Select genomic region:
Overview
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1.30
1.31
1.32
1.33
1.34
1.35
1.36
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1.38
1.39

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

NZ_CP034669.1 (Corallococcus coralloides)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | RiPP-like | 268,398 | 279,873 |
Region 2 | terpene | 892,194 | 920,111 | High | carotenoid | terpene
Region 3 | NRPS,T1PKS | 1,016,866 | 1,065,475 |
Region 4 | NRPS-like | 1,724,164 | 1,768,573 | High | VEPE/AEPE/TG-1 | other:nucleoside
Region 5 | NI-siderophore | 1,777,392 | 1,812,644 | Low | speibonoxamine/desoxy-desferrioxamine D1/desferrioxamine D1/desferrioxamine B/didesoxy-desferrioxamine D1/desoxy-desferrioxamine B/didesoxy-desferrioxamine B | other:other
Region 6 | T3PKS | 1,969,474 | 2,010,664 |
Region 7 | terpene | 2,021,660 | 2,044,667 |
Region 8 | T1PKS,NRPS | 2,288,616 | 2,345,118 |  |
Region 9 | T1PKS | 2,451,586 | 2,498,506 | Low | chloromyxamide | NRPS:Type I
Region 10 | NRPS | 2,640,640 | 2,706,808 |
Region 11 | RiPP-like | 2,833,880 | 2,844,728 |
Region 12 | T1PKS,NRPS-like,NRPS | 2,908,533 | 3,042,223 | Low | sinapigladioside | other:other
Region 13 | NRPS,T1PKS | 3,230,816 | 3,284,035 |
Region 14 | indole | 3,317,369 | 3,350,700 |
Region 15 | lanthipeptide-class-i,transAT-PKS,PKS-like,NRPS-like,NRPS,T1PKS | 3,789,728 | 3,966,492 | High | corallopyronin | NRPS:Type I+PKS
Region 16 | t3nrps-iterative,NRPS,T1PKS | 4,075,420 | 4,155,794 |
Region 17 | NRPS,T1PKS | 4,290,341 | 4,362,401 |
Region 18 | RiPP-like | 4,562,226 | 4,573,872 |
Region 19 | NRPS | 4,663,500 | 4,751,280 | Low | cadaside A/cadaside B | NRPS:Type I
Region 20 | lanthipeptide-class-ii | 4,834,866 | 4,857,709 |
Region 21 | NRPS,T1PKS | 5,022,882 | 5,149,058 | Medium | myxoprincomide-c506 | NRPS:Type I+PKS:Type I
Region 22 | RRE-containing | 5,170,959 | 5,191,273 |
Region 23 | terpene-precursor | 5,234,225 | 5,255,223 |
Region 24 | NRP-metallophore,NRPS,T1PKS | 5,257,423 | 5,364,319 | High | myxochelin A/myxochelin B | NRPS:Type I
Region 25 | RiPP-like | 5,414,952 | 5,425,824 |
Region 26 | azole-containing-RiPP | 5,540,042 | 5,566,759 |  |
Region 27 | terpene-precursor | 5,837,886 | 5,858,779 |
Region 28 | NRPS | 6,217,742 | 6,268,242 |
Region 29 | terpene | 6,606,232 | 6,627,203 |
Region 30 | thioamitides | 6,786,164 | 6,808,562 |
Region 31 | NRPS,T1PKS,linaridin | 6,845,891 | 6,923,698 | Low | nostopeptolide A2 | NRPS:Type I+PKS
Region 32 | NRPS,arylpolyene | 7,008,013 | 7,090,853 | Low | APE Vf | other:other
Region 33 | lanthipeptide-class-ii | 7,152,898 | 7,176,119 |
Region 34 | butyrolactone | 7,817,796 | 7,828,620 |
Region 35 | NRPS-like | 7,947,709 | 7,990,723 |
Region 36 | lanthipeptide-class-ii,phenazine | 7,992,849 | 8,032,695 |  |
Region 37 | T3PKS | 8,594,093 | 8,635,178 | Medium | alkylpyrone-407/alkylpyrone-393 | PKS
Region 38 | terpene | 8,772,940 | 8,795,198 | High | geosmin | terpene:Sesquiterpene
Region 39 | RiPP-like,RRE-containing | 9,018,680 | 9,040,279 |

NZ_CP034669.1 - Region 1 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 268,398 - 279,873 nt. (total: 11,476 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
EJ065_RS01180: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Transferases: glycosyltransferase
EJ065_RS01160: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000719.5 |  | 0.38 | saccharide | tobramycin | Streptoalloteichus hindustanus
BGC0000720.3 |  | 0.37 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0000721.4 |  | 0.32 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0000711.5 |  | 0.32 | saccharide | neomycin | Streptomyces fradiae
BGC0000709.5 |  | 0.31 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000702.5 |  | 0.31 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0000713.5 |  | 0.31 | saccharide | ribostamycin | Streptomyces ribosidificus
BGC0000907.5 |  | 0.30 | other (other) | lincomycin | Streptomyces lincolnensis
BGC0000914.5 |  | 0.30 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0000722.5 |  | 0.30 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. jinggangensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000719.5 |  | 0.38 | saccharide | tobramycin | Streptoalloteichus hindustanus
BGC0000720.3 |  | 0.37 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0000721.4 |  | 0.32 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0000711.5 |  | 0.32 | saccharide | neomycin | Streptomyces fradiae
BGC0000709.5 |  | 0.31 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000702.5 |  | 0.31 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0000713.5 |  | 0.31 | saccharide | ribostamycin | Streptomyces ribosidificus
BGC0000907.5 |  | 0.30 | other (other) | lincomycin | Streptomyces lincolnensis
BGC0000914.5 |  | 0.30 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0000722.5 |  | 0.30 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. jinggangensis

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.03 out of 29.72
Confidence: medium
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
NtrC | Nitrogen regulatory protein C

NZ_CP034669.1 - Region 2 - 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: 892,194 - 920,111 nt. (total: 27,918 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
EJ065_RS03910: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

EJ065_RS03920: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Hydrolases: esterase
EJ065_RS03890: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

Lyases: dehydratase
EJ065_RS03895: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthetase
EJ065_RS03905: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000648.3 |  | 0.84 | terpene | carotenoid | Myxococcus xanthus
BGC0000647.3 |  | 0.76 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000664.5 |  | 0.58 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.57 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000640.3 |  | 0.57 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000641.3 |  | 0.55 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000639.3 |  | 0.55 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000644.3 |  | 0.53 | terpene | carotenoid | Dietzia sp. CQ4
BGC0001227.3 |  | 0.53 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000633.3 |  | 0.53 | terpene | carotenoid | Streptomyces avermitilis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000648.3 |  | 0.84 | terpene | carotenoid | Myxococcus xanthus
BGC0000647.3 |  | 0.76 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000664.5 |  | 0.58 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.57 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000640.3 |  | 0.57 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000641.3 |  | 0.55 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000639.3 |  | 0.55 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000644.3 |  | 0.53 | terpene | carotenoid | Dietzia sp. CQ4
BGC0001227.3 |  | 0.53 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000633.3 |  | 0.53 | terpene | carotenoid | Streptomyces avermitilis

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

No significant matches found.

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

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

Genes with terpene domains:
EJ065_RS03905: PT_FPPS_like
Domain 1 (55 - 360): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

EJ065_RS03915: PT_phytoene_like
Domain 1 (21 - 313): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

EJ065_RS03935: Lycopene_cycl
Domain 1 (1 - 91): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

EJ065_RS03940: Lycopene_cycl
Domain 1 (6 - 99): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

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
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.22 out of 23.79
Confidence: medium
Additional weak hits (9):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.44 out of 31.73
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.62 out of 23.43
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.96 out of 30.22
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.21 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.21 out of 39.62
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.52 out of 32.74
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.23 out of 30.98
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.25 out of 36.53
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.80 out of 20.01
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
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism

NZ_CP034669.1 - Region 3 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,016,866 - 1,065,475 nt. (total: 48,610 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
EJ065_RS04540: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Ligases: ligase
EJ065_RS04470: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

EJ065_RS04535: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001249.5 |  |  | 0.82 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
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

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.72 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.67 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.48 out of 18.57
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.16 out of 30.11
Confidence: medium
Additional weak hits (11):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.12 out of 26.06
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.35 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.02 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.52 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.30 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.19 out of 30.11
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.08 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.96 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 3, location 1016865 - 1065475:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Phe - X - 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).
EJ065_RS04470: Phe - X - mal
Search NORINE for peptide: strict or relaxed
AMP-binding (15..410): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDAAFDASTLEGVLMVGGDLNSYGPTECTTSATA
  Nearest Stachelhaus code(s):
    Val DALWMGGTFK (79% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1059..1447): X
nrpys: Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LTVAFDFSVAEPMFAIGGEIQVYGPTEATVFTTA
  Nearest Stachelhaus code(s):
    Asn DVAMAGMVTK (62% 8Å match)
  Stachelhaus code match:
    70% (weak)

PKS_AT (2163..2441): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 97.1
  inactive: 60.2
  Methoxymalonyl-CoA: 55.6
  Methylmalonyl-CoA: 37.4
  Ethylmalonyl-CoA: 24.0
  2-Methylbutyryl-CoA: 14.9
  Acetyl-CoA: 13.8
  Isobutyryl-CoA: 13.6
  Propionyl-CoA: 13.0
  CHC-CoA: 11.7
  fatty_acid: 10.9
  Benzoyl-CoA: 10.6
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

