Select genomic region:
Overview
1.1
1.2
1.3
1.4
2.1
2.2
2.3
2.4
3.1
3.2
4.1
4.2
4.3
5.1
6.1
6.2
7.1
7.2
7.3
9.1
9.2
10.1
11.1
16.1
18.1
19.1
24.1

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

NZ_KB905813.1 (Streptomyces sulphureus DSM 40104)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | NI-siderophore | 1 | 18,535 | High | legonoxamine A/desferrioxamine B/legonoxamine B | other:other
Region 1.2 | T2PKS | 169,535 | 242,035 | Low | WS 79089B/benaphthamycin/WS 79089D/WS 79089A/WS 79089C | PKS
Region 1.3 | T3PKS,RiPP-like | 569,454 | 610,569 | High | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone/2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | PKS:Type III
Region 1.4 | T2PKS | 875,755 | 939,081 | Low | julichrome Q3-3/julichrome Q3-5 | PKS

NZ_KB905814.1 (Streptomyces sulphureus DSM 40104)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | lipolanthine,lanthipeptide-class-iii | 61,388 | 93,709 |  |
Region 2.2 | linaridin | 122,267 | 142,818 |  |
Region 2.3 | lassopeptide | 267,516 | 289,018 | Medium | ulleungdin | ribosomal:unmodified
Region 2.4 | NRPS,T1PKS | 455,124 | 529,144 |  |

NZ_KB905815.1 (Streptomyces sulphureus DSM 40104)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | ectoine | 53,961 | 64,365 | High | ectoine | other:ectoine
Region 3.2 | terpene-precursor | 487,959 | 509,026 |  |

NZ_KB905816.1 (Streptomyces sulphureus DSM 40104)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 4.1 | T1PKS | 89,785 | 168,918 | Low | phoslactomycin B | PKS
Region 4.2 | lanthipeptide-class-i | 527,115 | 574,350 |  |
Region 4.3 | terpene | 584,547 | 611,217 | Medium | hopene | terpene

NZ_KB905817.1 (Streptomyces sulphureus DSM 40104)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 5.1 | T1PKS,transAT-PKS-like,NRPS | 207,021 | 301,164 | Low | kirromycin | NRPS:Type I+PKS:Type I

NZ_KB905818.1 (Streptomyces sulphureus DSM 40104)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 6.1 | NI-siderophore | 44,692 | 77,255 | Low | kinamycin | PKS
Region 6.2 | T1PKS | 330,686 | 378,047 | Low | actinoallolide A | PKS

NZ_KB905819.1 (Streptomyces sulphureus DSM 40104)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 7.1 | lanthipeptide-class-i | 10,722 | 35,292 | High | planosporicin | ribosomal:RiPP:Lanthipeptide
Region 7.2 | azole-containing-RiPP | 51,102 | 83,722 |  |
Region 7.3 | NRPS | 207,993 | 258,573 | Low | TVA-YJ-2 | ribosomal:RiPP

NZ_KB905821.1 (Streptomyces sulphureus DSM 40104)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 9.1 | t3nrps-iterative,PKS-like,T3PKS | 95,802 | 150,458 | Low | rubiginone A2/rubiginone J/rubiginone K/rubiginone L/rubiginone M/rubiginone N/ochromycinone/rubiginone B2 | PKS
Region 9.2 | T1PKS | 306,804 | 349,537 | Low | armeniaspirol A/armeniaspirol B/armeniaspirol C | PKS

NZ_KB905822.1 (Streptomyces sulphureus DSM 40104)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 10.1 | NRP-metallophore,NRPS | 223,882 | 266,554 | Medium | coelibactin | NRPS:Type I

NZ_KB905823.1 (Streptomyces sulphureus DSM 40104)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 11.1 | T1PKS,NRPS | 101,016 | 173,007 | Low | microtermolide A | NRPS:Type I+PKS

NZ_KB905828.1 (Streptomyces sulphureus DSM 40104)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 16.1 | T2PKS | 1 | 56,627 | High | resistomycin/resistoflavine | PKS:Type II

NZ_KB905830.1 (Streptomyces sulphureus DSM 40104)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 18.1 | RRE-containing | 62,565 | 72,882 | Low | bottromycin A2 | ribosomal:RiPP:Bottromycin

NZ_KB905831.1 (Streptomyces sulphureus DSM 40104)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 19.1 | NRP-metallophore,NRPS | 1 | 47,640 | Medium | bacillibactin | NRPS:Type I

NZ_KB905836.1 (Streptomyces sulphureus DSM 40104)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 24.1 | RiPP-like,bottromycin | 1 | 9,160 | High | bottromycin D | ribosomal:RiPP:Bottromycin

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | NI-siderophore | 1 | 18,535 | High | legonoxamine A/desferrioxamine B/legonoxamine B | other:other
Region 1.2 | T2PKS | 169,535 | 242,035 | Low | WS 79089B/benaphthamycin/WS 79089D/WS 79089A/WS 79089C | PKS
Region 1.3 | T3PKS,RiPP-like | 569,454 | 610,569 | High | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone/2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | PKS:Type III
Region 1.4 | T2PKS | 875,755 | 939,081 | Low | julichrome Q3-3/julichrome Q3-5 | PKS
Region 2.1 | lipolanthine,lanthipeptide-class-iii | 61,388 | 93,709 |  |
Region 2.2 | linaridin | 122,267 | 142,818 |  |
Region 2.3 | lassopeptide | 267,516 | 289,018 | Medium | ulleungdin | ribosomal:unmodified
Region 2.4 | NRPS,T1PKS | 455,124 | 529,144 |  |
Region 3.1 | ectoine | 53,961 | 64,365 | High | ectoine | other:ectoine
Region 3.2 | terpene-precursor | 487,959 | 509,026 |  |
Region 4.1 | T1PKS | 89,785 | 168,918 | Low | phoslactomycin B | PKS
Region 4.2 | lanthipeptide-class-i | 527,115 | 574,350 |  |
Region 4.3 | terpene | 584,547 | 611,217 | Medium | hopene | terpene
Region 5.1 | T1PKS,transAT-PKS-like,NRPS | 207,021 | 301,164 | Low | kirromycin | NRPS:Type I+PKS:Type I
Region 6.1 | NI-siderophore | 44,692 | 77,255 | Low | kinamycin | PKS
Region 6.2 | T1PKS | 330,686 | 378,047 | Low | actinoallolide A | PKS
Region 7.1 | lanthipeptide-class-i | 10,722 | 35,292 | High | planosporicin | ribosomal:RiPP:Lanthipeptide
Region 7.2 | azole-containing-RiPP | 51,102 | 83,722 |  |
Region 7.3 | NRPS | 207,993 | 258,573 | Low | TVA-YJ-2 | ribosomal:RiPP
Region 9.1 | t3nrps-iterative,PKS-like,T3PKS | 95,802 | 150,458 | Low | rubiginone A2/rubiginone J/rubiginone K/rubiginone L/rubiginone M/rubiginone N/ochromycinone/rubiginone B2 | PKS
Region 9.2 | T1PKS | 306,804 | 349,537 | Low | armeniaspirol A/armeniaspirol B/armeniaspirol C | PKS
Region 10.1 | NRP-metallophore,NRPS | 223,882 | 266,554 | Medium | coelibactin | NRPS:Type I
Region 11.1 | T1PKS,NRPS | 101,016 | 173,007 | Low | microtermolide A | NRPS:Type I+PKS
Region 16.1 | T2PKS | 1 | 56,627 | High | resistomycin/resistoflavine | PKS:Type II
Region 18.1 | RRE-containing | 62,565 | 72,882 | Low | bottromycin A2 | ribosomal:RiPP:Bottromycin
Region 19.1 | NRP-metallophore,NRPS | 1 | 47,640 | Medium | bacillibactin | NRPS:Type I
Region 24.1 | RiPP-like,bottromycin | 1 | 9,160 | High | bottromycin D | ribosomal:RiPP:Bottromycin

No secondary metabolite regions were found in these records:
  NZ_KB905820.1 (Streptomyces sulphureus DSM 40104)
  NZ_KB905824.1 (Streptomyces sulphureus DSM 40104)
  NZ_KB905825.1 (Streptomyces sulphureus DSM 40104)
  NZ_KB905826.1 (Streptomyces sulphureus DSM 40104)
  NZ_KB905827.1 (Streptomyces sulphureus DSM 40104)
  NZ_KB905829.1 (Streptomyces sulphureus DSM 40104)
  NZ_KB905832.1 (Streptomyces sulphureus DSM 40104)
  NZ_KB905833.1 (Streptomyces sulphureus DSM 40104)
  NZ_KB905834.1 (Streptomyces sulphureus DSM 40104)
  NZ_KB905835.1 (Streptomyces sulphureus DSM 40104)
  NZ_KB905837.1 (Streptomyces sulphureus DSM 40104)
  NZ_KB905838.1 (Streptomyces sulphureus DSM 40104)

Compact view
NZ_KB905813.1 - Region 1 - 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: 1 - 18,535 nt. (total: 18,535 nt) Show pHMM detection rules used
Region on contig edge.
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
F603_RS0100030: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Lyases: decarboxylase
F603_RS0100035: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

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
--- | --- | --- | --- | --- | ---
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.79 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.72 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001572.3 |  | 0.67 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000940.5 |  | 0.64 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.64 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0002620.2 |  | 0.57 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002464.3 |  | 0.57 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0001531.5 |  | 0.54 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002690.2 |  | 0.51 | other (other) | FW0622 | Verrucosispora sp. FIM060022

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.79 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.72 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001572.3 |  | 0.67 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000940.5 |  | 0.64 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.64 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0002620.2 |  | 0.57 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002464.3 |  | 0.57 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0001531.5 |  | 0.54 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002690.2 |  | 0.51 | other (other) | FW0622 | Verrucosispora sp. FIM060022

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: 29.03 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.73 out of 36.53
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 (5):
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.88 out of 19.26
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.85 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.56 out of 36.53
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.38 out of 25.88
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.82 out of 18.57
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DmdR1 | Iron(II)-dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_KB905813.1 - Region 2 - 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: 169,535 - 242,035 nt. (total: 72,501 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
F603_RS0100790: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

F603_RS0100825: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

F603_RS0100835: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F603_RS0100895: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

F603_RS0100920: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F603_RS0100930: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

F603_RS0100955: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

F603_RS0100960: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

F603_RS0101010: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F603_RS0101025: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: methyltransferase
F603_RS0100910: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: deacetylase
F603_RS0100750: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

Lyases: cyclase hydratase
F603_RS0100855: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

F603_RS0100870: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

F603_RS0101035: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Isomerases: mutase
F603_RS0100975: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: synthase
F603_RS0100810: 1-deoxy-D-xylulose-5-phosphate synthase

