylmalonyl-CoA: 207.5
  Methoxymalonyl-CoA: 172.0
  2-Methylbutyryl-CoA: 146.9
  Propionyl-CoA: 112.2
  trans-1,2-CPDA: 110.3
  CHC-CoA: 106.4
  Malonyl-CoA: 102.0
  Benzoyl-CoA: 84.2
  Isobutyryl-CoA: 76.8
  Acetyl-CoA: 60.4
  3-Methylbutyryl-CoA: 35.1
  fatty_acid: 34.6
  inactive: 22.0

PKS_AT (3026..3318): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 195.8
  inactive: 76.0
  Methoxymalonyl-CoA: 69.8
  Methylmalonyl-CoA: 60.5
  Isobutyryl-CoA: 31.2
  Propionyl-CoA: 28.4
  Acetyl-CoA: 20.9
  Benzoyl-CoA: 18.9
  Ethylmalonyl-CoA: 17.9
  2-Methylbutyryl-CoA: 16.6
  CHC-CoA: 14.2
  fatty_acid: 11.8
  trans-1,2-CPDA: 8.5
  3-Methylbutyryl-CoA: 6.1

PKS_AT (4490..4785): 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: 206.3
  Ethylmalonyl-CoA: 188.1
  Methoxymalonyl-CoA: 178.4
  2-Methylbutyryl-CoA: 113.7
  trans-1,2-CPDA: 112.7
  Malonyl-CoA: 107.4
  CHC-CoA: 105.7
  Isobutyryl-CoA: 97.5
  Propionyl-CoA: 94.4
  Benzoyl-CoA: 87.1
  Acetyl-CoA: 59.6
  3-Methylbutyryl-CoA: 48.5
  inactive: 40.3
  fatty_acid: 36.1

SMF913_RS01070: X
AMP-binding (13..422): 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:
    NVAS--SSGSAVTITYVGSLQLYGTTEISGISML
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

SMF913_RS01080: mmal - mal - pk
PKS_AT (554..852): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 209.3
  Ethylmalonyl-CoA: 203.8
  Methoxymalonyl-CoA: 176.5
  2-Methylbutyryl-CoA: 134.8
  trans-1,2-CPDA: 126.3
  Propionyl-CoA: 112.5
  CHC-CoA: 95.7
  Isobutyryl-CoA: 85.6
  Malonyl-CoA: 80.1
  Benzoyl-CoA: 63.7
  Acetyl-CoA: 40.8
  3-Methylbutyryl-CoA: 37.9
  fatty_acid: 28.2
  inactive: 18.5

PKS_AT (1570..1865): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 208.9
  inactive: 95.4
  Methoxymalonyl-CoA: 70.6
  Methylmalonyl-CoA: 66.0
  Isobutyryl-CoA: 38.9
  Ethylmalonyl-CoA: 37.4
  Propionyl-CoA: 28.9
  Benzoyl-CoA: 24.7
  CHC-CoA: 22.1
  Acetyl-CoA: 20.8
  fatty_acid: 18.6
  trans-1,2-CPDA: 14.1
  2-Methylbutyryl-CoA: 12.1
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3334..3634): pk
ATSignature: Methoxymalonyl-CoA

Top 3 matches:
  Methoxymalonyl-CoA: 91.7%
  Methylmalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 185.7
  Ethylmalonyl-CoA: 184.8
  Methoxymalonyl-CoA: 180.4
  2-Methylbutyryl-CoA: 127.4
  Malonyl-CoA: 99.0
  trans-1,2-CPDA: 91.9
  Propionyl-CoA: 89.7
  Isobutyryl-CoA: 87.9
  CHC-CoA: 75.2
  Benzoyl-CoA: 51.5
  Acetyl-CoA: 50.2
  3-Methylbutyryl-CoA: 44.7
  inactive: 30.4
  fatty_acid: 28.1

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
IolR | Regulator of the inositol catabolism
MexT | Global virulence regulator
OsdR | Development and stress management regulator
RutR | Regulator of the pyrimidine and purine metabolism

NZ_LJIW01000001.1 - Region 2 - NAPAA
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: 563,322 - 597,509 nt. (total: 34,188 nt) Show pHMM detection rules used
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 reductase
SMF913_RS02215: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

SMF913_RS02245: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: methyltransferase
SMF913_RS02275: methyltransferase

smcogs
  SMCOG1089: methyltransferase

SMF913_RS02310: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: amidase hydrolase
SMF913_RS02235: amidase

smcogs
  SMCOG1105: amidase

SMF913_RS02260: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

SMF913_RS02365: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: dehydratase
SMF913_RS02340: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
SMF913_RS02295: 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 | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001833.4 |  | 0.60 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  | 0.59 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002276.2 |  | 0.58 | NRPS | choline | Aspergillus nidulans FGSC A4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001833.4 |  | 0.60 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  | 0.59 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002276.2 |  | 0.58 | NRPS | choline | Aspergillus nidulans FGSC A4

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: 16.54 out of 18.46
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.63 out of 18.46
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 (8):
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.77 out of 27.78
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.15 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.13 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.67 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.24 out of 29.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.82 out of 35.63
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 5, location 563321 - 597509:
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).
SMF913_RS02295: X
AMP-binding (60..455): 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:
    FVAMFDFSVEEVCCLVSGELNVYGPTEATVTATW
  Nearest Stachelhaus code(s):
    Ile or Val DFLCLGVVIK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

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

NZ_LJIW01000001.1 - Region 3 - 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: 878,743 - 921,481 nt. (total: 42,739 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 oxidoreductase
SMF913_RS03675: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

SMF913_RS03700: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

SMF913_RS03805: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: acetyltransferase aminotransferase methyltransferase
SMF913_RS03720: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

SMF913_RS03735: aminotransferase

smcogs
  SMCOG1019: aminotransferase

SMF913_RS03775: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Hydrolases: hydrolase
SMF913_RS03770: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: dehydratase
SMF913_RS03740: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
SMF913_RS03745: 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
--- | --- | --- | --- | --- | ---
BGC0002277.2 |  | 0.65 | NRPS | atromentin | Suillus grevillei
BGC0002274.2 |  | 0.64 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0002193.2 |  | 0.64 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.60 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.60 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000340.5 |  | 0.53 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35
BGC0000820.5 |  | 0.49 | other (other) | physostigmine | Streptomyces griseofuscus
BGC0001206.5 |  | 0.47 | other (other) | indolmycin | Streptomyces griseus subsp. griseus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002277.2 |  | 0.65 | NRPS | atromentin | Suillus grevillei
BGC0002274.2 |  | 0.64 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0002193.2 |  | 0.64 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.60 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.60 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000340.5 |  | 0.53 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35
BGC0000820.5 |  | 0.49 | other (other) | physostigmine | Streptomyces griseofuscus
BGC0001206.5 |  | 0.47 | other (other) | indolmycin | 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.
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: 19.26 out of 19.26
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (7):
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: 16.43 out of 29.38
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.46 out of 20.97
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.61 out of 29.51
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.86 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.47 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 6, location 878742 - 921481:
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).
SMF913_RS03745: X
AMP-binding (29..426): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AGKIHIAAIEALFTISGGEVPAFGMTETCAGSVF
  Nearest Stachelhaus code(s):
    Ppa VALFIGAAGK (71% 8Å match)
    4-ohPpa IAAFLGAAGK (68% 8Å match)
  Stachelhaus code match:
    80% (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
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000001.1 - Region 4 - NRPS,T1PKS,lanthipeptide-class-ii,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: 957,131 - 1,031,110 nt. (total: 73,980 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)
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))
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
Lanthipeptides
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
SMF913_RS04020: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

SMF913_RS04045: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

SMF913_RS04135: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

SMF913_RS04210: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

SMF913_RS04225: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

SMF913_RS04245: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: carbamoyltransferase methyltransferase
SMF913_RS04125: methyltransferase

smcogs
  SMCOG1089: methyltransferase

SMF913_RS47985: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

Hydrolases: phosphatase
SMF913_RS04095: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Lyases: cyclase
SMF913_RS04060: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Ligases: ligase synthase
SMF913_RS04085: 1-deoxy-D-xylulose-5-phosphate synthase

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

SMF913_RS04100: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS04105: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS04110: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

SMF913_RS04115: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS04120: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

SMF913_RS04150: 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 | lanthipeptide-class-ii | NRPS | T1PKS | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001833.4 |  |  |  |  | 0.84 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  |  |  | 0.82 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  |  |  | 0.81 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  |  |  |  | 0.79 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  |  |  | 0.79 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  |  |  |  | 0.76 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  |  |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  |  |  |  | 0.74 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  |  |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  |  |  |  | 0.72 | NRPS | enniatin | Fusarium equiseti

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.70 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  | 0.69 | 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.

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 SMF913_RS04060

SMF913_RS04065
Leader:
MNTTVTAWKNAMYREGLAVEPAHPAGA
Core:
V D L S A D L P D E T G T G A A E T L S T Q P F F D C C G
Core with dehydrations:
V D L Dha A D L P D E Dhb G Dhb G A A E Dhb L Dha Dhb Q P F F D Cys Cys G

#### antiSMASH-DB 4.0 matches for SMF913_RS04065

100.0%
NZ_BDFA01000012.1 and 6 others:
NZ_CP019458.1 Lanthipeptides: BV401_RS04085_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS43145_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS43375_lanthipeptide NZ_CP065050.1 Lanthipeptides: I1A49_RS03785_lanthipeptide NZ_JAALLH010000001.1 Lanthipeptides: SMALB_RS03525_lanthipeptide NZ_LJIW01000001.1 Lanthipeptides: SMF913_RS04065_lanthipeptide
Lanthipeptides: BGB88_RS46105_lanthipeptide
1
V D L S A D L P D E T G T G A A E T L S T Q P F F D C C G
29
V D L S A D L P D E T G T G A A E T L S T Q P F F D C C G
1
V D L S A D L P D E T G T G A A E T L S T Q P F F D C C G
29
48.3%
NZ_CP058693.1:
Lanthipeptides: HYQ63_RS37670_lanthipeptide
16
A E T L S T Q P F F D C C G
29
A E T L S T Q P F F D C C G
1
A E T L S T Q P F F D C C G
14
37.9%
NC_016582.1:
Lanthipeptides: SBI_RS52400_lanthipeptide
18
T L S T Q P F F D C C G
29
T L S T Q P F F C C G
2
T L S T Q P F F Q C C G
13
with 5 more sequence matches
37.9%
NZ_CP097290.1 and 1 other:
NZ_LIWB01000016.1 Lanthipeptides: AMK33_RS42540_lanthipeptide
Lanthipeptides: M4V62_RS43190_lanthipeptide
18
T L S T Q P F F D C C G
29
T L S T Q P F F+C C G
1
T L S T Q P F F N C C G
12
37.9%
NZ_NNBP01000002.1:
Lanthipeptides: CG747_RS46875_lanthipeptide
17
E T L S T Q P F F D C C G
29
+T L S T Q P F F+C C G
1
K T L S T Q P F F N C C G
13
31.0%
NZ_CP072827.1:
Lanthipeptides: J7W19_RS04815_lanthipeptide
11
T G T G A A E T L S T Q P F F D C C
28
+G T A +T+S P F+ C C
1
S G T I A I K T M S-A P F W T C C
17
26.5%
NZ_JACSPO010000013.1 and 1 other:
NZ_JACSPO010000013.1 Lanthipeptides: H9624_RS14885_lanthipeptide
Lanthipeptides: H9624_RS14885_lanthipeptide
1
V D L S A D L P D E T G T G A A E T
18
+ +S A L P D T G A T
15
I A I S A A L P D F C P T G A C T T
32
19.0%
NC_019757.1:
Lanthipeptides: allorf_3744133_3744366_lanthipeptide
10
E T G T G A A E T L S T Q
22
E T G T + +T L+T Q
25
E T G T K S R Q T L N T Q
37

#### MIBiG 4.0 matches for SMF913_RS04065

13.7%
BGC0002120.3 (NQE92413.1):
Lanthipeptide: nocathioamide A
9
D E T G T G A A E T L S T Q P F F D C C G
29
D E+ A A T C C
30
D E S S R P A A P A C H T L S S L P C C A
50
allorf_0961135_0961344
Leader:
MTVFLHCGEAWRHREMAMRGLVAG
Core:
P C S G I I S K R N L A P V K I R N V V P L G K P G S V R Q S R Q S R W C P A V E G A A R
Core with dehydrations:
P Cys Dha G I I Dha K R N L A P V K I R N V V P L G K P G Dha V R Q Dha R Q Dha R W Cys P A V E G A A R

#### antiSMASH-DB 4.0 matches for allorf_0961135_0961344

100.0%
NZ_LJIW01000001.1:
Lanthipeptides: allorf_0961135_0961344_lanthipeptide
1
P C S G I I S K R N L A P V K I R N V V P L G K P G S V R Q S R Q S R W C P A V E G A A R
45
P C S G I I S K R N L A P V K I R N V V P L G K P G S V R Q S R Q S R W C P A V E G A A R
1
P C S G I I S K R N L A P V K I R N V V P L G K P G S V R Q S R Q S R W C P A V E G A A R
45
77.8%
NZ_CP065050.1:
Lanthipeptides: allorf_00905184_00905363_lanthipeptide
1
P C S G I I S K R N L A P V K I R N V V P L G K P G S V R Q S R Q S R
35
P C S G I I S K R N L A P V K I R N V V P L G K P G S V R Q S R Q S R
1
P C S G I I S K R N L A P V K I R N V V P L G K P G S V R Q S R Q S R
35
62.2%
NZ_BDFA01000012.1:
Lanthipeptides: allorf_132034_132222_lanthipeptide
1
P C S G I I S K R N L A P V K I R N V V P L G K P G S V
28
P C S G I I S K R N L A P V K I R N V V P L G K P G S V
1
P C S G I I S K R N L A P V K I R N V V P L G K P G S V
28
allorf_0966751_0966921
Leader:
MSGGAAPGRVVSGRRPFARASCRTLARSSRRASVWGS
Core:
R R A C A H G S R H T S A W G S R R T
Core with dehydrations:
R R A Cys A H G Dha R H Dhb Dha A W G Dha R R Dhb

#### antiSMASH-DB 4.0 matches for allorf_0966751_0966921

100.0%
NZ_LJIW01000001.1:
Lanthipeptides: allorf_0966751_0966921_lanthipeptide
1
R R A C A H G S R H T S A W G S R R T
19
R R A C A H G S R H T S A W G S R R T
1
R R A C A H G S R H T S A W G S R R T
19
94.7%
NZ_BDFA01000012.1:
Lanthipeptides: allorf_126442_126612_lanthipeptide
1
R R A C A H G S R H T S A W G S R R T
19
R R A C A H G S R T S A W G S R R T
1
R R A C A H G S R P T S A W G S R R T
19
94.7%
NZ_CP029823.1:
Lanthipeptides: allorf_10622452_10622622_lanthipeptide
1
R R A C A H G S R H T S A W G S R R T
19
R R A C A H G S R H T S A W G R R T
1
R R A C A H G S R H T S A W G P R R T
19
with 4 more sequence matches
31.8%
NZ_CP024894.1:
Lanthipeptides: CU254_RS16295_lanthipeptide
6
H G S R H T S A W G S R R T
19
H G H S A W T
2
H G C S H Y S A W C G E S T
15
31.8%
NZ_CP091381.1:
Lanthipeptides: L3Q65_RS08355_lanthipeptide
6
H G S R H T S A W G S R R T
19
H G H S A W T
2
H G H S H Y S A W C G D S T
15
31.8%
NZ_SDLS01000004.1:
Lanthipeptides: EIZ45_RS09385_lanthipeptide
6
H G S R H T S A W G S R R T
19
H G H S A W T
2
H G H S H Y S A W C G E S T
15
21.1%
NZ_JXKZ01000002.1:
Lanthipeptides: allorf_047954_048064_lanthipeptide
1
R R A C A H G S R H T S A
13
++ C H G S++ +
5
Q Q V C K H G S K N D N C
17
allorf_0970795_0970926
Leader:
MRCGTTTASLSTGHLREVVSA
Core:
E S G G R D S V P V R V N V P M L C G D R P
Core with dehydrations:
E Dha G G R D Dha V P V R V N V P M L Cys G D R P

#### antiSMASH-DB 4.0 matches for allorf_0970795_0970926

100.0%
NZ_BDFA01000012.1 and 6 others:
NZ_CP019458.1 Lanthipeptides: allorf_00977752_00977883_lanthipeptide NZ_CP025018.1 Lanthipeptides: allorf_10559568_10559699_lanthipeptide NZ_CP029823.1 Lanthipeptides: allorf_10618447_10618578_lanthipeptide NZ_CP065050.1 Lanthipeptides: allorf_00914852_00914983_lanthipeptide NZ_JAALLH010000001.1 Lanthipeptides: allorf_0868461_0868592_lanthipeptide NZ_LJIW01000001.1 Lanthipeptides: allorf_0970795_0970926_lanthipeptide
Lanthipeptides: allorf_122437_122568_lanthipeptide
1
E S G G R D S V P V R V N V P M L C G D R P
22
E S G G R D S V P V R V N V P M L C G D R P
1
E S G G R D S V P V R V N V P M L C G D R P
22

#### MIBiG 4.0 matches for allorf_0970795_0970926

18.2%
BGC0000477.3 (ACA04491.1 (core 2)):
Cyanobactin: patellin 2 or patellin 3
13
N V P M L C
18
V P L C
1
T V P T L C
6
allorf_0970850_0971047
Leader:
MHSNLLGPDGRGRGGIGEWKTLCDIAGA
Core:
L I R E C T L P V A S M N A L W N N Y R L S I D W S P A R S G E R G E R R
Core with dehydrations:
L I R E Cys Dhb L P V A Dha M N A L W N N Y R L Dha I D W Dha P A R Dha G E R G E R R

#### antiSMASH-DB 4.0 matches for allorf_0970850_0971047

100.0%
NZ_BDFA01000012.1 and 5 others:
NZ_CP019458.1 Lanthipeptides: allorf_00977807_00978004_lanthipeptide NZ_CP025018.1 Lanthipeptides: allorf_10559447_10559644_lanthipeptide NZ_CP029823.1 Lanthipeptides: allorf_10618326_10618523_lanthipeptide NZ_CP065050.1 Lanthipeptides: allorf_00914907_00915104_lanthipeptide NZ_LJIW01000001.1 Lanthipeptides: allorf_0970850_0971047_lanthipeptide
Lanthipeptides: allorf_122316_122513_lanthipeptide
1
L I R E C T L P V A S M N A L W N N Y R L S I D W S P A R S G E R G E R R
37
L I R E C T L P V A S M N A L W N N Y R L S I D W S P A R S G E R G E R R
1
L I R E C T L P V A S M N A L W N N Y R L S I D W S P A R S G E R G E R R
37
97.3%
NZ_JAALLH010000001.1:
Lanthipeptides: allorf_0868516_0868713_lanthipeptide
1
L I R E C T L P V A S M N A L W N N Y R L S I D W S P A R S G E R G E R R
37
L I R E C T L P V A S M N A L W N N Y R L S D W S P A R S G E R G E R R
1
L I R E C T L P V A S M N A L W N N Y R L S T D W S P A R S G E R G E R R
37
21.6%
NZ_JAENHX010000011.1:
Lanthipeptides: JIN86_RS20375_lanthipeptide
9
V A S M N A L W N N Y R L S I D W S P A R S G
31
+A+ L N N Y ++ W S +G
11
I A N A V G L G N N Y G M A C T W S A E C N G
33
with 2 more sequence matches
18.4%
NC_017327.1 and 1 other:
NZ_CP021217.1 Lanthipeptides: allorf_1158639_1158842_lanthipeptide
Lanthipeptides: allorf_0125265_0125468_lanthipeptide
20
R L S I D W S P A R S G E R G E R
36
R ++ S P++ R G E R
7
R P A V G L S P S K P Q G R G E R
23
16.2%
NZ_RBZW01000021.1:
Lassopeptides: D8Y22_RS07925_lassopeptide
23
I D W S P A R S G E R G E R R
37
+D + +G R G R R
7
V D G N S G T T G N R G H R R
21
allorf_0970869_0970994
Leader:
MENVVRYRGSAHPGM
Core:
H A T G R F H E C A V E Q L P P L Y R L V T C E K W
Core with dehydrations:
H A Dhb G R F H E Cys A V E Q L P P L Y R L V Dhb Cys E K W

#### antiSMASH-DB 4.0 matches for allorf_0970869_0970994

100.0%
NZ_BDFA01000012.1 and 5 others:
NZ_CP025018.1 Lanthipeptides: allorf_10559500_10559625_lanthipeptide NZ_CP029823.1 Lanthipeptides: allorf_10618379_10618504_lanthipeptide NZ_CP065050.1 Lanthipeptides: allorf_00914926_00915051_lanthipeptide NZ_JAALLH010000001.1 Lanthipeptides: allorf_0868535_0868660_lanthipeptide NZ_LJIW01000001.1 Lanthipeptides: allorf_0970869_0970994_lanthipeptide
Lanthipeptides: allorf_122369_122494_lanthipeptide
1
H A T G R F H E C A V E Q L P P L Y R L V T C E K W
26
H A T G R F H E C A V E Q L P P L Y R L V T C E K W
1
H A T G R F H E C A V E Q L P P L Y R L V T C E K W
26
96.2%
NZ_CP019458.1:
Lanthipeptides: allorf_00977826_00977951_lanthipeptide
1
H A T G R F H E C A V E Q L P P L Y R L V T C E K W
26
H A T G R F H E C V E Q L P P L Y R L V T C E K W
1
H A T G R F H E C T V E Q L P P L Y R L V T C E K W
26
20.5%
NZ_KZ819178.1 and 1 other:
NZ_KZ819178.1 Lanthipeptides: allorf_4075416_4075610_lanthipeptide
Lanthipeptides: allorf_4075416_4075610_lanthipeptide
3
T G R F H E C A V E Q L P P L Y R L V T C
23
+G R F H A V P L C
10
S G R F H R P A V R P P S P L L L R P R C
30
with 2 more sequence matches
17.9%
NZ_CP039292.1 and 1 other:
NZ_CP039292.1 Lanthipeptides: allorf_0076338_0076511_lanthipeptide
Lanthipeptides: allorf_0076338_0076511_lanthipeptide
1
H A T G R F H E C A V E Q L P P L Y R
19
+G R +C + P Y+
6
E G S G R V S D C L C K G C G P T Y K
24
16.7%
NZ_KB217478.1:
Lanthipeptides: allorf_3684331_3684489_lanthipeptide
13
Q L P P L Y R L V T C
23
Q+P L Y L+ C
16
Q V P T L Y T L I N C
26

#### 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 |  | squalene | C30 | acyclic | none
triterpene |  | PSPP | C30 | acyclic | PP
triterpene | C30 carotenoid | diapophytoene | C30 | acyclic | none
tetraterpene | C40 carotenoid | phytoene | C40 | acyclic | none
triterpene |  | hydroxysqualene | C30 | acyclic | OH

Genes with terpene domains:
SMF913_RS04235: PT_phytoene_like
Domain 1 (18 - 281): Prenyltransferase; Phytoene synthase like
Subtype: unknown

Reactions:
  FPP → squalene
  FPP → PSPP
  FPP → diapophytoene
  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.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 20.47
Confidence: medium
Additional weak hits (15):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.27 out of 31.73
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.29 out of 20.97
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.27 out of 25.88
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.76 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.60 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.19 out of 18.57
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.20 out of 21.55
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.04 out of 19.26
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.79 out of 36.54
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.30 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.34 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
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
Lanthipeptides
NRPS/PKS products
NRPS/PKS substrates
Terpene
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.

SMF913_RS04065 - Class II
  Cleavage pHMM score: -6.00
  RODEO score: 0
  Monoisotopic mass: 2851.3 Da
  Molecular weight: 2853.0 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2871.0 Da N = 1
    2889.1 Da N = 2
    2907.1 Da N = 3
    2925.1 Da N = 4
allorf_0961135_0961344 - Class II
  Cleavage pHMM score: -6.80
  RODEO score: 0
  Monoisotopic mass: 4747.7 Da
  Molecular weight: 4750.5 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4768.6 Da N = 1
    4786.6 Da N = 2
    4804.6 Da N = 3
allorf_0966751_0966921 - Class II
  Cleavage pHMM score: -3.80
  RODEO score: 0
  Monoisotopic mass: 2062.1 Da
  Molecular weight: 2063.3 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2081.3 Da N = 1
    2099.3 Da N = 2
    2117.3 Da N = 3
    2135.3 Da N = 4
allorf_0970795_0970926 - Class II
  Cleavage pHMM score: -5.90
  RODEO score: 0
  Monoisotopic mass: 2303.1 Da
  Molecular weight: 2304.6 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2322.6 Da N = 1
allorf_0970850_0971047 - Class II
  Cleavage pHMM score: -1.80
  RODEO score: 0
  Monoisotopic mass: 4226.2 Da
  Molecular weight: 4228.8 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4246.8 Da N = 1
    4264.8 Da N = 2
    4282.8 Da N = 3
    4300.8 Da N = 4
allorf_0970869_0970994 - Class II
  Cleavage pHMM score: -5.60
  RODEO score: 0
  Monoisotopic mass: 3046.5 Da
  Molecular weight: 3048.5 Da
  Number of bridges: 2

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 7, location 957130 - 1031110:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Phe) + (ohmal) + (Pro) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 9, location 957493 - 1022392:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Phe) + (ohmal) + (Pro) + (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).
SMF913_RS04100: Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (481..879): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDASVWEMTAVAAGEVNAYGPTETTVAATA
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

SMF913_RS04105: mal
PKS_AT (568..859): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 99.0
  inactive: 49.3
  Methylmalonyl-CoA: 43.0
  Methoxymalonyl-CoA: 40.5
  Isobutyryl-CoA: 32.2
  Ethylmalonyl-CoA: 20.3
  Propionyl-CoA: 18.1
  Benzoyl-CoA: 11.7
  fatty_acid: 11.6
  2-Methylbutyryl-CoA: 10.5
  CHC-CoA: 5.6
  trans-1,2-CPDA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

SMF913_RS04110: Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (606..997): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VASVFDASVWEMYLITGGDFVAYGPTEGTIVQTW
  Nearest Stachelhaus code(s):
    Leu DAWIIGAIVK (59% 8Å match)
  Stachelhaus code match:
    90% (moderate)

SMF913_RS04115: Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (477..878): 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:
    MWEVFDVSAQETYMMTAGEENQYGSSECQVVSSL
  Nearest Stachelhaus code(s):
    Pro DVQFMAQVVK (62% 8Å match)
  Stachelhaus code match:
    90% (moderate)

SMF913_RS04150: X
AMP-binding (497..889): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VGLGFDVSLQQPDVISGGEFNCYGPTECTVNTTV
  Nearest Stachelhaus code(s):
    Cap DPQDIGIVNK (56% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LJIW01000001.1 - Region 5 - 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: 1,138,870 - 1,162,662 nt. (total: 23,793 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
SMF913_RS04825: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

SMF913_RS04830: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: aminotransferase sulfotransferase
SMF913_RS04850: aminotransferase

smcogs
  SMCOG1019: aminotransferase

SMF913_RS04860: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain

Ligases: synthetase
SMF913_RS04845: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002007.2 |  | 0.55 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0002584.2 |  | 0.54 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0000632.5 |  | 0.54 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0001206.5 |  | 0.43 | other (other) | indolmycin | Streptomyces griseus subsp. griseus
BGC0001485.4 |  | 0.43 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001896.4 |  | 0.43 | other (other) | carbazomycin B | Streptomyces luteoverticillatus
BGC0002019.3 |  | 0.42 | terpene | tiancilactone A, tiancilactone B, tiancilactone C, tiancilactone D, tiancilactone E, tiancilactone F, tiancilactone G, tiancilactone H | Streptomyces sp. CB03234
BGC0000665.5 |  | 0.42 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001529.5 |  | 0.41 | 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
BGC0000640.3 |  | 0.41 | terpene | carotenoid | Enterobacteriaceae bacterium DC404