EJ065_RS04535: X
AMP-binding (34..446): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    GITSWAKCAWGGCALSAGEREGYGQTETVVIVGI
  Nearest Stachelhaus code(s):
    Ala DVWCTAAVIK (35% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
ToxT | Regulator of MSHA biosynthesis

NZ_CP034669.1 - Region 4 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,724,164 - 1,768,573 nt. (total: 44,410 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: formyltransferase transferase
EJ065_RS07390: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

EJ065_RS07435: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Hydrolases: glucanase
EJ065_RS07480: Pullulanase, type I

smcogs
  SMCOG1297: Pullulanase, type I

Lyases: cyclase dehydratase
EJ065_RS07440: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

EJ065_RS07445: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

EJ065_RS07465: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
EJ065_RS07450: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000871.4 |  | 0.85 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622
BGC0000357.5 |  | 0.59 | 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
BGC0001285.5 |  | 0.47 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0002711.2 |  | 0.43 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000131.5 |  | 0.42 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0000898.5 |  | 0.42 | saccharide | desosamine, pikromycin, neomethymycin, narbomycin | Streptomyces venezuelae
BGC0000827.3 |  | 0.42 | other (other) | staurosporine | Salinispora arenicola CNS-205
BGC0000826.5 |  | 0.41 | other (other) | staurosporine | Streptomyces clavuligerus ATCC 27064
BGC0000880.4 |  | 0.41 | other (nucleoside) | tunicamycin B1 | Streptomyces chartreusis NRRL 3882
BGC0002347.3 |  | 0.41 | other (other) | cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D | Actinoalloteichus caeruleus WH1-2216-6

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000871.4 |  | 0.85 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622
BGC0000357.5 |  | 0.59 | 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
BGC0001285.5 |  | 0.47 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0002711.2 |  | 0.43 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000131.5 |  | 0.42 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0000898.5 |  | 0.42 | saccharide | desosamine, pikromycin, neomethymycin, narbomycin | Streptomyces venezuelae
BGC0000827.3 |  | 0.42 | other (other) | staurosporine | Salinispora arenicola CNS-205
BGC0000826.5 |  | 0.41 | other (other) | staurosporine | Streptomyces clavuligerus ATCC 27064
BGC0000880.4 |  | 0.41 | other (nucleoside) | tunicamycin B1 | Streptomyces chartreusis NRRL 3882
BGC0002347.3 |  | 0.41 | other (other) | cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D | Actinoalloteichus caeruleus WH1-2216-6

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.

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
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 1724163 - 1768573:
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).
EJ065_RS07450: X
AMP-binding (566..998): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LKLLFEFSAG-TIG-----RNR-----SSLNLGK
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

Link to PARAS substrate predictor
NZ_CP034669.1 - Region 5 - 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: 1,777,392 - 1,812,644 nt. (total: 35,253 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 reductase
EJ065_RS07615: alkyl hydroperoxide reductase/ Thiol specific

smcogs
  SMCOG1196: alkyl hydroperoxide reductase/ Thiol specific

EJ065_RS07655: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Transferases: aminotransferase
EJ065_RS07600: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Lyases: decarboxylase
EJ065_RS07670: 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
--- | --- | --- | --- | --- | ---
BGC0002469.2 |  | 0.63 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0001478.5 |  | 0.62 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002692.2 |  | 0.62 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0001572.3 |  | 0.62 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000941.3 |  | 0.60 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.59 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0002620.2 |  | 0.56 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0001499.5 |  | 0.56 | other (other) | aerobactin | Pantoea ananatis
BGC0001713.5 |  | 0.55 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0000295.5 |  | 0.55 | NRPS | acinetoferrin | Acinetobacter haemolyticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002469.2 |  | 0.63 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0001478.5 |  | 0.62 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002692.2 |  | 0.62 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0001572.3 |  | 0.62 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000941.3 |  | 0.60 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.59 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0002620.2 |  | 0.56 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0001499.5 |  | 0.56 | other (other) | aerobactin | Pantoea ananatis
BGC0001713.5 |  | 0.55 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0000295.5 |  | 0.55 | NRPS | acinetoferrin | Acinetobacter haemolyticus

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: 21.86 out of 28.19
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.25 out of 20.01
Confidence: medium
Additional weak hits (24):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.18 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.35 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.57 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.09 out of 29.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.83 out of 21.55
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.78 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.81 out of 20.01
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.85 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.49 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.97 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.92 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.44 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.66 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.09 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.51 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.14 out of 27.78
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.03 out of 30.22
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.20 out of 30.22
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.44 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.81 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.10 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.67 out of 24.78
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArgR | Regulator of arginine biosynthesis genes
ZuR variant 1 | Zinc-responsive repressor

NZ_CP034669.1 - Region 6 - 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: 1,969,474 - 2,010,664 nt. (total: 41,191 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
EJ065_RS08440: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

EJ065_RS08530: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

EJ065_RS08540: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

Transferases: aminotransferase
EJ065_RS08390: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: hydrolase
EJ065_RS08405: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

EJ065_RS08430: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: dehydratase
EJ065_RS08460: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
EJ065_RS08465: hydroxymethylglutaryl-CoA synthase

smcogs
  SMCOG1043: hydroxymethylglutaryl-CoA 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000841.5 |  | 0.44 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate, clavulanic acid | Streptomyces clavuligerus ATCC 27064
BGC0001374.5 |  | 0.43 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0001610.5 |  | 0.41 | other (other) | gougerotin | Streptomyces ahygroscopicus subsp. wuzhouensis
BGC0000207.5 |  | 0.41 | PKS | chartreusin | Streptomyces chartreusis
BGC0000255.5 |  | 0.41 | PKS | pederin | Uncultured bacterium
BGC0000679.5 |  | 0.40 | terpene | diazepinomicin | Micromonospora sp. M42
BGC0001880.3 |  | 0.40 | ribosomal | scytodecamide | Scytonema sp. UIC 10036
BGC0000205.3 |  | 0.40 | PKS | bryostatin | Candidatus Endobugula sertula
BGC0002584.2 |  | 0.40 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002561.3 |  | 0.40 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000841.5 |  | 0.44 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate, clavulanic acid | Streptomyces clavuligerus ATCC 27064
BGC0001374.5 |  | 0.43 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0001610.5 |  | 0.41 | other (other) | gougerotin | Streptomyces ahygroscopicus subsp. wuzhouensis
BGC0000207.5 |  | 0.41 | PKS | chartreusin | Streptomyces chartreusis
BGC0000255.5 |  | 0.41 | PKS | pederin | Uncultured bacterium
BGC0000679.5 |  | 0.40 | terpene | diazepinomicin | Micromonospora sp. M42
BGC0001880.3 |  | 0.40 | ribosomal | scytodecamide | Scytonema sp. UIC 10036
BGC0000205.3 |  | 0.40 | PKS | bryostatin | Candidatus Endobugula sertula
BGC0002584.2 |  | 0.40 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002561.3 |  | 0.40 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (17):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 22.07 out of 30.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.13 out of 21.55
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.60 out of 29.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.73 out of 20.97
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.00 out of 31.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.85 out of 31.73
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.14 out of 21.84
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.74 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.27 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.12 out of 18.57
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
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.17 out of 27.18
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.11 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.02 out of 18.57
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 19.29 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.12 out of 33.14
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.20 out of 30.11
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator

NZ_CP034669.1 - Region 7 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,021,660 - 2,044,667 nt. (total: 23,008 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
EJ065_RS08620: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

EJ065_RS08650: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Translocases: transport
EJ065_RS08640: 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
--- | --- | --- | --- | --- | ---
BGC0001248.3 |  | 0.77 | terpene | clavaric acid | Hypholoma sublateritium
BGC0001839.3 |  | 0.51 | terpene | squalestatin S1 | Aspergillus sp. Z5
BGC0000669.3 |  | 0.46 | terpene | marneral | Arabidopsis thaliana
BGC0000664.5 |  | 0.44 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001317.3 |  | 0.43 | terpene | lupeol | Lotus japonicus
BGC0000670.4 |  | 0.42 | terpene | thalianol, thaliandiol, thalianin | Arabidopsis thaliana
BGC0002402.2 |  | 0.42 | terpene | Yossoside I, Yossoside II, Yossoside III, Yossoside IV, Yossoside V | Spinacia oleracea
BGC0002449.2 |  | 0.42 | other (other) | sarasinoside | uncultured bacterium
BGC0000648.3 |  | 0.41 | terpene | carotenoid | Myxococcus xanthus
BGC0000637.3 |  | 0.41 | terpene | carotenoid | Corynebacterium glutamicum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001248.3 |  | 0.77 | terpene | clavaric acid | Hypholoma sublateritium
BGC0001839.3 |  | 0.51 | terpene | squalestatin S1 | Aspergillus sp. Z5
BGC0000669.3 |  | 0.46 | terpene | marneral | Arabidopsis thaliana
BGC0000664.5 |  | 0.44 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001317.3 |  | 0.43 | terpene | lupeol | Lotus japonicus
BGC0000670.4 |  | 0.42 | terpene | thalianol, thaliandiol, thalianin | Arabidopsis thaliana
BGC0002402.2 |  | 0.42 | terpene | Yossoside I, Yossoside II, Yossoside III, Yossoside IV, Yossoside V | Spinacia oleracea
BGC0002449.2 |  | 0.42 | other (other) | sarasinoside | uncultured bacterium
BGC0000648.3 |  | 0.41 | terpene | carotenoid | Myxococcus xanthus
BGC0000637.3 |  | 0.41 | terpene | carotenoid | Corynebacterium glutamicum

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

No significant matches found.