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

F603_RS0100880: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

F603_RS0100885: 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
--- | --- | --- | --- | --- | ---
BGC0000231.5 |  | 0.64 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000272.3 |  | 0.63 | PKS | spore pigment | Streptomyces collinus
BGC0001723.5 |  | 0.61 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000234.5 |  | 0.59 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000271.5 |  | 0.58 | PKS | spore pigment | Streptomyces avermitilis
BGC0000204.5 |  | 0.58 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200
BGC0001197.5 |  | 0.58 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001513.3 |  | 0.57 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000235.5 |  | 0.57 | PKS | kiamycin | Streptomyces sp. W007
BGC0001366.5 |  | 0.56 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000231.5 |  | 0.64 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000272.3 |  | 0.63 | PKS | spore pigment | Streptomyces collinus
BGC0001723.5 |  | 0.61 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000234.5 |  | 0.59 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000271.5 |  | 0.58 | PKS | spore pigment | Streptomyces avermitilis
BGC0000204.5 |  | 0.58 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200
BGC0001197.5 |  | 0.58 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001513.3 |  | 0.57 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000235.5 |  | 0.57 | PKS | kiamycin | Streptomyces sp. W007
BGC0001366.5 |  | 0.56 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
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:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.65 out of 18.46
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 24.07 out of 30.11
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (17):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.67 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 26.33
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.03 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.80 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.54 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.39 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.37 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.12 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 21.61 out of 36.54
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.37 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.68 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.85 out of 28.19
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.62 out of 20.01
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.76 out of 36.54
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.16 out of 36.53
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Type II PKS
TFBS Finder
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  169534 to 242035
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Product class(es):
  pentangular polyphenol
  tetracenomycin

F603_RS0100835
  KR (Score: 179.6; E-value: 2.1e-55)
F603_RS0100855
  CYC C4-C21/C2-C23|C2-C19 (Score: 134.9; E-value: 2.2e-42)
F603_RS0100865
  ACP (Score: 34.5; E-value: 3.6e-11)
F603_RS0100870
  CYC C9-C14 (Score: 241.3; E-value: 7.4e-75)
F603_RS0100875
  CYC C5-C18 (Score: 190.6; E-value: 2.1e-59)
F603_RS0100880
  KS (Score: 708.5; E-value: 5.8e-216)
F603_RS0100885
  CLF (Score: 463.3; E-value: 1.5e-141)
F603_RS0100910
  MET (Score: 221.3; E-value: 4.2e-68)
F603_RS0100920
  KR (Score: 169.0; E-value: 3.6e-52)
F603_RS0100955
  KR (Score: 62.8; E-value: 9.2e-20)
F603_RS0101010
  KR (Score: 133.0; E-value: 3.4e-41)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CelR | Cellobiose uptake repressor
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_KB905813.1 - Region 3 - RiPP-like,T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 569,454 - 610,569 nt. (total: 41,116 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS 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
F603_RS0102595: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F603_RS0102680: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

F603_RS0102690: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: acetyltransferase kinase methyltransferase
F603_RS0102645: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

F603_RS0102675: Methylation

MITE
  MITE0000155Methylation (identity: 64.10%)
smcogs
  SMCOG1150: isoprenylcysteine carboxyl methyltransferase

F603_RS0102685: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

F603_RS0102715: methyltransferase

smcogs
  SMCOG1089: methyltransferase

F603_RS0102770: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

Hydrolases: hydrolase
F603_RS0102635: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: synthase
F603_RS0102565: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

F603_RS0102660: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

F603_RS0102670: 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 | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000282.3 |  |  | 0.46 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002584.2 |  |  | 0.29 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0001294.5 |  |  | 0.24 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0000582.4 |  |  | 0.21 | ribosomal | cypemycin | Streptomyces sp. OH-4156
BGC0001513.3 |  |  | 0.21 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0001831.3 |  |  | 0.21 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001647.3 |  |  | 0.21 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0000632.5 |  |  | 0.20 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0000821.5 |  |  | 0.19 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0001985.4 |  |  | 0.19 | other (other) | Pyrazofurin | Streptomyces candidus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.76 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001831.3 |  | 0.54 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001077.4 |  | 0.50 | PKS | 6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone | Actinoplanes missouriensis 431
BGC0002362.3 |  | 0.46 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0002584.2 |  | 0.45 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0000131.5 |  | 0.45 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0002381.3 |  | 0.45 | PKS, other (other) | tambjamine BE-18591 | Streptomyces albus subsp. albus
BGC0000272.3 |  | 0.44 | PKS | spore pigment | Streptomyces collinus
BGC0000231.5 |  | 0.44 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000706.3 |  | 0.44 | saccharide | kanamycin | Streptomyces kanamyceticus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.39 out of 29.72
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (11):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.98 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.44 out of 18.57
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.89 out of 25.88
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.07 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.15 out of 30.97
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.03 out of 24.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.89 out of 25.88
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.95 out of 33.14
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_KB905813.1 - Region 4 - 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: 875,755 - 939,081 nt. (total: 63,327 nt) Show pHMM detection rules used
Region on contig edge.
T2PKS: (t2ks and t2clf)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
F603_RS0104070: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

F603_RS0104165: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F603_RS0104195: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

F603_RS0104265: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F603_RS0104275: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

F603_RS0104310: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase
F603_RS0104280: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: cyclase dehydratase
F603_RS0104025: L-carnitine dehydratase/bile acid-inducible

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

F603_RS0104160: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

F603_RS36360: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

Ligases: synthase
F603_RS0104175: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

F603_RS0104180: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000231.5 |  | 0.82 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.74 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001723.5 |  | 0.70 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002000.4 |  | 0.67 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0002514.3 |  | 0.61 | PKS | julichrome Q6.6 | Streptomyces sampsonii
BGC0001904.2 |  | 0.59 | PKS | fluostatin L, fluostatin D, difluostatin A, fluostatin C, fluostatin F, fluostatin G/H, fluostatin J, fluostatin K, rabelomycin | Micromonospora rosaria
BGC0002012.4 |  | 0.59 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772
BGC0000253.4 |  | 0.58 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000275.4 |  | 0.58 | PKS | tetracenomycin C | Streptomyces glaucescens
BGC0002712.2 |  | 0.58 | PKS | WS-5995 D, WS-5995 B, WS-5995 C, SEK 43 | Streptomyces yanglinensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000231.5 |  | 0.82 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.74 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001723.5 |  | 0.70 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002000.4 |  | 0.67 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0002514.3 |  | 0.61 | PKS | julichrome Q6.6 | Streptomyces sampsonii
BGC0001904.2 |  | 0.59 | PKS | fluostatin L, fluostatin D, difluostatin A, fluostatin C, fluostatin F, fluostatin G/H, fluostatin J, fluostatin K, rabelomycin | Micromonospora rosaria
BGC0002012.4 |  | 0.59 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772
BGC0000253.4 |  | 0.58 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000275.4 |  | 0.58 | PKS | tetracenomycin C | Streptomyces glaucescens
BGC0002712.2 |  | 0.58 | PKS | WS-5995 D, WS-5995 B, WS-5995 C, SEK 43 | Streptomyces yanglinensis

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: 16.26 out of 19.26
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.31 out of 23.79
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.17 out of 24.78
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.52 out of 29.72
Confidence: medium
Additional weak hits (21):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.61 out of 21.55
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.57 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.07 out of 30.11
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.74 out of 23.43
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.18 out of 25.75
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 21.45 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.18 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.16 out of 36.54
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.71 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.76 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.48 out of 27.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.15 out of 25.88
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.16 out of 29.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.66 out of 25.75
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.92 out of 18.57
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.35 out of 30.97
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.19 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.35 out of 28.19
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Type II PKS
TFBS Finder
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  875754 to 939081
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Malonyl elongations:
  8|9 (Score: 667.6; E-value: 1.2e-203)
Product class(es):
  angucycline
Product molecular weight(s):
  acetyl-CoA_8: 337 Da
  acetyl-CoA_9: 379 Da

F603_RS0104160
  CYC C7-C12 (Score: 445.9; E-value: 1.4e-136)
F603_RS0104165
  KR C9 (Score: 467.7; E-value: 2.2e-143)
F603_RS0104170
  ACP (Score: 112.3; E-value: 1.9e-35)
F603_RS0104175
  CLF 8|9 (Score: 667.6; E-value: 1.2e-203)
F603_RS0104180
  KS (Score: 765.6; E-value: 2.8e-233)
F603_RS0104265
  KR (Score: 200.0; E-value: 1.3e-61)
F603_RS0104310
  KR (Score: 177.3; E-value: 1.1e-54)
F603_RS36360
  CYC C4-C17/C2-C19 (Score: 149.0; E-value: 3.2e-46)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism
LexA variant 2 | Repressor of DNA damage response
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_KB905814.1 - Region 1 - lanthipeptide-class-iii,lipolanthine
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: 61,388 - 93,709 nt. (total: 32,322 nt) Show pHMM detection rules used
lipolanthine: (micKC and Flavoprotein)
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
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
F603_RS0104615: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: aminotransferase
F603_RS0104560: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Hydrolases: hydrolase
F603_RS0104565: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

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

Reference | lipolanthine | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000519.4 |  |  | 0.43 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000551.5 |  |  | 0.41 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000501.3 |  |  | 0.40 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000496.5 |  |  | 0.39 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000553.3 |  |  | 0.38 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000513.3 |  |  | 0.37 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000518.3 |  |  | 0.35 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002111.3 |  |  | 0.34 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000546.3 |  |  | 0.31 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0000527.5 |  |  | 0.30 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000519.4 |  | 0.54 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000551.5 |  | 0.53 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000501.3 |  | 0.52 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000496.5 |  | 0.52 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000553.3 |  | 0.51 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000513.3 |  | 0.50 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000518.3 |  | 0.49 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002111.3 |  | 0.48 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000546.3 |  | 0.46 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0001787.3 |  | 0.45 | ribosomal | suicin 3908 | 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.

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 F603_RS31580

F603_RS34610
Leader:
MTDFILDLQGMSSEDVE
Core:
V G E Q L A S S Y T T V L C G H S W T S I T C
Core with dehydrations:
V G E Q L A Dha Dha Y Dhb Dhb V L Cys G H Dha W Dhb Dha I Dhb Cys

#### antiSMASH-DB 4.0 matches for F603_RS34610

100.0%
NZ_KB905814.1:
Lanthipeptides: F603_RS34610_lanthipeptide
1
V G E Q L A S S Y T T V L C G H S W T S I T C
23
V G E Q L A S S Y T T V L C G H S W T S I T C
1
V G E Q L A S S Y T T V L C G H S W T S I T C
23
47.8%
NZ_CP019724.1:
Lanthipeptides: allorf_2155301_2155474_lanthipeptide
3
E Q L A S S Y T T V L C G H S W T S I T C
23
+ L A S S+T+V C S W S +C
3
D V L A S S W T S V C C K C S W V S T S C
23
47.8%
NZ_LZRD01000005.1 and 1 other:
NZ_LZRD01000005.1 Lanthipeptides: allorf_317314_317487_lanthipeptide
Lanthipeptides: allorf_317314_317487_lanthipeptide
3
E Q L A S S Y T T V L C G H S W T S I T C
23
+ L A S S+T+V C S W S +C
3
D V L A S S W T S V C C K C S W I S T S C
23
with 5 more sequence matches
36.0%
NZ_CP034350.1:
Lanthipeptides: D1J60_RS32970_lanthipeptide
1
V G E Q L A S S Y T T V L C G H S W T S I T
22
+G S + +L C G S S I T
1
L G G G G G S R A S L L L C G D S S L S I T
22
34.8%
NZ_RBWU01000007.1:
Lanthipeptides: BZB76_RS30440_lanthipeptide
11
T V L C G H S W T S I T
22
+V L C G H S S T
3
S V L C G H S S N S Q T
14
33.3%
NZ_BMVE01000003.1 and 12 others:
NZ_BMVL01000005.1 Lanthipeptides: IE257_RS16230_lanthipeptide NZ_CP011664.1 Lanthipeptides: M444_RS30240_lanthipeptide NZ_CP020039.1 Lanthipeptides: B4U39_RS34445_lanthipeptide NZ_CP020555.1 Lanthipeptides: B6R96_RS03515_lanthipeptide NZ_CP029189.1 Lanthipeptides: DEJ51_RS31910_lanthipeptide NZ_CP033581.1 Lanthipeptides: EES41_RS31595_lanthipeptide NZ_CP115936.1 Lanthipeptides: PET44_RS28650_lanthipeptide NZ_JAFLQY010000003.1 Lanthipeptides: J0X20_RS29030_lanthipeptide NZ_LIVP01000027.1 Lanthipeptides: AMK15_RS28680_lanthipeptide NZ_LWLD01000038.1 Lanthipeptides: A6A28_RS28600_lanthipeptide NZ_ML123038.1 Lanthipeptides: EES37_RS30340_lanthipeptide NZ_NNBM01000002.1 Lanthipeptides: CG724_RS07855_lanthipeptide
Lanthipeptides: IE248_RS10435_lanthipeptide
6
A S S Y T T V L C G H S W T S I T
22
S + +L C G S S I T
5
G S R A S L L L C G D S S L S I T
21
23.1%
NZ_KB467824.1:
Lanthipeptides: allorf_1564502_1564696_lanthipeptide
1
V G E Q L A S S Y T T V L C G H S W T S I T C
23
G Q S++ V C G T+I C
1
A G G Q A Q V S H S W V A C G Q C P T N I P C
23
19.4%
NZ_CP076356.1:
Lanthipeptides: allorf_0465169_0465315_lanthipeptide
1
V G E Q L A S S Y T T V L C
14
V G E+L A ++ L C
3
V G E K L A F K R S S E L C
16