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002007.2 |  | 0.55 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0002584.2 |  | 0.54 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0000632.5 |  | 0.54 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0001206.5 |  | 0.43 | other (other) | indolmycin | Streptomyces griseus subsp. griseus
BGC0001485.4 |  | 0.43 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001896.4 |  | 0.43 | other (other) | carbazomycin B | Streptomyces luteoverticillatus
BGC0002019.3 |  | 0.42 | terpene | tiancilactone A, tiancilactone B, tiancilactone C, tiancilactone D, tiancilactone E, tiancilactone F, tiancilactone G, tiancilactone H | Streptomyces sp. CB03234
BGC0000665.5 |  | 0.42 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001529.5 |  | 0.41 | 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
BGC0000640.3 |  | 0.41 | 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.
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
--- | --- | --- | --- | --- | ---
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:
SMF913_RS04835: T2TS
Domain 1 (271 - 551): Type 2 terpene synthase
Subtype: unknown
SMF913_RS04845: PT_FPPS_like
Domain 1 (44 - 336): 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:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.13 out of 29.72
Confidence: medium
Additional weak hits (6):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.77 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.56 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.69 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.19 out of 30.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.04 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 19.93 out of 33.14
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
--- | ---
NtrC | Nitrogen regulatory protein C

NZ_LJIW01000001.1 - Region 6 - 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: 1,185,337 - 1,264,086 nt. (total: 78,750 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 oxidoreductase oxygenase
SMF913_RS04995: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS05025: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

SMF913_RS05040: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS05055: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS05110: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS05125: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

Transferases: kinase
SMF913_RS05010: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

Hydrolases: hydrolase
SMF913_RS05045: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

SMF913_RS05075: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase
SMF913_RS05080: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

SMF913_RS05085: 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 | 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 |  | 0.73 | 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
BGC0001133.4 |  | 0.71 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001240.4 |  | 0.70 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

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 |  | 0.73 | 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
BGC0001133.4 |  | 0.71 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001240.4 |  | 0.70 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

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: 19.98 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
Additional weak hits (16):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.69 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.65 out of 20.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.87 out of 30.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.16 out of 25.88
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.67 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.92 out of 30.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 26.33
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.30 out of 20.01
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.47 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.93 out of 27.78
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.76 out of 20.97
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.66 out of 30.98
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.48 out of 35.63
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 12, location 1185336 - 1264086:
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 - X) + (D-X - Thr - D-Orn - 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).
SMF913_RS05080: Leu - Ala - Val - Ala - X
Search NORINE for peptide: strict or relaxed
AMP-binding (41..423): 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:
    FAASFDASVLESLIIVGAEVNSYGPTEATVVATW
  Nearest Stachelhaus code(s):
    Leu or 3OH-Leu DALLIGAVVK (76% 8Å match)
    Leu DALLIGAVVK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1085..1485): 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:
    LWATFDVSVFECSAVLAGEANLYGPTEATVYATA
  Nearest Stachelhaus code(s):
    Ala DVFSVALVYK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2605..3002): 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:
    LDRSFDASTYEVWLWTGGEVDGYGPTETTTFATR
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4123..4524): 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:
    LWATFDVSVFECSAVLAGEANIYGPTEATVYATA
  Nearest Stachelhaus code(s):
    Ala DVFSVAIVYK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5642..6021): X
nrpys: Leu, 3OH-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:
    FAESFDASVLEMLIIVGGDINAYGPTETTVVATW
  Nearest Stachelhaus code(s):
    Leu or 3OH-Leu DALLIGAVVK (85% 8Å match)
    Leu DALLIGAVVK (68% 8Å match)
  Stachelhaus code match:
    100% (strong)

SMF913_RS05085: X - Thr - Orn - Val - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (523..910): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGHAFDTSLEGLDLMLGGEYNFYGPTECTIDALA
  Nearest Stachelhaus code(s):
    Orn DTEDMGFVDK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2029..2447): 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:
    LETHFDFSVWEGSQVFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWSVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3115..3507): 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:
    LDHAFDTSWEGVDVMVGGEYNFYGPTECTVDAVY
  Nearest Stachelhaus code(s):
    Orn DTEDMGFVDK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4634..5012): 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:
    LDRSFDAATYEVWLWTGGDVDGYGPTETTTFATS
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5671..6049): 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:
    FAASFDASVLEVLIIVGGDVNSYGPTEATVVSTW
  Nearest Stachelhaus code(s):
    Leu or 3OH-Leu DALLIGAVVK (79% 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
--- | ---
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000001.1 - Region 7 - RiPP-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: 1,272,584 - 1,398,754 nt. (total: 126,171 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))
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)

#### 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
SMF913_RS05230: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS05245: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS05305: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

SMF913_RS05385: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: acetyltransferase glycosyltransferase methyltransferase
SMF913_RS05265: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

SMF913_RS05310: methyltransferase

smcogs
  SMCOG1089: methyltransferase

SMF913_RS49895: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Hydrolases: hydrolase
SMF913_RS05270: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase synthase
SMF913_RS05280: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

SMF913_RS05285: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

SMF913_RS05320: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS05325: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS05355: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

SMF913_RS05360: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS05365: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS50905: Beta-ketoacyl synthase

smcogs
  SMCOG1093: 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 | RiPP-like | T1PKS | hglE-KS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002497.3 |  |  |  | 1.17 | other (other) | hexacosalactone A | Streptomyces sp.
BGC0001276.3 |  |  |  | 0.75 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  |  |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  |  |  | 0.64 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001160.5 |  |  |  | 0.56 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  |  | 0.55 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000107.3 |  |  |  | 0.54 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0002192.3 |  |  |  | 0.54 | PKS | FR901512 | fungal sp. No.14919

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002497.3 |  | 0.92 | other (other) | hexacosalactone A | Streptomyces sp.
BGC0001276.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.75 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.75 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.72 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000067.5 |  | 0.66 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0001050.5 |  | 0.63 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0001160.5 |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822

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:
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: 18.44 out of 23.79
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (10):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.85 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.67 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.52 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.12 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.87 out of 30.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.49 out of 30.22
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.99 out of 29.65
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.32 out of 25.88
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 13, location 1272583 - 1398754:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk - ohmal - pk - pk) + (mal) + (Me-mal) + (Me-ohmal - ohmal - pk - ohmal) + (pk - ccmal) + (pk - ccmal - pk)
Non-colinear ordering:
  SMF913_RS49895 + SMF913_RS05285 + SMF913_RS05280 + SMF913_RS05275 + SMF913_RS05325 + SMF913_RS05320 + SMF913_RS50905

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 15, location 1274414 - 1398754:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk - ohmal - pk - pk) + (mal) + (Me-mal) + (Me-ohmal - ohmal - pk - ohmal) + (pk - ccmal) + (pk - ccmal - pk)
Non-colinear ordering:
  SMF913_RS49895 + SMF913_RS05285 + SMF913_RS05280 + SMF913_RS05275 + SMF913_RS05325 + SMF913_RS05320 + SMF913_RS50905

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).
SMF913_RS05280: mmal
PKS_AT (631..843): mmal
ATSignature: (unknown)
No matches above 50%
minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 8.5
  Malonyl-CoA: 4.6
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

SMF913_RS05285: mal
PKS_AT (1274..1566): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 58.3%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 71.4
  Methoxymalonyl-CoA: 34.4
  Methylmalonyl-CoA: 32.7
  inactive: 23.8
  Propionyl-CoA: 16.7
  CHC-CoA: 9.7
  Isobutyryl-CoA: 7.5
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

SMF913_RS50905: pk - mal - pk
PKS_AT (570..868): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 224.2
  Methylmalonyl-CoA: 224.1
  Methoxymalonyl-CoA: 179.8
  2-Methylbutyryl-CoA: 148.0
  trans-1,2-CPDA: 133.5
  Propionyl-CoA: 111.7
  CHC-CoA: 103.3
  Malonyl-CoA: 90.6
  Isobutyryl-CoA: 79.7
  Benzoyl-CoA: 66.0
  Acetyl-CoA: 43.1
  3-Methylbutyryl-CoA: 30.9
  fatty_acid: 27.0
  inactive: 25.4

PKS_AT (2351..2638): 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: 230.9
  inactive: 118.2
  Methoxymalonyl-CoA: 59.7
  Methylmalonyl-CoA: 48.5
  Propionyl-CoA: 35.7
  2-Methylbutyryl-CoA: 16.9
  Isobutyryl-CoA: 13.7
  Acetyl-CoA: 11.8
  Benzoyl-CoA: 9.3
  Ethylmalonyl-CoA: 5.2
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4189..4487): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 234.5
  Methylmalonyl-CoA: 229.2
  Methoxymalonyl-CoA: 185.8
  2-Methylbutyryl-CoA: 164.2
  trans-1,2-CPDA: 139.9
  Propionyl-CoA: 126.2
  CHC-CoA: 116.2
  Malonyl-CoA: 106.8
  Isobutyryl-CoA: 78.4
  Benzoyl-CoA: 73.7
  Acetyl-CoA: 49.3
  fatty_acid: 36.0
  3-Methylbutyryl-CoA: 30.9
  inactive: 28.2

SMF913_RS05320: pk - mal
PKS_AT (569..867): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 229.5
  Methylmalonyl-CoA: 225.8
  Methoxymalonyl-CoA: 182.0
  2-Methylbutyryl-CoA: 157.0
  trans-1,2-CPDA: 137.9
  Propionyl-CoA: 116.8
  CHC-CoA: 107.9
  Malonyl-CoA: 96.2
  Isobutyryl-CoA: 80.3
  Benzoyl-CoA: 72.3
  Acetyl-CoA: 40.4
  3-Methylbutyryl-CoA: 34.4
  fatty_acid: 29.7
  inactive: 26.6

PKS_AT (2337..2625): 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: 225.1
  inactive: 112.4
  Methoxymalonyl-CoA: 54.0
  Methylmalonyl-CoA: 45.0
  Propionyl-CoA: 34.9
  Isobutyryl-CoA: 19.8
  Acetyl-CoA: 16.3
  Benzoyl-CoA: 12.5
  2-Methylbutyryl-CoA: 8.0
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

SMF913_RS05325: mmal - mal - pk - mal
PKS_AT (576..874): 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: 229.2
  Ethylmalonyl-CoA: 228.4
  Methoxymalonyl-CoA: 184.7
  2-Methylbutyryl-CoA: 180.5
  trans-1,2-CPDA: 134.9
  Propionyl-CoA: 132.2
  CHC-CoA: 114.2
  Malonyl-CoA: 109.8
  Isobutyryl-CoA: 87.9
  Benzoyl-CoA: 69.7
  fatty_acid: 39.3
  Acetyl-CoA: 37.6
  3-Methylbutyryl-CoA: 36.0
  inactive: 28.3

PKS_AT (2150..2441): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 236.0
  inactive: 118.6
  Methoxymalonyl-CoA: 56.3
  Methylmalonyl-CoA: 44.6
  Propionyl-CoA: 31.4
  Isobutyryl-CoA: 20.2
  2-Methylbutyryl-CoA: 14.9
  Benzoyl-CoA: 12.7
  Ethylmalonyl-CoA: 11.0
  Acetyl-CoA: 10.1
  fatty_acid: 7.2
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3708..4006): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 238.1
  Methylmalonyl-CoA: 232.2
  Methoxymalonyl-CoA: 188.0
  2-Methylbutyryl-CoA: 165.2
  trans-1,2-CPDA: 149.0
  Propionyl-CoA: 127.2
  CHC-CoA: 111.3
  Malonyl-CoA: 110.0
  Isobutyryl-CoA: 70.2
  Benzoyl-CoA: 67.4
  Acetyl-CoA: 44.4
  fatty_acid: 40.0
  3-Methylbutyryl-CoA: 28.1
  inactive: 25.7

PKS_AT (5498..5787): 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: 226.5
  inactive: 117.9
  Methoxymalonyl-CoA: 59.6
  Methylmalonyl-CoA: 50.2
  Propionyl-CoA: 35.6
  2-Methylbutyryl-CoA: 18.3
  Isobutyryl-CoA: 15.0
  Acetyl-CoA: 13.6
  Benzoyl-CoA: 9.4
  fatty_acid: 5.4
  Ethylmalonyl-CoA: 4.8
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

SMF913_RS49895: pk - mal - pk - pk
PKS_AT (558..856): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 212.3
  Methylmalonyl-CoA: 208.5
  2-Methylbutyryl-CoA: 182.7
  Methoxymalonyl-CoA: 170.6
  trans-1,2-CPDA: 134.6
  Propionyl-CoA: 128.3
  CHC-CoA: 113.6
  Malonyl-CoA: 95.9
  Isobutyryl-CoA: 92.7
  Benzoyl-CoA: 67.2
  Acetyl-CoA: 53.1
  3-Methylbutyryl-CoA: 39.6
  fatty_acid: 34.0
  inactive: 23.9

PKS_AT (1585..1870): 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: 232.1
  inactive: 122.3
  Methoxymalonyl-CoA: 56.2
  Methylmalonyl-CoA: 46.5
  Propionyl-CoA: 35.3
  Isobutyryl-CoA: 19.6
  2-Methylbutyryl-CoA: 12.3
  Benzoyl-CoA: 11.8
  Acetyl-CoA: 11.6
  Ethylmalonyl-CoA: 6.1
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3070..3368): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 234.7
  Methylmalonyl-CoA: 228.1
  Methoxymalonyl-CoA: 185.7
  2-Methylbutyryl-CoA: 171.9
  trans-1,2-CPDA: 140.1
  Propionyl-CoA: 135.4
  CHC-CoA: 112.6
  Malonyl-CoA: 112.3
  Isobutyryl-CoA: 74.9
  Benzoyl-CoA: 68.7
  Acetyl-CoA: 45.0
  fatty_acid: 42.7
  inactive: 26.6
  3-Methylbutyryl-CoA: 22.0

PKS_AT (4404..4698): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 224.9
  Methylmalonyl-CoA: 222.2
  Methoxymalonyl-CoA: 178.4
  2-Methylbutyryl-CoA: 159.0
  trans-1,2-CPDA: 126.3
  Propionyl-CoA: 116.3
  CHC-CoA: 112.0
  Malonyl-CoA: 103.5
  Isobutyryl-CoA: 77.8
  Benzoyl-CoA: 64.5
  Acetyl-CoA: 40.0
  fatty_acid: 38.3
  3-Methylbutyryl-CoA: 33.3
  inactive: 27.9

SMF913_RS05360: X
AMP-binding (15..416): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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:
    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:
    TLRLHSGSGADLTLSYGGCLQFYGTTETSGISVL
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

SMF913_RS05365: X
AMP-binding (9..412): 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:
    NTTLHTFGQTGTMGFSGGSYEGYGLTEASPVVAY
  Nearest Stachelhaus code(s):
    Leu DFLYFGGVVK (29% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
CelR | Cellobiose uptake repressor
IolR | Regulator of the inositol catabolism

NZ_LJIW01000001.1 - Region 8 - 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: 1,480,101 - 1,501,183 nt. (total: 21,083 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: acetyltransferase methyltransferase
SMF913_RS05840: methyltransferase

smcogs
  SMCOG1248: methyltransferase

SMF913_RS05880: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Ligases: synthetase
SMF913_RS05825: 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
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
BGC0001911.3 |  | 0.38 | terpene | raimonol | Streptomyces anulatus
BGC0000665.5 |  | 0.37 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001810.3 |  | 0.37 | PKS | trehangelin | Polymorphospora rubra
BGC0000676.5 |  | 0.37 | terpene | aphidicolin, aphidicolan-16β-ol, 3-deoxyaphidicolin, 17-deoxyaphidicolin | Phoma betae
BGC0000688.4 |  | 0.36 | terpene | copalyl diphosphate | Diaporthe amygdali
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
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
BGC0001911.3 |  | 0.38 | terpene | raimonol | Streptomyces anulatus
BGC0000665.5 |  | 0.37 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001810.3 |  | 0.37 | PKS | trehangelin | Polymorphospora rubra
BGC0000676.5 |  | 0.37 | terpene | aphidicolin, aphidicolan-16β-ol, 3-deoxyaphidicolin, 17-deoxyaphidicolin | Phoma betae
BGC0000688.4 |  | 0.36 | terpene | copalyl diphosphate | Diaporthe amygdali
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488

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:
SMF913_RS05825: PT_FPPS_like
Domain 1 (64 - 359): 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:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.26 out of 27.04
Confidence: medium
Additional weak hits (9):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.08 out of 21.55
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.67 out of 25.75
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.32 out of 25.88
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.28 out of 26.33
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.97 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.16 out of 24.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75
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
--- | ---
DasR | N-acetylglucosamine dependent repressor

NZ_LJIW01000001.1 - Region 9 - 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: 1,533,386 - 1,613,403 nt. (total: 80,018 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 reductase
SMF913_RS06020: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

SMF913_RS06045: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

SMF913_RS06080: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS06120: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS06130: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

SMF913_RS06145: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

SMF913_RS06150: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: acylase methyltransferase
SMF913_RS06100: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

SMF913_RS06110: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

SMF913_RS06125: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

SMF913_RS06205: methyltransferase

smcogs
  SMCOG1248: methyltransferase

SMF913_RS49905: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase
SMF913_RS06025: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: synthase
SMF913_RS06105: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS06115: 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 | T1PKS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001276.3 |  |  | 0.90 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  |  | 0.90 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.89 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000075.5 |  |  | 0.87 | PKS | hygrocin A, hygrocin B | Streptomyces sp. LZ35
BGC0001244.3 |  |  | 0.81 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002191.2 |  |  | 0.62 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001164.3 |  |  | 0.58 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001284.4 |  |  | 0.58 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  |  | 0.58 | PKS | ACT-Toxin II | Alternaria alternata
BGC0000041.3 |  |  | 0.57 | PKS | oronofacic acid | Pseudomonas syringae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000075.5 |  | 0.83 | PKS | hygrocin A, hygrocin B | Streptomyces sp. LZ35
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.72 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002191.2 |  | 0.65 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001284.4 |  | 0.63 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  | 0.63 | PKS | ACT-Toxin II | Alternaria alternata
BGC0000041.3 |  | 0.62 | 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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26
Confidence: strong
Additional weak hits (10):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.06 out of 21.55
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.93 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.62 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.03 out of 29.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.43 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 23.02 out of 35.63
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.10 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 17, location 1533385 - 1613403:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (AHBA - Me-ccmal - mal - ohmal) + (redemal) + (ccmal) + (Me-redmal) + (Me-mal - ccmal)
Non-colinear ordering:
  SMF913_RS06125 + SMF913_RS49905 + SMF913_RS06120 + SMF913_RS06115 + SMF913_RS06110 + SMF913_RS06105 + SMF913_RS06100 + SMF913_RS06095

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).
SMF913_RS06095: mal
PKS_AT (0..217): mal
ATSignature: Malonyl-CoA, inactive

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 146.7
  inactive: 82.1
  Methoxymalonyl-CoA: 61.1
  Methylmalonyl-CoA: 44.8
  Propionyl-CoA: 30.3
  Acetyl-CoA: 19.1
  Isobutyryl-CoA: 15.7
  Ethylmalonyl-CoA: 15.0
  trans-1,2-CPDA: 9.4
  2-Methylbutyryl-CoA: 3.9
  fatty_acid: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

SMF913_RS06100: mmal
PKS_AT (564..863): 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: 195.8
  Ethylmalonyl-CoA: 174.4
  Methoxymalonyl-CoA: 144.3
  2-Methylbutyryl-CoA: 115.5
  Propionyl-CoA: 96.6
  trans-1,2-CPDA: 91.9
  Malonyl-CoA: 79.2
  CHC-CoA: 77.4
  Benzoyl-CoA: 59.4
  Isobutyryl-CoA: 57.5
  Acetyl-CoA: 39.5
  fatty_acid: 32.9
  inactive: 29.4
  3-Methylbutyryl-CoA: 20.0

SMF913_RS06105: mmal
PKS_AT (571..870): 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: 196.1
  Ethylmalonyl-CoA: 177.0
  Methoxymalonyl-CoA: 145.9
  2-Methylbutyryl-CoA: 112.8
  Propionyl-CoA: 96.5
  trans-1,2-CPDA: 96.3
  Malonyl-CoA: 82.1
  CHC-CoA: 77.8
  Isobutyryl-CoA: 62.3
  Benzoyl-CoA: 60.9
  Acetyl-CoA: 38.5
  fatty_acid: 33.6
  inactive: 28.6
  3-Methylbutyryl-CoA: 20.1

SMF913_RS06110: mal
PKS_AT (0..228): mal
ATSignature: Malonyl-CoA, inactive

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 168.3
  inactive: 93.6
  Methoxymalonyl-CoA: 58.7
  Methylmalonyl-CoA: 46.1
  Propionyl-CoA: 28.5
  Acetyl-CoA: 22.2
  Isobutyryl-CoA: 19.5
  Ethylmalonyl-CoA: 14.7
  trans-1,2-CPDA: 9.3
  fatty_acid: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

SMF913_RS06120: emal
PKS_AT (616..913): emal
ATSignature: Ethylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 187.5
  Methylmalonyl-CoA: 183.3
  Methoxymalonyl-CoA: 143.7
  2-Methylbutyryl-CoA: 117.4
  Propionyl-CoA: 104.9
  trans-1,2-CPDA: 95.6
  CHC-CoA: 87.9
  Malonyl-CoA: 80.7
  Isobutyryl-CoA: 78.1
  Benzoyl-CoA: 55.0
  Acetyl-CoA: 42.5
  fatty_acid: 36.0
  3-Methylbutyryl-CoA: 35.6
  inactive: 24.8

SMF913_RS49905: mal
PKS_AT (1..228): mal
ATSignature: Malonyl-CoA, inactive

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 142.1
  inactive: 86.3
  Methoxymalonyl-CoA: 57.9
  Methylmalonyl-CoA: 43.5
  Propionyl-CoA: 24.7
  Acetyl-CoA: 21.8
  Isobutyryl-CoA: 19.8
  Ethylmalonyl-CoA: 15.8
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

SMF913_RS06125: AHBA - mmal - mal
CAL_domain (34..442): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 404.5
  shikimic_acid: 245.8
  fatty_acid: 0.0
  NH2: 0.0
  Acetyl-CoA: 0.0

PKS_AT (1641..1940): 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: 207.4
  Ethylmalonyl-CoA: 193.6
  Methoxymalonyl-CoA: 156.8
  2-Methylbutyryl-CoA: 122.7
  trans-1,2-CPDA: 112.6
  Propionyl-CoA: 104.7
  Malonyl-CoA: 93.2
  CHC-CoA: 82.0
  Isobutyryl-CoA: 73.6
  Benzoyl-CoA: 64.2
  Acetyl-CoA: 53.4
  fatty_acid: 34.9
  inactive: 32.6
  3-Methylbutyryl-CoA: 22.6

PKS_AT (3362..3663): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 215.7
  inactive: 134.2
  Methoxymalonyl-CoA: 73.4
  Methylmalonyl-CoA: 49.1
  Propionyl-CoA: 34.9
  Benzoyl-CoA: 24.4
  Isobutyryl-CoA: 21.0
  Acetyl-CoA: 20.0
  Ethylmalonyl-CoA: 18.9
  2-Methylbutyryl-CoA: 13.7
  CHC-CoA: 3.0
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-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

NZ_LJIW01000001.1 - Region 10 - NRPS,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: 1,617,407 - 1,734,797 nt. (total: 117,391 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
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
SMF913_RS06315: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS06370: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS06505: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

SMF913_RS49925: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: glucosidase
SMF913_RS06480: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

Lyases: dehydratase
SMF913_RS06245: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Isomerases: racemase
SMF913_RS06500: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase synthase
SMF913_RS06450: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS06490: argininosuccinate synthase

smcogs
  SMCOG1291: argininosuccinate synthase

SMF913_RS49915: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS49920: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transporter
SMF913_RS06465: 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 | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000342.4 |  |  | 0.74 | NRPS | enniatin | Fusarium equiseti
BGC0002285.2 |  |  | 0.69 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0002135.2 |  |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000041.3 |  |  | 0.69 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001012.3 |  |  | 0.67 | NRPS, PKS | meridamycin | Streptomyces violaceusniger
BGC0001135.5 |  |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000307.4 |  |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001128.4 |  |  | 0.62 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  | 0.62 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001012.3 |  | 0.80 | NRPS, PKS | meridamycin | Streptomyces violaceusniger
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.72 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001011.5 |  | 0.71 | NRPS, PKS | meridamycin | Streptomyces sp. NRRL 30748
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0002285.2 |  | 0.68 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000166.5 |  | 0.65 | PKS | tylactone | Streptomyces fradiae
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

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:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.27 out of 23.79
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 20.58 out of 23.05
Confidence: strong
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 19.46 out of 20.01
Confidence: strong
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
Additional weak hits (10):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.27 out of 18.57
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.94 out of 33.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.64 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.70 out of 28.14
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.54 out of 30.22
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.49 out of 29.65
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.89 out of 20.01
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.48 out of 28.14
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.12 out of 25.88
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 18, location 1617406 - 1734797:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Hpr) + (mal - pk - pk - mal) + (pk - pk - pk - pk) + (ohmal - ohmal) + (pk - ohmal - ohmal - pk - ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 19, location 1617406 - 1729974:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Hpr) + (mal - pk - pk - mal) + (pk - pk - pk - pk) + (ohmal - ohmal) + (pk - ohmal - ohmal - pk - ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 20, location 1690027 - 1734797:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Hpr) + (mal - pk - pk - mal) + (pk - pk - pk - pk)

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).
SMF913_RS49915: pk - mal - mal - pk - mal
PKS_AT (809..1097): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 211.0
  Methylmalonyl-CoA: 208.7
  Methoxymalonyl-CoA: 166.9
  2-Methylbutyryl-CoA: 144.5
  trans-1,2-CPDA: 136.5
  CHC-CoA: 130.1
  Propionyl-CoA: 118.4
  Malonyl-CoA: 93.6
  Isobutyryl-CoA: 82.3
  Benzoyl-CoA: 68.7
  Acetyl-CoA: 54.2
  fatty_acid: 37.2
  3-Methylbutyryl-CoA: 27.1
  inactive: 25.6

PKS_AT (2350..2623): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 207.2
  inactive: 124.0
  Methoxymalonyl-CoA: 56.7
  Methylmalonyl-CoA: 51.4
  Isobutyryl-CoA: 38.5
  Propionyl-CoA: 37.1
  Ethylmalonyl-CoA: 25.6
  Benzoyl-CoA: 17.3
  Acetyl-CoA: 17.1
  CHC-CoA: 13.2
  2-Methylbutyryl-CoA: 13.2
  fatty_acid: 12.2
  trans-1,2-CPDA: 10.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3810..4083): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 206.1
  inactive: 113.6
  Methoxymalonyl-CoA: 60.0
  Methylmalonyl-CoA: 49.2
  Propionyl-CoA: 35.1
  Isobutyryl-CoA: 28.8
  Ethylmalonyl-CoA: 22.4
  Benzoyl-CoA: 21.0
  Acetyl-CoA: 17.6
  2-Methylbutyryl-CoA: 14.4
  fatty_acid: 13.4
  CHC-CoA: 12.3
  trans-1,2-CPDA: 10.2
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5352..5627): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 218.4
  Methylmalonyl-CoA: 210.2
  Methoxymalonyl-CoA: 166.8
  2-Methylbutyryl-CoA: 151.9
  trans-1,2-CPDA: 130.3
  CHC-CoA: 122.6
  Propionyl-CoA: 109.6
  Malonyl-CoA: 85.9
  Isobutyryl-CoA: 73.9
  Benzoyl-CoA: 63.7
  Acetyl-CoA: 48.5
  fatty_acid: 37.7
  3-Methylbutyryl-CoA: 21.3
  inactive: 19.4