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
triterpene | steroid |  | C30 | steroid skeleton | OH

Genes with terpene domains:
EJ065_RS08655: PT_phytoene_like
Domain 1 (15 - 271): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

EJ065_RS08660: T2TS
Domain 1 (3 - 633): Type 2 terpene synthase
Subtype: Oxidosqualene substrate

Reactions:
  2,3-oxidosqualene → steroid

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: 22.44 out of 23.79
Confidence: strong
Additional weak hits (8):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.65 out of 31.73
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.02 out of 32.93
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.34 out of 20.01
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.67 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.50 out of 29.25
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.33 out of 20.01
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.93 out of 29.38
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
--- | ---
FPP | Farnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
PSPP | Presqualene diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP034669.1 - Region 8 - 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: 2,288,616 - 2,345,118 nt. (total: 56,503 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase phosphate reductase
EJ065_RS10030: N-acetyl-gamma-glutamyl-phosphate reductase

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

EJ065_RS10045: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase acyltransferase kinase transketolase
EJ065_RS09995: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

EJ065_RS10010: transketolase

smcogs
  SMCOG1204: transketolase

EJ065_RS10050: acetylglutamate kinase

smcogs
  SMCOG1174: acetylglutamate kinase

EJ065_RS10080: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: deacetylase
EJ065_RS10055: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

Isomerases: mutase
EJ065_RS09980: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: ligase synthase
EJ065_RS09990: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

EJ065_RS10005: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

EJ065_RS10015: 1-deoxy-D-xylulose-5-phosphate synthase

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

EJ065_RS10065: pseudouridine synthase

smcogs
  SMCOG1279: pseudouridine 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
--- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  | 0.87 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.83 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  |  | 0.83 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  |  | 0.82 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.79 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  |  | 0.77 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  | 0.75 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0000307.4 |  |  | 0.72 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0000307.4 |  | 0.69 | 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:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.87 out of 26.85
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.00 out of 20.47
Confidence: medium
Additional weak hits (13):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.27 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.91 out of 27.78
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.76 out of 27.55
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.85 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.60 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.06 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.63 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.80 out of 26.06
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.11 out of 29.51
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.51 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.19 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.21 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.19 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 8, location 2288615 - 2345118:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val - Pro - Pro - X) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 9, location 2288615 - 2332284:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val - Pro - Pro - X) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 10, location 2292293 - 2345118:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val - Pro - Pro - X) + (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).
EJ065_RS09990: mal
PKS_AT (534..827): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 114.6
  inactive: 60.1
  Methoxymalonyl-CoA: 50.2
  Methylmalonyl-CoA: 39.2
  Propionyl-CoA: 29.8
  2-Methylbutyryl-CoA: 17.3
  Acetyl-CoA: 14.0
  Isobutyryl-CoA: 10.8
  CHC-CoA: 10.8
  fatty_acid: 10.2
  Benzoyl-CoA: 6.7
  Ethylmalonyl-CoA: 2.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

EJ065_RS09995: Val - Pro - Pro - X
Search NORINE for peptide: strict or relaxed
AMP-binding (499..896): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGVAFDAATLEGFLLTGGDTNGYGPTENTTFSAT
  Nearest Stachelhaus code(s):
    Val DALFLGGTFK (68% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1545..1947): Pro
nrpys: Pro

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MWQAFDVSFQEGFLITAGEENQYGPSETHAVSAW
  Nearest Stachelhaus code(s):
    Pro DVQFIAQVVK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2602..3004): Pro
nrpys: Pro

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MWQAFDVSFQEGFLITAGEENQYGPSETHAASAW
  Nearest Stachelhaus code(s):
    Pro DVQFIAQVVK (76% 8Å match)
    4Me-Pro DVQFIAHVAK (71% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (3665..4059): 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:
    LGLTFDATVFEPTLHVAGDLNCYGPTENTVIATS
  Nearest Stachelhaus code(s):
    OMe-Trp DAFTLGCVFK (47% 8Å match)
  Stachelhaus code match:
    70% (weak)

EJ065_RS10005: X
AMP-binding (5..426): X
nrpys: Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    ADTAFTYSYL-MYGATGSIHTLWGMTENGAVTIT
  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
--- | ---
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP034669.1 - Region 9 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,451,586 - 2,498,506 nt. (total: 46,921 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 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
EJ065_RS10520: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

EJ065_RS10530: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

EJ065_RS10535: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

EJ065_RS10545: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

EJ065_RS10560: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

EJ065_RS10565: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

EJ065_RS10605: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

EJ065_RS39770: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase methyltransferase
EJ065_RS10525: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

EJ065_RS10630: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

EJ065_RS10645: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
EJ065_RS10615: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: cyclase hydratase
EJ065_RS10555: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

EJ065_RS10635: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

EJ065_RS10660: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Ligases: ligase synthase
EJ065_RS10540: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

EJ065_RS10655: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

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
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.59 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002274.2 |  | 0.59 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0001945.3 |  | 0.53 | NRPS | chloromyxamide | Myxococcus sp.
BGC0002404.2 |  | 0.50 | other (other) | falcarindiol | Solanum lycopersicum
BGC0000866.5 |  | 0.50 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000894.4 |  | 0.50 | other (other) | citrinin | Monascus aurantiacus
BGC0000888.5 |  | 0.49 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000867.3 |  | 0.48 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0000231.5 |  | 0.45 | PKS | griseusin A, griseusin B | Streptomyces griseus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.59 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002274.2 |  | 0.59 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0001945.3 |  | 0.53 | NRPS | chloromyxamide | Myxococcus sp.
BGC0002404.2 |  | 0.50 | other (other) | falcarindiol | Solanum lycopersicum
BGC0000866.5 |  | 0.50 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000894.4 |  | 0.50 | other (other) | citrinin | Monascus aurantiacus
BGC0000888.5 |  | 0.49 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000867.3 |  | 0.48 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0000231.5 |  | 0.45 | PKS | griseusin A, griseusin B | Streptomyces griseus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 27.76 out of 30.22
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (6):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.11 out of 18.57
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.29 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.19 out of 28.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.20 out of 30.98
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
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).
EJ065_RS10540: X
AMP-binding (25..480): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    EAVLH---VAERFG----D--------AALESFR
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

EJ065_RS39770: mal
PKS_AT (204..501): mal
ATSignature: (unknown)
No matches above 50%
minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 45.1
  Methylmalonyl-CoA: 41.4
  Methoxymalonyl-CoA: 27.2
  Propionyl-CoA: 19.1
  Ethylmalonyl-CoA: 18.4
  trans-1,2-CPDA: 17.3
  2-Methylbutyryl-CoA: 17.0
  Acetyl-CoA: 8.7
  CHC-CoA: 1.4
  inactive: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
ClgR | Caseinolytic protease gene regulator

NZ_CP034669.1 - Region 10 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,640,640 - 2,706,808 nt. (total: 66,169 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
EJ065_RS11400: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Transferases: acetyltransferase acyltransferase
EJ065_RS11375: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

EJ065_RS11405: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Hydrolases: esterase
EJ065_RS11370: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

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

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
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001641.4 |  | 0.71 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.68 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001641.4 |  | 0.71 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.68 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.53 out of 25.88
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
Additional weak hits (8):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.22 out of 20.01
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.82 out of 23.43
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.10 out of 25.88
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.77 out of 36.54
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.07 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.69 out of 32.93
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.44 out of 27.04
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 12, location 2640639 - 2706808:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
EJ065_RS11375: Val - Val - Val - Ala - X - Ala - Ala - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (513..915): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGNGFDASTLEGWLLSGGDVHAYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (85% 8Å match)
    bOH-Val DALWLGGTFK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1571..1972): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGNAFDASTLEGWLLAGGDVNGYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (88% 8Å match)
    bOH-Val DALWLGGTFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2628..3029): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGNAFDASTLEGWLLAGGDVNGYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (88% 8Å match)
    bOH-Val DALWLGGTFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3685..4074): 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:
    FWATFDLSVFEANTNLAGEYNLYGPSEDTTYSTW
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4731..5128): X
nrpys: Gln, Glu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAHAFDASVQQVDCLVGGEFNVYGPTECTVDATA
  Nearest Stachelhaus code(s):
    Gln or Glu DAQDLGVVDK (85% 8Å match)
    Ile DAQDLGVVDK (82% 8Å match)
    Gln DAQDLGVVDK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5783..6172): 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:
    FWATFDLSVFEANTNLAGEYNLYGPSEDTTYSTW
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (6823..7212): 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:
    FWATFDLSVFEANTNLAGEYNLYGPSEDTTYSTW
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (7863..8265): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGNAFDASTLEGWLLAGGDVNGYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (88% 8Å match)
    bOH-Val DALWLGGTFK (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
--- | ---
AbrC3 | Antibiotic production activator
OsdR | Development and stress management regulator
PsrA | Oleic acid responsive regulator