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.99 out of 20.47
Confidence: medium
Additional weak hits (2):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.35 out of 30.25
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.09 out of 30.98
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

F603_RS34610 - Class III
  Cleavage pHMM score: 3.00
  RODEO score: 0
  Monoisotopic mass: 2252.1 Da
  Molecular weight: 2253.5 Da
  Number of bridges: 1
  Additional modifications: AviCys
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2271.6 Da N = 1
    2289.6 Da N = 2
    2307.6 Da N = 3
    2325.6 Da N = 4
    2343.6 Da N = 5
    2361.7 Da N = 6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_KB905814.1 - Region 2 - linaridin
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: 122,267 - 142,818 nt. (total: 20,552 nt) Show pHMM detection rules used
linaridin: (cypemycin or cypI)

#### 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
F603_RS0104835: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

F603_RS0104850: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: methyltransferase
F603_RS0104860: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: dehalogenase hydrolase
F603_RS0104855: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

F603_RS0104870: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

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 | linaridin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000495.5 |  | 0.44 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0000503.5 |  | 0.42 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0001374.5 |  | 0.42 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0000817.4 |  | 0.42 | other (other) | methylarcyriarubin | uncultured bacterium
BGC0000528.5 |  | 0.41 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001483.4 |  | 0.40 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000874.5 |  | 0.38 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0000706.3 |  | 0.38 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001336.5 |  | 0.38 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001277.4 |  | 0.38 | terpene | 15-acetyldeoxynivalenol, 3-decalonectrin | Fusarium graminearum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000495.5 |  | 0.44 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0000503.5 |  | 0.42 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0001374.5 |  | 0.42 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0000817.4 |  | 0.42 | other (other) | methylarcyriarubin | uncultured bacterium
BGC0000528.5 |  | 0.41 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001483.4 |  | 0.40 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000874.5 |  | 0.38 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0000706.3 |  | 0.38 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001336.5 |  | 0.38 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001277.4 |  | 0.38 | terpene | 15-acetyldeoxynivalenol, 3-decalonectrin | Fusarium graminearum

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:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.72 out of 27.04
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.19 out of 23.79
Confidence: medium
Additional weak hits (3):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.54 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.41 out of 27.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 24.17 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism

NZ_KB905814.1 - Region 3 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 267,516 - 289,018 nt. (total: 21,503 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
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 | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002053.3 |  | 0.74 | ribosomal | ulleungdin | Streptomyces sp.
BGC0002074.2 |  | 0.70 | ribosomal | huascopeptin | Streptomyces huasconensis
BGC0001507.3 |  | 0.69 | ribosomal | anantin C | Streptomyces olindensis
BGC0001645.3 |  | 0.65 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0001307.3 |  | 0.64 | ribosomal | chaxapeptin | Streptomyces leeuwenhoekii
BGC0001539.4 |  | 0.64 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001493.5 |  | 0.63 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001551.4 |  | 0.60 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0002318.2 |  | 0.60 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0001889.2 |  | 0.60 | ribosomal | fusilassin | Thermobifida fusca YX

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002053.3 |  | 0.74 | ribosomal | ulleungdin | Streptomyces sp.
BGC0002074.2 |  | 0.70 | ribosomal | huascopeptin | Streptomyces huasconensis
BGC0001507.3 |  | 0.69 | ribosomal | anantin C | Streptomyces olindensis
BGC0001645.3 |  | 0.65 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0001307.3 |  | 0.64 | ribosomal | chaxapeptin | Streptomyces leeuwenhoekii
BGC0001539.4 |  | 0.64 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001493.5 |  | 0.63 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001551.4 |  | 0.60 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0002318.2 |  | 0.60 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0001889.2 |  | 0.60 | ribosomal | fusilassin | Thermobifida fusca YX

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

No significant matches found.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.36 out of 19.26
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.57 out of 20.97
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.38 out of 29.72
Confidence: medium
Additional weak hits (8):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.44 out of 27.78
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.42 out of 26.12
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.41 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.08 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.27 out of 30.25
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: 19.59 out of 33.73
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (267515...289018)
F603_RS0105485
  RRE type: Stand_Alone_Lasso_RRE
  Location: 19 - 93
  Score: 81.0

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
NtrC | Nitrogen regulatory protein C

NZ_KB905814.1 - Region 4 - 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: 455,124 - 529,144 nt. (total: 74,021 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
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
F603_RS0106470: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

F603_RS31685: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acyltransferase glycosyltransferase methyltransferase
F603_RS0106260: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

F603_RS0106340: methyltransferase

smcogs
  SMCOG1089: methyltransferase

F603_RS0106345: methyltransferase

smcogs
  SMCOG1248: methyltransferase

F603_RS0106375: methyltransferase

smcogs
  SMCOG1089: methyltransferase

F603_RS0106430: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

Hydrolases: dehalogenase esterase hydrolase
F603_RS0106270: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

F603_RS0106305: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

F603_RS0106365: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase
F603_RS0106405: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

F603_RS0106485: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
F603_RS0106335: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

F603_RS0106400: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

F603_RS0106410: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F603_RS0106415: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F603_RS0106450: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

F603_RS0106475: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

F603_RS31675: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F603_RS33370: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

F603_RS33375: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001249.5 |  |  | 0.84 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  |  | 0.79 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  |  | 0.77 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  |  | 0.76 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002164.2 |  |  | 0.74 | NRPS | peramine | Epichloe festucae
BGC0001135.5 |  |  | 0.74 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  |  | 0.73 | NRPS | enniatin | Fusarium equiseti
BGC0001833.4 |  |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  | 0.71 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.70 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.70 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002164.2 |  | 0.70 | NRPS | peramine | Epichloe festucae
BGC0001135.5 |  | 0.70 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001833.4 |  | 0.69 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

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

No significant matches found.

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
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.68 out of 19.52
Confidence: medium
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 26.47 out of 30.22
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.17 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.19 out of 19.26
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 23.72 out of 27.18
Confidence: medium
Additional weak hits (28):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.31 out of 21.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.28 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.69 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.71 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.12 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.42 out of 31.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.02 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.97 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.33 out of 30.97
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.44 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.98 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.10 out of 26.06
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.62 out of 25.88
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.33 out of 39.62
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.99 out of 35.63
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.37 out of 29.25
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: 19.35 out of 28.19
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.82 out of 36.53
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.19 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.44 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
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.06 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.83 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.23 out of 26.06
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 455123 - 529144:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

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).
F603_RS33370: X - fatty_acid
AMP-binding (474..808): 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:
    SWLTLAASVHAWLLLTDGGHWLWALPEAGGFTAA
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

CAL_domain (1038..1455): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 23.8
  NH2: 22.4
  Acetyl-CoA: 9.9
  shikimic_acid: 0.0
  AHBA: 0.0

F603_RS33375: mal
PKS_AT (544..822): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 62.5%
  inactive: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 100.4
  Methoxymalonyl-CoA: 52.7
  inactive: 46.5
  Methylmalonyl-CoA: 40.3
  Propionyl-CoA: 29.5
  Ethylmalonyl-CoA: 19.4
  2-Methylbutyryl-CoA: 11.8
  fatty_acid: 7.6
  Isobutyryl-CoA: 6.7
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

F603_RS31675: Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (511..907): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWQAFDISVNELYIWCGGEYHGYGPAEATIGVSC
  Nearest Stachelhaus code(s):
    Orn DINYWGGIGK (94% 8Å match)
    Fo-OH-Orn DINYWGGIGK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

F603_RS0106400: mal
PKS_AT (535..816): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 140.2
  Methoxymalonyl-CoA: 63.7
  inactive: 63.4
  Methylmalonyl-CoA: 41.5
  Propionyl-CoA: 33.9
  fatty_acid: 21.4
  Ethylmalonyl-CoA: 17.9
  2-Methylbutyryl-CoA: 17.4
  Isobutyryl-CoA: 15.8
  CHC-CoA: 15.8
  trans-1,2-CPDA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

F603_RS0106410: Cys - Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (191..592): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDVSFDLSLWDGMGILGGDVGLGGNTEASILSCT
  Nearest Stachelhaus code(s):
    Leu DLLHLGLILK (35% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1254..1650): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AETTHDMSVFDGNSFLGGDVSVGGPTETTLWNIW
  Nearest Stachelhaus code(s):
    Cys DMFNFGVLWK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

F603_RS0106415: Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (14..403): 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:
    FWVSFDLSVFEGNTNLAGEHNLYGPSEDTTYSTW
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
ClgR | Caseinolytic protease gene regulator
IolR | Regulator of the inositol catabolism
NrdR | Represses ribonucleotide reductase encoding genes
VqsM | Regulator of quorum-sensing signalling systems

NZ_KB905815.1 - Region 1 - 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: 53,961 - 64,365 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
F603_RS0108360: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: aminotransferase
F603_RS0108345: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-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 | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.86 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.85 | 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
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
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 |  | 0.85 | 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
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
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:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
Additional weak hits (4):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.57 out of 21.55
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.30 out of 31.73
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.25 out of 20.01
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

NZ_KB905815.1 - Region 2 - 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: 487,959 - 509,026 nt. (total: 21,068 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
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
Hydrolases: peptidase
F603_RS0110225: gamma-glutamyltranspeptidase

smcogs
  SMCOG1274: gamma-glutamyltranspeptidase

Ligases: synthetase
F603_RS0110255: 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
BGC0002436.2 |  | 0.42 | other (other) | coformycin | Streptomyces citricolor
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000504.5 |  | 0.40 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000502.5 |  | 0.39 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0002698.2 |  | 0.39 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001075.5 |  | 0.36 | PKS, terpene | aurachin RE | Rhodococcus erythropolis