PKS_AT (7456..7763): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 75.0%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 200.3
  inactive: 97.5
  Methoxymalonyl-CoA: 64.3
  Methylmalonyl-CoA: 58.7
  Propionyl-CoA: 36.5
  Isobutyryl-CoA: 31.2
  Ethylmalonyl-CoA: 26.9
  Acetyl-CoA: 22.1
  fatty_acid: 15.7
  Benzoyl-CoA: 14.9
  2-Methylbutyryl-CoA: 14.5
  CHC-CoA: 11.6
  trans-1,2-CPDA: 10.0
  3-Methylbutyryl-CoA: 0.0

SMF913_RS06370: mal - mal
PKS_AT (571..844): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 208.0
  inactive: 119.8
  Methoxymalonyl-CoA: 50.1
  Methylmalonyl-CoA: 45.1
  Propionyl-CoA: 34.7
  Isobutyryl-CoA: 31.2
  Ethylmalonyl-CoA: 22.0
  Benzoyl-CoA: 19.3
  Acetyl-CoA: 18.5
  2-Methylbutyryl-CoA: 14.0
  CHC-CoA: 12.6
  fatty_acid: 11.9
  trans-1,2-CPDA: 8.8
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2024..2297): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 204.1
  inactive: 125.7
  Methoxymalonyl-CoA: 55.6
  Methylmalonyl-CoA: 49.9
  Isobutyryl-CoA: 35.4
  Propionyl-CoA: 34.8
  Ethylmalonyl-CoA: 25.2
  Benzoyl-CoA: 17.7
  Acetyl-CoA: 17.2
  CHC-CoA: 11.3
  2-Methylbutyryl-CoA: 10.4
  fatty_acid: 10.0
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

SMF913_RS49920: pk - pk - pk - pk
PKS_AT (558..856): pk
ATSignature: Methoxymalonyl-CoA

Top 3 matches:
  Methoxymalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 83.3%
  Methylmalonyl-CoA: 79.2%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 184.5
  Methylmalonyl-CoA: 177.6
  Methoxymalonyl-CoA: 150.6
  2-Methylbutyryl-CoA: 114.9
  trans-1,2-CPDA: 112.3
  Propionyl-CoA: 94.1
  CHC-CoA: 89.9
  Malonyl-CoA: 77.7
  Isobutyryl-CoA: 60.2
  fatty_acid: 36.8
  Benzoyl-CoA: 35.5
  Acetyl-CoA: 30.3
  inactive: 21.0
  3-Methylbutyryl-CoA: 12.5

PKS_AT (2357..2643): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 215.6
  Methylmalonyl-CoA: 208.4
  Methoxymalonyl-CoA: 169.9
  2-Methylbutyryl-CoA: 149.4
  trans-1,2-CPDA: 142.3
  Propionyl-CoA: 114.6
  CHC-CoA: 112.5
  Malonyl-CoA: 86.0
  Isobutyryl-CoA: 59.2
  Benzoyl-CoA: 55.9
  Acetyl-CoA: 41.4
  fatty_acid: 39.5
  3-Methylbutyryl-CoA: 28.7
  inactive: 19.3

PKS_AT (3917..4205): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 222.4
  Methylmalonyl-CoA: 219.2
  Methoxymalonyl-CoA: 177.8
  trans-1,2-CPDA: 151.2
  2-Methylbutyryl-CoA: 146.2
  CHC-CoA: 129.4
  Propionyl-CoA: 119.2
  Malonyl-CoA: 96.6
  Isobutyryl-CoA: 84.5
  Benzoyl-CoA: 73.0
  Acetyl-CoA: 55.8
  fatty_acid: 49.1
  inactive: 26.2
  3-Methylbutyryl-CoA: 15.3

PKS_AT (5974..6259): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 210.7
  Methylmalonyl-CoA: 207.4
  Methoxymalonyl-CoA: 168.1
  trans-1,2-CPDA: 138.5
  2-Methylbutyryl-CoA: 129.3
  CHC-CoA: 121.3
  Propionyl-CoA: 110.8
  Malonyl-CoA: 94.6
  Isobutyryl-CoA: 72.2
  Benzoyl-CoA: 70.6
  Acetyl-CoA: 44.7
  fatty_acid: 42.2
  inactive: 24.5
  3-Methylbutyryl-CoA: 9.3

SMF913_RS49925: mal - pk - pk - mal
PKS_AT (568..866): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 188.1
  inactive: 92.3
  Methoxymalonyl-CoA: 66.7
  Methylmalonyl-CoA: 50.5
  Acetyl-CoA: 27.5
  Propionyl-CoA: 22.9
  Isobutyryl-CoA: 22.9
  Ethylmalonyl-CoA: 19.3
  fatty_acid: 15.7
  Benzoyl-CoA: 12.6
  2-Methylbutyryl-CoA: 9.5
  CHC-CoA: 8.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (1587..1874): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 209.0
  Methylmalonyl-CoA: 205.2
  Methoxymalonyl-CoA: 166.2
  trans-1,2-CPDA: 134.8
  2-Methylbutyryl-CoA: 131.2
  CHC-CoA: 124.4
  Propionyl-CoA: 104.6
  Malonyl-CoA: 92.6
  Isobutyryl-CoA: 76.3
  Benzoyl-CoA: 69.0
  Acetyl-CoA: 43.7
  fatty_acid: 36.2
  inactive: 21.6
  3-Methylbutyryl-CoA: 14.2

PKS_AT (3039..3324): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 210.2
  Methylmalonyl-CoA: 209.4
  Methoxymalonyl-CoA: 168.8
  trans-1,2-CPDA: 143.0
  2-Methylbutyryl-CoA: 132.3
  CHC-CoA: 118.5
  Propionyl-CoA: 115.6
  Malonyl-CoA: 95.4
  Isobutyryl-CoA: 76.9
  Benzoyl-CoA: 68.0
  Acetyl-CoA: 46.4
  fatty_acid: 40.1
  inactive: 30.1
  3-Methylbutyryl-CoA: 9.0

PKS_AT (4717..4940): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 164.2
  inactive: 89.4
  Methoxymalonyl-CoA: 54.2
  Methylmalonyl-CoA: 40.3
  Ethylmalonyl-CoA: 27.8
  Propionyl-CoA: 24.6
  Acetyl-CoA: 23.9
  Isobutyryl-CoA: 21.3
  Benzoyl-CoA: 19.2
  2-Methylbutyryl-CoA: 16.7
  fatty_acid: 13.6
  CHC-CoA: 11.6
  trans-1,2-CPDA: 9.4
  3-Methylbutyryl-CoA: 0.0

SMF913_RS06450: Hpr
Search NORINE for peptide: strict or relaxed
AMP-binding (487..928): Hpr
nrpys: 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:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    pro (Pro)
  Single AA prediction:
    pro (Pro)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQAFDISLQESFVSQAGEHNHYGPSEAHVVTSY
  Nearest Stachelhaus code(s):
    Hpr DIQFSAHVVK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
ArgR | Regulator of arginine biosynthesis genes
IolR | Regulator of the inositol catabolism

NZ_LJIW01000001.1 - Region 11 - 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: 1,930,927 - 1,952,114 nt. (total: 21,188 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
Transferases: acetyltransferase
SMF913_RS07525: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Lyases: cyclase hydratase
SMF913_RS07485: Terpene synthase/cyclase metal-binding domain protein

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

SMF913_RS07515: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase
SMF913_RS07490: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS07520: 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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001746.3 |  | 0.79 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0000683.3 |  | 0.76 | terpene | avermitilol | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002708.2 |  | 0.75 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0001135.5 |  | 0.56 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002274.2 |  | 0.55 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0001758.4 |  | 0.55 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.55 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.55 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.55 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001746.3 |  | 0.79 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0000683.3 |  | 0.76 | terpene | avermitilol | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002708.2 |  | 0.75 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0001135.5 |  | 0.56 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002274.2 |  | 0.55 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0001758.4 |  | 0.55 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.55 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.55 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.55 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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 |  |  | C15 | C1-C11 | none

Genes with terpene domains:
SMF913_RS07485: T1TS
Domain 1 (1 - 341): Type 1 terpene synthase
Subtype: Isoafricanol synthase type

Reactions:
  FPP → sesquiterpene_C1-C11

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
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
Additional weak hits (3):
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.00 out of 27.04
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.39 out of 32.74
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.50 out of 25.75
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
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000001.1 - Region 12 - 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: 1,961,063 - 1,983,062 nt. (total: 22,000 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 oxygenase
SMF913_RS07580: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

SMF913_RS07615: Hydroxylation

MITE
  MITE0000061Hydroxylation (identity: 95.10%)
smcogs
  SMCOG1034: cytochrome P450

SMF913_RS07620: Hydroxylation

MITE
  MITE0000062Hydroxylation (identity: 94.30%)
smcogs
  SMCOG1034: cytochrome P450

SMF913_RS07625: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS07645: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Ligases: synthetase
SMF913_RS07605: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.91 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000660.5 |  | 0.59 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0002391.2 |  | 0.57 | terpene | zealexin B3, zealexin C2 | Zea mays
BGC0002736.2 |  | 0.57 | terpene | preaspterpenacid I | Aspergillus terreus NIH2624
BGC0000675.5 |  | 0.55 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001911.3 |  | 0.52 | terpene | raimonol | Streptomyces anulatus
BGC0001475.4 |  | 0.52 | terpene | aspterric acid | Aspergillus terreus NIH2624
BGC0001910.4 |  | 0.52 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.91 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000660.5 |  | 0.59 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0002391.2 |  | 0.57 | terpene | zealexin B3, zealexin C2 | Zea mays
BGC0002736.2 |  | 0.57 | terpene | preaspterpenacid I | Aspergillus terreus NIH2624
BGC0000675.5 |  | 0.55 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001911.3 |  | 0.52 | terpene | raimonol | Streptomyces anulatus
BGC0001475.4 |  | 0.52 | terpene | aspterric acid | Aspergillus terreus NIH2624
BGC0001910.4 |  | 0.52 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus

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:
SMF913_RS07605: PT_FPPS_like
Domain 1 (52 - 358): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

SMF913_RS07610: T1TS
Domain 1 (94 - 295): 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.07 out of 20.47
Confidence: medium
Additional weak hits (7):
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.75 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.07 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.07 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.48 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.56 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.24 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
--- | ---
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000001.1 - Region 13 - NRPS-like,T1PKS,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: 2,046,477 - 2,143,525 nt. (total: 97,049 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
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 oxygenase
SMF913_RS08155: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

SMF913_RS08175: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

SMF913_RS08185: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

SMF913_RS08210: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acetyltransferase acylase methyltransferase
SMF913_RS07970: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

SMF913_RS08100: methyltransferase

smcogs
  SMCOG1248: methyltransferase

SMF913_RS08140: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase phosphatase
SMF913_RS08170: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

SMF913_RS08220: HAD-superfamily hydrolase, subfamily IA, variant

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

Lyases: dehydratase hydratase lyase
SMF913_RS08020: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

SMF913_RS08025: L-carnitine dehydratase/bile acid-inducible

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

SMF913_RS08030: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

SMF913_RS08125: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Isomerases: racemase
SMF913_RS08110: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase synthase
SMF913_RS08015: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

SMF913_RS08035: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS08115: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

SMF913_RS08135: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS08145: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

SMF913_RS08200: 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 | betalactone | T1PKS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000068.5 |  |  |  | 1.04 | PKS | geldanamycin | Streptomyces hygroscopicus
BGC0000067.5 |  |  |  | 0.99 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0001275.3 |  |  |  | 0.83 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  |  |  | 0.75 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002191.2 |  |  |  | 0.59 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001276.3 |  |  |  | 0.59 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000066.5 |  |  |  | 0.58 | PKS | geldanamycin | Streptomyces hygroscopicus
BGC0001160.5 |  |  |  | 0.58 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  |  |  | 0.55 | PKS | FR901512 | fungal sp. No.14919
BGC0001268.4 |  |  |  | 0.53 | NRPS, PKS | fusarin C | Fusarium fujikuroi

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000068.5 |  | 0.94 | PKS | geldanamycin | Streptomyces hygroscopicus
BGC0000067.5 |  | 0.88 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0000066.5 |  | 0.73 | PKS | geldanamycin | Streptomyces hygroscopicus
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.70 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000074.5 |  | 0.66 | PKS | herbimycin A | Streptomyces hygroscopicus
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001160.5 |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919

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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.48 out of 23.79
Confidence: strong
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 26.33 out of 29.51
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.29 out of 23.79
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.52 out of 24.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.63 out of 28.19
Confidence: medium
Additional weak hits (19):
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.27 out of 32.93
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.10 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.12 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.52 out of 29.25
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: 20.24 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.96 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.11 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.15 out of 28.14
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.36 out of 29.38
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.49 out of 39.62
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.77 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.01 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.19 out of 28.19
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.03 out of 30.11
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.96 out of 32.93
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.32 out of 39.62
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 23, location 2046476 - 2143525:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (AHBA - Me-redmal - redmxmal - Me-ohmal) + (Me-ccmal - ohmxmal) + (redmal - Me-ccmal)
Non-colinear ordering:
  SMF913_RS08135 + SMF913_RS08140 + SMF913_RS08145

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 25, location 2060983 - 2143525:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (AHBA - Me-redmal - redmxmal - Me-ohmal) + (Me-ccmal - ohmxmal) + (redmal - Me-ccmal)
Non-colinear ordering:
  SMF913_RS08135 + SMF913_RS08140 + SMF913_RS08145

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).
SMF913_RS08035: X
AMP-binding (15..430): 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:
    DFSRHAGSTLSASGWV---VAGYGLSEASPNVAQ
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

SMF913_RS08135: AHBA - mmal - mxmal - mmal
CAL_domain (34..442): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 530.0
  shikimic_acid: 272.5
  Acetyl-CoA: 13.2
  fatty_acid: 0.0
  NH2: 0.0

PKS_AT (1686..1983): 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: 207.6
  Ethylmalonyl-CoA: 182.8
  Methoxymalonyl-CoA: 170.0
  2-Methylbutyryl-CoA: 127.2
  Propionyl-CoA: 109.8
  Malonyl-CoA: 103.3
  trans-1,2-CPDA: 95.9
  CHC-CoA: 76.8
  Isobutyryl-CoA: 70.8
  Benzoyl-CoA: 56.1
  Acetyl-CoA: 37.5
  3-Methylbutyryl-CoA: 35.2
  inactive: 24.0
  fatty_acid: 23.2

PKS_AT (3751..4051): mxmal
ATSignature: Methoxymalonyl-CoA

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

minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 194.1
  Methylmalonyl-CoA: 187.3
  Ethylmalonyl-CoA: 182.0
  2-Methylbutyryl-CoA: 125.7
  Malonyl-CoA: 97.5
  trans-1,2-CPDA: 95.5
  Propionyl-CoA: 90.2
  CHC-CoA: 76.2
  Isobutyryl-CoA: 64.8
  Benzoyl-CoA: 54.8
  Acetyl-CoA: 35.2
  3-Methylbutyryl-CoA: 29.5
  inactive: 28.2
  fatty_acid: 10.0

PKS_AT (5806..6103): 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: 206.3
  Ethylmalonyl-CoA: 185.6
  Methoxymalonyl-CoA: 171.8
  2-Methylbutyryl-CoA: 122.7
  Propionyl-CoA: 107.6
  Malonyl-CoA: 97.1
  trans-1,2-CPDA: 93.3
  CHC-CoA: 74.0
  Isobutyryl-CoA: 68.2
  Benzoyl-CoA: 56.3
  Acetyl-CoA: 39.7
  3-Methylbutyryl-CoA: 33.2
  fatty_acid: 27.2
  inactive: 21.2

SMF913_RS08140: mmal - mxmal
PKS_AT (573..872): 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: 209.0
  Ethylmalonyl-CoA: 187.3
  Methoxymalonyl-CoA: 172.1
  2-Methylbutyryl-CoA: 124.8
  Propionyl-CoA: 110.6
  Malonyl-CoA: 97.4
  trans-1,2-CPDA: 95.4
  CHC-CoA: 76.2
  Isobutyryl-CoA: 70.0
  Benzoyl-CoA: 56.5
  Acetyl-CoA: 38.1
  3-Methylbutyryl-CoA: 37.1
  fatty_acid: 24.6
  inactive: 23.2

PKS_AT (2336..2636): mxmal
ATSignature: Methoxymalonyl-CoA

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

minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 189.6
  Methylmalonyl-CoA: 184.4
  Ethylmalonyl-CoA: 178.5
  2-Methylbutyryl-CoA: 121.6
  trans-1,2-CPDA: 95.4
  Malonyl-CoA: 94.6
  Propionyl-CoA: 88.3
  CHC-CoA: 77.3
  Isobutyryl-CoA: 59.6
  Benzoyl-CoA: 52.2
  Acetyl-CoA: 33.2
  inactive: 28.2
  3-Methylbutyryl-CoA: 27.6
  fatty_acid: 8.2

SMF913_RS08145: mal - mmal
PKS_AT (580..888): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 230.9
  inactive: 124.4
  Methoxymalonyl-CoA: 67.1
  Methylmalonyl-CoA: 60.3
  Propionyl-CoA: 34.0
  Isobutyryl-CoA: 31.7
  Benzoyl-CoA: 28.8
  Acetyl-CoA: 19.9
  2-Methylbutyryl-CoA: 14.4
  Ethylmalonyl-CoA: 14.3
  CHC-CoA: 12.5
  trans-1,2-CPDA: 11.6
  fatty_acid: 10.2
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2652..2949): 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: 208.0
  Ethylmalonyl-CoA: 184.8
  Methoxymalonyl-CoA: 170.8
  2-Methylbutyryl-CoA: 122.2
  Propionyl-CoA: 111.0
  Malonyl-CoA: 100.8
  trans-1,2-CPDA: 96.0
  CHC-CoA: 81.7
  Isobutyryl-CoA: 71.3
  Benzoyl-CoA: 55.7
  Acetyl-CoA: 41.8
  3-Methylbutyryl-CoA: 38.1
  inactive: 26.2
  fatty_acid: 26.2

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

Regulator | Description
--- | ---
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism
LexA variant 2 | Repressor of DNA damage response
ZuR variant 1 | Zinc-responsive repressor

NZ_LJIW01000001.1 - Region 14 - PKS-like,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: 2,462,922 - 2,507,049 nt. (total: 44,128 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)
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
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
SMF913_RS09660: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS09720: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Transferases: acylase methyltransferase
SMF913_RS09690: methyltransferase

smcogs
  SMCOG1089: methyltransferase

SMF913_RS09705: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase
SMF913_RS09765: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

Lyases: cyclase dehydratase
SMF913_RS09675: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

SMF913_RS09685: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthase
SMF913_RS09710: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS09715: 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 | terpene | PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000658.3 |  |  | 1.22 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3 |  |  | 1.03 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000657.5 |  |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000065.5 |  |  | 0.39 | PKS | rustmicin | Streptomyces galbus
BGC0000275.4 |  |  | 0.25 | PKS | tetracenomycin C | Streptomyces glaucescens
BGC0002045.3 |  |  | 0.23 | PKS | persiamycin A | Streptomonospora sp. PA3
BGC0001580.3 |  |  | 0.23 | PKS | ebelactone | Kitasatospora aburaviensis
BGC0002514.3 |  |  | 0.23 | PKS | julichrome Q6.6 | Streptomyces sampsonii
BGC0002504.2 |  |  | 0.23 | PKS | nocardiopsistin A, nocardiopsistin B, nocardiopsistin C | Nocardiopsis sp.
BGC0001782.3 |  |  | 0.23 | 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

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000658.3 |  | 0.85 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3 |  | 0.79 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000065.5 |  | 0.58 | PKS | rustmicin | Streptomyces galbus
BGC0000657.5 |  | 0.55 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000675.5 |  | 0.50 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0000677.5 |  | 0.49 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001475.4 |  | 0.49 | terpene | aspterric acid | Aspergillus terreus NIH2624
BGC0002173.2 |  | 0.47 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000798.3 |  | 0.46 | saccharide | dhurrin | Sorghum bicolor
BGC0000886.4 |  | 0.46 | other (other) | allylmalonyl-CoA | Streptomyces tsukubensis

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
--- | --- | --- | --- | --- | ---
monoterpene |  | 2-methylisoborneol | C11 | C1-C6 | OH
monoterpene |  | 2-methylenebornane | C11 | C1-C6 | none

Genes with terpene domains:
SMF913_RS09685: T1TS
Domain 1 (13 - 436): Type 1 terpene synthase
Subtype: 2-Methylisoborneol synthase type

Reactions:
  2-MeGPP → 2-methylisoborneol
  2-MeGPP → 2-methylenebornane

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: 20.11 out of 23.05
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (19):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.54 out of 27.78
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.26 out of 20.01
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.15 out of 30.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.55 out of 30.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.52 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.93 out of 26.06
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.00 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.95 out of 29.38
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.14 out of 25.88
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.45 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.44 out of 28.19
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.65 out of 23.43
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.80 out of 36.54
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.90 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
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 26, location 2462921 - 2507049:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mxmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 28, location 2466020 - 2507049:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mxmal)

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).
SMF913_RS09705: mxmal
PKS_AT (20..290): mxmal
ATSignature: (unknown)
No matches above 50%
minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 20.9
  Malonyl-CoA: 19.3
  Methylmalonyl-CoA: 18.2
  2-Methylbutyryl-CoA: 10.0
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Acronym | Full name
--- | ---
2-MeGPP | 2-methylgeranyl diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production

NZ_LJIW01000001.1 - Region 15 - 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: 2,581,817 - 2,658,607 nt. (total: 76,791 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 oxygenase
SMF913_RS10170: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS10210: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

SMF913_RS10220: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

SMF913_RS10320: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS10345: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

SMF913_RS10375: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

SMF913_RS48030: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS49990: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS49995: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase
SMF913_RS10315: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: dehalogenase phosphatase
SMF913_RS10160: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

SMF913_RS10205: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Ligases: synthase
SMF913_RS10325: 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 | T1PKS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  | 0.86 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.86 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  |  | 0.85 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000041.3 |  |  | 0.68 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000067.5 |  |  | 0.63 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0001160.5 |  |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002191.2 |  |  | 0.60 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001164.3 |  |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001284.4 |  |  | 0.57 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  |  | 0.57 | PKS | FR901512 | fungal sp. No.14919

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000018.5 |  | 0.66 | PKS | angolamycin | Streptomyces eurythermus
BGC0000067.5 |  | 0.65 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002191.2 |  | 0.64 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.63 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15

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: 17.92 out of 20.47
Confidence: medium
Additional weak hits (10):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.83 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.38 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.73 out of 18.57
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.65 out of 22.40
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 21.84
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.27 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.52 out of 29.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.23 out of 33.14
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 29, location 2581816 - 2658607:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (AHBA - pk - redmal) + (pk) + (Me-ccmal - pk) + (ccmal)
Non-colinear ordering:
  SMF913_RS49990 + SMF913_RS48030 + SMF913_RS10315 + SMF913_RS10320 + SMF913_RS49995 + SMF913_RS10325

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).
SMF913_RS49990: AHBA - pk - mal
CAL_domain (34..440): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 382.8
  shikimic_acid: 254.8
  NH2: 10.6
  fatty_acid: 0.0
  Acetyl-CoA: -4.1

PKS_AT (1508..1802): pk
ATSignature: Methoxymalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 175.1
  Methylmalonyl-CoA: 164.0
  Methoxymalonyl-CoA: 151.4
  trans-1,2-CPDA: 110.0
  2-Methylbutyryl-CoA: 104.4
  CHC-CoA: 88.6
  Propionyl-CoA: 86.9
  Malonyl-CoA: 82.4
  Benzoyl-CoA: 54.8
  Acetyl-CoA: 34.4
  Isobutyryl-CoA: 34.2
  inactive: 13.8
  fatty_acid: 13.3
  3-Methylbutyryl-CoA: 11.8

PKS_AT (3177..3371): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 66.7%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 112.9
  inactive: 55.6
  Methoxymalonyl-CoA: 47.8
  Methylmalonyl-CoA: 37.8
  Ethylmalonyl-CoA: 26.6
  Propionyl-CoA: 17.4
  Isobutyryl-CoA: 12.9
  CHC-CoA: 12.7
  Benzoyl-CoA: 12.1
  2-Methylbutyryl-CoA: 11.5
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

SMF913_RS10315: pk
PKS_AT (569..863): pk
ATSignature: Methoxymalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 178.5
  Methylmalonyl-CoA: 168.2
  Methoxymalonyl-CoA: 154.4
  trans-1,2-CPDA: 112.2
  2-Methylbutyryl-CoA: 104.8
  Propionyl-CoA: 89.2
  CHC-CoA: 86.9
  Malonyl-CoA: 80.1
  Benzoyl-CoA: 48.3
  Isobutyryl-CoA: 32.4
  Acetyl-CoA: 27.9
  inactive: 15.1
  3-Methylbutyryl-CoA: 12.6
  fatty_acid: 8.9

SMF913_RS10320: mmal - pk
PKS_AT (550..839): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 196.7
  Ethylmalonyl-CoA: 187.9
  Methoxymalonyl-CoA: 156.6
  2-Methylbutyryl-CoA: 129.3
  trans-1,2-CPDA: 101.6
  Propionyl-CoA: 93.8
  CHC-CoA: 90.2
  Malonyl-CoA: 84.7
  Isobutyryl-CoA: 71.6
  Benzoyl-CoA: 62.2
  Acetyl-CoA: 53.5
  fatty_acid: 37.0
  3-Methylbutyryl-CoA: 31.5
  inactive: 22.2

PKS_AT (2211..2505): pk
ATSignature: Methoxymalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 181.5
  Methylmalonyl-CoA: 170.8
  Methoxymalonyl-CoA: 159.5
  trans-1,2-CPDA: 113.0
  2-Methylbutyryl-CoA: 107.4
  Propionyl-CoA: 92.3
  CHC-CoA: 87.9
  Malonyl-CoA: 83.7
  Benzoyl-CoA: 52.0
  Isobutyryl-CoA: 36.7
  Acetyl-CoA: 30.4
  3-Methylbutyryl-CoA: 14.7
  inactive: 13.5
  fatty_acid: 11.4

SMF913_RS10325: mal
PKS_AT (552..835): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 173.6
  inactive: 82.2
  Methoxymalonyl-CoA: 65.7
  Methylmalonyl-CoA: 55.1
  Ethylmalonyl-CoA: 29.6
  Propionyl-CoA: 28.6
  Isobutyryl-CoA: 14.6
  2-Methylbutyryl-CoA: 13.7
  CHC-CoA: 12.4
  Benzoyl-CoA: 12.1
  trans-1,2-CPDA: 8.5
  fatty_acid: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

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

NZ_LJIW01000001.1 - Region 16 - 2dos,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: 2,703,603 - 2,786,829 nt. (total: 83,227 nt) Show pHMM detection rules used
2dos: ((DOIS or DHQ_synthase or ValA or salQ) and DegT_DnrJ_EryC1 and (LipV or ADSI-DH or cds(ADH_N and ADH_zinc_N)))
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 reductase
SMF913_RS10685: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

SMF913_RS10700: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

SMF913_RS10720: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

SMF913_RS10795: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

SMF913_RS10820: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

SMF913_RS10835: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

SMF913_RS48685: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase
SMF913_RS10725: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: hydrolase
SMF913_RS10715: HAD-superfamily hydrolase, subfamily IA, variant

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

Lyases: dehydratase
SMF913_RS10655: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
SMF913_RS10675: 3-oxoacyl-(acyl carrier protein) synthase III

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

SMF913_RS10680: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS10705: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS10735: 3-dehydroquinate synthase

smcogs
  SMCOG1183: 3-dehydroquinate synthase

SMF913_RS10745: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS10750: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS10770: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS10775: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

Translocases: permease
SMF913_RS10810: 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 | 2dos | T1PKS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  |  | 1.31 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  |  | 1.28 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  |  | 1.28 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  |  |  | 1.26 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001164.3 |  |  |  | 1.02 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  | 1.01 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000041.3 |  |  |  | 1.00 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002191.2 |  |  |  | 0.89 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001254.3 |  |  |  | 0.89 | PKS | ACT-Toxin II | Alternaria alternata
BGC0000018.5 |  |  |  | 0.87 | PKS | angolamycin | Streptomyces eurythermus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001164.3 |  | 0.70 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.70 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000018.5 |  | 0.65 | PKS | angolamycin | Streptomyces eurythermus
BGC0000041.3 |  | 0.64 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001254.3 |  | 0.64 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001163.3 |  | 0.64 | PKS | 1-heptadecene | Moorea producens 3L