NZ_CP034669.1 - Region 11 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,833,880 - 2,844,728 nt. (total: 10,849 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: esterase
EJ065_RS12060: thioesterase superfamily protein

smcogs
  SMCOG1144: thioesterase superfamily 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 | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002665.2 |  | 0.33 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0001486.4 |  | 0.31 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0000065.5 |  | 0.19 | PKS | rustmicin | Streptomyces galbus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002665.2 |  | 0.33 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0001486.4 |  | 0.31 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0000065.5 |  | 0.19 | PKS | rustmicin | Streptomyces galbus

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.58 out of 23.79
Confidence: medium
Additional weak hits (1):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.52 out of 29.38
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP034669.1 - Region 12 - NRPS,NRPS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,908,533 - 3,042,223 nt. (total: 133,691 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
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
EJ065_RS12460: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

EJ065_RS12490: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase acyltransferase aminotransferase glycosyltransferase sulfotransferase
EJ065_RS12400: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

EJ065_RS12500: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

EJ065_RS12525: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

EJ065_RS12595: glutathione S-transferase

smcogs
  SMCOG1193: glutathione S-transferase

EJ065_RS12605: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: esterase
EJ065_RS12405: thioesterase

smcogs
  SMCOG1004: thioesterase

EJ065_RS12415: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: lyase
EJ065_RS12590: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Isomerases: isomerase
EJ065_RS12395: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
EJ065_RS12430: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

EJ065_RS12495: 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 | T1PKS | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001833.4 |  |  |  | 1.05 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  | 1.02 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  | 1.02 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  |  | 1.01 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  |  |  | 0.94 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002154.2 |  |  |  | 0.90 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0000107.3 |  |  |  | 0.89 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0001257.3 |  |  |  | 0.89 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002191.2 |  |  |  | 0.89 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0002274.2 |  |  |  | 0.89 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.75 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002071.2 |  | 0.75 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.22 out of 23.43
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.49 out of 25.31
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.25 out of 20.01
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
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
Additional weak hits (9):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.92 out of 30.22
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.71 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.72 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.05 out of 27.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.89 out of 29.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.79 out of 30.97
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.27 out of 29.65
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.15 out of 32.93
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.68 out of 29.65
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 14, location 2908532 - 3042223:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ohmal) + (NH2) + (mal - Cys) + (X - Leu - Glu - Val - Val - Glu - Ala - Ala - Val) + (X - X - Val - Val - Ala - Ala - Ala)

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).
EJ065_RS12400: mal
PKS_AT (550..829): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 75.0%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 121.7
  inactive: 76.4
  Methoxymalonyl-CoA: 51.5
  Methylmalonyl-CoA: 43.4
  Propionyl-CoA: 22.8
  Isobutyryl-CoA: 13.2
  2-Methylbutyryl-CoA: 10.9
  Ethylmalonyl-CoA: 10.3
  3-Methylbutyryl-CoA: 9.8
  CHC-CoA: 9.6
  Benzoyl-CoA: 9.1
  fatty_acid: 8.5
  Acetyl-CoA: 8.4
  trans-1,2-CPDA: 0.0

EJ065_RS12410: NH2
CAL_domain (194..609): NH2
minowa: NH2

Prediction, score:
  NH2: 15.2
  fatty_acid: 8.8
  shikimic_acid: 0.0
  Acetyl-CoA: 0.0
  AHBA: -0.4

EJ065_RS12430: mal - Cys
Search NORINE for peptide: strict or relaxed
PKS_AT (592..871): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 75.0%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 121.7
  inactive: 76.4
  Methoxymalonyl-CoA: 51.5
  Methylmalonyl-CoA: 43.4
  Propionyl-CoA: 22.8
  Isobutyryl-CoA: 13.2
  2-Methylbutyryl-CoA: 10.9
  Ethylmalonyl-CoA: 10.3
  3-Methylbutyryl-CoA: 9.8
  CHC-CoA: 9.6
  Benzoyl-CoA: 9.1
  fatty_acid: 8.5
  Acetyl-CoA: 8.4
  trans-1,2-CPDA: 0.0

AMP-binding (3210..3609): 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:
    TDISFDLSVYDGNSMLSGDASLGGATEASIWSII
  Nearest Stachelhaus code(s):
    Cys DLYNMSLIWK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

EJ065_RS12495: X - Leu - Glu - Val - Val - Glu - Ala - Ala - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (506..899): 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:
    LHEAFDLSVEETSLISGGELNTYGPTEATVIATF
  Nearest Stachelhaus code(s):
    Lys DAESIGTVIK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1557..1947): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHAFDASTWEPFMLTGGDFNHYGPTESTVVATF
  Nearest Stachelhaus code(s):
    Leu DAWFLGHVVK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2604..3002): Glu
nrpys: Glu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LALAFDASVKQQDCLVGGEFNVYGPTECTVDATA
  Nearest Stachelhaus code(s):
    Glu DAKDLGVVDK (74% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3662..4061): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGSAFDASTLEGWLLAGGDLNGYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (88% 8Å match)
    bOH-Val DALWLGGTFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4720..5119): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MGSAFDASTLEGFLLSGGDHNAYGPTESTTLATT
  Nearest Stachelhaus code(s):
    Val DALFLGGTFK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (5777..6175): Glu
nrpys: Glu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LALAFDASVKQQDCLVGGEFNVYGPTECTVDATA
  Nearest Stachelhaus code(s):
    Glu DAKDLGVVDK (74% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (6834..7222): 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:
    FWATFDLSVFEANTNLAGEFNLYGPSEDTTYSTA
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (7879..8267): 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:
    FWATFDLSVFEANTNLAGEFNLYGPSEDTTYSTA
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (8923..9322): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGSAFDASTLEGWLLAGGDLNGYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (88% 8Å match)
    bOH-Val DALWLGGTFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

EJ065_RS12500: X - X - Val - Val - Ala - Ala - Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (506..899): 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:
    LHEAFDLSVEETSLISGGELNTYGPTEATVIATF
  Nearest Stachelhaus code(s):
    Lys DAESIGTVIK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1556..1954): X
nrpys: Gln, Glu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGLAFDASVQQVDCLVGGEFNVYGPTECTVDATA
  Nearest Stachelhaus code(s):
    Gln or Glu DAQDLGVVDK (91% 8Å match)
    Ile DAQDLGVVDK (88% 8Å match)
    Gln DAQDLGVVDK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2614..3013): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGSAFDASTLEGWLLTGGEVHAYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (85% 8Å match)
    bOH-Val DALWLGGTFK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (3671..4070): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGSAFDASTLEGWLLTGGDIHAYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (85% 8Å match)
    bOH-Val DALWLGGTFK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (4729..5117): 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:
    FWATFDLSVFEANTNLAGEFNLYGPSEDTTYSTA
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5774..6162): 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:
    FWATFDLSVFEANTNLAGEFNLYGPSEDTTYSTA
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (6819..7207): 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:
    FWATFDLSVFEANTNLAGEFNLYGPSEDTTYSTA
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (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
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
ArgR | Regulator of arginine biosynthesis genes
BldD | Development and antibiotic global regulator
CatR | H2O2-responsive repressor

NZ_CP034669.1 - Region 13 - 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: 3,230,816 - 3,284,035 nt. (total: 53,220 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: oxidoreductase
EJ065_RS13600: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: acyltransferase aminotransferase
EJ065_RS13495: aminotransferase

smcogs
  SMCOG1019: aminotransferase

EJ065_RS13530: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Lyases: dehydratase
EJ065_RS13610: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
EJ065_RS13535: 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 | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001261.3 |  |  | 0.82 | NRPS | AM-toxin | Alternaria alternata
BGC0002135.2 |  |  | 0.80 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  |  | 0.77 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  |  | 0.76 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001166.5 |  |  | 0.69 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000307.4 |  |  | 0.68 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0002135.2 |  | 0.72 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.68 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001166.5 |  | 0.68 | NRPS | HC-toxin | Alternaria jesenskae
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.