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
BGC0002436.2 |  | 0.42 | other (other) | coformycin | Streptomyces citricolor
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000504.5 |  | 0.40 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000502.5 |  | 0.39 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0002698.2 |  | 0.39 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001075.5 |  | 0.36 | PKS, terpene | aurachin RE | Rhodococcus erythropolis

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:
F603_RS0110255: PT_FPPS_like
Domain 1 (64 - 353): 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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.56 out of 20.97
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.39 out of 25.31
Confidence: medium
Additional weak hits (8):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.63 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.66 out of 20.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.83 out of 26.12
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.78 out of 21.55
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
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
--- | ---
CatR | H2O2-responsive repressor
CcpA | Catabolite control protein A

NZ_KB905816.1 - Region 1 - 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: 89,785 - 168,918 nt. (total: 79,134 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
F603_RS0112400: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

F603_RS0112495: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F603_RS0112500: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F603_RS0112515: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

F603_RS0112535: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

F603_RS32010: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: acylase
F603_RS0112480: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

F603_RS0112485: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase
F603_RS0112525: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase
F603_RS0112465: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
F603_RS0112415: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F603_RS0112475: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

F603_RS0112490: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

F603_RS0112545: 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 | T1PKS | 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 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000041.3 |  | 0.64 | PKS | oronofacic acid | Pseudomonas syringae
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
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1

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 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000041.3 |  | 0.64 | PKS | oronofacic acid | Pseudomonas syringae
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
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002191.2 |  | 0.63 | 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.
No hits above weak threshold.
Weak hits (14):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.05 out of 27.55
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.58 out of 26.12
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.00 out of 18.57
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 18.77 out of 33.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.83 out of 31.73
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.07 out of 32.74
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.40 out of 24.78
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.37 out of 30.98
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.31 out of 32.93
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.03 out of 25.88
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.92 out of 23.43
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.58 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.30 out of 33.14
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.46 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 1, location 89784 - 168918:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk - ccmal) + (ccmal - pk) + (ohmal) + (Me-redmal) + (ohemal) + (ohmal)
Non-colinear ordering:
  F603_RS0112475 + F603_RS0112480 + F603_RS0112485 + F603_RS0112495 + F603_RS0112500 + F603_RS0112490

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).
F603_RS0112415: X
AMP-binding (12..391): 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:
    SALLHGLILG-GFGVSGSAVERYGMTETLMNTSV
  Nearest Stachelhaus code(s):
    nohBza GLGLVGAIIK (44% 8Å match)
  Stachelhaus code match:
    60% (weak)

F603_RS0112475: pk - mal
PKS_AT (231..525): pk
ATSignature: CHC-CoA

Top 3 matches:
  CHC-CoA: 95.8%
  Ethylmalonyl-CoA: 66.7%
  Methoxymalonyl-CoA: 66.7%

minowa: CHC-CoA

Prediction, score:
  CHC-CoA: 198.0
  Ethylmalonyl-CoA: 156.2
  Methylmalonyl-CoA: 154.1
  Methoxymalonyl-CoA: 128.9
  2-Methylbutyryl-CoA: 113.4
  trans-1,2-CPDA: 105.4
  Propionyl-CoA: 99.5
  Malonyl-CoA: 78.6
  Isobutyryl-CoA: 63.9
  Benzoyl-CoA: 60.2
  Acetyl-CoA: 28.2
  fatty_acid: 26.7
  3-Methylbutyryl-CoA: 14.2
  inactive: 11.4

PKS_AT (1197..1461): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 62.5%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 121.3
  Methoxymalonyl-CoA: 65.7
  inactive: 50.6
  Methylmalonyl-CoA: 35.2
  Isobutyryl-CoA: 22.1
  Acetyl-CoA: 21.3
  Propionyl-CoA: 19.1
  Ethylmalonyl-CoA: 15.5
  trans-1,2-CPDA: 11.3
  CHC-CoA: 8.8
  fatty_acid: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

F603_RS0112480: mal - pk
PKS_AT (555..823): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 62.5%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 119.7
  Methoxymalonyl-CoA: 70.0
  inactive: 53.7
  Methylmalonyl-CoA: 39.2
  Acetyl-CoA: 25.2
  Ethylmalonyl-CoA: 21.8
  Propionyl-CoA: 18.9
  Isobutyryl-CoA: 16.6
  trans-1,2-CPDA: 13.6
  CHC-CoA: 11.1
  fatty_acid: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

PKS_AT (2250..2541): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 213.8
  Methylmalonyl-CoA: 207.7
  Methoxymalonyl-CoA: 171.5
  2-Methylbutyryl-CoA: 130.3
  Malonyl-CoA: 119.6
  trans-1,2-CPDA: 117.1
  Propionyl-CoA: 111.7
  CHC-CoA: 105.2
  Isobutyryl-CoA: 80.3
  Benzoyl-CoA: 72.7
  Acetyl-CoA: 61.7
  fatty_acid: 40.8
  inactive: 38.3
  3-Methylbutyryl-CoA: 21.6

F603_RS0112485: mal
PKS_AT (571..859): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 178.6
  inactive: 79.8
  Methoxymalonyl-CoA: 75.7
  Methylmalonyl-CoA: 57.4
  Propionyl-CoA: 27.7
  Acetyl-CoA: 22.8
  CHC-CoA: 21.3
  Benzoyl-CoA: 18.1
  fatty_acid: 18.0
  2-Methylbutyryl-CoA: 17.8
  Isobutyryl-CoA: 16.9
  Ethylmalonyl-CoA: 12.9
  trans-1,2-CPDA: 10.7
  3-Methylbutyryl-CoA: 0.0

F603_RS0112490: mal
PKS_AT (558..831): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 176.3
  inactive: 100.2
  Methoxymalonyl-CoA: 73.8
  Methylmalonyl-CoA: 60.5
  Propionyl-CoA: 41.6
  Isobutyryl-CoA: 38.9
  Acetyl-CoA: 35.5
  Ethylmalonyl-CoA: 32.2
  2-Methylbutyryl-CoA: 32.0
  CHC-CoA: 31.0
  Benzoyl-CoA: 25.6
  trans-1,2-CPDA: 21.9
  fatty_acid: 18.3
  3-Methylbutyryl-CoA: 7.5

F603_RS0112495: mmal
PKS_AT (573..872): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 201.4
  Ethylmalonyl-CoA: 184.9
  Methoxymalonyl-CoA: 161.8
  2-Methylbutyryl-CoA: 139.9
  Malonyl-CoA: 110.3
  Propionyl-CoA: 107.2
  CHC-CoA: 99.2
  trans-1,2-CPDA: 97.8
  Isobutyryl-CoA: 81.0
  Benzoyl-CoA: 79.4
  Acetyl-CoA: 78.3
  fatty_acid: 43.9
  3-Methylbutyryl-CoA: 39.9
  inactive: 36.3

F603_RS0112500: emal
PKS_AT (574..873): emal
ATSignature: Ethylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 183.0
  Methylmalonyl-CoA: 180.1
  Methoxymalonyl-CoA: 150.3
  2-Methylbutyryl-CoA: 113.9
  Malonyl-CoA: 97.5
  CHC-CoA: 97.4
  trans-1,2-CPDA: 95.6
  Propionyl-CoA: 93.7
  Isobutyryl-CoA: 76.0
  Benzoyl-CoA: 63.5
  Acetyl-CoA: 61.0
  fatty_acid: 36.5
  inactive: 22.6
  3-Methylbutyryl-CoA: 19.4

F603_RS0112545: X
AMP-binding (457..886): X
nrpys: Asp, Asn, Glu, Gln, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AMESHTGFLYGLQAVATGACGAFGTTETCLAALS
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

Regulator | Description
--- | ---

NZ_KB905816.1 - Region 2 - 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: 527,115 - 574,350 nt. (total: 47,236 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 oxidoreductase
F603_RS0114390: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

F603_RS0114410: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Lyases: cyclase dehydratase
F603_RS0114340: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

F603_RS0114345: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

F603_RS0114450: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

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

Reference | lanthipeptide-class-i | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002707.2 |  |  | 0.23 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0002535.2 |  |  | 0.20 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0001226.4 |  |  | 0.18 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000563.4 |  |  | 0.17 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0002514.3 |  |  | 0.17 | PKS | julichrome Q6.6 | Streptomyces sampsonii
BGC0001300.5 |  |  | 0.16 | PKS | anthracimycin | Streptomyces sp. CNH365
BGC0001579.4 |  |  | 0.16 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0002220.2 |  |  | 0.16 | terpene | Ent-kauren-16alpha-ol | Punctularia strigosozonata HHB-11173 SS5
BGC0000221.5 |  |  | 0.15 | PKS | erdacin | uncultured soil bacterium V167
BGC0001965.4 |  |  | 0.15 | other (other) | nybomycin | Streptomyces albus subsp. chlorinus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001226.4 |  | 0.49 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000563.4 |  | 0.48 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0002635.2 |  | 0.48 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0001727.3 |  | 0.48 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0001579.4 |  | 0.47 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000540.5 |  | 0.46 | ribosomal | paenibacillin | Paenibacillus polymyxa OSY-DF
BGC0000503.5 |  | 0.45 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0001229.4 |  | 0.45 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0001660.3 |  | 0.45 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000605.5 |  | 0.45 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365

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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (8):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.24 out of 31.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.00 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.84 out of 29.38
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.27 out of 20.01
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.76 out of 18.57
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.55 out of 26.12
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.88 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
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 (527114...552323)
F603_RS0114340
  RRE type: Lanthipeptide_LanB_RRE
  Location: 156 - 247
  Score: 59.8

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_KB905816.1 - Region 3 - 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: 584,547 - 611,217 nt. (total: 26,671 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
F603_RS0114650: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

Transferases: aminotransferase transferase
F603_RS0114580: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

F603_RS0114655: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Ligases: synthetase
F603_RS0114600: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Translocases: transport
F603_RS0114625: 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
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.65 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.58 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000664.5 |  | 0.50 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000852.5 |  | 0.48 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.65 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.58 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000664.5 |  | 0.50 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000852.5 |  | 0.48 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163

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
--- | --- | --- | --- | --- | ---
triterpene | hopanoid |  | C30 | hopanoid skeleton | unknown
triterpene | polypodane |  | C30 | polypodane skeleton | unknown

Genes with terpene domains:
F603_RS0114595: T2TS
Domain 1 (51 - 686): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

F603_RS0114600: PT_FPPS_like
Domain 1 (61 - 354): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

F603_RS0114610: PT_phytoene_like
Domain 1 (17 - 300): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

F603_RS0114615: PT_phytoene_like
Domain 1 (11 - 279): 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:
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: 17.23 out of 19.52
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.67 out of 19.26
Confidence: medium
Additional weak hits (5):
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.65 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.31 out of 24.78
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.37 out of 30.98
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.33 out of 29.25
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.00 out of 32.38
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
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein

NZ_KB905817.1 - Region 1 - NRPS,T1PKS,transAT-PKS-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: 207,021 - 301,164 nt. (total: 94,144 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))
transAT-PKS-like: cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS) and not PKS_AT)
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
F603_RS0116340: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

F603_RS0116350: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

F603_RS0116365: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

F603_RS0116415: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase acylase glycosyltransferase methyltransferase transferase
F603_RS0116330: methyltransferase

smcogs
  SMCOG1089: methyltransferase

F603_RS0116335: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

F603_RS0116380: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

F603_RS0116385: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

F603_RS0116435: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: amidase back translocase esterase
F603_RS0116375: amidase

smcogs
  SMCOG1105: amidase

F603_RS0116445: thioesterase

smcogs
  SMCOG1004: thioesterase

F603_RS0116460: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

F603_RS0116465: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

Lyases: dehydratase
F603_RS0116355: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