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:
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11
Confidence: strong
Additional weak hits (14):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.50 out of 21.55
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.71 out of 27.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.86 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.27 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.57 out of 27.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.73 out of 25.75
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.90 out of 30.22
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.28 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.90 out of 21.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.30 out of 29.65
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.69 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.00 out of 29.25
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.09 out of 35.63
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 30, location 2703602 - 2786829:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (AHBA - Me-ccmal - mal - pk) + (Me-redmal) + (Me-redmal) + (Me-ccmal) + (pk)
Non-colinear ordering:
  SMF913_RS10775 + SMF913_RS10770 + SMF913_RS48685 + SMF913_RS10750 + SMF913_RS10745

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).
SMF913_RS10680: Acetyl-CoA
CAL_domain (45..497): Acetyl-CoA
minowa: Acetyl-CoA

Prediction, score:
  Acetyl-CoA: 49.0
  fatty_acid: 15.3
  AHBA: 2.7
  NH2: 2.2
  shikimic_acid: -4.9

SMF913_RS10705: X
AMP-binding (47..462): X
nrpys: Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AAIL---ITVSSTAFSEGARATYGMTELSIGTWT
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

SMF913_RS10745: pk
PKS_AT (572..871): pk
ATSignature: Ethylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 184.2
  Ethylmalonyl-CoA: 178.2
  Methoxymalonyl-CoA: 157.3
  trans-1,2-CPDA: 129.9
  2-Methylbutyryl-CoA: 115.3
  Malonyl-CoA: 99.3
  CHC-CoA: 97.3
  Propionyl-CoA: 95.3
  Isobutyryl-CoA: 87.3
  Benzoyl-CoA: 61.6
  fatty_acid: 50.1
  3-Methylbutyryl-CoA: 44.5
  Acetyl-CoA: 40.0
  inactive: 28.6

SMF913_RS10750: mmal
PKS_AT (570..868): 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: 206.6
  Ethylmalonyl-CoA: 200.3
  Methoxymalonyl-CoA: 168.4
  2-Methylbutyryl-CoA: 126.1
  trans-1,2-CPDA: 123.0
  Propionyl-CoA: 105.8
  CHC-CoA: 89.3
  Malonyl-CoA: 82.3
  Isobutyryl-CoA: 78.6
  Benzoyl-CoA: 66.6
  fatty_acid: 34.8
  Acetyl-CoA: 30.0
  3-Methylbutyryl-CoA: 25.3
  inactive: 20.7

SMF913_RS48685: mmal
PKS_AT (566..859): mmal
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 83.3%
  Methoxymalonyl-CoA: 83.3%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 172.9
  Ethylmalonyl-CoA: 164.2
  Methoxymalonyl-CoA: 148.2
  trans-1,2-CPDA: 101.3
  Isobutyryl-CoA: 97.0
  2-Methylbutyryl-CoA: 96.1
  Propionyl-CoA: 86.4
  Malonyl-CoA: 79.3
  CHC-CoA: 79.3
  Benzoyl-CoA: 51.7
  fatty_acid: 44.7
  3-Methylbutyryl-CoA: 31.6
  Acetyl-CoA: 22.6
  inactive: 17.0

SMF913_RS10770: mmal
PKS_AT (570..869): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Malonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 184.9
  Ethylmalonyl-CoA: 175.4
  Methoxymalonyl-CoA: 149.8
  trans-1,2-CPDA: 111.7
  2-Methylbutyryl-CoA: 96.0
  Propionyl-CoA: 90.6
  Isobutyryl-CoA: 90.4
  CHC-CoA: 80.7
  Malonyl-CoA: 80.1
  Benzoyl-CoA: 56.1
  Acetyl-CoA: 32.0
  fatty_acid: 28.2
  3-Methylbutyryl-CoA: 22.1
  inactive: 17.1

SMF913_RS10775: AHBA - mmal - mal - pk
CAL_domain (33..448): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 411.8
  shikimic_acid: 231.1
  Acetyl-CoA: 10.5
  fatty_acid: 0.0
  NH2: 0.0

PKS_AT (1568..1867): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Malonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 192.9
  Ethylmalonyl-CoA: 185.0
  Methoxymalonyl-CoA: 154.5
  trans-1,2-CPDA: 114.9
  2-Methylbutyryl-CoA: 106.6
  Isobutyryl-CoA: 98.6
  Propionyl-CoA: 97.4
  CHC-CoA: 87.2
  Malonyl-CoA: 84.6
  Benzoyl-CoA: 63.2
  fatty_acid: 49.2
  3-Methylbutyryl-CoA: 37.3
  Acetyl-CoA: 34.9
  inactive: 19.1

PKS_AT (3264..3558): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 79.2%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 194.9
  inactive: 82.8
  Methoxymalonyl-CoA: 68.5
  Methylmalonyl-CoA: 52.7
  Isobutyryl-CoA: 38.0
  Propionyl-CoA: 33.0
  Ethylmalonyl-CoA: 25.2
  trans-1,2-CPDA: 17.6
  Acetyl-CoA: 15.6
  Benzoyl-CoA: 12.8
  2-Methylbutyryl-CoA: 12.0
  CHC-CoA: 7.2
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4574..4875): pk
ATSignature: Ethylmalonyl-CoA, Methoxymalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 191.1
  Ethylmalonyl-CoA: 186.2
  Methoxymalonyl-CoA: 150.5
  2-Methylbutyryl-CoA: 131.4
  CHC-CoA: 108.9
  trans-1,2-CPDA: 103.0
  Malonyl-CoA: 100.2
  Isobutyryl-CoA: 99.2
  Propionyl-CoA: 99.1
  Benzoyl-CoA: 51.0
  Acetyl-CoA: 50.5
  fatty_acid: 47.1
  3-Methylbutyryl-CoA: 25.2
  inactive: 23.7

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

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor

NZ_LJIW01000001.1 - Region 17 - 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: 2,973,705 - 3,002,770 nt. (total: 29,066 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
SMF913_RS11700: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Lyases: lyase
SMF913_RS11725: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Isomerases: isomerase
SMF913_RS11670: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase synthetase
SMF913_RS11685: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

SMF913_RS11690: 1-deoxy-D-xylulose-5-phosphate synthase

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

SMF913_RS11710: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transport
SMF913_RS11730: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport 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
--- | --- | --- | --- | --- | ---
BGC0002458.3 |  | 0.65 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0000665.5 |  | 0.52 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002591.2 |  | 0.50 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000666.5 |  | 0.49 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0000663.5 |  | 0.48 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000937.5 |  | 0.47 | other (other) | fosfazinomycin A, fosfazinomycin B | Streptomyces sp. WM6372
BGC0001850.4 |  | 0.47 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0000668.5 |  | 0.46 | other (other), terpene | 12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole | Hapalosiphon welwitschii UTEX B 1830

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002458.3 |  | 0.65 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0000665.5 |  | 0.52 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002591.2 |  | 0.50 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000666.5 |  | 0.49 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0000663.5 |  | 0.48 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000937.5 |  | 0.47 | other (other) | fosfazinomycin A, fosfazinomycin B | Streptomyces sp. WM6372
BGC0001850.4 |  | 0.47 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0000668.5 |  | 0.46 | other (other), terpene | 12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole | Hapalosiphon welwitschii UTEX B 1830

Similar known clusters from MIBiG 4.0
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
--- | --- | --- | --- | --- | ---
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:
SMF913_RS11685: PT_FPPS_like
Domain 1 (61 - 349): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

SMF913_RS11715: TS_Pyr4
Domain 1 (4 - 213): 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.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
Additional weak hits (3):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.54 out of 23.43
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.92 out of 27.78
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.60 out of 30.98
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_LJIW01000001.1 - Region 18 - 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: 3,036,382 - 3,068,159 nt. (total: 31,778 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
SMF913_RS11885: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: methyltransferase transferase
SMF913_RS11880: methyltransferase

smcogs
  SMCOG1089: methyltransferase

SMF913_RS11970: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Lyases: decarboxylase
SMF913_RS11950: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: synthase
SMF913_RS11920: carbamoyl phosphate synthase small subunit

smcogs
  SMCOG1249: carbamoyl phosphate synthase small subunit

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
--- | --- | --- | --- | --- | ---
BGC0002527.2 |  | 0.60 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0001408.5 |  | 0.60 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0000946.5 |  | 0.59 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0000947.5 |  | 0.50 | other (other) | vibrioferrin | Vibrio alginolyticus
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
BGC0000844.5 |  | 0.48 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002127.3 |  | 0.48 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0002031.3 |  | 0.47 | other (other) | kitasetaline | Kitasatospora setae KM-6054

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002527.2 |  | 0.60 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0001408.5 |  | 0.60 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0000946.5 |  | 0.59 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0000947.5 |  | 0.50 | other (other) | vibrioferrin | Vibrio alginolyticus
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
BGC0000844.5 |  | 0.48 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002127.3 |  | 0.48 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0002031.3 |  | 0.47 | other (other) | kitasetaline | Kitasatospora setae KM-6054

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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.62 out of 20.97
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.60 out of 19.26
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.90 out of 36.53
Confidence: medium
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 26.17 out of 29.65
Confidence: medium
Additional weak hits (8):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.66 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.84 out of 29.38
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.34 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.96 out of 30.25
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.26 out of 35.63
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.73 out of 24.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
DmdR1 | Iron(II)-dependent repressor
LexA variant 1 | Repressor of DNA damage response

NZ_LJIW01000001.1 - Region 19 - 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: 3,223,361 - 3,233,765 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
Oxidoreductases: dehydrogenase
SMF913_RS12745: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: aminotransferase
SMF913_RS12725: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

SMF913_RS12740: 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 |  | 0.86 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.86 | other (other) | ectoine | Streptomyces anulatus
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000857.3 |  | 0.63 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.63 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.62 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.86 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.86 | other (other) | ectoine | Streptomyces anulatus
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000857.3 |  | 0.63 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.63 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.62 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

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: 16.52 out of 19.26
Confidence: medium
Additional weak hits (4):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.61 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.40 out of 30.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.12 out of 26.12
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LJIW01000001.1 - Region 20 - 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: 3,976,215 - 4,002,677 nt. (total: 26,463 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
SMF913_RS16295: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Lyases: cyclase dehydratase
SMF913_RS16240: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

SMF913_RS16245: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase 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 | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.52 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000560.5 |  | 0.45 | ribosomal | subtilomycin | Bacillus subtilis
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000544.4 |  | 0.42 | ribosomal | planosporicin | Planomonospora alba
BGC0001727.3 |  | 0.42 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0002120.3 |  | 0.37 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000529.5 |  | 0.36 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0001625.5 |  | 0.31 | PKS | Isofuranonaphthoquinone A, Isofuranonaphthoquinone B, Isofuranonaphthoquinone C, Isofuranonaphthoquinone D, Isofuranonaphthoquinone E, Isofuranonaphthoquinone F | Streptomyces sp. CB01883
BGC0001386.5 |  | 0.31 | PKS | JBIR-76, JBIR-77 | Streptomyces sp. RI-77

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.52 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000560.5 |  | 0.45 | ribosomal | subtilomycin | Bacillus subtilis
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000544.4 |  | 0.42 | ribosomal | planosporicin | Planomonospora alba
BGC0001727.3 |  | 0.42 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0002120.3 |  | 0.37 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000529.5 |  | 0.36 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0001625.5 |  | 0.31 | PKS | Isofuranonaphthoquinone A, Isofuranonaphthoquinone B, Isofuranonaphthoquinone C, Isofuranonaphthoquinone D, Isofuranonaphthoquinone E, Isofuranonaphthoquinone F | Streptomyces sp. CB01883
BGC0001386.5 |  | 0.31 | PKS | JBIR-76, JBIR-77 | Streptomyces sp. RI-77

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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
Additional weak hits (8):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.95 out of 29.51
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.09 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.91 out of 32.74
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.73 out of 30.22
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: 20.61 out of 29.65
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.09 out of 32.93
Confidence: weak
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.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (3976214...4002677)
SMF913_RS16245
  RRE type: Lanthipeptide_LanB_RRE
  Location: 158 - 250
  Score: 58.9

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_LJIW01000001.1 - Region 21 - 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: 4,340,792 - 4,523,551 nt. (total: 182,760 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
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
SMF913_RS17770: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS17850: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS17960: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

SMF913_RS17965: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

Transferases: acetyltransferase acylase
SMF913_RS17750: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

SMF913_RS17860: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

SMF913_RS17895: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Hydrolases: dehalogenase esterase hydrolase
SMF913_RS17735: thioesterase

smcogs
  SMCOG1004: thioesterase

SMF913_RS17760: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

SMF913_RS17815: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

SMF913_RS17935: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: synthase
SMF913_RS17855: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS17880: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS17885: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS17890: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS17900: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS50180: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002498.3 |  | 0.77 | other (other) | desulfoclethramycin, clethramycin | Streptomyces sp.
BGC0002355.2 |  | 0.74 | PKS, other (other) | tetrafibricin | Streptomyces neyagawaensis
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
BGC0000041.3 |  | 0.73 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002357.3 |  | 0.71 | PKS, other (other) | neomediomycin B | Streptomyces sp. RK95-74
BGC0001662.4 |  | 0.68 | PKS | mediomycin A | Kitasatospora mediocidica
BGC0002356.3 |  | 0.68 | PKS, other (other) | mediomycin A | Streptomyces blastmyceticus
BGC0000018.5 |  | 0.64 | PKS | angolamycin | Streptomyces eurythermus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002498.3 |  | 0.77 | other (other) | desulfoclethramycin, clethramycin | Streptomyces sp.
BGC0002355.2 |  | 0.74 | PKS, other (other) | tetrafibricin | Streptomyces neyagawaensis
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
BGC0000041.3 |  | 0.73 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002357.3 |  | 0.71 | PKS, other (other) | neomediomycin B | Streptomyces sp. RK95-74
BGC0001662.4 |  | 0.68 | PKS | mediomycin A | Kitasatospora mediocidica
BGC0002356.3 |  | 0.68 | PKS, other (other) | mediomycin A | Streptomyces blastmyceticus
BGC0000018.5 |  | 0.64 | PKS | angolamycin | Streptomyces eurythermus

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: 17.68 out of 20.47
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 23.52 out of 26.33
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.50 out of 20.47
Confidence: medium
Additional weak hits (17):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.20 out of 20.97
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.69 out of 26.85
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.69 out of 26.85
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.67 out of 29.72
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.39 out of 27.78
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.73 out of 19.26
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.54 out of 31.73
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.37 out of 25.88
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.88 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.20 out of 30.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.02 out of 25.88
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.78 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.38 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.80 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.21 out of 23.43
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.24 out of 32.38
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 35, location 4340791 - 4523551:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (ohmal - ohmal - ccmal - ohmal - ohmal) + (ccmal - ohmal) + (ccmal - ohmal - ccmal - ohmal - ccmal) + (Me-ohmal) + (ohmal - ccmal - ccmal) + (ccmal - ccmal - ccmal - ccmal) + (Me-ohmal - Me-ohmal) + (ccmal - redmal - ccmal) + (ccmal - Me-ccmal)
Non-colinear ordering:
  SMF913_RS17900 + SMF913_RS17895 + SMF913_RS17890 + SMF913_RS17885 + SMF913_RS17880 + SMF913_RS50180 + SMF913_RS17860 + SMF913_RS17855 + SMF913_RS17850

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).
SMF913_RS17750: pk
PKS_AT (11..274): pk
ATSignature: (unknown)
No matches above 50%
minowa: CHC-CoA

Prediction, score:
  CHC-CoA: 14.1
  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

SMF913_RS17850: mal - mmal
PKS_AT (591..884): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 230.6
  inactive: 117.9
  Methoxymalonyl-CoA: 69.2
  Methylmalonyl-CoA: 64.0
  Propionyl-CoA: 39.9
  Ethylmalonyl-CoA: 27.5
  Isobutyryl-CoA: 26.8
  Acetyl-CoA: 25.4
  trans-1,2-CPDA: 22.5
  Benzoyl-CoA: 21.8
  2-Methylbutyryl-CoA: 19.3
  CHC-CoA: 16.8
  fatty_acid: 11.1
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2374..2673): 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: 224.5
  Ethylmalonyl-CoA: 218.5
  Methoxymalonyl-CoA: 178.1
  2-Methylbutyryl-CoA: 142.6
  trans-1,2-CPDA: 132.7
  Propionyl-CoA: 104.4
  Malonyl-CoA: 100.8
  CHC-CoA: 96.4
  Isobutyryl-CoA: 90.7
  Benzoyl-CoA: 68.9
  3-Methylbutyryl-CoA: 59.4
  Acetyl-CoA: 45.0
  fatty_acid: 40.3
  inactive: 32.8

SMF913_RS17855: mal - mal - mal
PKS_AT (575..865): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 235.8
  inactive: 125.5
  Methoxymalonyl-CoA: 77.2
  Methylmalonyl-CoA: 67.0
  Isobutyryl-CoA: 43.6
  Propionyl-CoA: 39.0
  Ethylmalonyl-CoA: 33.9
  Benzoyl-CoA: 29.7
  2-Methylbutyryl-CoA: 24.8
  Acetyl-CoA: 22.8
  CHC-CoA: 18.6
  trans-1,2-CPDA: 15.2
  fatty_acid: 13.3
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2335..2628): 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: 241.3
  inactive: 128.6
  Methoxymalonyl-CoA: 67.1
  Methylmalonyl-CoA: 65.4
  Propionyl-CoA: 43.7
  Isobutyryl-CoA: 36.0
  Acetyl-CoA: 27.2
  Benzoyl-CoA: 25.3
  2-Methylbutyryl-CoA: 22.1
  trans-1,2-CPDA: 14.5
  CHC-CoA: 14.1
  fatty_acid: 11.6
  3-Methylbutyryl-CoA: 0.0
  Ethylmalonyl-CoA: -2.7

PKS_AT (4415..4703): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 237.8
  inactive: 125.6
  Methoxymalonyl-CoA: 74.4
  Methylmalonyl-CoA: 71.7
  Propionyl-CoA: 44.8
  Ethylmalonyl-CoA: 36.3
  2-Methylbutyryl-CoA: 28.1
  Isobutyryl-CoA: 27.8
  Acetyl-CoA: 27.3
  Benzoyl-CoA: 27.1
  CHC-CoA: 18.6
  trans-1,2-CPDA: 16.6
  fatty_acid: 14.5
  3-Methylbutyryl-CoA: 0.0

SMF913_RS17860: mmal - mmal
PKS_AT (570..869): 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: 224.4
  Ethylmalonyl-CoA: 221.0
  Methoxymalonyl-CoA: 178.1
  2-Methylbutyryl-CoA: 143.4
  trans-1,2-CPDA: 130.3
  Propionyl-CoA: 106.6
  Malonyl-CoA: 99.3
  CHC-CoA: 96.9
  Isobutyryl-CoA: 82.6
  Benzoyl-CoA: 65.5
  3-Methylbutyryl-CoA: 55.5
  Acetyl-CoA: 42.6
  fatty_acid: 41.2
  inactive: 30.8

PKS_AT (2117..2416): 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: 225.4
  Ethylmalonyl-CoA: 219.1
  Methoxymalonyl-CoA: 179.0
  2-Methylbutyryl-CoA: 150.5
  trans-1,2-CPDA: 128.1
  Propionyl-CoA: 103.9
  Malonyl-CoA: 103.1
  CHC-CoA: 103.1
  Isobutyryl-CoA: 95.6
  Benzoyl-CoA: 74.7
  3-Methylbutyryl-CoA: 65.9
  Acetyl-CoA: 51.2
  fatty_acid: 40.3
  inactive: 31.8

SMF913_RS50180: mal - mal - mal - mal
PKS_AT (575..866): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 242.0
  inactive: 127.2
  Methoxymalonyl-CoA: 74.7
  Methylmalonyl-CoA: 70.5
  Propionyl-CoA: 45.0
  Isobutyryl-CoA: 43.9
  Benzoyl-CoA: 33.5
  Ethylmalonyl-CoA: 31.5
  Acetyl-CoA: 25.2
  2-Methylbutyryl-CoA: 24.9
  trans-1,2-CPDA: 20.9
  CHC-CoA: 19.6
  fatty_acid: 14.7
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2389..2678): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 242.6
  inactive: 119.2
  Methoxymalonyl-CoA: 69.7
  Methylmalonyl-CoA: 67.9
  Propionyl-CoA: 46.3
  Isobutyryl-CoA: 29.2
  Benzoyl-CoA: 27.1
  Ethylmalonyl-CoA: 25.7
  Acetyl-CoA: 22.8
  2-Methylbutyryl-CoA: 20.1
  trans-1,2-CPDA: 18.2
  CHC-CoA: 17.7
  fatty_acid: 14.1
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4181..4472): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 236.6
  inactive: 125.0
  Methoxymalonyl-CoA: 71.2
  Methylmalonyl-CoA: 64.5
  Propionyl-CoA: 46.0
  Isobutyryl-CoA: 33.2
  Benzoyl-CoA: 21.6
  Ethylmalonyl-CoA: 21.1
  2-Methylbutyryl-CoA: 21.0
  Acetyl-CoA: 20.2
  CHC-CoA: 12.2
  trans-1,2-CPDA: 10.1
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5993..6281): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 232.8
  inactive: 117.8
  Methoxymalonyl-CoA: 66.0
  Methylmalonyl-CoA: 63.7
  Propionyl-CoA: 42.5
  Benzoyl-CoA: 26.8
  Acetyl-CoA: 26.7
  Isobutyryl-CoA: 26.5
  Ethylmalonyl-CoA: 22.3
  trans-1,2-CPDA: 19.4
  2-Methylbutyryl-CoA: 17.0
  CHC-CoA: 14.4
  fatty_acid: 10.8
  3-Methylbutyryl-CoA: 0.0

SMF913_RS17880: mal - mal - mal
PKS_AT (572..866): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 244.6
  inactive: 118.3
  Methoxymalonyl-CoA: 70.4
  Methylmalonyl-CoA: 61.1
  Propionyl-CoA: 36.2
  Isobutyryl-CoA: 29.2
  Benzoyl-CoA: 21.1
  2-Methylbutyryl-CoA: 20.6
  Ethylmalonyl-CoA: 20.3
  Acetyl-CoA: 17.5
  CHC-CoA: 10.4
  trans-1,2-CPDA: 7.1
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2134..2426): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 239.1
  inactive: 116.9
  Methoxymalonyl-CoA: 67.6
  Methylmalonyl-CoA: 60.7
  Propionyl-CoA: 37.4
  Benzoyl-CoA: 24.4
  Isobutyryl-CoA: 23.3
  Acetyl-CoA: 20.2
  Ethylmalonyl-CoA: 17.6
  trans-1,2-CPDA: 14.1
  CHC-CoA: 11.6
  2-Methylbutyryl-CoA: 10.4
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3890..4192): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 219.0
  inactive: 107.0
  Methoxymalonyl-CoA: 62.7
  Methylmalonyl-CoA: 61.1
  Propionyl-CoA: 38.4
  Isobutyryl-CoA: 27.3
  Ethylmalonyl-CoA: 21.2
  2-Methylbutyryl-CoA: 21.1
  Acetyl-CoA: 19.1
  Benzoyl-CoA: 16.6
  trans-1,2-CPDA: 13.9
  CHC-CoA: 12.9
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

SMF913_RS17885: mmal
PKS_AT (567..866): 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: 224.4
  Ethylmalonyl-CoA: 223.2
  Methoxymalonyl-CoA: 177.3
  2-Methylbutyryl-CoA: 142.9
  trans-1,2-CPDA: 127.3
  CHC-CoA: 110.2
  Propionyl-CoA: 102.1
  Malonyl-CoA: 96.6
  Isobutyryl-CoA: 82.3
  Benzoyl-CoA: 67.4
  3-Methylbutyryl-CoA: 56.1
  Acetyl-CoA: 42.2
  fatty_acid: 41.3
  inactive: 28.5

SMF913_RS17890: mal - mal - mal - mal - mal
PKS_AT (567..858): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 240.6
  inactive: 128.7
  Methoxymalonyl-CoA: 72.0
  Methylmalonyl-CoA: 71.6
  Propionyl-CoA: 46.7
  Ethylmalonyl-CoA: 32.1
  Isobutyryl-CoA: 30.5
  Benzoyl-CoA: 27.9
  2-Methylbutyryl-CoA: 27.8
  Acetyl-CoA: 24.6
  trans-1,2-CPDA: 18.1
  CHC-CoA: 17.3
  fatty_acid: 10.4
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2396..2687): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 237.7
  inactive: 125.0
  Methoxymalonyl-CoA: 73.1
  Methylmalonyl-CoA: 70.4
  Propionyl-CoA: 45.2
  Isobutyryl-CoA: 31.3
  Acetyl-CoA: 29.2
  2-Methylbutyryl-CoA: 27.1
  Ethylmalonyl-CoA: 25.2
  Benzoyl-CoA: 20.5
  CHC-CoA: 15.2
  trans-1,2-CPDA: 13.9
  fatty_acid: 10.1
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3874..4167): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 237.2
  inactive: 118.0
  Methoxymalonyl-CoA: 71.6
  Methylmalonyl-CoA: 67.2
  Propionyl-CoA: 46.3
  Isobutyryl-CoA: 35.0
  Ethylmalonyl-CoA: 29.7
  2-Methylbutyryl-CoA: 29.3
  Benzoyl-CoA: 26.8
  Acetyl-CoA: 23.0
  trans-1,2-CPDA: 17.8
  CHC-CoA: 15.5
  fatty_acid: 12.8
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5743..6034): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 234.4
  inactive: 117.9
  Methoxymalonyl-CoA: 65.9
  Methylmalonyl-CoA: 65.6
  Propionyl-CoA: 43.3
  Acetyl-CoA: 29.1
  Isobutyryl-CoA: 28.4
  Ethylmalonyl-CoA: 24.6
  Benzoyl-CoA: 23.4
  2-Methylbutyryl-CoA: 23.4
  trans-1,2-CPDA: 20.9
  CHC-CoA: 14.0
  fatty_acid: 10.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (7301..7593): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 234.7
  inactive: 118.0
  Methoxymalonyl-CoA: 67.7
  Methylmalonyl-CoA: 65.4
  Propionyl-CoA: 42.5
  Isobutyryl-CoA: 25.1
  Benzoyl-CoA: 24.4
  Acetyl-CoA: 24.0
  Ethylmalonyl-CoA: 21.9
  2-Methylbutyryl-CoA: 19.3
  trans-1,2-CPDA: 16.6
  CHC-CoA: 15.1
  fatty_acid: 9.5
  3-Methylbutyryl-CoA: 0.0

SMF913_RS17895: mal - mal
PKS_AT (576..867): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 240.0
  inactive: 121.2
  Methoxymalonyl-CoA: 71.4
  Methylmalonyl-CoA: 68.9
  Propionyl-CoA: 44.1
  Isobutyryl-CoA: 36.3
  Acetyl-CoA: 28.5
  Ethylmalonyl-CoA: 27.8
  Benzoyl-CoA: 24.8
  2-Methylbutyryl-CoA: 22.3
  CHC-CoA: 15.3
  trans-1,2-CPDA: 14.0
  fatty_acid: 10.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2366..2658): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 241.2
  inactive: 121.1
  Methoxymalonyl-CoA: 73.3
  Methylmalonyl-CoA: 73.0
  Propionyl-CoA: 44.7
  Isobutyryl-CoA: 32.4
  Ethylmalonyl-CoA: 32.0
  Acetyl-CoA: 25.1
  2-Methylbutyryl-CoA: 24.1
  Benzoyl-CoA: 21.7
  CHC-CoA: 17.4
  trans-1,2-CPDA: 14.3
  fatty_acid: 9.3
  3-Methylbutyryl-CoA: 0.0