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.05 out of 22.40
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.00 out of 20.47
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.17 out of 25.88
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (13):
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.02 out of 32.93
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.99 out of 32.93
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.82 out of 23.43
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.90 out of 20.01
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.51 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.36 out of 27.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.77 out of 24.78
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.00 out of 32.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.64 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.23 out of 31.73
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.76 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.25 out of 28.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 20.60 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 15, location 3230815 - 3284035:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Pro - mal) + (Gly - Gly)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
EJ065_RS13530: Gly - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (490..879): 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:
    FTMTFDIAVLELQALVGGEWNMYGPTETTVWSTT
  Nearest Stachelhaus code(s):
    Gly DILQLGMVWK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1540..1929): 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:
    FTMTFDIAVLELQALVGGEWNMYGPTETTVWSTT
  Nearest Stachelhaus code(s):
    Gly DILQLGMVWK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

EJ065_RS13535: Pro - mal
Search NORINE for peptide: strict or relaxed
AMP-binding (12..417): Pro
nrpys: Pro

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQSFDVSFQEGFLVTAGEHNHYGPSETHVVSSY
  Nearest Stachelhaus code(s):
    Pro DVQFVAHVVK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

PKS_AT (1141..1436): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 79.2%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 155.6
  inactive: 85.9
  Methoxymalonyl-CoA: 61.7
  Methylmalonyl-CoA: 53.9
  Isobutyryl-CoA: 40.4
  Propionyl-CoA: 35.4
  Ethylmalonyl-CoA: 23.9
  2-Methylbutyryl-CoA: 23.5
  3-Methylbutyryl-CoA: 20.3
  Benzoyl-CoA: 19.3
  CHC-CoA: 16.3
  Acetyl-CoA: 16.1
  fatty_acid: 14.8
  trans-1,2-CPDA: 12.8

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
HypR | L-hydroxyproline utilization repressor
PsrA | Oleic acid responsive regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP034669.1 - Region 14 - indole
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,317,369 - 3,350,700 nt. (total: 33,332 nt) Show pHMM detection rules used
indole: (indsynth or dmat or indole_PTase)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: sulfotransferase
EJ065_RS13850: glutathione S-transferase

smcogs
  SMCOG1193: glutathione S-transferase

EJ065_RS13910: glutathione S-transferase

smcogs
  SMCOG1193: glutathione S-transferase

Hydrolases: hydrolase
EJ065_RS13920: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold 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 | indole | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002330.2 |  | 0.38 | ribosomal | landornamide A | Kamptonema sp. PCC 6506
BGC0001245.3 |  | 0.37 | PKS | lasiodiplodin | Lasiodiplodia theobromae
BGC0002805.2 |  | 0.36 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0001626.3 |  | 0.36 | PKS | isoindolinone | Stachybotrys chlorohalonata IBT 40285
BGC0000076.3 |  | 0.35 | PKS | hypothemycin | Hypomyces subiculosus
BGC0000077.3 |  | 0.34 | PKS | hypothemycin | Hypomyces subiculosus
BGC0001363.5 |  | 0.34 | NRPS, PKS | ralsolamycin | Ralstonia solanacearum GMI1000
BGC0000335.4 |  | 0.33 | NRPS, PKS | cystomanamide A, cystomanamide B, cystomanamide C, cystomanamide D | Cystobacter fuscus
BGC0001369.3 |  | 0.32 | PKS | metatricycloene | uncultured bacterium
BGC0001835.2 |  | 0.32 | PKS | gynuellalide | Gynuella sunshinyii YC6258

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002330.2 |  | 0.38 | ribosomal | landornamide A | Kamptonema sp. PCC 6506
BGC0001245.3 |  | 0.37 | PKS | lasiodiplodin | Lasiodiplodia theobromae
BGC0002805.2 |  | 0.36 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0001626.3 |  | 0.36 | PKS | isoindolinone | Stachybotrys chlorohalonata IBT 40285
BGC0000076.3 |  | 0.35 | PKS | hypothemycin | Hypomyces subiculosus
BGC0000077.3 |  | 0.34 | PKS | hypothemycin | Hypomyces subiculosus
BGC0001363.5 |  | 0.34 | NRPS, PKS | ralsolamycin | Ralstonia solanacearum GMI1000
BGC0000335.4 |  | 0.33 | NRPS, PKS | cystomanamide A, cystomanamide B, cystomanamide C, cystomanamide D | Cystobacter fuscus
BGC0001369.3 |  | 0.32 | PKS | metatricycloene | uncultured bacterium
BGC0001835.2 |  | 0.32 | PKS | gynuellalide | Gynuella sunshinyii YC6258

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (6):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.68 out of 30.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.36 out of 31.73
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.02 out of 32.93
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.60 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.41 out of 28.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.56 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP034669.1 - Region 15 - NRPS,NRPS-like,PKS-like,T1PKS,lanthipeptide-class-i,transAT-PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,789,728 - 3,966,492 nt. (total: 176,765 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))
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))
PKS-like: (t2pks2 or ksIII)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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
Lanthipeptides
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
EJ065_RS15880: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

EJ065_RS15960: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

EJ065_RS15965: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

EJ065_RS15980: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

EJ065_RS15985: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Transferases: acylase aminotransferase glycosyltransferase methyltransferase
EJ065_RS15910: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

EJ065_RS16075: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

EJ065_RS16080: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

EJ065_RS16090: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

EJ065_RS16175: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: esterase
EJ065_RS15975: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: cyclase dehydratase hydratase
EJ065_RS15835: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

EJ065_RS15840: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

EJ065_RS15935: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

EJ065_RS15940: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
EJ065_RS15915: 3-oxoacyl-(acyl carrier protein) synthase III

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

EJ065_RS15925: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

EJ065_RS15930: hydroxymethylglutaryl-CoA synthase

smcogs
  SMCOG1043: hydroxymethylglutaryl-CoA synthase

EJ065_RS15955: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

EJ065_RS16060: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

EJ065_RS16065: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

EJ065_RS16070: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

EJ065_RS16095: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

EJ065_RS38975: 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 | transAT-PKS | PKS-like | NRPS-like | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001091.5 |  |  |  |  |  |  | 1.84 | NRPS, PKS | corallopyronin | Corallococcus coralloides
BGC0001164.3 |  |  |  |  |  |  | 1.77 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  |  |  |  | 1.76 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001161.5 |  |  |  |  |  |  | 1.01 | PKS | 1-heptadecene | Moorea bouillonii PNG
BGC0002135.2 |  |  |  |  |  |  | 0.94 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001876.2 |  |  |  |  |  |  | 0.93 | NRPS | thalassospiramide A | Thalassospira sp. CNJ-328
BGC0001163.3 |  |  |  |  |  |  | 0.90 | PKS | 1-heptadecene | Moorea producens 3L
BGC0000402.4 |  |  |  |  |  |  | 0.90 | NRPS | paenilarvin A, paenilarvin B, paenilarvin C | Paenibacillus larvae subsp. larvae DSM 25430
BGC0001050.5 |  |  |  |  |  |  | 0.89 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0001273.3 |  |  |  |  |  |  | 0.89 | PKS | asperlactone | Aspergillus ochraceus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001091.5 |  | 0.96 | NRPS, PKS | corallopyronin | Corallococcus coralloides
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.73 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  | 0.72 | NRPS | AM-toxin | Alternaria alternata

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

No significant matches found.

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:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.03 out of 29.72
Confidence: medium
Additional weak hits (26):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.97 out of 39.62
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.46 out of 25.88
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.28 out of 23.43
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.69 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.75 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.13 out of 28.14
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.73 out of 19.26
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.13 out of 30.97
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.42 out of 29.65
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.09 out of 27.04
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.26 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.02 out of 26.06
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.26 out of 32.93
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.53 out of 32.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.39 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.80 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.50 out of 32.74
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.76 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.91 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.79 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.93 out of 35.63
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.85 out of 20.01
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.64 out of 26.06
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.14 out of 32.93
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.48 out of 32.38
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Lanthipeptides
NRPS/PKS products
NRPS/PKS substrates
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.
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 17, location 3789727 - 3966492:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - mal) + (Me-ccmal - mal - mal) + (ccmal - ccmal - mal) + (ccmal - mal - Me-ccmal - mal) + (X - D-X - X) + (ohmal) + (Acetyl-CoA - pk - Asp - D-Thr - Asn - D-Ser - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 19, location 3804061 - 3902940:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - mal) + (Me-ccmal - mal - mal) + (ccmal - ccmal - mal) + (ccmal - mal - Me-ccmal - mal)
Non-colinear ordering:
  EJ065_RS15950 + EJ065_RS15955 + EJ065_RS15960 + EJ065_RS15965

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 20, location 3884218 - 3966492:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Acetyl-CoA - pk - Asp - D-Thr - Asn - D-Ser - X) + (ohmal) + (X - D-X - X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
EJ065_RS15910: mal
PKS_AT (0..277): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 108.7
  Methoxymalonyl-CoA: 37.4
  inactive: 35.9
  Methylmalonyl-CoA: 27.0
  Propionyl-CoA: 23.0
  fatty_acid: 15.1
  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
  2-Methylbutyryl-CoA: 0.0

EJ065_RS15950: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (1156..1552): 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:
    FAMTFDIAGLELQALCGGEWNLYGPTETTIWSTL
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

EJ065_RS16060: X - X - X
AMP-binding (514..906): 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:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAEAFDISVEETSLISGGEFNTYGPTEGTVVATL
  Nearest Stachelhaus code(s):
    Lys DIESIGTVLK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1569..1966): X
nrpys: Gln, Glu, Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LALAFDASVQQRDCLVGGEFNVYGPTECTVDSTC
  Nearest Stachelhaus code(s):
    Gln or Glu DAQDLGVVDK (88% 8Å match)
    Ile DAQDLGVVDK (88% 8Å match)
    Gln DAQDLGVVDK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3086..3477): X
nrpys: Phe, 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:
    TAAAFDASVCESTLISAGELNAYGPTEASVCASI
  Nearest Stachelhaus code(s):
    Tyr or Pro DASTIAAVCK (76% 8Å match)
    Tyr DASTIAAVCK (71% 8Å match)
    Phe DAWTIAAVCK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

EJ065_RS16065: mal
PKS_AT (535..832): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 79.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 170.3
  inactive: 102.1
  Methoxymalonyl-CoA: 78.3
  Methylmalonyl-CoA: 56.0
  Ethylmalonyl-CoA: 28.5
  Propionyl-CoA: 26.7
  CHC-CoA: 24.1
  2-Methylbutyryl-CoA: 22.7
  Isobutyryl-CoA: 20.0
  trans-1,2-CPDA: 11.3
  Acetyl-CoA: 10.8
  fatty_acid: 9.2
  Benzoyl-CoA: 8.6
  3-Methylbutyryl-CoA: 8.5