F603_RS0116390: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
F603_RS0116400: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

F603_RS0116405: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

F603_RS0116410: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

F603_RS0116420: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

F603_RS0116425: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

F603_RS0116430: 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 | transAT-PKS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001160.5 |  |  |  | 0.77 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  |  | 0.77 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000041.3 |  |  |  | 0.67 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001135.5 |  |  |  | 0.60 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  |  | 0.59 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  |  |  | 0.59 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  |  |  | 0.58 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  | 0.58 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  | 0.58 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000357.5 |  |  |  | 0.58 | 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

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002276.2 |  | 0.64 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.63 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001268.4 |  | 0.63 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002164.2 |  | 0.63 | NRPS | peramine | Epichloe festucae

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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (3):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.78 out of 39.62
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.65 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 1, location 207020 - 301164:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 214903 - 301164:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - ccmal) + (Me-ohmal - ohmal - mal) + (Gly - ccmal) + (Me-ccmal - mal - ohmal - ohmal - ccmal) + (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).
F603_RS0116335: pk - mal
PKS_AT (7..297): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 58.3%

minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 32.4
  Malonyl-CoA: 26.7
  Methylmalonyl-CoA: 21.6
  Isobutyryl-CoA: 17.0
  Propionyl-CoA: 13.1
  inactive: 11.9
  fatty_acid: 8.9
  trans-1,2-CPDA: 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

PKS_AT (339..618): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 121.2
  inactive: 35.9
  Methoxymalonyl-CoA: 35.8
  Methylmalonyl-CoA: 33.3
  Propionyl-CoA: 31.8
  2-Methylbutyryl-CoA: 16.7
  fatty_acid: 9.9
  trans-1,2-CPDA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

F603_RS0116420: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (529..923): 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:
    FSMTFDIAGLELQALCGGEWNMYGPTETTIWSSV
  Nearest Stachelhaus code(s):
    Gly DILQLGMIWK (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
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production

NZ_KB905818.1 - Region 1 - 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: 44,692 - 77,255 nt. (total: 32,564 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
F603_RS0117535: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

Isomerases: mutase
F603_RS0117540: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.55 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000942.4 |  | 0.54 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001713.5 |  | 0.52 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0000941.3 |  | 0.51 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002469.2 |  | 0.50 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0000939.5 |  | 0.50 | other (other) | aerobactin | Grimontia hollisae
BGC0002305.2 |  | 0.49 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0002633.2 |  | 0.47 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002683.2 |  | 0.47 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.55 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000942.4 |  | 0.54 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001713.5 |  | 0.52 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0000941.3 |  | 0.51 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002469.2 |  | 0.50 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0000939.5 |  | 0.50 | other (other) | aerobactin | Grimontia hollisae
BGC0002305.2 |  | 0.49 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0002633.2 |  | 0.47 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002683.2 |  | 0.47 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.91 out of 19.26
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.29 out of 23.79
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.93 out of 24.78
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 23.01 out of 27.18
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.44 out of 27.18
Confidence: medium
Additional weak hits (9):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.34 out of 25.88
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.15 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.51 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
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
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.32 out of 27.18
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.39 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.46 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism
LexA variant 2 | Repressor of DNA damage response
NrdR | Represses ribonucleotide reductase encoding genes
RpoN | Regulator of nitrogen assimilation and virulence

NZ_KB905818.1 - Region 2 - 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: 330,686 - 378,047 nt. (total: 47,362 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
F603_RS0118720: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

F603_RS0118745: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

F603_RS0118770: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

F603_RS32380: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Transferases: kinase
F603_RS32375: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Hydrolases: hydrolase
F603_RS0118750: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase
F603_RS0118740: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transport
F603_RS0118680: 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 |  | 0.72 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001276.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  | 0.66 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.66 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.60 | PKS | ACT-Toxin II | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002191.2 |  | 0.72 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001276.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  | 0.66 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.66 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.60 | 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:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.07 out of 30.12
Confidence: medium
Additional weak hits (9):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.61 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.61 out of 21.55
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.23 out of 26.85
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.04 out of 29.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.98 out of 25.88
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.11 out of 30.22
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.49 out of 33.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.04 out of 23.43
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 2, location 330685 - 378047:
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).
F603_RS0118740: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (26..432): diOH-Bz
nrpys: diOH-Bz

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VNALFTCAHPGGALQVGGAQQVYGMSEGLLSFTR
  Nearest Stachelhaus code(s):
    diOH-Bz PLPAQGVLCK (71% 8Å match)
    Sal PLPAQGVLNK (65% 8Å match)
  Stachelhaus code match:
    70% (weak)

F603_RS0118745: pk
PKS_AT (536..832): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  Methylmalonyl-CoA: 66.7%
  Methoxymalonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 109.1
  Methoxymalonyl-CoA: 97.7
  Malonyl-CoA: 90.8
  Ethylmalonyl-CoA: 69.3
  2-Methylbutyryl-CoA: 64.0
  Isobutyryl-CoA: 58.0
  Propionyl-CoA: 53.1
  trans-1,2-CPDA: 45.9
  fatty_acid: 33.9
  Acetyl-CoA: 26.3
  CHC-CoA: 23.1
  inactive: 17.0
  Benzoyl-CoA: 15.7
  3-Methylbutyryl-CoA: 3.5

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_KB905819.1 - Region 1 - 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: 10,722 - 35,292 nt. (total: 24,571 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
Lyases: cyclase dehydratase
F603_RS0119400: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

F603_RS0119405: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

Ligases: ligase
F603_RS0119370: 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-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000544.4 |  | 0.79 | ribosomal | planosporicin | Planomonospora alba
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002635.2 |  | 0.70 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0002274.2 |  | 0.56 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001289.5 |  | 0.55 | ribosomal | penisin | Paenibacillus ehimensis
BGC0001579.4 |  | 0.53 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0001660.3 |  | 0.52 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000542.3 |  | 0.52 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.51 | ribosomal | paenicidin A | Paenibacillus polymyxa

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000544.4 |  | 0.79 | ribosomal | planosporicin | Planomonospora alba
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002635.2 |  | 0.70 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0002274.2 |  | 0.56 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001289.5 |  | 0.55 | ribosomal | penisin | Paenibacillus ehimensis
BGC0001579.4 |  | 0.53 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0001660.3 |  | 0.52 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000542.3 |  | 0.52 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.51 | ribosomal | paenicidin A | Paenibacillus polymyxa

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 F603_RS0119405

F603_RS34750
Leader:
MGINSPADVRNDEGLLDLDLEIGVEKSVAGPA
Core:
V T S I S Y C T P G C T S E G G G S G C S H C C
Core with dehydrations:
V Dhb Dha I Dha Y Cys Dhb P G Cys Dhb Dha E G G G Dha G Cys Dha H Cys Cys

#### antiSMASH-DB 4.0 matches for F603_RS34750

100.0%
NZ_KB905819.1:
Lanthipeptides: F603_RS34750_lanthipeptide
1
V T S I S Y C T P G C T S E G G G S G C S H C C
24
V T S I S Y C T P G C T S E G G G S G C S H C C
1
V T S I S Y C T P G C T S E G G G S G C S H C C
24
95.8%
NZ_CP007699.2:
Lanthipeptides: T261_RS08380_lanthipeptide
1
V T S I S Y C T P G C T S E G G G S G C S H C C
24
V T S I S Y C T P G C T S+G G G S G C S H C C
1
V T S I S Y C T P G C T S D G G G S G C S H C C
24
95.8%
NZ_CP048882.1 and 1 other:
NZ_CP048882.1 Lanthipeptides: G4Z16_RS06545_lanthipeptide
Lanthipeptides: G4Z16_RS06545_lanthipeptide
1
V T S I S Y C T P G C T S E G G G S G C S H C C
24
+T S I S Y C T P G C T S E G G G S G C S H C C
1
I T S I S Y C T P G C T S E G G G S G C S H C C
24
with 103 more sequence matches
Only the first 10 are displayed here.
95.8%
NZ_JAMTCQ010000009.1:
Lanthipeptides: LY41_RS11610_lanthipeptide
1
V T S I S Y C T P G C T S E G G G S G C S H C C
24
V T S+S Y C T P G C T S E G G G S G C S H C C
1
V T S V S Y C T P G C T S E G G G S G C S H C C
24
91.7%
NZ_FMHI01000015.1 and 1 other:
NZ_LIXJ01000007.1 Lanthipeptides: AMK22_RS13160_lanthipeptide
Lanthipeptides: H180DRAFT_RS21560_lanthipeptide
1
V T S I S Y C T P G C T S E G G G S G C S H C C
24
+T S+S Y C T P G C T S E G G G S G C S H C C
1
I T S V S Y C T P G C T S E G G G S G C S H C C
24
91.7%
NZ_JADDUE010000020.1:
Lanthipeptides: INP57_RS28495_lanthipeptide
1
V T S I S Y C T P G C T S E G G G S G C S H C C
24
V T S+S Y C T P G C T S E G G G S C S H C C
1
V T S V S Y C T P G C T S E G G G S N C S H C C
24
87.5%
NZ_JAMHJQ010000009.1 and 2 others:
NZ_KN039946.1 Lanthipeptides: FM21_RS35825_lanthipeptide NZ_LIPF01000002.1 Lanthipeptides: AMK11_RS10850_lanthipeptide
Lanthipeptides: M1203_RS22635_lanthipeptide
1
V T S I S Y C T P G C T S E G G G S G C S H C C
24
+T S+S+C T P G C T S E G G G S G C S H C C
1
I T S V S W C T P G C T S E G G G S G C S H C C
24
87.5%
NZ_LIVZ01000011.1:
Lanthipeptides: AMK31_RS29125_lanthipeptide
1
V T S I S Y C T P G C T S E G G G S G C S H C C
24
+T S+S Y C T P G C T S+G G G S G C S H C C
1
I T S V S Y C T P G C T S D G G G S G C S H C C
24
83.3%
NZ_JACHEM010000003.1:
Lanthipeptides: HNQ79_RS07795_lanthipeptide
1
V T S I S Y C T P G C T S E G G G S G C S H C C
24
+T S+S+C T P G C T S+G G G S G C S H C C
1
I T S V S W C T P G C T S D G G G S G C S H C C
24
79.2%
NZ_AXWW01000016.1 and 1 other:
NZ_JAMTCO010000009.1 Lanthipeptides: LV75_RS20160_lanthipeptide
Lanthipeptides: H504_RS39505_lanthipeptide
1
V T S I S Y C T P G C T S E G G G S G C S H C C
24
+T S I S C T P G C T S G G G S C S C C
1
I T S I S L C T P G C T S A G G G S N C S F C C
24
79.2%
NZ_FMZZ01000002.1:
Lanthipeptides: BLS56_RS30480_lanthipeptide
1
V T S I S Y C T P G C T S E G G G S G C S H C C
24
V T S+S C T P G C T S G G G S C S C C
1
V T S V S L C T P G C T S P G G G S N C S F C C
24
79.2%
NZ_KI866523.1:
Lanthipeptides: MPTA5024_RS39835_lanthipeptide
1
V T S I S Y C T P G C T S E G G G S G C S H C C
24
V T S S C T P G C T S G G G S C S C C
1
V T S W S L C T P G C T S P G G G S N C S F C C
24
75.0%
NZ_AP023356.1:
Lanthipeptides: Aiant_RS23765_lanthipeptide
1
V T S I S Y C T P G C T S E G G G S G C S H C C
24
+T S+S C T P G C T S G G G S C S C C
1
I T S V S L C T P G C T S A G G G S Q C S F C C
24

#### MIBiG 4.0 matches for F603_RS34750

35.3%
BGC0000535.4 (ADJ56352.1):
Lanthipeptide: nisin A
1
V T S I S Y C T P G C T S E G G G S G C S
21
+T S I S C T P G C + G G C+
1
I T S I S L C T P G C K T-G A L M G C N
20

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.23 out of 27.18
Confidence: medium
Additional weak hits (6):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.56 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.76 out of 29.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.41 out of 35.63
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.31 out of 32.93
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.34 out of 29.65
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.45 out of 30.98
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.