SMF913_RS17900: mal - mal - mal - mal - mal
PKS_AT (674..972): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 229.9
  inactive: 123.4
  Methoxymalonyl-CoA: 77.5
  Methylmalonyl-CoA: 75.1
  Isobutyryl-CoA: 48.9
  Propionyl-CoA: 39.2
  Acetyl-CoA: 35.2
  Ethylmalonyl-CoA: 27.1
  2-Methylbutyryl-CoA: 23.2
  Benzoyl-CoA: 20.1
  CHC-CoA: 14.7
  trans-1,2-CPDA: 10.2
  fatty_acid: 8.3
  3-Methylbutyryl-CoA: 5.9

PKS_AT (2224..2515): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 238.6
  inactive: 128.0
  Methylmalonyl-CoA: 66.1
  Methoxymalonyl-CoA: 65.7
  Propionyl-CoA: 42.5
  Isobutyryl-CoA: 28.4
  Acetyl-CoA: 23.1
  trans-1,2-CPDA: 22.1
  Benzoyl-CoA: 21.5
  2-Methylbutyryl-CoA: 21.5
  Ethylmalonyl-CoA: 20.7
  CHC-CoA: 11.3
  fatty_acid: 8.7
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3751..4042): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 236.4
  inactive: 121.5
  Methoxymalonyl-CoA: 67.6
  Methylmalonyl-CoA: 66.3
  Propionyl-CoA: 42.9
  Benzoyl-CoA: 25.7
  Acetyl-CoA: 24.2
  Isobutyryl-CoA: 24.1
  Ethylmalonyl-CoA: 23.3
  2-Methylbutyryl-CoA: 18.7
  CHC-CoA: 17.8
  trans-1,2-CPDA: 16.5
  fatty_acid: 9.8
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5578..5869): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 237.1
  inactive: 127.2
  Methoxymalonyl-CoA: 69.5
  Methylmalonyl-CoA: 67.6
  Propionyl-CoA: 46.1
  Ethylmalonyl-CoA: 32.3
  Isobutyryl-CoA: 31.7
  2-Methylbutyryl-CoA: 24.9
  Acetyl-CoA: 24.8
  Benzoyl-CoA: 24.2
  trans-1,2-CPDA: 19.4
  CHC-CoA: 17.9
  fatty_acid: 10.3
  3-Methylbutyryl-CoA: 0.0

PKS_AT (7120..7415): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 227.2
  inactive: 119.9
  Methoxymalonyl-CoA: 75.8
  Methylmalonyl-CoA: 75.5
  Isobutyryl-CoA: 50.5
  Propionyl-CoA: 42.2
  Ethylmalonyl-CoA: 34.1
  Acetyl-CoA: 22.6
  Benzoyl-CoA: 21.8
  2-Methylbutyryl-CoA: 19.6
  3-Methylbutyryl-CoA: 15.2
  trans-1,2-CPDA: 13.9
  CHC-CoA: 13.8
  fatty_acid: 0.0

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000001.1 - 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: 4,661,194 - 4,673,590 nt. (total: 12,397 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 oxygenase
SMF913_RS18585: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS18595: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

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
--- | --- | --- | --- | --- | ---
BGC0002584.2 |  | 0.43 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002115.3 |  | 0.41 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0000483.5 |  | 0.41 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0000477.3 |  | 0.40 | ribosomal | patellin 2, patellin 3 | uncultured Prochloron sp. 06037A
BGC0000565.5 |  | 0.40 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0002485.2 |  | 0.38 | other (other), ribosomal | muscoride A, muscoride B | Desmonostoc sp. PCC 7906
BGC0002551.2 |  | 0.38 | other (other), ribosomal, terpene | muscoride A, muscoride B | Nostoc sp. UHCC-0398
BGC0000583.5 |  | 0.38 | ribosomal | grisemycin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000193.3 |  | 0.38 | PKS | aclacinomycin | Streptomyces galilaeus
BGC0000471.4 |  | 0.37 | ribosomal | viridisamide A | Oscillatoria nigro-viridis PCC 7112

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002584.2 |  | 0.43 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002115.3 |  | 0.41 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0000483.5 |  | 0.41 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0000477.3 |  | 0.40 | ribosomal | patellin 2, patellin 3 | uncultured Prochloron sp. 06037A
BGC0000565.5 |  | 0.40 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0002485.2 |  | 0.38 | other (other), ribosomal | muscoride A, muscoride B | Desmonostoc sp. PCC 7906
BGC0002551.2 |  | 0.38 | other (other), ribosomal, terpene | muscoride A, muscoride B | Nostoc sp. UHCC-0398
BGC0000583.5 |  | 0.38 | ribosomal | grisemycin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000193.3 |  | 0.38 | PKS | aclacinomycin | Streptomyces galilaeus
BGC0000471.4 |  | 0.37 | ribosomal | viridisamide A | Oscillatoria nigro-viridis PCC 7112

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: 18.62 out of 23.79
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.07 out of 23.43
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
Additional weak hits (7):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.87 out of 29.38
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.56 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.49 out of 28.19
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.88 out of 27.18
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.94 out of 35.63
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.81 out of 23.43
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RiPP-like protocluster (4661193...4673590)
SMF913_RS18610
  RRE type: Goadsporin_CD_RRE
  Location: 3 - 106
  Score: 63.2
  RRE type: NHLP_CD_RRE
  Location: 3 - 103
  Score: 53.6
  RRE type: Cyanobactin_D_RRE
  Location: 3 - 88
  Score: 44.3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
BldD | Development and antibiotic global regulator
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000001.1 - Region 23 - HR-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: 4,680,361 - 4,730,634 nt. (total: 50,274 nt) Show pHMM detection rules used
HR-T2PKS: (hr-t2pks-ksa and (t2fas or APE_KS2 or ketoacyl-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 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
SMF913_RS18665: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

SMF913_RS18745: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS18790: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS18840: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

SMF913_RS18845: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Transferases: PPTase acylase carboxylase
SMF913_RS18720: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

SMF913_RS18730: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

SMF913_RS18765: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: amidase dehalogenase hydrolase
SMF913_RS18670: amidase

smcogs
  SMCOG1105: amidase

SMF913_RS18715: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

SMF913_RS18725: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

SMF913_RS18735: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: synthase
SMF913_RS18770: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

SMF913_RS18800: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS18815: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS18820: 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 | HR-T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000234.5 |  | 0.54 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001987.2 |  | 0.52 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0000867.3 |  | 0.51 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0002510.2 |  | 0.50 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0000218.5 |  | 0.49 | PKS | doxorubicin | Streptomyces peucetius
BGC0001177.4 |  | 0.49 | PKS | mensacaricin | Streptomyces bottropensis
BGC0002477.3 |  | 0.49 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0000225.5 |  | 0.48 | PKS | frenolicin B | Streptomyces roseofulvus
BGC0002369.2 |  | 0.48 | PKS | maduralactomycin A, maduralactomycin B, actinospirol A, actinospirol B | Actinomadura rubteroloni

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000234.5 |  | 0.54 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001987.2 |  | 0.52 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0000867.3 |  | 0.51 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0002510.2 |  | 0.50 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0000218.5 |  | 0.49 | PKS | doxorubicin | Streptomyces peucetius
BGC0001177.4 |  | 0.49 | PKS | mensacaricin | Streptomyces bottropensis
BGC0002477.3 |  | 0.49 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0000225.5 |  | 0.48 | PKS | frenolicin B | Streptomyces roseofulvus
BGC0002369.2 |  | 0.48 | PKS | maduralactomycin A, maduralactomycin B, actinospirol A, actinospirol B | Actinomadura rubteroloni

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:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.68 out of 27.04
Confidence: medium
Additional weak hits (13):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.52 out of 29.25
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.05 out of 30.97
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.77 out of 32.74
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.08 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.68 out of 27.78
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.35 out of 26.33
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.07 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.20 out of 24.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.81 out of 27.04
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.02 out of 18.57
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.79 out of 25.88
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
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).
SMF913_RS18765: mal
PKS_AT (20..306): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 107.0
  Methylmalonyl-CoA: 45.6
  Methoxymalonyl-CoA: 42.7
  Propionyl-CoA: 39.0
  inactive: 35.5
  Ethylmalonyl-CoA: 18.2
  CHC-CoA: 17.6
  trans-1,2-CPDA: 10.7
  2-Methylbutyryl-CoA: 10.3
  Acetyl-CoA: 9.3
  fatty_acid: 6.0
  Isobutyryl-CoA: 2.9
  Benzoyl-CoA: 0.7
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
DasR | N-acetylglucosamine dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000001.1 - Region 24 - 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: 4,780,519 - 4,824,529 nt. (total: 44,011 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
SMF913_RS19195: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

SMF913_RS19305: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

Hydrolases: deacetylase hydrolase
SMF913_RS19280: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

SMF913_RS19300: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

Ligases: ligase
SMF913_RS19290: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter
SMF913_RS19335: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Similar known clusters from MIBiG 4.0
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: 19.73 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.69 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.29 out of 30.11
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.00 out of 20.47
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.44 out of 27.04
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (18):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.31 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.28 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.82 out of 29.38
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 26.33
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.82 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.18 out of 27.78
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.88 out of 19.26
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.71 out of 29.25
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.91 out of 19.26
Confidence: weak
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
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.26 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.23 out of 20.01
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.05 out of 25.88
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.53 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.16 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.75 out of 33.14
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 38, location 4780518 - 4824529:
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).
SMF913_RS19290: X
AMP-binding (471..874): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    CWMTFDASVCEWQFSSGGENNLYGPTETTIQIAH
  Nearest Stachelhaus code(s):
    Gln DAWQFGLIQK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CRP | Cyclic AMP receptor protein
CelR | Cellobiose uptake repressor
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000001.1 - Region 25 - indole
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: 5,023,833 - 5,044,981 nt. (total: 21,149 nt) Show pHMM detection rules used
indole: (indsynth or dmat or indole_PTase)

#### 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
SMF913_RS20190: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS20215: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Isomerases: racemase
SMF913_RS20175: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

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 | indole | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001483.4 |  | 0.57 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0001294.5 |  | 0.56 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002643.2 |  | 0.46 | other (other) | aetokthonotoxin | Aetokthonos hydrillicola Thurmond2011
BGC0000844.5 |  | 0.46 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001911.3 |  | 0.45 | terpene | raimonol | Streptomyces anulatus
BGC0002128.3 |  | 0.45 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001910.4 |  | 0.44 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001483.4 |  | 0.57 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0001294.5 |  | 0.56 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002643.2 |  | 0.46 | other (other) | aetokthonotoxin | Aetokthonos hydrillicola Thurmond2011
BGC0000844.5 |  | 0.46 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001911.3 |  | 0.45 | terpene | raimonol | Streptomyces anulatus
BGC0002128.3 |  | 0.45 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001910.4 |  | 0.44 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus

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
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.76 out of 25.31
Confidence: medium
Additional weak hits (3):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.04 out of 25.88
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.60 out of 29.25
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CatR | H2O2-responsive repressor

NZ_LJIW01000001.1 - 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: 5,664,428 - 5,686,824 nt. (total: 22,397 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: oxidoreductase oxygenase
SMF913_RS23050: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

SMF913_RS23085: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Hydrolases: amidase
SMF913_RS23055: amidase

smcogs
  SMCOG1105: amidase

Lyases: cyclase
SMF913_RS23060: 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 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001746.3 |  | 0.75 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0000658.3 |  | 0.56 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001224.5 |  | 0.46 | other (other) | reductasporine | uncultured bacterium
BGC0001336.5 |  | 0.45 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0000851.5 |  | 0.44 | other (other) | albonoursin | Streptomyces noursei ATCC 11455
BGC0001485.4 |  | 0.43 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001223.5 |  | 0.41 | other (other) | hydroxysporine | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001746.3 |  | 0.75 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0000658.3 |  | 0.56 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001224.5 |  | 0.46 | other (other) | reductasporine | uncultured bacterium
BGC0001336.5 |  | 0.45 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0000851.5 |  | 0.44 | other (other) | albonoursin | Streptomyces noursei ATCC 11455
BGC0001485.4 |  | 0.43 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001223.5 |  | 0.41 | other (other) | hydroxysporine | uncultured bacterium

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:
SMF913_RS23060: T1TS + T1TS
Domain 1 (2 - 326): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (376 - 739): 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.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.15 out of 23.79
Confidence: medium
Additional weak hits (7):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.14 out of 27.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.98 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.93 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.47 out of 31.73
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.15 out of 30.97
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.24 out of 27.55
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
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
--- | ---
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000002.1 - Region 1 - NRPS,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: 5,774 - 66,037 nt. (total: 60,264 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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
Transferases: acyltransferase
SMF913_RS25535: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Ligases: ligase synthetase
SMF913_RS25530: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS25625: 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 | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001825.4 |  |  | 0.41 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  |  | 0.38 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  |  | 0.37 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  | 0.36 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.36 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.35 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0000342.4 |  |  | 0.35 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  |  | 0.35 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  | 0.33 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  |  | 0.33 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

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:
SMF913_RS25625: PT_FPPS_like
Domain 1 (63 - 361): 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
Additional weak hits (19):
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.88 out of 19.26
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.24 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.11 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.58 out of 29.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.30 out of 32.74
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.81 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.38 out of 29.38
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.39 out of 32.93
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.83 out of 32.93
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.42 out of 26.12
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.81 out of 25.88
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.14 out of 39.62
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.81 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.29 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.68 out of 30.98
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.48 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.87 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
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 1, location 5773 - 66037:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-X - Ser - Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 5773 - 57197:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-X - Ser - Val)

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).
SMF913_RS25530: X
AMP-binding (18..336): X
nrpys: Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    NRTPCNALVMSGSIITAAARQGYGLTEA-VNFSF
  Nearest Stachelhaus code(s):
    Tyr DAMSIGAVIK (38% 8Å match)
    Phe DAWTIAGVCK (35% 8Å match)
  Stachelhaus code match:
    60% (weak)

SMF913_RS25535: X - Ser - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (465..867): X
nrpys: Val, aIle

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:
    LDRSFDAFNLEVWLWTGGDVNGYGPTETTVFATR
  Nearest Stachelhaus code(s):
    Val or aIle DALWWGGVFK (91% 8Å match)
    Ile DALWWGGVFK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1941..2335): 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:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LVTHFDVSVWETNQVCAGEVNMYGITETTVHATY
  Nearest Stachelhaus code(s):
    Ser DVWNVAMVHK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2992..3368): 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:
    LALAFDMCKPELQAAVGGELACYGPTETTVWSTA
  Nearest Stachelhaus code(s):
    D-Ala DMPQLGMVWK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

SMF913_RS50380: mmal
PKS_AT (35..193): mmal
ATSignature: (unknown)
No matches above 50%
minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 44.2
  Methoxymalonyl-CoA: 43.5
  CHC-CoA: 33.6
  Ethylmalonyl-CoA: 32.1
  2-Methylbutyryl-CoA: 31.6
  Propionyl-CoA: 27.9
  trans-1,2-CPDA: 24.2
  Isobutyryl-CoA: 11.7
  3-Methylbutyryl-CoA: 7.6
  inactive: 0.0
  fatty_acid: 0.0
  Malonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0

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
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000002.1 - Region 2 - NRPS,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: 362,619 - 468,577 nt. (total: 105,959 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))
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
SMF913_RS27205: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS27210: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS27235: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

SMF913_RS27240: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

SMF913_RS27285: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS27310: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

SMF913_RS27355: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS27360: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS27390: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

SMF913_RS27405: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

SMF913_RS50555: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: aminotransferase
SMF913_RS27315: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: deaminase hydrolase peptidase
SMF913_RS27215: HAD-superfamily hydrolase, subfamily IA, variant

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

SMF913_RS27265: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

SMF913_RS27345: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

SMF913_RS27415: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

SMF913_RS27420: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Ligases: ligase synthase
SMF913_RS27220: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

SMF913_RS27275: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

SMF913_RS27280: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS27290: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

SMF913_RS27335: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS51020: 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 | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000342.4 |  |  |  |  | 1.39 | NRPS | enniatin | Fusarium equiseti
BGC0001250.4 |  |  |  |  | 1.34 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  |  |  |  | 1.34 | NRPS | epichloenin A | Epichloe festucae
BGC0002135.2 |  |  |  |  | 1.34 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  |  |  | 1.30 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  |  |  |  | 1.25 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001833.4 |  |  |  |  | 1.25 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000307.4 |  |  |  |  | 1.23 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001128.4 |  |  |  |  | 1.22 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  |  | 1.20 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001250.4 |  | 0.68 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.68 | NRPS | epichloenin A | Epichloe festucae
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.66 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.66 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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: 17.23 out of 19.52
Confidence: medium
Additional weak hits (7):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.69 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.43 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.73 out of 30.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.43 out of 33.14
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.33 out of 32.93
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.17 out of 32.93
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.34 out of 27.18
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 4, location 362618 - 468577:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (shikimic_acid - redemal - ccmal - ccmal - ccmal) + (Hpr) + (Me-redmal - Me-ccmal - ccmal - Me-redmal - mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 362618 - 405861:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (shikimic_acid - redemal - ccmal - ccmal - ccmal) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 375587 - 468577:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (shikimic_acid - redemal - ccmal - ccmal - ccmal) + (Hpr) + (Me-redmal - Me-ccmal - ccmal - Me-redmal - 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).
SMF913_RS27280: X
AMP-binding (9..433): 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:
    FEAFFDGSVSESMSLFGGETNCYGPTETTIVITG
  Nearest Stachelhaus code(s):
    Phe DVSTCGCIIK (62% 8Å match)
    bOH-Tyr DASTLGAICK (56% 8Å match)
  Stachelhaus code match:
    60% (weak)

SMF913_RS27290: X
AMP-binding (483..877): 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:
    LWQAFDVSFQEPFLCVSGEVNLYGPTETNAATVH
  Nearest Stachelhaus code(s):
    Aze DVQFISQIAK (68% 8Å match)
  Stachelhaus code match:
    70% (weak)

SMF913_RS51020: shikimic_acid - emal - mal - mal - mal
CAL_domain (34..439): shikimic_acid
minowa: shikimic_acid

Prediction, score:
  shikimic_acid: 505.1
  AHBA: 306.0
  fatty_acid: 0.0
  Acetyl-CoA: 0.0
  NH2: -1.8

PKS_AT (1754..2029): emal
ATSignature: Methylmalonyl-CoA, Ethylmalonyl-CoA, Methoxymalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 153.1
  Methylmalonyl-CoA: 142.3
  Methoxymalonyl-CoA: 112.8
  trans-1,2-CPDA: 67.9
  Propionyl-CoA: 61.2
  Malonyl-CoA: 59.4
  CHC-CoA: 58.2
  2-Methylbutyryl-CoA: 55.5
  Isobutyryl-CoA: 39.2
  Benzoyl-CoA: 29.6
  fatty_acid: 22.8
  Acetyl-CoA: 20.1
  inactive: 13.5
  3-Methylbutyryl-CoA: 12.2

PKS_AT (3685..3946): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 161.2
  Methoxymalonyl-CoA: 74.4
  inactive: 68.5
  Methylmalonyl-CoA: 50.2
  Isobutyryl-CoA: 30.5
  Acetyl-CoA: 23.3
  Ethylmalonyl-CoA: 18.8
  Propionyl-CoA: 14.7
  fatty_acid: 14.6
  Benzoyl-CoA: 11.9
  CHC-CoA: 11.5
  2-Methylbutyryl-CoA: 9.7
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5189..5449): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 157.7
  Methoxymalonyl-CoA: 75.9
  inactive: 69.3
  Methylmalonyl-CoA: 49.0
  Isobutyryl-CoA: 29.3
  Acetyl-CoA: 23.4
  Ethylmalonyl-CoA: 20.4
  Propionyl-CoA: 14.7
  fatty_acid: 14.6
  Benzoyl-CoA: 11.9
  CHC-CoA: 11.4
  2-Methylbutyryl-CoA: 9.5
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (6785..7048): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 160.2
  Methoxymalonyl-CoA: 73.0
  inactive: 68.2
  Methylmalonyl-CoA: 50.1
  Isobutyryl-CoA: 28.2
  Acetyl-CoA: 22.3
  Ethylmalonyl-CoA: 17.0
  Propionyl-CoA: 16.6
  fatty_acid: 14.3
  Benzoyl-CoA: 11.1
  CHC-CoA: 10.8
  2-Methylbutyryl-CoA: 9.5
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

SMF913_RS27335: Hpr
Search NORINE for peptide: strict or relaxed
AMP-binding (487..883): Hpr
nrpys: 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:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    pro (Pro)
  Single AA prediction:
    pip (Hpr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQIFDYSVQESYACQGGEHNHYGPAESQLVTGY
  Nearest Stachelhaus code(s):
    Hpr DYQYLGHLVK (94% 8Å match)
  Stachelhaus code match:
    90% (moderate)

SMF913_RS50555: mmal - mmal - mal - mmal - mal
PKS_AT (543..815): 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: 174.9
  Ethylmalonyl-CoA: 166.9
  Methoxymalonyl-CoA: 146.9
  2-Methylbutyryl-CoA: 86.6
  Malonyl-CoA: 84.3
  Propionyl-CoA: 83.8
  trans-1,2-CPDA: 83.7
  CHC-CoA: 75.2
  Isobutyryl-CoA: 63.2
  Benzoyl-CoA: 59.4
  Acetyl-CoA: 35.1
  inactive: 21.9
  fatty_acid: 21.3
  3-Methylbutyryl-CoA: 19.2

PKS_AT (2483..2776): 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: 204.2
  Ethylmalonyl-CoA: 202.4
  Methoxymalonyl-CoA: 160.3
  2-Methylbutyryl-CoA: 110.6
  Malonyl-CoA: 100.4
  Propionyl-CoA: 98.8
  trans-1,2-CPDA: 92.0
  Isobutyryl-CoA: 88.5
  CHC-CoA: 80.8
  Benzoyl-CoA: 62.0
  Acetyl-CoA: 38.6
  inactive: 30.2
  3-Methylbutyryl-CoA: 25.8
  fatty_acid: 24.7

PKS_AT (4172..4432): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 162.5
  Methoxymalonyl-CoA: 74.6
  inactive: 68.3
  Methylmalonyl-CoA: 50.1
  Isobutyryl-CoA: 31.5
  Acetyl-CoA: 21.6
  Ethylmalonyl-CoA: 20.7
  Propionyl-CoA: 18.9
  fatty_acid: 14.6
  Benzoyl-CoA: 11.7
  CHC-CoA: 11.4
  2-Methylbutyryl-CoA: 9.9
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5670..5943): 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: 172.4
  Ethylmalonyl-CoA: 158.6
  Methoxymalonyl-CoA: 144.1
  2-Methylbutyryl-CoA: 91.8
  Malonyl-CoA: 81.5
  Propionyl-CoA: 81.0
  trans-1,2-CPDA: 78.5
  CHC-CoA: 74.7
  Isobutyryl-CoA: 62.5
  Benzoyl-CoA: 56.8
  Acetyl-CoA: 34.1
  inactive: 22.5
  fatty_acid: 17.0
  3-Methylbutyryl-CoA: 15.7

PKS_AT (7635..7924): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 66.7%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 143.0
  Methoxymalonyl-CoA: 58.5
  Methylmalonyl-CoA: 54.6
  inactive: 50.0
  Isobutyryl-CoA: 28.8
  Propionyl-CoA: 27.5
  Ethylmalonyl-CoA: 27.1
  Benzoyl-CoA: 19.9
  fatty_acid: 14.0
  trans-1,2-CPDA: 11.1
  Acetyl-CoA: 9.7
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: -0.3

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_LJIW01000002.1 - Region 3 - 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: 552,127 - 599,383 nt. (total: 47,257 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
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
SMF913_RS27795: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS27860: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS27890: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

SMF913_RS27940: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: acetyltransferase
SMF913_RS27835: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Ligases: synthase
SMF913_RS27875: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS27885: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS48985: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.77 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.77 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001164.3 |  | 0.67 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.67 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001276.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002191.2 |  | 0.65 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  | 0.63 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  | 0.63 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.62 | PKS | ACT-Toxin II | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.77 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.77 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001164.3 |  | 0.67 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.67 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001276.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002191.2 |  | 0.65 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  | 0.63 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  | 0.63 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.62 | PKS | ACT-Toxin II | 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:
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: 20.38 out of 23.79
Confidence: medium
Additional weak hits (8):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.53 out of 33.73
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.19 out of 30.22
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.80 out of 30.25
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.14 out of 19.26
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.13 out of 24.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.66 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.61 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.06 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 7, location 552126 - 599383:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal)

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).
SMF913_RS27875: mal
PKS_AT (1184..1479): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 179.9
  inactive: 136.6
  Methylmalonyl-CoA: 68.1
  Methoxymalonyl-CoA: 67.6
  Propionyl-CoA: 51.3
  Isobutyryl-CoA: 49.8
  Ethylmalonyl-CoA: 26.0
  Acetyl-CoA: 22.6
  Benzoyl-CoA: 22.4
  trans-1,2-CPDA: 21.5
  2-Methylbutyryl-CoA: 19.1
  CHC-CoA: 16.3
  3-Methylbutyryl-CoA: 9.3
  fatty_acid: 9.1

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism

NZ_LJIW01000002.1 - Region 4 - NRPS,arylpolyene
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: 658,964 - 731,781 nt. (total: 72,818 nt) Show pHMM detection rules used
arylpolyene: (APE_KS1 or APE_KS2)
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 oxidoreductase oxygenase
SMF913_RS28285: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS28295: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

SMF913_RS28300: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

SMF913_RS28305: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

SMF913_RS28310: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

SMF913_RS28340: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS28410: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS28460: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS28485: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: kinase
SMF913_RS28515: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Hydrolases: deacetylase deaminase
SMF913_RS28415: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

SMF913_RS28500: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

Ligases: ligase synthase
SMF913_RS28385: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS28390: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

SMF913_RS28395: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS28420: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

SMF913_RS28440: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

SMF913_RS28445: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter
SMF913_RS28325: 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 | arylpolyene | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002510.2 |  |  | 1.77 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0002378.3 |  |  | 0.65 | NRPS | coprisamide C, coprisamide D | Streptomyces sp.
BGC0001268.4 |  |  | 0.49 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002547.2 |  |  | 0.45 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces youssoufiensis
BGC0002135.2 |  |  | 0.43 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.40 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  | 0.40 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  | 0.39 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  | 0.38 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001133.4 |  |  | 0.38 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002510.2 |  | 0.96 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002378.3 |  | 0.74 | NRPS | coprisamide C, coprisamide D | Streptomyces sp.
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001133.4 |  | 0.70 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

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:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.83 out of 26.33
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.26 out of 23.79
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.42 out of 20.47
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.31 out of 27.04
Confidence: medium
Additional weak hits (16):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.07 out of 30.97
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.35 out of 25.75
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.69 out of 29.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.28 out of 31.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.50 out of 21.55
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.82 out of 23.43
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.19 out of 25.75
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.91 out of 39.62
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.45 out of 20.97
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.45 out of 20.97
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.09 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.39 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 8, location 658963 - 731781:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Ala - D-Ser) + (D-X - Val - X - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 9, location 658963 - 700094:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-X - Val - X - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 10, location 667563 - 731781:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Ala - D-Ser) + (D-X - Val - X - 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).
SMF913_RS28440: X - Val - X - X
Search NORINE for peptide: strict or relaxed
AMP-binding (465..861): X
nrpys: 3OH-Leu, 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAAAFDAAVLEMLIVVGGDVNAYGPTESTVAATM
  Nearest Stachelhaus code(s):
    3OH-Leu DALLVGAVAK (82% 8Å match)
    Leu DALLVGAVAK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2005..2409): 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:
    LDGSFDASTYEVWLWSGGDGDGYGPTETTTFAAY
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3071..3479): X
nrpys: Dpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HAKAFDISVWQSEVMVTGEVNAYGPTECSDDVTH
  Nearest Stachelhaus code(s):
    Dpr DIWEMTADDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4142..4549): X
nrpys: bMe-Asp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YFASFDLSVTAVKALLGGELNMYGPTETTVNCSQ
  Nearest Stachelhaus code(s):
    bMe-Asp DLTKLGMVNK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