EJ065_RS16070: Acetyl-CoA - pk - Asp - Thr - Asn - Ser - X
Search NORINE for peptide: strict or relaxed
CAL_domain (43..494): Acetyl-CoA
minowa: Acetyl-CoA

Prediction, score:
  Acetyl-CoA: 58.3
  NH2: 27.8
  fatty_acid: 26.3
  AHBA: 13.5
  shikimic_acid: 0.0

PKS_AT (1231..1528): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  Methylmalonyl-CoA: 66.7%
  Ethylmalonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 121.5
  Methoxymalonyl-CoA: 108.2
  Isobutyryl-CoA: 99.5
  Malonyl-CoA: 99.3
  Ethylmalonyl-CoA: 82.0
  Benzoyl-CoA: 66.1
  Propionyl-CoA: 61.1
  Acetyl-CoA: 57.8
  CHC-CoA: 54.3
  3-Methylbutyryl-CoA: 49.1
  trans-1,2-CPDA: 44.1
  2-Methylbutyryl-CoA: 38.9
  fatty_acid: 30.0
  inactive: 28.6

AMP-binding (2684..3097): Asp
nrpys: Asp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HVLAFDISVWQTQVIPTGELNAYGPAECSDDVTL
  Nearest Stachelhaus code(s):
    Asp DIWQSTADDK (62% 8Å match)
    dnmeProp or Dab DIWQSTADDK (59% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (3759..4166): 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:
    LATHFDFSVWEGNQVFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5280..5681): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWCSFDLTVTSLKLVIGGEINEYGPTEAVVGCCV
  Nearest Stachelhaus code(s):
    Asn DLTKVGEVGK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (6339..6738): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFICSGEHNLYGPTEAAVDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHISLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (7858..8249): X
nrpys: Phe, 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:
    TAAAFDASVCESTLISAGELNAYGPTEASVCASI
  Nearest Stachelhaus code(s):
    Tyr or Pro DASTIAAVCK (76% 8Å match)
    Tyr DASTIAAVCK (71% 8Å match)
    Phe DAWTIAAVCK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (3789727...3814715)
EJ065_RS15835
  RRE type: Lanthipeptide_LanB_RRE
  Location: 173 - 261
  Score: 43.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP034669.1 - Region 16 - NRPS,T1PKS,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: 4,075,420 - 4,155,794 nt. (total: 80,375 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)
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
Transferases: acylase acyltransferase methyltransferase
EJ065_RS16785: methyltransferase

smcogs
  SMCOG1089: methyltransferase

EJ065_RS16830: acyltransferase

smcogs
  SMCOG1141: acyltransferase

EJ065_RS40660: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase protease
EJ065_RS16635: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

EJ065_RS39395: HAD-superfamily hydrolase, subfamily IA, variant

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

Lyases: decarboxylase
EJ065_RS16795: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase
EJ065_RS39850: 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 | t3nrps-iterative | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001164.3 |  |  |  | 0.78 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  | 0.78 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001051.5 |  |  |  | 0.54 | NRPS, PKS | thuggacin A | Sorangium cellulosum
BGC0000143.5 |  |  |  | 0.50 | PKS | salinomycin | Streptomyces albus
BGC0001163.3 |  |  |  | 0.50 | PKS | 1-heptadecene | Moorea producens 3L
BGC0001162.3 |  |  |  | 0.50 | PKS | 1-heptadecene | Moorea producens JHB
BGC0001161.5 |  |  |  | 0.49 | PKS | 1-heptadecene | Moorea bouillonii PNG
BGC0000353.5 |  |  |  | 0.41 | NRPS | tacrolimus | Streptomyces sp. MA6548
BGC0002749.2 |  |  |  | 0.41 | NRPS, PKS | aspcandine | Aspergillus candidus
BGC0001876.2 |  |  |  | 0.41 | NRPS | thalassospiramide A | Thalassospira sp. CNJ-328

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
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
BGC0001051.5 |  | 0.52 | NRPS, PKS | thuggacin A | Sorangium cellulosum
BGC0000143.5 |  | 0.50 | PKS | salinomycin | Streptomyces albus
BGC0001844.4 |  | 0.49 | NRPS | holrhizin A, holrhizin B, holrhizin C, holrhizin D | Paraburkholderia rhizoxinica HKI 454
BGC0001873.3 |  | 0.48 | NRPS | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0001163.3 |  | 0.48 | PKS | 1-heptadecene | Moorea producens 3L
BGC0001162.3 |  | 0.48 | PKS | 1-heptadecene | Moorea producens JHB
BGC0001161.5 |  | 0.47 | PKS | 1-heptadecene | Moorea bouillonii PNG

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.54 out of 23.79
Confidence: medium
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.40 out of 22.40
Confidence: strong
Additional weak hits (10):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.71 out of 39.62
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.62 out of 18.57
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.39 out of 21.55
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.12 out of 26.12
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.27 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.87 out of 20.01
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.50 out of 28.14
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.37 out of 32.93
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.66 out of 29.65
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.42 out of 27.04
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 21, location 4075419 - 4155794:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Cys - ohmal - ohmal)

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).
EJ065_RS39850: Cys - mal
Search NORINE for peptide: strict or relaxed
AMP-binding (506..911): 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:
    TDISFDLSVWDGNTMLSGDVALGGATEASIWSNF
  Nearest Stachelhaus code(s):
    Cys DLWNLSLIWK (88% 8Å match)
  Stachelhaus code match:
    90% (moderate)

PKS_AT (1547..1832): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 70.8%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 124.3
  inactive: 67.0
  Methoxymalonyl-CoA: 62.3
  Methylmalonyl-CoA: 57.6
  Propionyl-CoA: 47.0
  Isobutyryl-CoA: 40.2
  Benzoyl-CoA: 33.7
  fatty_acid: 27.2
  Ethylmalonyl-CoA: 25.9
  Acetyl-CoA: 25.2
  3-Methylbutyryl-CoA: 20.6
  2-Methylbutyryl-CoA: 20.0
  CHC-CoA: 14.9
  trans-1,2-CPDA: 11.3

EJ065_RS40660: mal
PKS_AT (5..293): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 70.8%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 128.8
  Methoxymalonyl-CoA: 66.3
  inactive: 63.3
  Methylmalonyl-CoA: 58.4
  Propionyl-CoA: 48.3
  Isobutyryl-CoA: 38.9
  fatty_acid: 30.9
  Benzoyl-CoA: 29.4
  Ethylmalonyl-CoA: 27.1
  3-Methylbutyryl-CoA: 19.6
  Acetyl-CoA: 19.3
  2-Methylbutyryl-CoA: 16.3
  CHC-CoA: 13.8
  trans-1,2-CPDA: 9.2

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

Regulator | Description
--- | ---
HypR | L-hydroxyproline utilization repressor
IolR | Regulator of the inositol catabolism

NZ_CP034669.1 - Region 17 - 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: 4,290,341 - 4,362,401 nt. (total: 72,061 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 oxidoreductase
EJ065_RS17590: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

EJ065_RS17615: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

EJ065_RS17655: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Hydrolases: hydrolase
EJ065_RS17530: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

Lyases: cyclase
EJ065_RS17660: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Ligases: synthase
EJ065_RS17580: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

EJ065_RS17610: hydroxymethylglutaryl-CoA synthase

smcogs
  SMCOG1043: hydroxymethylglutaryl-CoA 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
--- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  | 0.87 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  |  | 0.84 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  |  | 0.83 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  |  | 0.79 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.78 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  | 0.75 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001641.4 |  |  | 0.74 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  |  | 0.71 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001240.4 |  |  | 0.71 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.73 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001641.4 |  | 0.69 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.68 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001240.4 |  | 0.68 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.22 out of 18.46
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.73 out of 18.46
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 21.40 out of 23.05
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.59 out of 23.05
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.30 out of 24.78
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.75 out of 23.05
Confidence: medium
Additional weak hits (12):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.08 out of 25.75
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.25 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.67 out of 30.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.82 out of 32.74
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.63 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.68 out of 30.25
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.99 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.22 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.59 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.32 out of 30.98
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 22, location 4290340 - 4362401:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser - X - Phe - Val - mal - Ser - Val - Glu)

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).
EJ065_RS17580: Ser - X - Phe - Val - mal - X - Ser - Val - Glu
Search NORINE for peptide: strict or relaxed
AMP-binding (483..884): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWELHFVCSGEHNLYGPTEAAVDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHVSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1540..1941): X
nrpys: Val, bOH-Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDSAFDASTLEGWLLAGGDINGYGPTENTTFSAT
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (85% 8Å match)
    bOH-Val DALWLGGTFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2600..3001): Phe
nrpys: Phe

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    N/A
  Single AA prediction:
    phe (Phe)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDTGFDLATFEGLFLYAGEVNLYGPTETTVGVTT
  Nearest Stachelhaus code(s):
    Pro DLFYLALVCK (53% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (3659..4057): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGAAFDASTLEGYLFVGGDVNGYGPTEATVFTCC
  Nearest Stachelhaus code(s):
    Ile or Val DALWMGGVFK (68% 8Å match)
    Val DALWMGGVFK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