F603_RS34750 - Class I
  Cleavage pHMM score: 9.60
  RODEO score: 27
  Monoisotopic mass: 2150.8 Da
  Molecular weight: 2152.4 Da
  Number of bridges: 5
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2170.4 Da N = 1
    2188.4 Da N = 2
    2206.4 Da N = 3

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (10721...35292)
F603_RS0119405
  RRE type: Lanthipeptide_LanB_RRE
  Location: 174 - 264
  Score: 50.9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_KB905819.1 - Region 2 - azole-containing-RiPP
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 51,102 - 83,722 nt. (total: 32,621 nt) Show pHMM detection rules used
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
Azole RiPPs
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
Ligases: ligase
F603_RS0119590: 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 | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.54 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000662.5 |  | 0.52 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001146.5 |  | 0.50 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0001592.5 |  | 0.50 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0002826.2 |  | 0.50 | other (other) | closoxazole A, closoxazole B | Clostridium cavendishii DSM 21758
BGC0000606.5 |  | 0.50 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0000889.5 |  | 0.50 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0002311.3 |  | 0.49 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0001295.5 |  | 0.49 | other (other) | cremeomycin | Streptomyces cremeus
BGC0001145.5 |  | 0.48 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.54 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000662.5 |  | 0.52 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001146.5 |  | 0.50 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0001592.5 |  | 0.50 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0002826.2 |  | 0.50 | other (other) | closoxazole A, closoxazole B | Clostridium cavendishii DSM 21758
BGC0000606.5 |  | 0.50 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0000889.5 |  | 0.50 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0002311.3 |  | 0.49 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0001295.5 |  | 0.49 | other (other) | cremeomycin | Streptomyces cremeus
BGC0001145.5 |  | 0.48 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847

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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.40 out of 20.97
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.36 out of 25.31
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (8):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.50 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.42 out of 20.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.25 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.33 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.36 out of 29.25
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: 20.12 out of 29.65
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
RREFinder
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (51101...83722)
F603_RS0119620
  RRE type: Thiopeptide_F_RRE
  Location: 0 - 82
  Score: 37.6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor
CcpA | Catabolite control protein A

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
NZ_KB905819.1 - Region 3 - 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: 207,993 - 258,573 nt. (total: 50,581 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 synthase
F603_RS0120215: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

F603_RS0120230: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

F603_RS0120295: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Hydrolases: synthase
F603_RS0120230: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

Ligases: ligase synthase
F603_RS0120285: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

F603_RS0120315: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.70 | 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 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti

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 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.70 | 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 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
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.

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: 19.79 out of 23.79
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
Additional weak hits (21):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.45 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.60 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.36 out of 21.55
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.56 out of 28.14
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.76 out of 26.85
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.28 out of 26.33
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.21 out of 23.43
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.71 out of 26.85
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.17 out of 20.97
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.24 out of 25.88
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.50 out of 25.88
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.58 out of 33.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.33 out of 23.43
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
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.01 out of 36.54
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.29 out of 33.73
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.80 out of 35.63
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 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
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 3, location 207992 - 258573:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Orn - Orn - 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).
F603_RS0120315: Orn - Orn - Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (473..950): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LHHAFDAAWDPWETALGGEYNFYGPTEATVDAVT
  Nearest Stachelhaus code(s):
    Lys DADDAGTVDK (68% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1613..2015): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LHHAFDASWDPWETALGGEWNLYGPTEATVDSTA
  Nearest Stachelhaus code(s):
    OH-Orn DAQEGGLVDK (74% 8Å match)
    Lys DADDAGTVDK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2674..3075): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LHHAFDASWDPWETALGGEWNLYGPTEATVDTLC
  Nearest Stachelhaus code(s):
    OH-Orn DAQEGGLVDK (71% 8Å match)
    Lys DADDAGTVDK (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
--- | ---
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence

NZ_KB905821.1 - Region 1 - PKS-like,T3PKS,t3nrps-iterative
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 95,802 - 150,458 nt. (total: 54,657 nt) Show pHMM detection rules used
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)
PKS-like: (t2pks2 or ksIII)
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 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
F603_RS0123020: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

F603_RS0123060: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F603_RS35605: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

Transferases: glycosyltransferase halogenase methyltransferase
F603_RS0123035: halogenase

smcogs
  SMCOG1119: halogenase

F603_RS0123130: methyltransferase

smcogs
  SMCOG1089: methyltransferase

F603_RS32655: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

Hydrolases: hydrolase
F603_RS0123030: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

F603_RS0123135: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: decarboxylase dehydratase
F603_RS0123090: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

F603_RS0123105: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase
F603_RS0123045: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

F603_RS0123075: 3-oxoacyl-(acyl carrier protein) synthase III

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

F603_RS0123085: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F603_RS0123100: 3-oxoacyl-(acyl carrier protein) synthase III

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

F603_RS32635: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | t3nrps-iterative | PKS-like | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000866.5 |  |  |  | 0.61 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000286.3 |  |  |  | 0.59 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0000218.5 |  |  |  | 0.57 | PKS | doxorubicin | Streptomyces peucetius
BGC0002547.2 |  |  |  | 0.57 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces youssoufiensis
BGC0000217.5 |  |  |  | 0.55 | PKS | daunorubicin | Streptomyces sp.
BGC0000192.3 |  |  |  | 0.52 | PKS | aclacinomycin | Streptomyces galilaeus
BGC0001197.5 |  |  |  | 0.52 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002510.2 |  |  |  | 0.52 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0000191.5 |  |  |  | 0.51 | PKS | aclacinomycin | Streptomyces galilaeus
BGC0001596.3 |  |  |  | 0.50 | PKS | fluostatin M, fluostatin N, fluostatin O, fluostatin P, fluostatin Q | Streptomyces albus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000866.5 |  | 0.53 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000286.3 |  | 0.52 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0002547.2 |  | 0.51 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces youssoufiensis
BGC0000218.5 |  | 0.51 | PKS | doxorubicin | Streptomyces peucetius
BGC0000909.3 |  | 0.51 | other (other) | melanin | Streptomyces avermitilis
BGC0000217.5 |  | 0.50 | PKS | daunorubicin | Streptomyces sp.
BGC0002510.2 |  | 0.49 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0000192.3 |  | 0.49 | PKS | aclacinomycin | Streptomyces galilaeus
BGC0000191.5 |  | 0.49 | PKS | aclacinomycin | Streptomyces galilaeus
BGC0001197.5 |  | 0.49 | PKS | frankiamicin | Frankia sp. EAN1pec

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: 19.00 out of 20.47
Confidence: strong
Additional weak hits (13):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.71 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.69 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.50 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.65 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.16 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.80 out of 27.78
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.13 out of 39.62
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.03 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.17 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.24 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.24 out of 32.93
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).
F603_RS0123085: X
AMP-binding (11..405): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AAILFDYGLYQLAGTNTGAQLMYGLTECKRATIM
  Nearest Stachelhaus code(s):
    Asp DYYPTTMRAK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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_KB905821.1 - Region 2 - 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: 306,804 - 349,537 nt. (total: 42,734 nt) Show pHMM detection rules used
Region on contig edge.
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### 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
F603_RS0124095: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

F603_RS0124120: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

F603_RS32740: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

F603_RS32750: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acylase halogenase
F603_RS0124055: flavin-dependent pyrrole halogenase

halogenases
  flavin-dependent pyrrole halogenase
smcogs
  SMCOG1119: halogenase

F603_RS0124060: ambiguous flavin-dependent halogenase

halogenases
  ambiguous flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

F603_RS0124080: flavin-dependent pyrrole halogenase

halogenases
  flavin-dependent pyrrole halogenase
smcogs
  SMCOG1119: halogenase

F603_RS32760: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: ligase synthase
F603_RS0124100: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F603_RS0124115: 3-oxoacyl-(acyl carrier protein) synthase III

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

F603_RS32755: 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
--- | --- | --- | --- | --- | ---
BGC0002341.2 |  | 0.76 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
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
BGC0000131.5 |  | 0.61 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0001275.3 |  | 0.60 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  | 0.60 | PKS | asperlactone | Aspergillus ochraceus
BGC0001257.3 |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0001244.3 |  | 0.60 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.60 | PKS | 6-methylsalicyclic acid | Aspergillus terreus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002341.2 |  | 0.76 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
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
BGC0000131.5 |  | 0.61 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0001275.3 |  | 0.60 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  | 0.60 | PKS | asperlactone | Aspergillus ochraceus
BGC0001257.3 |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0001244.3 |  | 0.60 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.60 | PKS | 6-methylsalicyclic acid | Aspergillus terreus

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.
No hits above weak threshold.
Weak hits (10):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.29 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.17 out of 26.06
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.98 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.63 out of 30.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.01 out of 20.97
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.71 out of 25.75
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.81 out of 30.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.04 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.72 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.62 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 2, location 306803 - 349537:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (mal - Me-ohmal)
Non-colinear ordering:
  F603_RS32755 + F603_RS32760

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).
F603_RS32755: mal
PKS_AT (572..867): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 66.7%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 167.8
  inactive: 100.2
  Methoxymalonyl-CoA: 77.5
  Methylmalonyl-CoA: 69.8
  Ethylmalonyl-CoA: 67.2
  Propionyl-CoA: 44.7
  2-Methylbutyryl-CoA: 39.6
  trans-1,2-CPDA: 39.1
  CHC-CoA: 38.1
  Isobutyryl-CoA: 32.1
  Acetyl-CoA: 28.1
  fatty_acid: 20.5
  Benzoyl-CoA: 15.7
  3-Methylbutyryl-CoA: 7.3

F603_RS32760: mal - mmal
PKS_AT (539..827): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  Methylmalonyl-CoA: 70.8%
  Propionyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 114.9
  Methylmalonyl-CoA: 106.9
  Methoxymalonyl-CoA: 95.7
  Isobutyryl-CoA: 69.8
  Ethylmalonyl-CoA: 65.9
  inactive: 52.3
  Propionyl-CoA: 41.4
  CHC-CoA: 38.5
  fatty_acid: 37.2
  Acetyl-CoA: 37.1
  2-Methylbutyryl-CoA: 27.5
  Benzoyl-CoA: 25.5
  3-Methylbutyryl-CoA: 24.3
  trans-1,2-CPDA: 21.6