SMF913_RS28445: Ala - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (476..877): 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:
    LWATFDVSVFEGSAVLAGEANIYGPTEATVYATA
  Nearest Stachelhaus code(s):
    Ala DVFSVAIVYK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1993..2399): 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:
    RWTTFDVSVWEWHFLCSGEHNLYGPTEASVDVTS
  Nearest Stachelhaus code(s):
    Ser DVWHLSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AfsR | Pleiotropic regulatory for antibiotic production
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000002.1 - Region 5 - NRP-metallophore,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: 962,332 - 1,020,665 nt. (total: 58,334 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
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 electron transfer oxidoreductase oxygenase
SMF913_RS29660: flavodoxin

smcogs
  SMCOG1134: flavodoxin

SMF913_RS29760: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

SMF913_RS29780: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

SMF913_RS29795: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: formyltransferase
SMF913_RS29765: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

Hydrolases: dehalogenase esterase hydrolase
SMF913_RS29720: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

SMF913_RS29770: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

SMF913_RS29810: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Isomerases: mutase
SMF913_RS29835: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: ligase
SMF913_RS29730: 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 | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000325.5 |  |  | 1.10 | NRPS | coelichelin | Streptomyces coelicolor A3(2)
BGC0000357.5 |  |  | 0.69 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001825.4 |  |  | 0.62 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  |  | 0.57 | NRPS | AM-toxin | Alternaria alternata
BGC0000307.4 |  |  | 0.57 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001641.4 |  |  | 0.57 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.57 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  |  | 0.56 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.56 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001137.5 |  |  | 0.47 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000325.5 |  | 0.81 | NRPS | coelichelin | Streptomyces coelicolor A3(2)
BGC0000357.5 |  | 0.68 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  | 0.62 | NRPS | AM-toxin | Alternaria alternata
BGC0000307.4 |  | 0.62 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.62 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.61 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.61 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001137.5 |  | 0.57 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans

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: 17.13 out of 19.26
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 30.12 out of 30.12
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 27.49 out of 30.12
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.37 out of 30.12
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.90 out of 30.12
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 33.36 out of 36.53
Confidence: strong
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.05 out of 22.40
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.30 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.84 out of 36.53
Confidence: medium
Additional weak hits (15):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.36 out of 29.51
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.14 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.87 out of 27.78
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.70 out of 26.33
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 26.02 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.24 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.25 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.99 out of 36.53
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.95 out of 39.62
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.12 out of 36.53
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.61 out of 23.43
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.27 out of 20.01
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.81 out of 21.84
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 962331 - 1020665:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

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).
SMF913_RS29730: Fo-OH-Orn - Thr - OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (144..542): Fo-OH-Orn
nrpys: Fo-OH-Orn

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWQAFDISINELYLWCGGEYHGYGPAETTIGVSH
  Nearest Stachelhaus code(s):
    Fo-OH-Orn DINYWGGIGK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1625..2037): 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:
    LNTHFDFAVWEGNQIFGGEVNMYGITETTVHVTH
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3050..3450): OH-Orn
nrpys: OH-Orn

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    MNHVFDMSWEEWNVLLGGEYNLYGPTEYTINTLG
  Nearest Stachelhaus code(s):
    OH-Orn DMENLGLINK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
DmdR1 | Iron(II)-dependent repressor
HypR | L-hydroxyproline utilization repressor
OsdR | Development and stress management regulator

NZ_LJIW01000002.1 - Region 6 - NRPS,NRPS-like,T1PKS,T3PKS,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: 1,044,703 - 1,165,355 nt. (total: 120,653 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)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
betalactone: (HMGL-like and AMP-binding)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
SMF913_RS30050: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

SMF913_RS30055: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS30205: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS30240: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

SMF913_RS30245: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

SMF913_RS30250: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

SMF913_RS30315: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: aminotransferase halogenase methyltransferase sulfotransferase
SMF913_RS30040: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

SMF913_RS30045: Sulfotransferase domain

extras
  Sulfotransfer_1: Sulfotransferase domain

SMF913_RS30060: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

SMF913_RS30075: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

SMF913_RS30110: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: esterase hydrolase
SMF913_RS30030: thioesterase

smcogs
  SMCOG1004: thioesterase

SMF913_RS30260: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: hydratase lyase
SMF913_RS30005: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

SMF913_RS30015: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

SMF913_RS30115: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

SMF913_RS30120: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Isomerases: racemase
SMF913_RS30305: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase synthase
SMF913_RS30020: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

SMF913_RS30065: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS30070: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS30090: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

SMF913_RS30225: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

SMF913_RS48235: 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-like | NRPS | betalactone | T1PKS | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002341.2 |  |  |  |  |  | 1.45 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0001132.4 |  |  |  |  |  | 1.38 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  |  |  | 1.38 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002608.2 |  |  |  |  |  | 1.35 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0001833.4 |  |  |  |  |  | 1.34 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  |  |  |  | 1.33 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  |  |  |  | 1.31 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001050.5 |  |  |  |  |  | 1.29 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0002135.2 |  |  |  |  |  | 1.26 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  |  |  |  | 1.23 | NRPS | AM-toxin | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002341.2 |  | 0.77 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0001132.4 |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.76 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001275.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0002608.2 |  | 0.75 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0001273.3 |  | 0.75 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.75 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.74 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

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: 18.37 out of 20.47
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.87 out of 29.72
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
Additional weak hits (5):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.00 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.26 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.26 out of 26.06
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.84 out of 32.38
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 12, location 1044702 - 1154931:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal - Me-ccmal) + (Me-redmal - ohmal) + (Thr - Ala - Dab - Val - Ile) + (Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 13, location 1044702 - 1087927:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly) + (Thr - Ala - Dab - Val - Ile)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 14, location 1048142 - 1106970:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-redmal - ohmal) + (Thr - Ala - Dab - Val - Ile) + (Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 15, location 1077708 - 1154931:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal - Me-ccmal) + (Me-redmal - ohmal) + (Thr - Ala - Dab - Val - Ile)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 16, location 1124281 - 1165355:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal - Me-ccmal)

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).
SMF913_RS30065: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (147..550): Gly
nrpys: Gly

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:
    HAKAFDISLWQSQVAVTGEVNCYGLTEVSDDSNH
  Nearest Stachelhaus code(s):
    Gly DIWQATCDDK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

SMF913_RS30070: Thr - Ala - Dab - Val - Ile
Search NORINE for peptide: strict or relaxed
AMP-binding (470..887): 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:
    LTAHFDFSVWEGSQVFGGEVNMYGITETTVHVTH
  Nearest Stachelhaus code(s):
    Thr DFWSVGMVHK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1595..1992): Ala
nrpys: Ala

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:
    Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LFRAFDVATWETQLLVAGEGNAYGPTEITVIAAA
  Nearest Stachelhaus code(s):
    Ala DVWQLAAVIK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3295..3690): Dab
nrpys: Dab

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:
    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:
    LDRAFDGSTVEVHMLTGADRSSYGPTEVTVIGTQ
  Nearest Stachelhaus code(s):
    Dab DGVHLGSVIK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4370..4773): 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:
    LPAAFDCTTFEIVLLTGGDINGYGPTESTTYTHS
  Nearest Stachelhaus code(s):
    Dhpg or cl-me-dHpg DSFLLGGTYK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (5444..5858): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    QWMAFDASVWEWQLLCIGEHNLYGPTEASVAVTS
  Nearest Stachelhaus code(s):
    Ile DAWQLLLVAK (91% 8Å match)
  Stachelhaus code match:
    90% (moderate)

SMF913_RS48235: mmal - mal
PKS_AT (557..851): 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: 192.7
  Ethylmalonyl-CoA: 182.9
  Methoxymalonyl-CoA: 155.7
  2-Methylbutyryl-CoA: 128.1
  trans-1,2-CPDA: 122.6
  Propionyl-CoA: 102.3
  CHC-CoA: 88.5
  Malonyl-CoA: 73.2
  Isobutyryl-CoA: 56.0
  Benzoyl-CoA: 49.1
  Acetyl-CoA: 25.3
  inactive: 22.9
  fatty_acid: 22.2
  3-Methylbutyryl-CoA: 16.6

PKS_AT (2675..2970): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 198.8
  inactive: 96.8
  Methoxymalonyl-CoA: 56.0
  Methylmalonyl-CoA: 43.6
  Propionyl-CoA: 37.8
  Isobutyryl-CoA: 19.5
  Acetyl-CoA: 16.9
  Ethylmalonyl-CoA: 15.3
  Benzoyl-CoA: 10.7
  fatty_acid: 10.4
  2-Methylbutyryl-CoA: 7.1
  trans-1,2-CPDA: 4.1
  CHC-CoA: 1.2
  3-Methylbutyryl-CoA: 0.0

SMF913_RS49010: mal - mmal - mmal
PKS_AT (549..799): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 44.9
  inactive: 9.7
  Acetyl-CoA: 9.6
  Propionyl-CoA: 4.4
  Methoxymalonyl-CoA: 0.4
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0
  Methylmalonyl-CoA: -0.2

PKS_AT (1511..1806): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 196.5
  Ethylmalonyl-CoA: 187.6
  Methoxymalonyl-CoA: 148.3
  trans-1,2-CPDA: 116.3
  2-Methylbutyryl-CoA: 112.7
  Propionyl-CoA: 102.8
  Malonyl-CoA: 98.9
  CHC-CoA: 98.9
  Isobutyryl-CoA: 71.4
  Benzoyl-CoA: 65.6
  Acetyl-CoA: 51.9
  inactive: 33.4
  fatty_acid: 29.9
  3-Methylbutyryl-CoA: 19.4

PKS_AT (3289..3511): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 166.5
  Ethylmalonyl-CoA: 163.7
  Methoxymalonyl-CoA: 132.1
  trans-1,2-CPDA: 101.5
  CHC-CoA: 97.5
  2-Methylbutyryl-CoA: 92.9
  Propionyl-CoA: 82.6
  Malonyl-CoA: 75.8
  Benzoyl-CoA: 58.2
  Isobutyryl-CoA: 54.9
  Acetyl-CoA: 34.8
  inactive: 28.4
  fatty_acid: 25.3
  3-Methylbutyryl-CoA: 13.6

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
NtrC | Nitrogen regulatory protein C
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000002.1 - Region 7 - 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: 1,280,067 - 1,291,062 nt. (total: 10,996 nt) Show pHMM detection rules used
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
Lyases: dehydratase
SMF913_RS30825: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

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
--- | --- | --- | --- | --- | ---
BGC0001458.4 |  | 0.53 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0000850.5 |  | 0.51 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.38 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002584.2 |  | 0.37 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002443.3 |  | 0.32 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0000528.5 |  | 0.32 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002386.2 |  | 0.32 | NRPS, PKS | cyclo(n-Me-L-Leu-L-Val), cyclo(n-Me-L-Leu-L-Leu), cyclo(n-Me-L-Leu-L-Ile) | Sorangium cellulosum So0157-2
BGC0002316.2 |  | 0.32 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000219.4 |  | 0.31 | PKS, saccharide | elloramycin | Streptomyces olivaceus
BGC0002805.2 |  | 0.31 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001458.4 |  | 0.53 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0000850.5 |  | 0.51 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.38 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002584.2 |  | 0.37 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002443.3 |  | 0.32 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0000528.5 |  | 0.32 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002386.2 |  | 0.32 | NRPS, PKS | cyclo(n-Me-L-Leu-L-Val), cyclo(n-Me-L-Leu-L-Leu), cyclo(n-Me-L-Leu-L-Ile) | Sorangium cellulosum So0157-2
BGC0002316.2 |  | 0.32 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000219.4 |  | 0.31 | PKS, saccharide | elloramycin | Streptomyces olivaceus
BGC0002805.2 |  | 0.31 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A

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 (2):
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.62 out of 29.65
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.58 out of 20.01
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LJIW01000002.1 - Region 8 - 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: 1,321,466 - 1,409,740 nt. (total: 88,275 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
SMF913_RS30965: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

SMF913_RS31065: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

SMF913_RS31080: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

SMF913_RS31155: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Hydrolases: deaminase hydrolase
SMF913_RS31020: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

SMF913_RS31030: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

SMF913_RS31170: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: lyase
SMF913_RS31090: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

SMF913_RS31095: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase
SMF913_RS30960: cobalamin synthesis protein/P47K family protein

smcogs
  SMCOG1178: cobalamin synthesis protein/P47K family protein

SMF913_RS31040: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS31045: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS31050: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS31070: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS31085: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS31100: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

Translocases: transport
SMF913_RS31025: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport 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 | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001833.4 |  |  | 0.86 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  |  | 0.85 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  |  | 0.83 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  |  | 0.82 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  |  | 0.81 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.81 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  | 0.80 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  |  | 0.78 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  |  | 0.78 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  |  | 0.78 | NRPS | enniatin | Fusarium equiseti

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.77 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.77 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.74 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4 |  | 0.74 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001825.4 |  | 0.74 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

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:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.88 out of 20.97
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.88 out of 27.04
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31
Confidence: medium
Additional weak hits (14):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.32 out of 20.97
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.41 out of 36.54
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.81 out of 26.12
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.60 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.81 out of 26.06
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.59 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.52 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.67 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.79 out of 30.97
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.34 out of 39.62
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.14 out of 21.55
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.63 out of 27.18
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.49 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 18, location 1321465 - 1409740:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu - Pro) + (Gly - X - Gly - X - Gly - D-Thr) + (X - D-Hpr) + (Asp)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 19, location 1321465 - 1399224:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu - Pro) + (Gly - X - Gly - X - Gly - D-Thr) + (X - D-Hpr) + (Asp)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 20, location 1366449 - 1409740:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly - X - Gly - X - Gly - D-Thr) + (X - D-Hpr) + (Asp)

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).
SMF913_RS31040: Leu - Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (468..864): 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:
    val (Val)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRSFDASTYEVFLWTGGEVDVYGPTETTTFAVR
  Nearest Stachelhaus code(s):
    Leu DAYFWGVTFK (94% 8Å match)
    Val DAYFWGVTFK (91% 8Å match)
    Ile DAYFWGVTFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1539..1952): 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:
    LWHTFDVSVQESYAVQAGEHNHYGPAETHVVTAC
  Nearest Stachelhaus code(s):
    Pro DVQYVAHVVK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

SMF913_RS31045: Gly - X - Gly - X - Gly - Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (466..865): 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:
    FAMTFDIAGLEVQALVGGETNMYGPTETTIWSTA
  Nearest Stachelhaus code(s):
    Gly DILQLGMIWK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1532..1906): X
nrpys: Dpr

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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    YRASFDLTVTATKVITGGEVNAYGPTEATVNCAD
  Nearest Stachelhaus code(s):
    Dpr DLTKIGAVNK (94% 8Å match)
    Asp DLTKIGAVNK (79% 8Å match)
    OH-Asp or OMe-Asp DLTKIGAVNK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2571..2971): 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:
    FSMTFDIAGLEVQALVGGETNLYGPTETTIWSTA
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3637..4011): X
nrpys: Dpr

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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    YRASFDLTVTATKVITGGEVNAYGPTEATVNCAD
  Nearest Stachelhaus code(s):
    Dpr DLTKIGAVNK (94% 8Å match)
    Asp DLTKIGAVNK (79% 8Å match)
    OH-Asp or OMe-Asp DLTKIGAVNK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4677..5075): 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:
    FSMTFDIAGLEVQALVGGETNLYGPTETTIWSTA
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5797..6185): 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:
    LSTHFDFSVWEGNQVFGGEVNMYGITETTVHVTH
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
    Val DFWNVGMVHK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

SMF913_RS31050: X - Hpr
Search NORINE for peptide: strict or relaxed
AMP-binding (479..853): X
nrpys: Dpr

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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    YRASFDLTVTATKVITGGEVNAYGPTEATVNCAD
  Nearest Stachelhaus code(s):
    Dpr DLTKIGAVNK (94% 8Å match)
    Asp DLTKIGAVNK (79% 8Å match)
    OH-Asp or OMe-Asp DLTKIGAVNK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2187..2598): Hpr
nrpys: 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:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    pro (Pro)
  Single AA prediction:
    pip (Hpr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHLFDFAVQEQFAFQGGEHNIYGPAETHAATST
  Nearest Stachelhaus code(s):
    Hpr DFQFFGIAAK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

SMF913_RS31070: NH2
CAL_domain (42..470): NH2
minowa: NH2

Prediction, score:
  NH2: 129.1
  fatty_acid: 28.5
  Acetyl-CoA: 10.6
  AHBA: 10.4
  shikimic_acid: 0.0

SMF913_RS31085: Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (246..653): Asp
nrpys: Asp

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:
    HAKAFDISLWQAQVSVTGEVNAYGATETSDDPMH
  Nearest Stachelhaus code(s):
    Asp DIWQSTADDK (91% 8Å match)
    dnmeProp or Dab DIWQSTADDK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CatR | H2O2-responsive repressor
CcpA | Catabolite control protein A
DasR | N-acetylglucosamine dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000002.1 - Region 9 - 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: 1,435,569 - 1,573,992 nt. (total: 138,424 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
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
SMF913_RS31345: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

SMF913_RS31385: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS31480: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acylase
SMF913_RS31425: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

SMF913_RS31445: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Lyases: hydratase
SMF913_RS31375: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

Ligases: ligase synthase
SMF913_RS31430: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS31435: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS31450: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

SMF913_RS31455: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS31460: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS31465: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS31470: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: permease
SMF913_RS31370: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001523.5 |  | 0.83 | PKS | azalomycin F3a | Streptomyces sp. 211726
BGC0001273.3 |  | 0.73 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001700.5 |  | 0.70 | PKS | niphimycin C, niphimycin D, niphimycin E, 17-O-methylniphimycin, niphimycin Iα, 19-O-malonylniphimycin | Streptomyces sp. IMB7-145
BGC0000041.3 |  | 0.68 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000018.5 |  | 0.68 | PKS | angolamycin | Streptomyces eurythermus
BGC0000067.5 |  | 0.66 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001523.5 |  | 0.83 | PKS | azalomycin F3a | Streptomyces sp. 211726
BGC0001273.3 |  | 0.73 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001700.5 |  | 0.70 | PKS | niphimycin C, niphimycin D, niphimycin E, 17-O-methylniphimycin, niphimycin Iα, 19-O-malonylniphimycin | Streptomyces sp. IMB7-145
BGC0000041.3 |  | 0.68 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000018.5 |  | 0.68 | PKS | angolamycin | Streptomyces eurythermus
BGC0000067.5 |  | 0.66 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822

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: 19.14 out of 23.79
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 23.24 out of 27.18
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: 18.71 out of 23.79
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.04 out of 18.57
Confidence: medium
Additional weak hits (19):
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.04 out of 19.26
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.75 out of 29.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.19 out of 18.57
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.73 out of 29.25
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.43 out of 26.85
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.88 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.48 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.14 out of 30.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.50 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.22 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.65 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.45 out of 30.25
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.28 out of 36.53
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.58 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.94 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.28 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 out of 28.19
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52
Confidence: weak
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 21, location 1435568 - 1573992:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (redmal) + (pk - ohmal) + (Me-ccmal - pk - ccmal) + (ohmal - ohmal - ohmal) + (ohmal - ohmal - mal - pk - redmal) + (pk - ohmal) + (pk - ccmal) + (pk)
Non-colinear ordering:
  SMF913_RS31435 + SMF913_RS31465 + SMF913_RS31470 + SMF913_RS31460 + SMF913_RS31455 + SMF913_RS31450 + SMF913_RS31445 + SMF913_RS31440

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).
SMF913_RS31425: pk
PKS_AT (26..305): pk
ATSignature: (unknown)
No matches above 50%
minowa: trans-1,2-CPDA

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

SMF913_RS31430: X
AMP-binding (10..375): 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:
    NRNLHQYGLSMIDACSGAALDSYGSTEAGNVSFA
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

SMF913_RS31435: mal
PKS_AT (672..975): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 234.2
  inactive: 138.2
  Methoxymalonyl-CoA: 75.5
  Methylmalonyl-CoA: 63.8
  Isobutyryl-CoA: 36.8
  Ethylmalonyl-CoA: 29.9
  Propionyl-CoA: 26.0
  Benzoyl-CoA: 21.6
  Acetyl-CoA: 15.8
  trans-1,2-CPDA: 14.0
  2-Methylbutyryl-CoA: 12.3
  fatty_acid: 11.6
  CHC-CoA: 9.4
  3-Methylbutyryl-CoA: 0.0

SMF913_RS31440: pk
PKS_AT (578..876): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 230.3
  Methylmalonyl-CoA: 228.3
  Methoxymalonyl-CoA: 181.9
  2-Methylbutyryl-CoA: 160.3
  trans-1,2-CPDA: 126.5
  Propionyl-CoA: 116.2
  CHC-CoA: 113.9
  Malonyl-CoA: 112.7
  Isobutyryl-CoA: 80.4
  Benzoyl-CoA: 61.5
  3-Methylbutyryl-CoA: 50.2
  inactive: 49.1
  Acetyl-CoA: 43.3
  fatty_acid: 27.6

SMF913_RS31445: pk - mal
PKS_AT (569..867): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 233.0
  Methylmalonyl-CoA: 230.2
  Methoxymalonyl-CoA: 186.6
  2-Methylbutyryl-CoA: 157.0
  trans-1,2-CPDA: 134.6
  CHC-CoA: 119.5
  Malonyl-CoA: 116.1
  Propionyl-CoA: 115.3
  Isobutyryl-CoA: 82.5
  Benzoyl-CoA: 60.1
  3-Methylbutyryl-CoA: 46.8
  inactive: 44.4
  Acetyl-CoA: 40.8
  fatty_acid: 32.5

PKS_AT (2139..2442): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 244.1
  inactive: 118.5
  Methoxymalonyl-CoA: 76.7
  Methylmalonyl-CoA: 68.0
  Propionyl-CoA: 40.3
  Isobutyryl-CoA: 32.6
  Ethylmalonyl-CoA: 24.3
  Acetyl-CoA: 20.3
  2-Methylbutyryl-CoA: 19.1
  Benzoyl-CoA: 17.3
  CHC-CoA: 10.5
  fatty_acid: 10.0
  trans-1,2-CPDA: 9.4
  3-Methylbutyryl-CoA: 0.0

SMF913_RS31450: pk - mal
PKS_AT (566..864): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 231.0
  Methylmalonyl-CoA: 230.0
  Methoxymalonyl-CoA: 186.5
  2-Methylbutyryl-CoA: 156.8
  trans-1,2-CPDA: 135.0
  CHC-CoA: 118.5
  Malonyl-CoA: 118.2
  Propionyl-CoA: 117.2
  Isobutyryl-CoA: 84.9
  Benzoyl-CoA: 62.3
  3-Methylbutyryl-CoA: 49.9
  inactive: 49.8
  Acetyl-CoA: 40.7
  fatty_acid: 31.8

PKS_AT (2117..2418): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 241.3
  inactive: 112.4
  Methoxymalonyl-CoA: 70.8
  Methylmalonyl-CoA: 62.4
  Propionyl-CoA: 39.4
  Isobutyryl-CoA: 30.0
  Ethylmalonyl-CoA: 29.1
  Acetyl-CoA: 21.7
  Benzoyl-CoA: 18.6
  fatty_acid: 16.3
  2-Methylbutyryl-CoA: 13.5
  trans-1,2-CPDA: 12.3
  CHC-CoA: 11.2
  3-Methylbutyryl-CoA: 0.0

SMF913_RS31455: mal - mal - mal - pk - mal
PKS_AT (568..869): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 244.9
  inactive: 122.5
  Methoxymalonyl-CoA: 80.8
  Methylmalonyl-CoA: 68.8
  Propionyl-CoA: 35.7
  Isobutyryl-CoA: 31.3
  Ethylmalonyl-CoA: 24.5
  Acetyl-CoA: 22.3
  Benzoyl-CoA: 22.0
  2-Methylbutyryl-CoA: 13.9
  trans-1,2-CPDA: 13.7
  fatty_acid: 13.7
  CHC-CoA: 13.7
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2121..2422): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 242.2
  inactive: 118.8
  Methoxymalonyl-CoA: 73.9
  Methylmalonyl-CoA: 66.1
  Propionyl-CoA: 37.2
  Isobutyryl-CoA: 31.9
  Acetyl-CoA: 24.2
  Ethylmalonyl-CoA: 22.8
  Benzoyl-CoA: 18.5
  fatty_acid: 13.4
  2-Methylbutyryl-CoA: 12.7
  trans-1,2-CPDA: 11.6
  CHC-CoA: 9.6
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3675..3981): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 239.8
  inactive: 125.5
  Methoxymalonyl-CoA: 79.3
  Methylmalonyl-CoA: 69.8
  Propionyl-CoA: 38.5
  Isobutyryl-CoA: 32.0
  Ethylmalonyl-CoA: 30.9
  trans-1,2-CPDA: 21.1
  Benzoyl-CoA: 20.1
  Acetyl-CoA: 20.0
  fatty_acid: 18.0
  2-Methylbutyryl-CoA: 12.5
  CHC-CoA: 11.2
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5032..5330): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 231.7
  Methylmalonyl-CoA: 229.4
  Methoxymalonyl-CoA: 185.0
  2-Methylbutyryl-CoA: 153.1
  trans-1,2-CPDA: 133.1
  Malonyl-CoA: 115.7
  CHC-CoA: 114.7
  Propionyl-CoA: 114.1
  Isobutyryl-CoA: 88.4
  Benzoyl-CoA: 65.6
  3-Methylbutyryl-CoA: 47.4
  inactive: 46.5
  Acetyl-CoA: 41.5
  fatty_acid: 28.1

PKS_AT (6606..6908): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 91.7%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 241.1
  inactive: 120.3
  Methoxymalonyl-CoA: 77.1
  Methylmalonyl-CoA: 67.9
  Propionyl-CoA: 33.1
  Isobutyryl-CoA: 30.6
  Acetyl-CoA: 25.2
  Benzoyl-CoA: 18.7
  Ethylmalonyl-CoA: 18.6
  fatty_acid: 16.7
  trans-1,2-CPDA: 13.0
  2-Methylbutyryl-CoA: 12.0
  CHC-CoA: 7.0
  3-Methylbutyryl-CoA: 0.0

SMF913_RS31460: mal - mal - mal
PKS_AT (573..875): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 91.7%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 250.8
  inactive: 123.9
  Methoxymalonyl-CoA: 77.0
  Methylmalonyl-CoA: 67.8
  Propionyl-CoA: 38.3
  Isobutyryl-CoA: 32.8
  Ethylmalonyl-CoA: 27.5
  Acetyl-CoA: 23.6
  Benzoyl-CoA: 19.5
  fatty_acid: 15.2
  2-Methylbutyryl-CoA: 14.8
  trans-1,2-CPDA: 14.1
  CHC-CoA: 7.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2125..2426): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 248.8
  inactive: 121.9
  Methoxymalonyl-CoA: 74.4
  Methylmalonyl-CoA: 67.0
  Propionyl-CoA: 37.4
  Isobutyryl-CoA: 35.8
  Ethylmalonyl-CoA: 26.6
  Acetyl-CoA: 25.4
  Benzoyl-CoA: 18.4
  2-Methylbutyryl-CoA: 16.5
  fatty_acid: 13.1
  trans-1,2-CPDA: 11.1
  CHC-CoA: 8.7
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3678..3981): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 91.7%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 228.8
  inactive: 120.5
  Methoxymalonyl-CoA: 71.1
  Methylmalonyl-CoA: 59.9
  Propionyl-CoA: 36.0
  Isobutyryl-CoA: 34.0
  Benzoyl-CoA: 31.4
  Ethylmalonyl-CoA: 23.2
  Acetyl-CoA: 19.5
  2-Methylbutyryl-CoA: 18.4
  fatty_acid: 14.4
  trans-1,2-CPDA: 8.2
  CHC-CoA: 8.2
  3-Methylbutyryl-CoA: 0.0