PKS_AT (4888..5187): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 117.2
  Methoxymalonyl-CoA: 83.4
  Methylmalonyl-CoA: 74.2
  Ethylmalonyl-CoA: 54.4
  inactive: 51.1
  Propionyl-CoA: 49.0
  Isobutyryl-CoA: 46.7
  CHC-CoA: 31.4
  2-Methylbutyryl-CoA: 26.2
  Benzoyl-CoA: 23.6
  trans-1,2-CPDA: 21.3
  Acetyl-CoA: 20.2
  fatty_acid: 15.2
  3-Methylbutyryl-CoA: 14.4

A-OX (5915..6638): X
No predictions made
AMP-binding (7151..7552): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFMCSGEHNLYGPTEAAVDVTS
  Nearest Stachelhaus code(s):
    Ser DVWHMSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (8223..8638): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSNAFDASTLEGWLLAGGDVNGYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (85% 8Å match)
    bOH-Val DALWLGGTFK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (9299..9719): Glu
nrpys: Glu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LALAFDASVYQWDVLVGGEFNTYGPTECTVATTA
  Nearest Stachelhaus code(s):
    Gln or Glu DAQDLGVVDK (76% 8Å match)
    Ile DAQDLGVVDK (74% 8Å match)
    Dhpg DAYNLGTLCK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
LexA variant 2 | Repressor of DNA damage response
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP034669.1 - Region 18 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,562,226 - 4,573,872 nt. (total: 11,647 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
EJ065_RS18445: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001928.2 |  | 0.46 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000866.5 |  | 0.45 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000902.4 |  | 0.42 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0001184.4 |  | 0.42 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0002496.3 |  | 0.38 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0000671.3 |  | 0.36 | terpene | momilactone B | Oryza sativa Japonica Group
BGC0002387.2 |  | 0.35 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0000218.5 |  | 0.35 | PKS | doxorubicin | Streptomyces peucetius
BGC0001605.3 |  | 0.34 | terpene | gibberellin | Sinorhizobium fredii NGR234

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001928.2 |  | 0.46 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000866.5 |  | 0.45 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000902.4 |  | 0.42 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0001184.4 |  | 0.42 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0002496.3 |  | 0.38 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0000671.3 |  | 0.36 | terpene | momilactone B | Oryza sativa Japonica Group
BGC0002387.2 |  | 0.35 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0000218.5 |  | 0.35 | PKS | doxorubicin | Streptomyces peucetius
BGC0001605.3 |  | 0.34 | terpene | gibberellin | Sinorhizobium fredii NGR234

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.73 out of 18.46
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.42 out of 20.47
Confidence: medium
Additional weak hits (4):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.58 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.22 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.98 out of 26.06
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.70 out of 26.12
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP034669.1 - Region 19 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,663,500 - 4,751,280 nt. (total: 87,781 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
EJ065_RS19010: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

EJ065_RS19020: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

EJ065_RS19025: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

EJ065_RS19060: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

EJ065_RS19065: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Lyases: dehydratase
EJ065_RS18925: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

EJ065_RS19035: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

EJ065_RS19095: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
EJ065_RS19000: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

EJ065_RS19030: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

EJ065_RS19040: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.77 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.77 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.74 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.74 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.77 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.77 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.74 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.74 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.44 out of 23.79
Confidence: medium
Additional weak hits (5):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.81 out of 21.55
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.52 out of 20.01
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.49 out of 39.62
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 24, location 4663499 - 4751280:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser - NMe-Gly) + (AHBA - Ala - Ala - Phe - Val - Asp - X - Tyr - Asn - Thr)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
EJ065_RS19000: AHBA - Ala - Ala - Phe - Val - Asp - X - Tyr - Asn - Thr
Search NORINE for peptide: strict or relaxed
CAL_domain (44..494): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 24.1
  fatty_acid: 23.6
  NH2: 23.6
  Acetyl-CoA: 3.8
  shikimic_acid: 2.3

AMP-binding (1171..1564): 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:
    FWATFDLSVFEANTNLAGEYNLYGPTEDTTYSTY
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2217..2610): 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:
    FWATFDISVFEANTNLAGEYNFYGPTEDTTYSTY
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (85% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (3264..3656): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TQAAFDASVWESTLVSAGEINAYGPTETTVCATL
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (71% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4317..4716): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGPAFDASTFEGWLLAGGDINGYGPTENTTFTAC
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5386..5789): Asp
nrpys: Asp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YGVSADLGHTAPKIVLGGEFNHYGPTETTVGVLT
  Nearest Stachelhaus code(s):
    Asp DLTKVGHVGK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (6452..6843): X
nrpys: R-bohPhe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TRAAFDASVWESTLVSAGEINAYGPTEATVCATL
  Nearest Stachelhaus code(s):
    R-bohPhe DAWTVAAVCK (76% 8Å match)
    Phe DAWTVAAVCK (71% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (7509..7900): Tyr
nrpys: Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TQAAFDASVCEGTLISAGEINAYGPTEATVCATL
  Nearest Stachelhaus code(s):
    Tyr DASTIAAVCK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (8562..8965): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWCSFDLTVTSAKLVIGGEINEYGPTETVVGCSV
  Nearest Stachelhaus code(s):
    Asn DLTKVGEVGK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (9625..10033): 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:
    LGTHFDFSVWEGNQVFGGEVNMYGITETTVHVTW
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

EJ065_RS19030: NH2
CAL_domain (42..481): NH2
minowa: NH2

Prediction, score:
  NH2: 138.7
  AHBA: 14.5
  Acetyl-CoA: 11.4
  shikimic_acid: 3.5
  fatty_acid: 1.0

EJ065_RS19040: Ser - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (468..871): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFMCSGEHNLYGPTEASIDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHMSLIDK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1538..1946): 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:
    FGMTFDISVLEWQSLVGGEFNMYGPTETTVWSTV
  Nearest Stachelhaus code(s):
    Gly DILQLGMVWK (82% 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_CP034669.1 - Region 20 - lanthipeptide-class-ii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,834,866 - 4,857,709 nt. (total: 22,844 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### 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: oxidoreductase
EJ065_RS19490: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Lyases: cyclase
EJ065_RS19475: lanthionine synthetase C family protein

smcogs
  SMCOG1070: 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-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001579.4 |  | 0.46 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0002704.2 |  | 0.46 | ribosomal | archalan β | Halorussus salinus
BGC0002698.2 |  | 0.43 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001660.3 |  | 0.43 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000503.5 |  | 0.42 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000517.4 |  | 0.41 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125
BGC0002346.3 |  | 0.40 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0001364.3 |  | 0.39 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001579.4 |  | 0.46 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0002704.2 |  | 0.46 | ribosomal | archalan β | Halorussus salinus
BGC0002698.2 |  | 0.43 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001660.3 |  | 0.43 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000503.5 |  | 0.42 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000517.4 |  | 0.41 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125
BGC0002346.3 |  | 0.40 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0001364.3 |  | 0.39 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919

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

No significant matches found.

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

No significant matches found.

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

#### Lanthipeptide(s) for EJ065_RS19475

EJ065_RS19470
Leader:
MTKNASVHDVVQGWLSGDEESHGM
Core:
T N P A G P V F V G G L R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
Core with dehydrations:
Dhb N P A G P V F V G G L R Dhb E Q A L Dhb E Dha N L V E N Dhb G Cys Dha Dha Cys Dha A Dha Dhb Dhb G F Cys Cys