PKS_AT (1555..1846): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 66.7%
  Malonyl-CoA: 62.5%
  Ethylmalonyl-CoA: 58.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 135.7
  Ethylmalonyl-CoA: 127.8
  Methoxymalonyl-CoA: 117.4
  Propionyl-CoA: 98.0
  2-Methylbutyryl-CoA: 90.5
  Malonyl-CoA: 79.5
  CHC-CoA: 74.1
  trans-1,2-CPDA: 73.0
  Isobutyryl-CoA: 62.9
  Acetyl-CoA: 57.5
  Benzoyl-CoA: 53.9
  fatty_acid: 45.5
  inactive: 30.3
  3-Methylbutyryl-CoA: 22.9

F603_RS0124100: Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (9..405): 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:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FWAAFDLSVLDVYSLFAGELNLYGPTETNVCTAY
  Nearest Stachelhaus code(s):
    Pro DLLYLALVCK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---

NZ_KB905822.1 - Region 1 - 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: 223,882 - 266,554 nt. (total: 42,673 nt) Show pHMM detection rules used
Region on contig edge.
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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 oxygenase
F603_RS0125385: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

F603_RS0125415: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

F603_RS0125445: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

Hydrolases: esterase hydrolase
F603_RS0125365: isochorismatase

smcogs
  SMCOG1027: isochorismatase

F603_RS0125410: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

F603_RS0125420: thioesterase

smcogs
  SMCOG1004: thioesterase

Isomerases: isomerase
F603_RS32925: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase
F603_RS0125450: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F603_RS0125460: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F603_RS32915: 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
--- | --- | --- | --- | --- | --- | ---
BGC0001833.4 |  |  | 0.61 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  | 0.61 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
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
BGC0001641.4 |  |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  | 0.60 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  |  | 0.59 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  |  | 0.59 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001135.5 |  |  | 0.59 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  |  | 0.58 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.63 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.63 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001135.5 |  | 0.63 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans

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:
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 25.13 out of 28.19
Confidence: strong
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.95 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.93 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.95 out of 28.19
Confidence: medium
Additional weak hits (21):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.22 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.35 out of 31.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.48 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 21.55 out of 36.54
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.04 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.16 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.42 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.52 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.60 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.03 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.40 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.18 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.01 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.39 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.50 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.78 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.38 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.86 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.32 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.32 out of 30.98
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.00 out of 24.78
Confidence: weak
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 223881 - 266554:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

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).
F603_RS32915: Ser - Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (563..941): 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:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Small clusters prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Single AA prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDLSFDLSVFDANCLLGGDVALGGTTETAIHSTV
  Nearest Stachelhaus code(s):
    Ser DLFNLGLIHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1581..1977): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDVSFDLSVYDGNSLVSGDVALGGATEAAIWSNA
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

F603_RS0125450: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (543..939): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDIAFDLSVFDGDSLLSGDVSLGGATEAAIWSIH
  Nearest Stachelhaus code(s):
    Cys DLFNLSLIWK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

F603_RS0125460: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (32..435): diOH-Bz
nrpys: diOH-Bz

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    NASLFPLACPGGALQVGGAQQVFGMAEGLVNYTR
  Nearest Stachelhaus code(s):
    diOH-Bz PLPAQGVVNK (91% 8Å match)
    diOH-Bz or Sal PLPAQGVVNK (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
--- | ---
ZuR variant 1 | Zinc-responsive repressor

NZ_KB905823.1 - Region 1 - 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: 101,016 - 173,007 nt. (total: 71,992 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: electron transfer
F603_RS0126020: flavodoxin

smcogs
  SMCOG1134: flavodoxin

Transferases: acylase carboxylase methyltransferase transferase
F603_RS0126080: methyltransferase

smcogs
  SMCOG1089: methyltransferase

F603_RS0126090: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

F603_RS0126110: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

F603_RS32945: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: back translocase esterase hydrolase peptidase
F603_RS0126030: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

F603_RS0126045: HAD-superfamily hydrolase, subfamily IA, variant

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

F603_RS0126140: gamma-glutamyltranspeptidase

smcogs
  SMCOG1274: gamma-glutamyltranspeptidase

F603_RS32950: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase synthase
F603_RS0126060: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

F603_RS0126065: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

F603_RS0126070: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

F603_RS0126100: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F603_RS0126105: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F603_RS32940: 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 | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  | 0.89 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.88 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  | 0.87 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000342.4 |  |  | 0.75 | NRPS | enniatin | Fusarium equiseti
BGC0001758.4 |  |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  |  | 0.70 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  | 0.69 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  |  | 0.67 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.75 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000342.4 |  | 0.70 | NRPS | enniatin | Fusarium equiseti
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.68 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
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
BGC0002135.2 |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.67 | NRPS | AbT1 | Aureobasidium pullulans

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: 20.58 out of 23.79
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.52 out of 23.79
Confidence: medium
Additional weak hits (4):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.37 out of 26.85
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.62 out of 26.12
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.37 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.88 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 1, location 101015 - 173007:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk) + (pk) + (Me-redmal) + (Me-ccmal) + (D-mal) + (NMe-X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 101015 - 167798:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk) + (pk) + (Me-redmal) + (Me-ccmal) + (D-mal) + (NMe-X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 127811 - 173007:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk) + (Me-redmal) + (Me-ccmal) + (D-mal) + (NMe-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).
F603_RS32940: pk
PKS_AT (562..858): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  Methylmalonyl-CoA: 75.0%
  Propionyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 129.0
  Ethylmalonyl-CoA: 107.7
  Malonyl-CoA: 97.9
  Methoxymalonyl-CoA: 96.9
  2-Methylbutyryl-CoA: 83.4
  Propionyl-CoA: 73.9
  trans-1,2-CPDA: 61.7
  Isobutyryl-CoA: 50.8
  CHC-CoA: 42.7
  Acetyl-CoA: 42.7
  inactive: 42.4
  Benzoyl-CoA: 37.7
  fatty_acid: 25.6
  3-Methylbutyryl-CoA: 24.8

F603_RS0126060: pk
PKS_AT (557..849): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  Methylmalonyl-CoA: 70.8%
  Methoxymalonyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 118.1
  Methoxymalonyl-CoA: 92.0
  Ethylmalonyl-CoA: 86.2
  Malonyl-CoA: 82.6
  Isobutyryl-CoA: 64.1
  2-Methylbutyryl-CoA: 62.5
  trans-1,2-CPDA: 57.9
  Propionyl-CoA: 53.3
  Acetyl-CoA: 47.0
  fatty_acid: 41.3
  CHC-CoA: 40.4
  Benzoyl-CoA: 37.8
  3-Methylbutyryl-CoA: 32.4
  inactive: 31.6

F603_RS0126065: mmal
PKS_AT (571..858): mmal
ATSignature: Methoxymalonyl-CoA, Malonyl-CoA, Methylmalonyl-CoA

Top 3 matches:
  Methoxymalonyl-CoA: 62.5%
  Malonyl-CoA: 62.5%
  Methylmalonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 125.5
  Methoxymalonyl-CoA: 112.7
  Ethylmalonyl-CoA: 92.9
  Malonyl-CoA: 79.0
  Isobutyryl-CoA: 74.7
  trans-1,2-CPDA: 69.4
  2-Methylbutyryl-CoA: 69.2
  Propionyl-CoA: 63.0
  Acetyl-CoA: 60.3
  fatty_acid: 56.9
  CHC-CoA: 38.4
  Benzoyl-CoA: 36.8
  inactive: 36.3
  3-Methylbutyryl-CoA: 19.7

F603_RS0126070: mmal
PKS_AT (574..871): mmal
ATSignature: Malonyl-CoA, Methylmalonyl-CoA

Top 3 matches:
  Malonyl-CoA: 70.8%
  Methylmalonyl-CoA: 70.8%
  Ethylmalonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 121.5
  Ethylmalonyl-CoA: 106.1
  Methoxymalonyl-CoA: 93.2
  Malonyl-CoA: 85.5
  Propionyl-CoA: 83.7
  trans-1,2-CPDA: 79.6
  2-Methylbutyryl-CoA: 62.5
  Isobutyryl-CoA: 54.7
  fatty_acid: 45.5
  Acetyl-CoA: 31.2
  CHC-CoA: 24.0
  Benzoyl-CoA: 23.0
  3-Methylbutyryl-CoA: 19.8
  inactive: 17.0

F603_RS32945: mal
PKS_AT (553..835): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 70.8%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 138.0
  inactive: 72.3
  Methoxymalonyl-CoA: 69.9
  Methylmalonyl-CoA: 61.4
  Isobutyryl-CoA: 40.6
  Propionyl-CoA: 38.0
  Ethylmalonyl-CoA: 31.5
  trans-1,2-CPDA: 17.6
  Benzoyl-CoA: 16.7
  fatty_acid: 16.0
  CHC-CoA: 14.0
  2-Methylbutyryl-CoA: 10.1
  Acetyl-CoA: 2.4
  3-Methylbutyryl-CoA: 1.9

F603_RS0126080: X
AMP-binding (468..858): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TVRASYLYLFSTVLVVTGELSLYGSAETAGAAVL
  Nearest Stachelhaus code(s):
    D-Ala DLFTVCLIAK (29% 8Å match)
  Stachelhaus code match:
    60% (weak)

F603_RS0126100: Acetyl-CoA
CAL_domain (46..496): Acetyl-CoA
minowa: Acetyl-CoA

Prediction, score:
  Acetyl-CoA: 48.6
  fatty_acid: 28.8
  NH2: 8.8
  AHBA: 3.3
  shikimic_acid: 0.0

F603_RS0126105: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (21..408): 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:
    LACHFDFSVWEGSQVLGGEYNMYGITEITVHATV
  Nearest Stachelhaus code(s):
    Thr DFWSVGMVHK (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
--- | ---
IolR | Regulator of the inositol catabolism

NZ_KB905828.1 - Region 1 - T2PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 56,627 nt. (total: 56,627 nt) Show pHMM detection rules used
Region on contig edge.
T2PKS: (t2ks and t2clf)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
F603_RS0129160: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

F603_RS0129250: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F603_RS33185: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: acetyltransferase acylase methyltransferase
F603_RS0129085: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

F603_RS0129130: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

F603_RS0129135: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

F603_RS0129245: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Lyases: cyclase
F603_RS0129105: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

Ligases: ligase synthase
F603_RS0129120: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

F603_RS0129125: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

F603_RS0129240: 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 | T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000264.5 |  | 0.76 | PKS | resistomycin, resistoflavine | Streptomyces resistomycificus
BGC0000231.5 |  | 0.62 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001257.3 |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.59 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0002274.2 |  | 0.59 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0000234.5 |  | 0.57 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001513.3 |  | 0.55 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000866.5 |  | 0.55 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000264.5 |  | 0.76 | PKS | resistomycin, resistoflavine | Streptomyces resistomycificus
BGC0000231.5 |  | 0.62 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001257.3 |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.59 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0002274.2 |  | 0.59 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0000234.5 |  | 0.57 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001513.3 |  | 0.55 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000866.5 |  | 0.55 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242

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:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.49 out of 25.31
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.67 out of 23.79
Confidence: medium
Additional weak hits (14):
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: 19.22 out of 36.54
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.10 out of 26.12
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.37 out of 29.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.75 out of 21.55
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.61 out of 32.74
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: 17.28 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.00 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.16 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.19 out of 29.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.05 out of 20.97
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.59 out of 31.73
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.59 out of 35.63
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).
F603_RS0129085: mal
PKS_AT (99..388): mal
ATSignature: (unknown)
No matches above 50%
minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 51.1
  Methoxymalonyl-CoA: 37.6
  inactive: 30.6
  Methylmalonyl-CoA: 29.6
  Isobutyryl-CoA: 13.3
  Ethylmalonyl-CoA: 12.7
  2-Methylbutyryl-CoA: 11.5
  fatty_acid: 11.4
  CHC-CoA: 11.0
  Propionyl-CoA: 10.6
  3-Methylbutyryl-CoA: 10.5
  Benzoyl-CoA: 9.8
  trans-1,2-CPDA: 0.0
  Acetyl-CoA: 0.0