SMF913_RS31465: pk - mal
PKS_AT (565..863): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 232.4
  Methylmalonyl-CoA: 231.5
  Methoxymalonyl-CoA: 187.9
  2-Methylbutyryl-CoA: 150.7
  trans-1,2-CPDA: 133.9
  Malonyl-CoA: 114.5
  Propionyl-CoA: 113.2
  CHC-CoA: 108.3
  Isobutyryl-CoA: 87.5
  Benzoyl-CoA: 64.0
  Acetyl-CoA: 44.0
  3-Methylbutyryl-CoA: 43.0
  inactive: 38.9
  fatty_acid: 26.8

PKS_AT (2295..2596): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 91.7%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 241.1
  inactive: 120.1
  Methoxymalonyl-CoA: 74.3
  Methylmalonyl-CoA: 60.7
  Isobutyryl-CoA: 34.3
  Propionyl-CoA: 33.9
  Acetyl-CoA: 25.4
  Benzoyl-CoA: 18.1
  Ethylmalonyl-CoA: 16.0
  2-Methylbutyryl-CoA: 10.2
  fatty_acid: 9.7
  CHC-CoA: 4.9
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

SMF913_RS31470: mmal - pk - mal
PKS_AT (573..871): 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: 229.3
  Ethylmalonyl-CoA: 228.7
  Methoxymalonyl-CoA: 185.7
  2-Methylbutyryl-CoA: 152.8
  trans-1,2-CPDA: 130.3
  Malonyl-CoA: 114.8
  Propionyl-CoA: 110.8
  CHC-CoA: 103.4
  Isobutyryl-CoA: 85.9
  Benzoyl-CoA: 63.7
  3-Methylbutyryl-CoA: 47.4
  Acetyl-CoA: 45.5
  inactive: 37.5
  fatty_acid: 36.9

PKS_AT (2303..2601): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 232.3
  Methylmalonyl-CoA: 230.7
  Methoxymalonyl-CoA: 188.1
  2-Methylbutyryl-CoA: 150.5
  trans-1,2-CPDA: 138.8
  Malonyl-CoA: 116.9
  Propionyl-CoA: 113.9
  CHC-CoA: 105.9
  Isobutyryl-CoA: 85.6
  Benzoyl-CoA: 64.3
  inactive: 45.9
  3-Methylbutyryl-CoA: 45.3
  Acetyl-CoA: 39.0
  fatty_acid: 33.1

PKS_AT (3863..4166): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 224.1
  inactive: 114.7
  Methoxymalonyl-CoA: 74.8
  Methylmalonyl-CoA: 65.6
  Isobutyryl-CoA: 39.6
  Propionyl-CoA: 38.2
  Acetyl-CoA: 31.5
  Ethylmalonyl-CoA: 21.9
  2-Methylbutyryl-CoA: 18.8
  fatty_acid: 18.4
  Benzoyl-CoA: 13.7
  CHC-CoA: 7.9
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
IolR | Regulator of the inositol catabolism
NrdR | Represses ribonucleotide reductase encoding genes
ToxT | Regulator of MSHA biosynthesis

NZ_LJIW01000002.1 - Region 10 - 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: 1,786,623 - 1,961,609 nt. (total: 174,987 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
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Gene details
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
SMF913_RS32540: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

SMF913_RS32555: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS32640: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

SMF913_RS32645: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

SMF913_RS32705: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS32730: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

SMF913_RS32740: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

SMF913_RS50625: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase aminotransferase kinase methyltransferase
SMF913_RS32520: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

SMF913_RS32525: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

SMF913_RS32565: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

SMF913_RS32585: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

SMF913_RS32595: methyltransferase

smcogs
  SMCOG1089: methyltransferase

SMF913_RS32680: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

SMF913_RS32760: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: dehalogenase esterase
SMF913_RS32560: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

SMF913_RS32695: thioesterase

smcogs
  SMCOG1004: thioesterase

Isomerases: isomerase
SMF913_RS32765: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
SMF913_RS32485: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS32570: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS32575: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS32580: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS32590: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

SMF913_RS32745: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS49040: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS49045: 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 | T1PKS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000114.5 |  |  | 0.82 | PKS | nigericin | Streptomyces violaceusniger
BGC0001276.3 |  |  | 0.77 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  |  | 0.65 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  |  | 0.61 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002191.2 |  |  | 0.60 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001164.3 |  |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001254.3 |  |  | 0.56 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002192.3 |  |  | 0.56 | PKS | FR901512 | fungal sp. No.14919

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000114.5 |  | 0.91 | PKS | nigericin | Streptomyces violaceusniger
BGC0001276.3 |  | 0.77 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.67 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  | 0.66 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001160.5 |  | 0.66 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002038.2 |  | 0.66 | PKS | nigericin | Streptomyces sp. DASNCL29
BGC0001164.3 |  | 0.66 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002191.2 |  | 0.64 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1

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:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
Additional weak hits (20):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.55 out of 26.06
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.29 out of 27.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.91 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.74 out of 27.78
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.36 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.79 out of 23.43
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.77 out of 24.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.15 out of 28.14
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.95 out of 32.93
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.90 out of 29.65
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.55 out of 18.57
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.27 out of 20.01
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.08 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.08 out of 26.06
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: 19.95 out of 26.85
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.01 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 22, location 1786622 - 1961609:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal - Me-mal) + (Me-redmal) + (ccmal - Me-redmal) + (Me-ccmal - redmal) + (Me-ccmal - Me-redmal) + (Me-ohmal) + (ohmal - ohmal) + (ohmal) + (Me-redmal) + (Me-ccmal) + (Me-redmal)
Non-colinear ordering:
  SMF913_RS32590 + SMF913_RS32585 + SMF913_RS32580 + SMF913_RS32575 + SMF913_RS32570 + SMF913_RS32565 + SMF913_RS50625 + SMF913_RS49040 + SMF913_RS32520 + SMF913_RS32525 + SMF913_RS32740

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 23, location 1786622 - 1920020:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal - Me-mal) + (Me-redmal) + (ccmal - Me-redmal) + (Me-ccmal - redmal) + (Me-ccmal - Me-redmal) + (Me-ohmal) + (ohmal - ohmal) + (ohmal) + (Me-redmal) + (Me-ccmal)
Non-colinear ordering:
  SMF913_RS32590 + SMF913_RS32585 + SMF913_RS32580 + SMF913_RS32575 + SMF913_RS32570 + SMF913_RS32565 + SMF913_RS50625 + SMF913_RS49040 + SMF913_RS32520 + SMF913_RS32525

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 24, location 1915180 - 1961609:
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).
SMF913_RS32485: X
AMP-binding (27..439): 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:
    FYQAWAYGYFAGAASAAGERDHYGSTELGMVVAH
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

SMF913_RS50625: mal - mal
PKS_AT (574..875): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 169.3
  inactive: 74.9
  Methoxymalonyl-CoA: 57.0
  Methylmalonyl-CoA: 52.3
  Isobutyryl-CoA: 31.7
  fatty_acid: 29.7
  Propionyl-CoA: 29.0
  Ethylmalonyl-CoA: 18.3
  2-Methylbutyryl-CoA: 17.8
  Acetyl-CoA: 15.9
  Benzoyl-CoA: 14.8
  trans-1,2-CPDA: 12.2
  CHC-CoA: 9.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2140..2427): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 177.2
  inactive: 75.1
  Methoxymalonyl-CoA: 65.9
  Methylmalonyl-CoA: 57.3
  Propionyl-CoA: 34.1
  fatty_acid: 33.4
  Ethylmalonyl-CoA: 21.7
  2-Methylbutyryl-CoA: 21.3
  Isobutyryl-CoA: 19.8
  trans-1,2-CPDA: 13.3
  Acetyl-CoA: 11.5
  Benzoyl-CoA: 11.0
  CHC-CoA: 9.2
  3-Methylbutyryl-CoA: 0.0

SMF913_RS49040: mal
PKS_AT (1314..1607): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 171.0
  inactive: 73.0
  Methoxymalonyl-CoA: 65.9
  Methylmalonyl-CoA: 58.5
  fatty_acid: 38.5
  Propionyl-CoA: 32.3
  Ethylmalonyl-CoA: 26.0
  Isobutyryl-CoA: 22.9
  2-Methylbutyryl-CoA: 20.0
  Acetyl-CoA: 17.6
  trans-1,2-CPDA: 11.9
  Benzoyl-CoA: 11.6
  CHC-CoA: 10.3
  3-Methylbutyryl-CoA: 0.0

SMF913_RS32520: mmal
PKS_AT (577..877): 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: 204.4
  Ethylmalonyl-CoA: 192.1
  Methoxymalonyl-CoA: 170.7
  2-Methylbutyryl-CoA: 146.8
  trans-1,2-CPDA: 123.3
  Propionyl-CoA: 120.8
  Malonyl-CoA: 102.2
  CHC-CoA: 89.4
  Isobutyryl-CoA: 71.1
  fatty_acid: 52.5
  Benzoyl-CoA: 48.7
  Acetyl-CoA: 43.6
  3-Methylbutyryl-CoA: 36.6
  inactive: 17.2

SMF913_RS32525: mmal
PKS_AT (576..876): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 205.3
  Ethylmalonyl-CoA: 197.2
  Methoxymalonyl-CoA: 170.2
  2-Methylbutyryl-CoA: 148.0
  trans-1,2-CPDA: 125.5
  Propionyl-CoA: 121.3
  Malonyl-CoA: 102.0
  CHC-CoA: 95.0
  Isobutyryl-CoA: 70.3
  fatty_acid: 50.1
  Acetyl-CoA: 48.3
  Benzoyl-CoA: 46.2
  3-Methylbutyryl-CoA: 39.0
  inactive: 17.7

SMF913_RS32565: mmal
PKS_AT (587..887): 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: 208.0
  Ethylmalonyl-CoA: 206.2
  Methoxymalonyl-CoA: 175.6
  trans-1,2-CPDA: 127.7
  2-Methylbutyryl-CoA: 127.2
  Propionyl-CoA: 110.7
  Malonyl-CoA: 105.6
  CHC-CoA: 92.2
  Isobutyryl-CoA: 64.6
  Benzoyl-CoA: 43.3
  Acetyl-CoA: 41.8
  fatty_acid: 38.2
  inactive: 21.8
  3-Methylbutyryl-CoA: 19.7

SMF913_RS32570: mmal - mmal
PKS_AT (567..867): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 211.9
  Ethylmalonyl-CoA: 204.9
  Methoxymalonyl-CoA: 174.6
  trans-1,2-CPDA: 145.8
  2-Methylbutyryl-CoA: 135.0
  Propionyl-CoA: 111.6
  Malonyl-CoA: 109.0
  CHC-CoA: 103.4
  Isobutyryl-CoA: 71.6
  Benzoyl-CoA: 64.0
  fatty_acid: 43.7
  Acetyl-CoA: 41.7
  3-Methylbutyryl-CoA: 36.4
  inactive: 22.1

PKS_AT (2376..2679): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 209.5
  Ethylmalonyl-CoA: 201.8
  Methoxymalonyl-CoA: 171.7
  trans-1,2-CPDA: 143.2
  2-Methylbutyryl-CoA: 133.8
  Propionyl-CoA: 108.4
  Malonyl-CoA: 105.2
  CHC-CoA: 102.3
  Isobutyryl-CoA: 70.6
  Benzoyl-CoA: 58.7
  fatty_acid: 39.8
  Acetyl-CoA: 37.1
  3-Methylbutyryl-CoA: 35.9
  inactive: 19.8

SMF913_RS32575: mmal - mal
PKS_AT (565..865): 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: 210.9
  Ethylmalonyl-CoA: 207.5
  Methoxymalonyl-CoA: 175.4
  2-Methylbutyryl-CoA: 138.3
  trans-1,2-CPDA: 135.3
  Propionyl-CoA: 115.8
  CHC-CoA: 113.8
  Malonyl-CoA: 110.2
  Isobutyryl-CoA: 64.8
  Benzoyl-CoA: 62.3
  fatty_acid: 49.2
  Acetyl-CoA: 49.2
  3-Methylbutyryl-CoA: 40.8
  inactive: 24.3

PKS_AT (2362..2650): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 181.7
  inactive: 95.6
  Methoxymalonyl-CoA: 62.1
  Methylmalonyl-CoA: 61.3
  fatty_acid: 34.6
  Isobutyryl-CoA: 33.4
  Propionyl-CoA: 33.3
  2-Methylbutyryl-CoA: 26.2
  Ethylmalonyl-CoA: 21.7
  Acetyl-CoA: 19.4
  trans-1,2-CPDA: 13.6
  CHC-CoA: 13.5
  Benzoyl-CoA: 7.5
  3-Methylbutyryl-CoA: 0.0

SMF913_RS32580: mal - mmal
PKS_AT (596..895): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 225.6
  inactive: 121.5
  Methoxymalonyl-CoA: 55.5
  Methylmalonyl-CoA: 44.8
  Propionyl-CoA: 28.5
  Isobutyryl-CoA: 27.4
  Acetyl-CoA: 21.1
  Benzoyl-CoA: 16.5
  Ethylmalonyl-CoA: 11.5
  2-Methylbutyryl-CoA: 9.4
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2398..2701): 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: 214.0
  Ethylmalonyl-CoA: 209.2
  Methoxymalonyl-CoA: 179.6
  trans-1,2-CPDA: 149.8
  2-Methylbutyryl-CoA: 140.5
  Propionyl-CoA: 123.5
  Malonyl-CoA: 111.1
  CHC-CoA: 99.4
  Isobutyryl-CoA: 74.0
  Benzoyl-CoA: 63.0
  Acetyl-CoA: 55.7
  fatty_acid: 53.1
  3-Methylbutyryl-CoA: 31.2
  inactive: 24.8

SMF913_RS32585: mmal
PKS_AT (564..867): 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: 210.7
  Ethylmalonyl-CoA: 206.8
  Methoxymalonyl-CoA: 174.4
  trans-1,2-CPDA: 135.7
  2-Methylbutyryl-CoA: 131.2
  Propionyl-CoA: 111.4
  Malonyl-CoA: 110.8
  CHC-CoA: 108.4
  Isobutyryl-CoA: 73.3
  Benzoyl-CoA: 68.8
  fatty_acid: 48.0
  Acetyl-CoA: 46.1
  3-Methylbutyryl-CoA: 36.4
  inactive: 20.9

SMF913_RS32590: mal - mmal
PKS_AT (541..847): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 208.8
  inactive: 92.2
  Methoxymalonyl-CoA: 73.6
  Methylmalonyl-CoA: 64.1
  Isobutyryl-CoA: 42.6
  Ethylmalonyl-CoA: 30.0
  Acetyl-CoA: 29.1
  Propionyl-CoA: 28.0
  Benzoyl-CoA: 26.8
  CHC-CoA: 18.5
  fatty_acid: 13.9
  3-Methylbutyryl-CoA: 12.6
  2-Methylbutyryl-CoA: 11.4
  trans-1,2-CPDA: -0.0

PKS_AT (1572..1875): 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: 207.6
  Ethylmalonyl-CoA: 204.0
  Methoxymalonyl-CoA: 176.3
  trans-1,2-CPDA: 140.4
  2-Methylbutyryl-CoA: 133.1
  Propionyl-CoA: 115.9
  Malonyl-CoA: 107.3
  CHC-CoA: 94.0
  Isobutyryl-CoA: 69.7
  Benzoyl-CoA: 54.3
  fatty_acid: 45.7
  Acetyl-CoA: 43.5
  3-Methylbutyryl-CoA: 26.3
  inactive: 22.0

SMF913_RS32740: mmal
PKS_AT (568..863): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 147.0
  Ethylmalonyl-CoA: 131.9
  Methoxymalonyl-CoA: 124.8
  Malonyl-CoA: 96.7
  2-Methylbutyryl-CoA: 92.4
  Isobutyryl-CoA: 89.2
  Propionyl-CoA: 85.4
  trans-1,2-CPDA: 79.0
  Acetyl-CoA: 62.9
  CHC-CoA: 49.5
  fatty_acid: 39.6
  3-Methylbutyryl-CoA: 37.3
  inactive: 34.3
  Benzoyl-CoA: 19.9

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

NZ_LJIW01000002.1 - Region 11 - 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: 2,053,609 - 2,133,513 nt. (total: 79,905 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
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
SMF913_RS33235: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

SMF913_RS33255: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

SMF913_RS33265: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

SMF913_RS33310: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS33370: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Transferases: acylase glycosyltransferase transferase transketolase
SMF913_RS33230: transketolase

smcogs
  SMCOG1204: transketolase

SMF913_RS33300: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

SMF913_RS33320: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

SMF913_RS33360: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Hydrolases: esterase
SMF913_RS33305: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase
SMF913_RS33225: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

SMF913_RS33270: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

SMF913_RS33355: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
SMF913_RS33315: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS33325: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

SMF913_RS49650: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002291.3 |  | 0.96 | PKS | efomycin K, efomycin L | Streptomyces sp. M56
BGC0000053.5 |  | 0.85 | PKS | elaiophylin | Unknown. Unclassified.
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000041.3 |  | 0.73 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.64 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0000166.5 |  | 0.63 | PKS | tylactone | Streptomyces fradiae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002291.3 |  | 0.96 | PKS | efomycin K, efomycin L | Streptomyces sp. M56
BGC0000053.5 |  | 0.85 | PKS | elaiophylin | Unknown. Unclassified.
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000041.3 |  | 0.73 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.64 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0000166.5 |  | 0.63 | PKS | tylactone | Streptomyces fradiae

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
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.09 out of 20.47
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.71 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
Additional weak hits (21):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.86 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.88 out of 30.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.04 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.05 out of 30.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.26 out of 28.14
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.22 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.77 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.29 out of 18.57
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: 19.35 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.01 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.75 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.19 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.74 out of 27.78
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.28 out of 29.51
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.61 out of 24.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.89 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.95 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.89 out of 32.93
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.71 out of 25.75
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.06 out of 27.18
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 25, location 2053608 - 2133513:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal - ccemal - ohmal) + (Me-ohmal) + (pk) + (pk - ccmal) + (ccmal)
Non-colinear ordering:
  SMF913_RS49650 + SMF913_RS33325 + SMF913_RS33320 + SMF913_RS33315 + SMF913_RS33310

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).
SMF913_RS33310: mal
PKS_AT (566..861): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 189.1
  inactive: 93.0
  Methoxymalonyl-CoA: 59.2
  Methylmalonyl-CoA: 45.3
  Propionyl-CoA: 31.2
  Ethylmalonyl-CoA: 24.2
  Acetyl-CoA: 23.0
  Benzoyl-CoA: 21.5
  Isobutyryl-CoA: 20.7
  CHC-CoA: 14.2
  2-Methylbutyryl-CoA: 11.9
  fatty_acid: 8.7
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

SMF913_RS33315: pk - mal
PKS_AT (572..863): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 222.5
  Methylmalonyl-CoA: 219.8
  Methoxymalonyl-CoA: 178.9
  2-Methylbutyryl-CoA: 153.5
  trans-1,2-CPDA: 130.5
  Propionyl-CoA: 113.9
  CHC-CoA: 104.8
  Malonyl-CoA: 100.8
  Isobutyryl-CoA: 71.3
  Benzoyl-CoA: 56.4
  3-Methylbutyryl-CoA: 51.1
  Acetyl-CoA: 44.3
  fatty_acid: 34.3
  inactive: 27.2

PKS_AT (2102..2401): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 215.4
  inactive: 115.9
  Methoxymalonyl-CoA: 58.3
  Methylmalonyl-CoA: 39.9
  Propionyl-CoA: 28.6
  Benzoyl-CoA: 19.5
  Acetyl-CoA: 19.4
  Ethylmalonyl-CoA: 12.4
  Isobutyryl-CoA: 10.6
  2-Methylbutyryl-CoA: 10.1
  fatty_acid: 9.6
  CHC-CoA: 5.4
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

SMF913_RS33320: pk
PKS_AT (568..859): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 224.0
  Methylmalonyl-CoA: 221.0
  Methoxymalonyl-CoA: 178.0
  2-Methylbutyryl-CoA: 156.6
  trans-1,2-CPDA: 130.0
  Propionyl-CoA: 111.9
  CHC-CoA: 110.2
  Malonyl-CoA: 94.4
  Isobutyryl-CoA: 77.3
  3-Methylbutyryl-CoA: 58.9
  Benzoyl-CoA: 58.8
  Acetyl-CoA: 40.5
  fatty_acid: 36.8
  inactive: 22.3

SMF913_RS33325: mmal
PKS_AT (595..889): 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: 215.5
  Ethylmalonyl-CoA: 210.7
  Methoxymalonyl-CoA: 177.2
  2-Methylbutyryl-CoA: 152.1
  trans-1,2-CPDA: 129.1
  Propionyl-CoA: 118.1
  CHC-CoA: 116.0
  Malonyl-CoA: 101.0
  Isobutyryl-CoA: 87.4
  Benzoyl-CoA: 64.7
  3-Methylbutyryl-CoA: 64.6
  Acetyl-CoA: 53.2
  fatty_acid: 44.5
  inactive: 33.6

SMF913_RS49650: mal - emal - mal
PKS_AT (530..820): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 202.2
  inactive: 112.2
  Methoxymalonyl-CoA: 57.4
  Methylmalonyl-CoA: 41.3
  Isobutyryl-CoA: 25.6
  Benzoyl-CoA: 25.3
  Propionyl-CoA: 20.0
  Acetyl-CoA: 17.6
  Ethylmalonyl-CoA: 15.7
  fatty_acid: 15.2
  CHC-CoA: 9.1
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

PKS_AT (1538..1836): emal
ATSignature: Ethylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 216.2
  Methylmalonyl-CoA: 195.9
  Methoxymalonyl-CoA: 177.9
  trans-1,2-CPDA: 143.2
  2-Methylbutyryl-CoA: 139.7
  CHC-CoA: 115.8
  Malonyl-CoA: 111.9
  Propionyl-CoA: 106.2
  Isobutyryl-CoA: 75.8
  Benzoyl-CoA: 73.4
  3-Methylbutyryl-CoA: 46.7
  Acetyl-CoA: 45.5
  fatty_acid: 42.9
  inactive: 18.9

PKS_AT (3380..3670): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 212.0
  inactive: 115.8
  Methoxymalonyl-CoA: 59.0
  Methylmalonyl-CoA: 45.2
  Benzoyl-CoA: 26.9
  Propionyl-CoA: 22.6
  Acetyl-CoA: 22.4
  Isobutyryl-CoA: 19.9
  fatty_acid: 19.5
  Ethylmalonyl-CoA: 12.5
  2-Methylbutyryl-CoA: 9.1
  CHC-CoA: 9.0
  trans-1,2-CPDA: 8.0
  3-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
IolR | Regulator of the inositol catabolism
MexT | Global virulence regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000002.1 - Region 12 - 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: 2,160,780 - 2,182,871 nt. (total: 22,092 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
Oxidoreductases: dehydrogenase
SMF913_RS33560: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: glycosyltransferase
SMF913_RS33550: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

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
--- | --- | --- | --- | --- | ---
BGC0000518.3 |  | 0.41 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000528.5 |  | 0.40 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002316.2 |  | 0.40 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0001221.5 |  | 0.40 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0000515.4 |  | 0.39 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0002535.2 |  | 0.39 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0002346.3 |  | 0.39 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000506.4 |  | 0.39 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000511.5 |  | 0.39 | ribosomal | ericin S | Bacillus subtilis
BGC0001789.3 |  | 0.39 | ribosomal | suicin 90-1330 | Streptococcus suis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000518.3 |  | 0.41 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000528.5 |  | 0.40 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002316.2 |  | 0.40 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0001221.5 |  | 0.40 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0000515.4 |  | 0.39 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0002535.2 |  | 0.39 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0002346.3 |  | 0.39 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000506.4 |  | 0.39 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000511.5 |  | 0.39 | ribosomal | ericin S | Bacillus subtilis
BGC0001789.3 |  | 0.39 | ribosomal | suicin 90-1330 | Streptococcus suis

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: 28.03 out of 36.53
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.80 out of 29.51
Confidence: medium
Additional weak hits (5):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.39 out of 20.97
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.63 out of 26.12
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.35 out of 30.25
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.36 out of 27.55
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.49 out of 30.22
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (2160779...2182871)
SMF913_RS33570
  RRE type: PqqD_RRE
  Location: 13 - 93
  Score: 64.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DmdR1 | Iron(II)-dependent repressor
DosR | Hypoxia stress response regulator

NZ_LJIW01000002.1 - Region 13 - hserlactone
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: 2,295,766 - 2,316,524 nt. (total: 20,759 nt) Show pHMM detection rules used
hserlactone: Autoind_synth

#### 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
SMF913_RS34190: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

Transferases: acyltransferase methyltransferase
SMF913_RS34135: methyltransferase

smcogs
  SMCOG1089: methyltransferase

SMF913_RS34160: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Hydrolases: deformylase
SMF913_RS34150: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Ligases: ligase
SMF913_RS34165: 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 | hserlactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002128.3 |  | 0.47 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001682.3 |  | 0.45 | other (other) | N-acyl lysine, N-acyl ornithine | Pseudomonas aeruginosa LESB58
BGC0002545.3 |  | 0.36 | PKS | sungeidine C, sungeidine B, sungeidine D, sungeidine H, sungeidine A, sungeidine E, sungeidine F, sungeidine G | Micromonospora sp.
BGC0001765.3 |  | 0.36 | saccharide | salecan | Agrobacterium tumefaciens
BGC0002362.3 |  | 0.36 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0001380.3 |  | 0.35 | saccharide | salecan | Agrobacterium sp. ZX09
BGC0000896.5 |  | 0.34 | other (other) | cycloserine | Streptomyces lavendulae subsp. lavendulae
BGC0001377.5 |  | 0.33 | PKS | uncialamycin | Streptomyces uncialis
BGC0002372.3 |  | 0.33 | PKS, other (other), terpene | marinoterpin B, marinoterpin A, marinoterpin C | Streptomyces sp.
BGC0000692.5 |  | 0.32 | saccharide | apramycin | Streptoalloteichus hindustanus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002128.3 |  | 0.47 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001682.3 |  | 0.45 | other (other) | N-acyl lysine, N-acyl ornithine | Pseudomonas aeruginosa LESB58
BGC0002545.3 |  | 0.36 | PKS | sungeidine C, sungeidine B, sungeidine D, sungeidine H, sungeidine A, sungeidine E, sungeidine F, sungeidine G | Micromonospora sp.
BGC0001765.3 |  | 0.36 | saccharide | salecan | Agrobacterium tumefaciens
BGC0002362.3 |  | 0.36 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0001380.3 |  | 0.35 | saccharide | salecan | Agrobacterium sp. ZX09
BGC0000896.5 |  | 0.34 | other (other) | cycloserine | Streptomyces lavendulae subsp. lavendulae
BGC0001377.5 |  | 0.33 | PKS | uncialamycin | Streptomyces uncialis
BGC0002372.3 |  | 0.33 | PKS, other (other), terpene | marinoterpin B, marinoterpin A, marinoterpin C | Streptomyces sp.
BGC0000692.5 |  | 0.32 | saccharide | apramycin | Streptoalloteichus hindustanus

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: 19.35 out of 20.47
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.15 out of 27.04
Confidence: medium
Additional weak hits (2):
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.85 out of 27.04
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.69 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000002.1 - Region 14 - 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: 2,327,642 - 2,338,577 nt. (total: 10,936 nt) Show pHMM detection rules used
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 oxidoreductase
SMF913_RS34280: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS34290: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Hydrolases: hydrolase
SMF913_RS34265: HAD-superfamily hydrolase, subfamily IA, variant

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

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 |  | 0.76 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.75 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.57 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.44 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0001659.3 |  | 0.37 | terpene | mangicol A | Fusarium equiseti
BGC0000914.5 |  | 0.35 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0001909.3 |  | 0.34 | PKS | strobilurin A | Strobilurus tenacellus
BGC0000723.5 |  | 0.33 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. limoneus
BGC0002571.2 |  | 0.33 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0000843.5 |  | 0.32 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.76 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.75 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.57 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.44 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0001659.3 |  | 0.37 | terpene | mangicol A | Fusarium equiseti
BGC0000914.5 |  | 0.35 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0001909.3 |  | 0.34 | PKS | strobilurin A | Strobilurus tenacellus
BGC0000723.5 |  | 0.33 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. limoneus
BGC0002571.2 |  | 0.33 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0000843.5 |  | 0.32 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064

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 (10):
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 17.67 out of 22.40
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.82 out of 39.62
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.60 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.90 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.73 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.63 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.28 out of 28.14
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.18 out of 18.57
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.49 out of 33.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 30.98
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LJIW01000002.1 - Region 15 - 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: 2,509,112 - 2,557,505 nt. (total: 48,394 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
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
SMF913_RS35200: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

SMF913_RS35245: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Lyases: dehydratase
SMF913_RS35210: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Translocases: transport
SMF913_RS35225: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002191.2 |  | 0.62 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002164.2 |  | 0.58 | NRPS | peramine | Epichloe festucae
BGC0002138.2 |  | 0.44 | PKS | fuelimycin A, fuelimicin B, fuelimicin C | Streptomyces albireticuli NRRL B-1670
BGC0002515.2 |  | 0.43 | PKS | solanapyrone A | Ascochyta rabiei
BGC0001858.2 |  | 0.40 | PKS | alternapyrone B, alternapyrone C, alternapyrone D, alternapyrone E, alternapyrone F | Parastagonospora nodorum SN15
BGC0001161.5 |  | 0.39 | PKS | 1-heptadecene | Moorea bouillonii PNG
BGC0001162.3 |  | 0.39 | PKS | 1-heptadecene | Moorea producens JHB
BGC0001163.3 |  | 0.39 | PKS | 1-heptadecene | Moorea producens 3L
BGC0002525.3 |  | 0.39 | PKS | fusarubin, 1233A, 1233B, NG-391, lucilactaene | Fusarium sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002191.2 |  | 0.62 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002164.2 |  | 0.58 | NRPS | peramine | Epichloe festucae
BGC0002138.2 |  | 0.44 | PKS | fuelimycin A, fuelimicin B, fuelimicin C | Streptomyces albireticuli NRRL B-1670
BGC0002515.2 |  | 0.43 | PKS | solanapyrone A | Ascochyta rabiei
BGC0001858.2 |  | 0.40 | PKS | alternapyrone B, alternapyrone C, alternapyrone D, alternapyrone E, alternapyrone F | Parastagonospora nodorum SN15
BGC0001161.5 |  | 0.39 | PKS | 1-heptadecene | Moorea bouillonii PNG
BGC0001162.3 |  | 0.39 | PKS | 1-heptadecene | Moorea producens JHB
BGC0001163.3 |  | 0.39 | PKS | 1-heptadecene | Moorea producens 3L
BGC0002525.3 |  | 0.39 | PKS | fusarubin, 1233A, 1233B, NG-391, lucilactaene | Fusarium 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.
Binding sites found:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.61 out of 20.97
Confidence: medium
Additional weak hits (10):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.06 out of 31.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.25 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.82 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.60 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.08 out of 26.06
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.98 out of 27.04
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.82 out of 25.88
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.44 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 29, location 2509111 - 2557505:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-pk)

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).
SMF913_RS35200: pk
PKS_AT (753..1057): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  Methylmalonyl-CoA: 70.8%
  CE-Malonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 117.1
  Methoxymalonyl-CoA: 105.5
  Malonyl-CoA: 86.1
  Ethylmalonyl-CoA: 79.4
  Propionyl-CoA: 73.6
  2-Methylbutyryl-CoA: 71.5
  Isobutyryl-CoA: 68.7
  fatty_acid: 47.8
  trans-1,2-CPDA: 44.4
  Benzoyl-CoA: 41.5
  CHC-CoA: 37.2
  Acetyl-CoA: 23.5
  3-Methylbutyryl-CoA: 22.1
  inactive: 18.3

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
CatR | H2O2-responsive repressor
CcpA | Catabolite control protein A

NZ_LJIW01000002.1 - 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: 2,887,638 - 2,914,091 nt. (total: 26,454 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
SMF913_RS36860: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS36885: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

Transferases: aminotransferase transferase
SMF913_RS36805: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

SMF913_RS36890: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Ligases: synthase synthetase
SMF913_RS36810: 1-deoxy-D-xylulose-5-phosphate synthase

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

SMF913_RS36835: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.74 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.51 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0001361.3 |  | 0.48 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.48 | terpene | sodorifen | Serratia plymuthica
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000651.5 |  | 0.48 | terpene | KS-505a | Streptomyces argenteolus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.74 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.51 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0001361.3 |  | 0.48 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.48 | terpene | sodorifen | Serratia plymuthica
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000651.5 |  | 0.48 | terpene | KS-505a | Streptomyces argenteolus

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:
SMF913_RS36830: T2TS
Domain 1 (12 - 639): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

SMF913_RS36835: PT_FPPS_like
Domain 1 (69 - 355): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

SMF913_RS36845: PT_phytoene_like
Domain 1 (13 - 308): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

SMF913_RS36850: PT_phytoene_like
Domain 1 (6 - 266): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  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.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.50 out of 20.47
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.03 out of 29.72
Confidence: medium
Additional weak hits (5):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.78 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.89 out of 30.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.82 out of 36.54
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.74 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.39 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
PSPP | Presqualene diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000002.1 - Region 17 - triceptide
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: 2,940,510 - 2,961,670 nt. (total: 21,161 nt) Show pHMM detection rules used
triceptide: ((cds(PF04055 and (TIGR04085 or SPASM)) and triceptide_precursor) or triceptide_rSAM)

#### 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: acetyltransferase
SMF913_RS36990: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Lyases: dehydratase
SMF913_RS36995: L-carnitine dehydratase/bile acid-inducible

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

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 | triceptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000866.5 |  | 0.42 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.40 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0001122.4 |  | 0.33 | NRPS, PKS | dihydroisoflavipucine, isoflavipucine | Aspergillus terreus NIH2624
BGC0001387.5 |  | 0.32 | other (other) | nucleocidin | Streptomyces calvus
BGC0000453.5 |  | 0.29 | NRPS | valinomycin | Streptomyces tsusimaensis
BGC0002467.2 |  | 0.27 | NRPS | thermochelin | Thermocrispum agreste DSM 44070
BGC0000466.5 |  | 0.26 | NRPS | yatakemycin | Streptomyces sp. TP-A2060
BGC0001945.3 |  | 0.26 | NRPS | chloromyxamide | Myxococcus sp.
BGC0001941.3 |  | 0.26 | PKS | Fulvuthiacene A, Fulvuthiacene B | Myxococcus fulvus
BGC0000925.5 |  | 0.26 | other (other) | quinolobactin | Pseudomonas fluorescens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000866.5 |  | 0.42 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.40 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0001122.4 |  | 0.33 | NRPS, PKS | dihydroisoflavipucine, isoflavipucine | Aspergillus terreus NIH2624
BGC0001387.5 |  | 0.32 | other (other) | nucleocidin | Streptomyces calvus
BGC0000453.5 |  | 0.29 | NRPS | valinomycin | Streptomyces tsusimaensis
BGC0002467.2 |  | 0.27 | NRPS | thermochelin | Thermocrispum agreste DSM 44070
BGC0000466.5 |  | 0.26 | NRPS | yatakemycin | Streptomyces sp. TP-A2060
BGC0001945.3 |  | 0.26 | NRPS | chloromyxamide | Myxococcus sp.
BGC0001941.3 |  | 0.26 | PKS | Fulvuthiacene A, Fulvuthiacene B | Myxococcus fulvus
BGC0000925.5 |  | 0.26 | other (other) | quinolobactin | 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.

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: 21.32 out of 26.85
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.25 out of 20.01
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
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
Additional weak hits (7):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.27 out of 32.74
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.09 out of 29.25
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.87 out of 26.85
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.95 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.17 out of 20.01
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.95 out of 20.01
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArgR | Regulator of arginine biosynthesis genes
CRP | Cyclic AMP receptor protein
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000002.1 - Region 18 - 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: 3,107,092 - 3,179,607 nt. (total: 72,516 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: oxidase oxidoreductase oxygenase
SMF913_RS37755: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

SMF913_RS37880: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

SMF913_RS37965: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

SMF913_RS37970: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

Transferases: PPTase acetyltransferase aminotransferase methyltransferase
SMF913_RS37930: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

SMF913_RS37945: aminotransferase

smcogs
  SMCOG1019: aminotransferase

SMF913_RS38010: methyltransferase

smcogs
  SMCOG1089: methyltransferase

SMF913_RS38035: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

SMF913_RS38040: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: deacetylase hydrolase
SMF913_RS37855: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

SMF913_RS38050: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

Lyases: cyclase
SMF913_RS37910: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

SMF913_RS37915: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

Ligases: ligase synthase
SMF913_RS37740: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS37895: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS37900: Beta-ketoacyl synthase

smcogs
  SMCOG1093: 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
--- | --- | --- | --- | --- | ---
BGC0000271.5 |  | 0.76 | PKS | spore pigment | Streptomyces avermitilis
BGC0000272.3 |  | 0.73 | PKS | spore pigment | Streptomyces collinus
BGC0000215.5 |  | 0.72 | PKS | curamycin | Streptomyces cyaneus
BGC0000231.5 |  | 0.61 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001513.3 |  | 0.59 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000234.5 |  | 0.58 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000275.4 |  | 0.57 | PKS | tetracenomycin C | Streptomyces glaucescens
BGC0001197.5 |  | 0.57 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002000.4 |  | 0.55 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0001895.4 |  | 0.55 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000271.5 |  | 0.76 | PKS | spore pigment | Streptomyces avermitilis
BGC0000272.3 |  | 0.73 | PKS | spore pigment | Streptomyces collinus
BGC0000215.5 |  | 0.72 | PKS | curamycin | Streptomyces cyaneus
BGC0000231.5 |  | 0.61 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001513.3 |  | 0.59 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000234.5 |  | 0.58 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000275.4 |  | 0.57 | PKS | tetracenomycin C | Streptomyces glaucescens
BGC0001197.5 |  | 0.57 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002000.4 |  | 0.55 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0001895.4 |  | 0.55 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001

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: 20.47 out of 20.47
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.87 out of 27.04
Confidence: medium
Additional weak hits (9):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.12 out of 18.57
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.63 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.43 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.48 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.41 out of 26.06
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.90 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.66 out of 29.38
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.23 out of 30.98
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).
SMF913_RS37740: X
AMP-binding (23..477): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    ENILFGRMVE-VLA---------GIFERAVDVAV
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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:
  3107091 to 3179607
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Product class(es):
  pentangular polyphenol
  tetracenomycin

SMF913_RS37850
  OXY (Score: 33.8; E-value: 4.4e-11)
SMF913_RS37880
  OXY (Score: 266.6; E-value: 1.1e-81)
SMF913_RS37890
  CYC C5-C18 (Score: 214.7; E-value: 8e-67)
SMF913_RS37895
  KS (Score: 707.0; E-value: 1.6e-215)
SMF913_RS37900
  CLF (Score: 543.3; E-value: 7.6e-166)
SMF913_RS37905
  ACP (Score: 63.0; E-value: 4.6e-20)
SMF913_RS37910
  CYC C9-C14 (Score: 246.6; E-value: 1.7e-76)
SMF913_RS37915
  CYC C4-C21/C2-C23|C2-C19 (Score: 148.6; E-value: 1.2e-46)
SMF913_RS37930
  MET C6|C8 (Score: 497.6; E-value: 3.2e-152)
SMF913_RS38010
  MET (Score: 29.5; E-value: 9.3e-10)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000002.1 - Region 19 - 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: 3,290,528 - 3,353,153 nt. (total: 62,626 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
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: oxidase oxidoreductase oxygenase
SMF913_RS38595: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

SMF913_RS38615: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

SMF913_RS38720: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Hydrolases: back translocase
SMF913_RS38770: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

Ligases: synthase
SMF913_RS49660: Beta-ketoacyl synthase

smcogs
  SMCOG1093: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000041.3 |  | 0.71 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001268.4 |  | 0.58 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0000024.5 |  | 0.55 | PKS | aureothin | Streptomyces thioluteus
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002228.3 |  | 0.51 | NRPS | CIML B, CIML A, CIML D, CIML C | Colletotrichum incanum
BGC0000844.5 |  | 0.51 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001665.3 |  | 0.50 | PKS | methylated alkyl-resorcinol, methylated acyl-phloroglucinol | Mycobacterium marinum M
BGC0000067.5 |  | 0.50 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000041.3 |  | 0.71 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001268.4 |  | 0.58 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0000024.5 |  | 0.55 | PKS | aureothin | Streptomyces thioluteus
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002228.3 |  | 0.51 | NRPS | CIML B, CIML A, CIML D, CIML C | Colletotrichum incanum
BGC0000844.5 |  | 0.51 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001665.3 |  | 0.50 | PKS | methylated alkyl-resorcinol, methylated acyl-phloroglucinol | Mycobacterium marinum M
BGC0000067.5 |  | 0.50 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus

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: 19.26 out of 19.26
Confidence: strong
Additional weak hits (10):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.22 out of 29.51
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.54 out of 27.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.22 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.97 out of 26.06
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.59 out of 33.14
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 33, location 3290527 - 3353153:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - Me-mal - Me-ccmal) + (Me-redmal - Me-mal)
Non-colinear ordering:
  SMF913_RS49660 + SMF913_RS50725

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).
SMF913_RS49660: mmal - mmal - mmal
PKS_AT (577..858): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 189.5
  Ethylmalonyl-CoA: 181.0
  Methoxymalonyl-CoA: 160.4
  2-Methylbutyryl-CoA: 118.3
  trans-1,2-CPDA: 112.6
  Malonyl-CoA: 112.1
  Propionyl-CoA: 98.6
  CHC-CoA: 94.8
  Isobutyryl-CoA: 69.7
  Acetyl-CoA: 45.9
  Benzoyl-CoA: 43.3
  inactive: 33.3
  3-Methylbutyryl-CoA: 28.9
  fatty_acid: 27.2

PKS_AT (1581..1878): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 205.7
  Ethylmalonyl-CoA: 187.6
  Methoxymalonyl-CoA: 167.3
  2-Methylbutyryl-CoA: 126.4
  trans-1,2-CPDA: 117.7
  Propionyl-CoA: 104.0
  CHC-CoA: 103.9
  Malonyl-CoA: 98.4
  Isobutyryl-CoA: 80.2
  Benzoyl-CoA: 66.3
  Acetyl-CoA: 54.2
  inactive: 38.9
  3-Methylbutyryl-CoA: 35.7
  fatty_acid: 30.5

PKS_AT (2598..2883): 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: 213.5
  Ethylmalonyl-CoA: 200.7
  Methoxymalonyl-CoA: 176.0
  2-Methylbutyryl-CoA: 141.5
  Malonyl-CoA: 124.2
  trans-1,2-CPDA: 119.0
  CHC-CoA: 112.5
  Propionyl-CoA: 109.3
  Isobutyryl-CoA: 94.1
  Benzoyl-CoA: 61.1
  inactive: 53.1
  Acetyl-CoA: 49.9
  3-Methylbutyryl-CoA: 46.1
  fatty_acid: 34.8

SMF913_RS50725: mmal - mmal
PKS_AT (566..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: 204.6
  Ethylmalonyl-CoA: 190.7
  Methoxymalonyl-CoA: 168.0
  2-Methylbutyryl-CoA: 130.4
  trans-1,2-CPDA: 116.5
  Malonyl-CoA: 111.9
  CHC-CoA: 104.7
  Propionyl-CoA: 103.3
  Isobutyryl-CoA: 79.5
  Acetyl-CoA: 64.6
  Benzoyl-CoA: 51.7
  inactive: 36.2
  3-Methylbutyryl-CoA: 31.6
  fatty_acid: 17.2

PKS_AT (2652..2956): 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: 219.2
  Ethylmalonyl-CoA: 208.2
  Methoxymalonyl-CoA: 183.4
  Malonyl-CoA: 128.2
  2-Methylbutyryl-CoA: 128.2
  trans-1,2-CPDA: 122.1
  Propionyl-CoA: 103.0
  Isobutyryl-CoA: 93.0
  CHC-CoA: 90.9
  Benzoyl-CoA: 71.9
  Acetyl-CoA: 71.4
  3-Methylbutyryl-CoA: 60.7
  inactive: 49.9
  fatty_acid: 32.9

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

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

NZ_LJIW01000002.1 - Region 20 - 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: 3,410,713 - 3,422,215 nt. (total: 11,503 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
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 | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002387.2 |  | 0.28 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0001377.5 |  | 0.25 | PKS | uncialamycin | Streptomyces uncialis
BGC0000874.5 |  | 0.25 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0002788.2 |  | 0.24 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0000495.5 |  | 0.24 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0002713.2 |  | 0.24 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0001060.5 |  | 0.22 | PKS | dynemicin A | Micromonospora chersina
BGC0001984.3 |  | 0.21 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0001514.5 |  | 0.20 | other (other) | aristeromycin | Streptomyces citricolor
BGC0000241.5 |  | 0.19 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora tropica CNB-440

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002387.2 |  | 0.28 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0001377.5 |  | 0.25 | PKS | uncialamycin | Streptomyces uncialis
BGC0000874.5 |  | 0.25 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0002788.2 |  | 0.24 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0000495.5 |  | 0.24 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0002713.2 |  | 0.24 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0001060.5 |  | 0.22 | PKS | dynemicin A | Micromonospora chersina
BGC0001984.3 |  | 0.21 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0001514.5 |  | 0.20 | other (other) | aristeromycin | Streptomyces citricolor
BGC0000241.5 |  | 0.19 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora tropica CNB-440

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:
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.04 out of 23.43
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.93 out of 26.85
Confidence: medium
Additional weak hits (3):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.81 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.60 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.73 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
RutR | Regulator of the pyrimidine and purine metabolism

NZ_LJIW01000002.1 - Region 21 - NRPS,aminocoumarin,arylpolyene,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: 3,539,445 - 3,620,587 nt. (total: 81,143 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
aminocoumarin: (novK or novJ or novI or novH or SpcDK_cou)
arylpolyene: (APE_KS1 or APE_KS2)
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
SMF913_RS39610: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

SMF913_RS39640: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS39675: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS39780: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SMF913_RS39790: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acyltransferase glycosyltransferase methyltransferase transferase
SMF913_RS39570: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

SMF913_RS39575: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

SMF913_RS39635: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

SMF913_RS39655: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

SMF913_RS39800: methyltransferase

smcogs
  SMCOG1089: methyltransferase

SMF913_RS39810: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: esterase
SMF913_RS39730: thioesterase

smcogs
  SMCOG1004: thioesterase

Isomerases: isomerase
SMF913_RS39765: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase synthetase
SMF913_RS39585: 3-oxoacyl-(acyl carrier protein) synthase III

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

SMF913_RS39590: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS39615: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS39645: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

SMF913_RS39660: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SMF913_RS39665: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

SMF913_RS39695: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS39710: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS39715: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS39720: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMF913_RS39785: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

SMF913_RS39820: 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 | NRPS | aminocoumarin | arylpolyene | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001132.4 |  |  |  |  | 1.20 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  |  | 1.16 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  |  |  |  | 1.15 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  |  |  | 1.14 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001529.5 |  |  |  |  | 1.13 | 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
BGC0002286.3 |  |  |  |  | 1.13 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  |  |  | 1.11 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  |  |  | 1.11 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  |  |  |  | 1.08 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  |  |  |  | 1.08 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001529.5 |  | 0.79 | 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
BGC0001132.4 |  | 0.77 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002075.3 |  | 0.76 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  | 0.76 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001261.3 |  | 0.75 | NRPS | AM-toxin | Alternaria alternata
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.75 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001249.5 |  | 0.74 | NRPS | dimethylcoprogen | 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.

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:
SMF913_RS39785: PT_FPPS_like
Domain 1 (58 - 344): 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:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 30.12 out of 30.12
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):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.62 out of 32.74
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.07 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.56 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.01 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.46 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.01 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.78 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.65 out of 39.62
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.66 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.46 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.92 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.53 out of 23.43
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.53 out of 32.93
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.40 out of 20.01
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.13 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
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 35, location 3539444 - 3620587:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - D-Leu) + (Ser - D-Asp) + (Ala - Ser) + (Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 36, location 3539444 - 3605314:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - D-Leu) + (Ser - D-Asp) + (Ala - Ser) + (Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 37, location 3572237 - 3613371:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - D-Leu) + (Ser - D-Asp)

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).
SMF913_RS39590: NH2
CAL_domain (44..486): NH2
minowa: NH2

Prediction, score:
  NH2: 111.0
  Acetyl-CoA: 38.1
  fatty_acid: 10.9
  shikimic_acid: 0.0
  AHBA: 0.0

SMF913_RS39645: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (464..873): 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:
    LATHFDFSVWEGNQVFGGEVNMYGITETTVHVSY
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

SMF913_RS39655: Ala - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (464..864): 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:
    LWATFDVSVFEGSALLCGEANVYGPTEATVYAAA
  Nearest Stachelhaus code(s):
    Ala DVFSLAVVYK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1521..1928): 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:
    RWMTFDVSVWEWHFLCSGEHNLYGPTEASVDVTS
  Nearest Stachelhaus code(s):
    Ser DVWHLSLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

SMF913_RS39660: Ser - Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (463..869): 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:
    RWMTFDVSVWEWHFLCSGEHNLYGPTEASVDVTY
  Nearest Stachelhaus code(s):
    Ser DVWHLSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1529..1932): Asp
nrpys: Asp

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

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

SMF913_RS39665: Thr - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (13..422): 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:
    LSTHFDFSVWEGNQVFGGEVNMYGITETTVHVSY
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1081..1479): Leu
nrpys: Leu

SVM prediction details:
  Predicted physicochemical class:
    N/A
  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:
    FTEAFDAAVLEMLIIVGGEVNAYGPTESTVAATT
  Nearest Stachelhaus code(s):
    Leu DALLIGAVAK (85% 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
--- | ---
OsdR | Development and stress management regulator

NZ_LJIW01000002.1 - Region 22 - 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: 3,689,075 - 3,719,258 nt. (total: 30,184 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
SMF913_RS40145: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

Transferases: aminotransferase
SMF913_RS40180: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Isomerases: mutase
SMF913_RS40130: 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 |  | 0.54 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002633.2 |  | 0.50 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0000852.5 |  | 0.49 | other (other) | ectoine | Sporosarcina pasteurii
BGC0002683.2 |  | 0.49 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000859.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000858.3 |  | 0.48 | other (other) | ectoine | Methylobacter marinus
BGC0002470.2 |  | 0.48 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0000855.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000856.3 |  | 0.48 | other (other) | ectoine | Methylophaga thalassica
BGC0000857.3 |  | 0.48 | other (other) | ectoine | Methylophaga alcalica

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002469.2 |  | 0.54 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002633.2 |  | 0.50 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0000852.5 |  | 0.49 | other (other) | ectoine | Sporosarcina pasteurii
BGC0002683.2 |  | 0.49 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000859.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000858.3 |  | 0.48 | other (other) | ectoine | Methylobacter marinus
BGC0002470.2 |  | 0.48 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0000855.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000856.3 |  | 0.48 | other (other) | ectoine | Methylophaga thalassica
BGC0000857.3 |  | 0.48 | other (other) | ectoine | Methylophaga alcalica

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:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.07 out of 26.85
Confidence: medium
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
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 20.58 out of 23.05
Confidence: strong
Additional weak hits (13):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.67 out of 26.33
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.99 out of 30.97
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.22 out of 27.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.19 out of 29.65
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.51 out of 27.18
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.32 out of 27.18
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.84 out of 26.85
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
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 30.11
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.88 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
LexA variant 2 | Repressor of DNA damage response
RutR | Regulator of the pyrimidine and purine metabolism

NZ_LJIW01000002.1 - Region 23 - 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: 4,255,263 - 4,298,109 nt. (total: 42,847 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 oxidoreductase
SMF913_RS42535: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMF913_RS42555: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

SMF913_RS42590: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: methyltransferase
SMF913_RS42615: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: dehydratase
SMF913_RS42565: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
SMF913_RS42570: 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
--- | --- | --- | --- | --- | ---
BGC0000340.5 |  | 0.95 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35
BGC0002277.2 |  | 0.65 | NRPS | atromentin | Suillus grevillei
BGC0002274.2 |  | 0.65 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0002193.2 |  | 0.64 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0001164.3 |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001295.5 |  | 0.47 | other (other) | cremeomycin | Streptomyces cremeus
BGC0001844.4 |  | 0.46 | NRPS | holrhizin A, holrhizin B, holrhizin C, holrhizin D | Paraburkholderia rhizoxinica HKI 454
BGC0001873.3 |  | 0.46 | NRPS | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0002404.2 |  | 0.46 | other (other) | falcarindiol | Solanum lycopersicum
BGC0000197.5 |  | 0.45 | PKS, saccharide | aranciamycin | Streptomyces echinatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000340.5 |  | 0.95 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35
BGC0002277.2 |  | 0.65 | NRPS | atromentin | Suillus grevillei
BGC0002274.2 |  | 0.65 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0002193.2 |  | 0.64 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0001164.3 |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001295.5 |  | 0.47 | other (other) | cremeomycin | Streptomyces cremeus
BGC0001844.4 |  | 0.46 | NRPS | holrhizin A, holrhizin B, holrhizin C, holrhizin D | Paraburkholderia rhizoxinica HKI 454
BGC0001873.3 |  | 0.46 | NRPS | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0002404.2 |  | 0.46 | other (other) | falcarindiol | Solanum lycopersicum
BGC0000197.5 |  | 0.45 | PKS, saccharide | aranciamycin | Streptomyces echinatus

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
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.50 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.36 out of 19.26
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.82 out of 21.84
Confidence: medium
Additional weak hits (9):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.80 out of 23.43
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.89 out of 33.73
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.17 out of 25.88
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.78 out of 30.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.58 out of 31.73
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.82 out of 27.55
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.81 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.12 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 40, location 4255262 - 4298109:
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).
SMF913_RS42570: X
AMP-binding (44..450): X
nrpys: Ppa

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:
    SGKIHVAALLELFTVSGGEWPAFGMTETCAGSIY
  Nearest Stachelhaus code(s):
    Ppa VALFVGAAGK (100% 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
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism
MexT | Global virulence regulator
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_LJIW01000002.1 - Region 24 - NI-siderophore,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: 4,807,378 - 4,858,226 nt. (total: 50,849 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC
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 oxygenase
SMF913_RS45040: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

SMF913_RS45060: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Lyases: cyclase decarboxylase dehydratase
SMF913_RS45035: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

SMF913_RS45160: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

SMF913_RS45165: 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 | NI-siderophore | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001478.5 |  |  | 0.59 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  |  | 0.59 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000941.3 |  |  | 0.58 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000940.5 |  |  | 0.44 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  |  | 0.43 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001572.3 |  |  | 0.37 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002464.3 |  |  | 0.29 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002690.2 |  |  | 0.27 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002620.2 |  |  | 0.22 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002469.2 |  |  | 0.21 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001478.5 |  | 0.84 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.83 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000941.3 |  | 0.83 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000940.5 |  | 0.74 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.74 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002464.3 |  | 0.63 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002690.2 |  | 0.60 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0001531.5 |  | 0.56 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002620.2 |  | 0.55 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina

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.

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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 36.53
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 22.22 out of 23.05
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 22.22 out of 23.05
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (10):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.55 out of 21.55
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.72 out of 26.12
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.07 out of 39.62
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.04 out of 26.06
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.88 out of 20.97
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.04 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.00 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.36 out of 23.43
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 19.15 out of 33.14
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.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (4833038...4858226)
SMF913_RS45160
  RRE type: Lanthipeptide_LanB_RRE
  Location: 152 - 240
  Score: 61.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
DmdR1 | Iron(II)-dependent repressor