F603_RS0129240: X
AMP-binding (56..508): 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:
    TATAFDRGAR-I--ICGGSYEGYGLTETTAAATA
  Nearest Stachelhaus code(s):
    nDodec DVLFIGGVAK (32% 8Å match)
  Stachelhaus code match:
    60% (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:
  0 to 56627
Starter unit(s):
  2-methylbutyryl-CoA (Score: 116.0; E-value: 2.78e-31)

F603_RS0129085
  AT (Score: 155.5; E-value: 4e-48)
  AT ADB23379.1_TLN-05220/TLN-05223_2-methylbutyryl-CoA (Score: 116.0; E-value: 2.78e-31)
F603_RS0129090
  CYC C5-C14/C3-C16 (Score: 319.5; E-value: 3.8e-98)
F603_RS0129105
  CYC C9-C14 (Score: 127.5; E-value: 7.7e-40)
F603_RS0129110
  ACP (Score: 34.1; E-value: 4.8e-11)
F603_RS0129120
  CLF (Score: 431.0; E-value: 9.8e-132)
F603_RS0129125
  KS (Score: 514.9; E-value: 3.3e-157)
F603_RS0129130
  MET (Score: 144.6; E-value: 8.8e-45)
F603_RS0129135
  MET (Score: 172.4; E-value: 3.3e-53)
F603_RS0129250
  KR (Score: 131.4; E-value: 1.1e-40)
F603_RS33185
  OXY (Score: 126.3; E-value: 3.8e-39)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_KB905830.1 - Region 1 - RRE-containing
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 62,565 - 72,882 nt. (total: 10,318 nt) Show pHMM detection rules used
Region on contig edge.
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
F603_RS0130255: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: Methylation
F603_RS34500: Methylation

MITE
  MITE0000049Methylation (identity: 66.30%)

Hydrolases: Hydrolysis hydrolase
F603_RS0130260: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

F603_RS0130265: Hydrolysis

MITE
  MITE0000048Hydrolysis (identity: 69.20%)

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

Reference | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000470.6 |  | 0.46 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000468.5 |  | 0.42 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.42 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000469.6 |  | 0.39 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0000507.5 |  | 0.36 | ribosomal | epicidin | Staphylococcus epidermidis
BGC0000217.5 |  | 0.35 | PKS | daunorubicin | Streptomyces sp.
BGC0002181.3 |  | 0.35 | terpene | pleuromutilin | Rhodocybe pseudopiperita
BGC0002716.2 |  | 0.35 | NRPS | gamexpeptide A, gamexpeptide B, gamexpeptide E, luminmide B, luminmide D, luminmide E, luminmide F, luminmide G | Photorhabdus laumondii subsp. laumondii
BGC0001882.3 |  | 0.35 | PKS | chrysoxanthone A, chrysoxanthone B, chrysoxanthone C | Penicillium rubens Wisconsin 54-1255
BGC0000631.5 |  | 0.34 | terpene | Botrydial, 8,9-epibotrydial, 1-epibotrydial, Dihydrobotrydial, 10-Oxo-dihydrobotrydial, 10-dehydroxy dihydrobotrydialone, 10-epi-dihydrobotrydial, Botryendial, Botryenalol, Botrydienal, Norbotrydialone acetate, 10-Oxodihydrobotry-1(9),4(5)-diendial, 10-Oxodehydrodihydrobotrydial, Dehydrobotrydienol, 11-Hydroxydehydrobotrydienol, 12-hydroxydehydrobotrydienol, Secobotrytriendiol, Secobotrytriene-10,12,15-triol, Secobotrydiene-3,10,15-triol, Secobotrydiene-3,4,10,15-tetraol, 4β-Acetoxytetrahydrobotryslactone | Botrytis cinerea B05.10

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000470.6 |  | 0.46 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000468.5 |  | 0.42 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.42 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000469.6 |  | 0.39 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0000507.5 |  | 0.36 | ribosomal | epicidin | Staphylococcus epidermidis
BGC0000217.5 |  | 0.35 | PKS | daunorubicin | Streptomyces sp.
BGC0002181.3 |  | 0.35 | terpene | pleuromutilin | Rhodocybe pseudopiperita
BGC0002716.2 |  | 0.35 | NRPS | gamexpeptide A, gamexpeptide B, gamexpeptide E, luminmide B, luminmide D, luminmide E, luminmide F, luminmide G | Photorhabdus laumondii subsp. laumondii
BGC0001882.3 |  | 0.35 | PKS | chrysoxanthone A, chrysoxanthone B, chrysoxanthone C | Penicillium rubens Wisconsin 54-1255
BGC0000631.5 |  | 0.34 | terpene | Botrydial, 8,9-epibotrydial, 1-epibotrydial, Dihydrobotrydial, 10-Oxo-dihydrobotrydial, 10-dehydroxy dihydrobotrydialone, 10-epi-dihydrobotrydial, Botryendial, Botryenalol, Botrydienal, Norbotrydialone acetate, 10-Oxodihydrobotry-1(9),4(5)-diendial, 10-Oxodehydrodihydrobotrydial, Dehydrobotrydienol, 11-Hydroxydehydrobotrydienol, 12-hydroxydehydrobotrydienol, Secobotrytriendiol, Secobotrytriene-10,12,15-triol, Secobotrydiene-3,10,15-triol, Secobotrydiene-3,4,10,15-tetraol, 4β-Acetoxytetrahydrobotryslactone | Botrytis cinerea B05.10

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 (1):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.08 out of 30.22
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (62564...72882)
F603_RS34500
  RRE type: Bottromycin_Methyltransferase_RRE
  Location: 0 - 57
  Score: 93.5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_KB905831.1 - Region 1 - 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: 1 - 47,640 nt. (total: 47,640 nt) Show pHMM detection rules used
Region on contig edge.
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
F603_RS0130295: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

F603_RS0130335: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

F603_RS0130365: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: glycosyltransferase kinase transferase
F603_RS0130310: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

F603_RS0130325: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

F603_RS0130420: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

F603_RS0130455: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

F603_RS0130465: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Hydrolases: esterase hydrolase phosphatase
F603_RS0130350: inositol monophosphatase

smcogs
  SMCOG1207: inositol monophosphatase

F603_RS0130380: isochorismatase

smcogs
  SMCOG1027: isochorismatase

F603_RS0130450: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

Isomerases: isomerase mutase racemase
F603_RS0130315: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

F603_RS0130370: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

F603_RS0130405: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase
F603_RS0130375: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F603_RS0130390: 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
--- | --- | --- | --- | --- | --- | ---
BGC0002075.3 |  |  | 0.87 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001185.5 |  |  | 0.77 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0001825.4 |  |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  |  | 0.69 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  | 0.68 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000401.5 |  |  | 0.67 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0001641.4 |  |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

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
BGC0001185.5 |  | 0.71 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0001825.4 |  | 0.68 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000401.5 |  | 0.67 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0000706.3 |  | 0.66 | saccharide | kanamycin | Streptomyces kanamyceticus

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:
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.96 out of 29.65
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 32.19 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.90 out of 36.53
Confidence: medium
Additional weak hits (6):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.15 out of 28.14
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.29 out of 33.73
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.94 out of 20.01
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 19.26
Confidence: weak
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 0 - 47640:
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).
F603_RS0130375: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (45..453): diOH-Bz
nrpys: diOH-Bz

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    SGSLFPMSSPGGGMLVGGAMQVFGMAEGLVNYTR
  Nearest Stachelhaus code(s):
    diOH-Bz PLPGLGVVNK (91% 8Å match)
  Stachelhaus code match:
    90% (moderate)

F603_RS0130390: X
AMP-binding (474..873): X
nrpys: Ala, 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:
    RWMTFDVSVWEWHFFCSGEHNLYGPTEAAVDVTH
  Nearest Stachelhaus code(s):
    Ala or Ser DVWHFSLVDK (100% 8Å match)
    Ser DVWHFSLVDK (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
--- | ---
DmdR1 | Iron(II)-dependent repressor
LexA variant 1 | Repressor of DNA damage response

NZ_KB905836.1 - Region 1 - RiPP-like,bottromycin
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 - 9,160 nt. (total: 9,160 nt) Show pHMM detection rules used
Region on contig edge.
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))
bottromycin: botH

#### 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: Cyclization oxygenase
F603_RS0131235: Cyclization

MITE
  MITE0000053Cyclization (identity: 77.50%)

F603_RS0131255: Decarboxylation, Oxidation

MITE
  MITE0000044Decarboxylation, Oxidation (identity: 74.00%)
smcogs
  SMCOG1007: cytochrome P450

Transferases: Methylation
F603_RS0131240: Methylation

MITE
  MITE0000046Methylation (identity: 78.00%)

F603_RS0131260: Methylation

MITE
  MITE0000047Methylation (identity: 70.90%)

F603_RS34890: Methylation

MITE
  MITE0000049Methylation (identity: 68.40%)

Hydrolases: Hydrolysis dehalogenase
F603_RS0131250: Hydrolysis

MITE
  MITE0000050Hydrolysis (identity: 66.10%)

F603_RS33305: Epimerization

MITE
  MITE0000051Epimerization (identity: 68.20%)
smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: oxygenase
F603_RS0131255: Decarboxylation, Oxidation

MITE
  MITE0000044Decarboxylation, Oxidation (identity: 74.00%)
smcogs
  SMCOG1007: cytochrome P450

Isomerases: dehalogenase
F603_RS33305: Epimerization

MITE
  MITE0000051Epimerization (identity: 68.20%)
smcogs
  SMCOG1262: haloalkane dehalogenase

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 | bottromycin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000470.6 |  |  | 1.38 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000469.6 |  |  | 0.93 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0001157.6 |  |  | 0.93 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000468.5 |  |  | 0.92 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001201.3 |  |  | 0.38 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0001310.5 |  |  | 0.36 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0000844.5 |  |  | 0.29 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0000598.5 |  |  | 0.27 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0002120.3 |  |  | 0.26 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000902.4 |  |  | 0.25 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000470.6 |  | 0.88 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000469.6 |  | 0.76 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0001157.6 |  | 0.76 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000468.5 |  | 0.76 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001201.3 |  | 0.51 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0001310.5 |  | 0.49 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0000844.5 |  | 0.45 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0000598.5 |  | 0.42 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0002120.3 |  | 0.41 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000902.4 |  | 0.41 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338

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: 19.33 out of 23.79
Confidence: medium
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RiPP-like protocluster (0...9160)
F603_RS34890
  RRE type: Bottromycin_Methyltransferase_RRE
  Location: 0 - 57
  Score: 93.8
F603_RS0131240
  RRE type: Bottromycin_Methyltransferase_RRE
  Location: 531 - 609
  Score: 112.9
bottromycin protocluster (0...9160)
F603_RS34890
  RRE type: Bottromycin_Methyltransferase_RRE
  Location: 0 - 57
  Score: 93.8
F603_RS0131240
  RRE type: Bottromycin_Methyltransferase_RRE
  Location: 531 - 609
  Score: 112.9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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