#### antiSMASH-DB 4.0 matches for EJ065_RS19470

100.0%
NZ_CP034669.1:
Lanthipeptides: EJ065_RS19470_lanthipeptide
1
T N P A G P V F V G G L R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
T N P A G P V F V G G L R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
1
T N P A G P V F V G G L R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
97.6%
NC_017030.1:
Lanthipeptides: COCOR_RS20320_lanthipeptide
1
T N P A G P V F V G G L R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
T N P A G P V F V G G+R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
1
T N P A G P V F V G G M R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
97.6%
NZ_CP114039.1:
Lanthipeptides: O0N60_RS29095_lanthipeptide
1
T N P A G P V F V G G L R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
T N P A G P V F V G G R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
1
T N P A G P V F V G G Q R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
with 68 more sequence matches
Only the first 10 are displayed here.
82.9%
NZ_CP079946.1:
Lanthipeptides: KYK13_RS20175_lanthipeptide
1
T N P A G P V F V G G L R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
T N P A G P V F V G G T E+A L T E S N L V +T G C S S C+A S T T F C C
1
T N P A G P V F V G G T S T E K A L T E S N L V A D T G C S S C T A S T T A F C C
41
53.8%
NZ_CP012109.1:
Lanthipeptides: A176_RS31295_lanthipeptide
1
T N P A G P V F V G G L R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
+N P A G P++V G G T E A L T+ +L+ T G C S S C S A S T G F C C
12
S N P A G P L Y V G G D A T E A A L T D E S L M I F T G C S S C S A S G T G F C C
52
53.7%
NZ_CP069396.1:
Lanthipeptides: JRI60_RS03735_lanthipeptide
2
N P A G P V F V G G L R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
N P A G P++V G G T E A L T+++ T C S S C S S +C C
2
N P A G P L Y V G G A A T E N A L T D A S D A L V T R C S S C S G S A G S Y C C
41
51.2%
NZ_CP010407.1 and 4 others:
NZ_CP010407.1 Lanthipeptides: SVTN_RS37515_lanthipeptide NZ_CP010407.1 Lanthipeptides: SVTN_RS37515_lanthipeptide NZ_CP010407.1 Lanthipeptides: SVTN_RS37515_lanthipeptide NZ_JACHJY010000017.1 Lanthipeptides: GGE06_RS39715_lanthipeptide
Lanthipeptides: SVTN_RS37515_lanthipeptide
2
N P A G P V F V G G L R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
N P A G P++V G G E A L T+ T G C S S C+ S +C C
2
N P A G P L Y V G G A A G E A A L T D G T E A L L T G C S S C T G S L H S Y C C
41
51.2%
NZ_CP029194.1 and 1 other:
NZ_CP059991.1 Lanthipeptides: H4W23_RS35675_lanthipeptide
Lanthipeptides: DEJ46_RS04155_lanthipeptide
2
N P A G P V F V G G L R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
N P A G P++V G G E A L T++ T G C S S C+ S +C C
2
N P A G P L Y V G G A A G E A A L T D A T E A L L T G C S S C T G S W H S Y C C
41
51.2%
NZ_JH941044.1:
Lanthipeptides: Y19_RS0126875_lanthipeptide
2
N P A G P V F V G G L R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
N P A G P++V G G E A L T++ T G C S S C+ S +C C
2
N P A G P L Y V G G A A G E A A L T D A T E A L F T G C S S C T G S W H S Y C C
41
47.6%
NZ_BMUQ01000012.1 and 9 others:
NZ_CP041604.2 Lanthipeptides: FNV64_RS07000_lanthipeptide NZ_CP041610.2 Lanthipeptides: FNV62_RS03705_lanthipeptide NZ_CP041611.1 Lanthipeptides: FNV63_RS03970_lanthipeptide NZ_CP041613.2 Lanthipeptides: FNV68_RS05855_lanthipeptide NZ_CP041650.2 Lanthipeptides: FNV59_RS05275_lanthipeptide NZ_CP050974.1 Lanthipeptides: HEP84_RS02235_lanthipeptide NZ_CP051010.1 Lanthipeptides: HEP87_RS03725_lanthipeptide NZ_FONR01000009.1 Lanthipeptides: BM303_RS25620_lanthipeptide NZ_KQ948493.1 Lanthipeptides: AQJ27_RS49365_lanthipeptide
Lanthipeptides: IE289_RS27575_lanthipeptide
1
T N P A G P V F V G G L R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
T N P A G P++V G G E A L T+ + C S S S S +C C
2
T N P A G P L Y V G G A A A E A A L T D P S D S L Y G F C S S P S G S H G S W C C
42
47.6%
NZ_BMUU01000006.1 and 2 others:
NZ_BMUZ01000004.1 Lanthipeptides: IE267_RS12185_lanthipeptide NZ_CP070373.1 Lanthipeptides: GWQ54_RS15625_lanthipeptide
Lanthipeptides: IE233_RS19480_lanthipeptide
2
N P A G P V F V G G L R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
N P A G P++V G G E A L T+S+ C S S S S +C C
3
N P A G P L Y V G G A A A E A A L T D S S D S L Y G F C S S P S G S H G S W C C
42
46.5%
NZ_CP077072.1:
Lanthipeptides: KR767_RS10085_lanthipeptide
2
N P A G P V F V G G L-R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
N P A G ++ G L +T A+T + T C S S C+A S G F C C
3
N P A G S L Y T E G L A K T M N A M T N P E V A I G T N C S S C T A S R P G F C C
43
45.2%
NZ_BMNG01000007.1:
Lanthipeptides: IEY91_RS17560_lanthipeptide
1
T N P A G P V F V G G L R T E Q A L T E S N L V E N T G C S S C S A S T T G F C C
41
+N P A G P++V G G E A L T++ C S S S S +C C
2
S N P A G P L Y V G G T V G E A A L T D A T D S L Y G F C S S P S G S L G S W C C
42
EJ065_RS39045
Leader:
MSSIWTPPNPILGTSGYWTPAGSATSKGS
Core:
T T A T C K T T L V G L G S N G N Y T W A L S M Q
Core with dehydrations:
Dhb Dhb A Dhb Cys K Dhb Dhb L V G L G Dha N G N Y Dhb W A L Dha M Q

#### antiSMASH-DB 4.0 matches for EJ065_RS39045

100.0%
NZ_CP034669.1:
Lanthipeptides: EJ065_RS39045_lanthipeptide
1
T T A T C K T T L V G L G S N G N Y T W A L S M Q
25
T T A T C K T T L V G L G S N G N Y T W A L S M Q
1
T T A T C K T T L V G L G S N G N Y T W A L S M Q
25

#### MIBiG 4.0 matches for EJ065_RS39045

14.3%
BGC0000517.4 (BAB04173.1):
Lanthipeptide: haloduracin β or haloduracin α
12
L G S N G N Y
18
L G+ G Y
10
L G N K G A Y
16
13.3%
BGC0002110.3 (QKV49893.1):
Lanthipeptide: birimositide
12
L G S N G
16
L G+N G
12
L G N N G
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:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.28 out of 26.33
Confidence: medium
Additional weak hits (5):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.42 out of 26.12
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.47 out of 27.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.20 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.73 out of 27.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.82 out of 24.78
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.

EJ065_RS19470 - Class II
  Cleavage pHMM score: 0.10
  RODEO score: 0
  Monoisotopic mass: 3909.8 Da
  Molecular weight: 3912.3 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3930.3 Da N = 1
    3948.3 Da N = 2
    3966.3 Da N = 3
    3984.4 Da N = 4
    4002.4 Da N = 5
    4020.4 Da N = 6
    4038.4 Da N = 7
EJ065_RS39045 - Class II
  Cleavage pHMM score: -6.30
  RODEO score: 0
  Monoisotopic mass: 2473.3 Da
  Molecular weight: 2474.8 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2492.8 Da N = 1
    2510.8 Da N = 2
    2528.8 Da N = 3
    2546.9 Da N = 4
    2564.9 Da N = 5
    2582.9 Da N = 6
    2600.9 Da N = 7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator

NZ_CP034669.1 - Region 21 - 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: 5,022,882 - 5,149,058 nt. (total: 126,177 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
EJ065_RS20210: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

EJ065_RS20225: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

EJ065_RS20235: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

EJ065_RS20360: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

EJ065_RS20460: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: acetyltransferase transferase
EJ065_RS20245: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

EJ065_RS20465: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Hydrolases: esterase
EJ065_RS20365: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: hydratase
EJ065_RS20215: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

EJ065_RS20475: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
EJ065_RS20300: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

EJ065_RS20305: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

EJ065_RS20315: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

EJ065_RS20335: carbamoyl phosphate synthase small subunit

smcogs
  SMCOG1249: carbamoyl phosphate synthase small subunit

EJ065_RS20370: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

EJ065_RS20375: 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 | T1PKS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001132.4 |  |  |  | 1.40 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  | 1.38 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  |  | 1.38 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  |  | 1.37 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  |  |  | 1.37 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  |  |  | 1.37 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  |  | 1.35 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001249.5 |  |  |  | 1.32 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001261.3 |  |  |  | 1.31 | NRPS | AM-toxin | Alternaria alternata
BGC0001641.4 |  |  |  | 1.27 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.78 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.77 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.77 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.77 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.77 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.76 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.76 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001249.5 |  | 0.75 | NRPS | dimethylcoprogen | Alternaria alternata

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.81 out of 25.88
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.95 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.71 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (8):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.68 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.53 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.70 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.95 out of 31.73
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.71 out of 25.88
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.94 out of 20.01
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 26, location 5022881 - 5149058:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu - X) + (mal) + (NH2 - X) + (X - X - X - X) + (Acetyl-CoA - Gly - Ser - Glu - mal - D-Ser - Arg - X - X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
EJ065_RS20300: Acetyl-CoA - Gly - Ser - Glu - mal - X - Ser - Arg - X - X
Search NORINE for peptide: strict or relaxed
CAL_domain (42..489): Acetyl-CoA
minowa: Acetyl-CoA

Prediction, score:
  Acetyl-CoA: 51.6
  NH2: 25.2
  AHBA: 23.4
  fatty_acid: 17.8
  shikimic_acid: 8.6

AMP-binding (1178..1571): 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:
    FAMTFDISVLEWQCLVGGELNMYGPTETTVWSSM
  Nearest Stachelhaus code(s):
    Gly DILQLGMVWK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2218..2616): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFVCSGEHNLYGPTEAAVDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHVSLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3277..3675): Glu
nrpys: Glu

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:
    glu (Glu)

Stachelhaus prediction details:
  Stachelhaus sequence:
    VAAAFDGSVLEMHMHTGGDTNGYGPSECSIVATA
  Nearest Stachelhaus code(s):
    Val DGLYIGGIMK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

PKS_AT (4407..4701): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 132.5
  Methoxymalonyl-CoA: 85.8
  Methylmalonyl-CoA: 75.5
  Isobutyryl-CoA: 51.3
  Propionyl-CoA: 48.1
  inactive: 45.6
  Ethylmalonyl-CoA: 43.9
  CHC-CoA: 37.9
  Benzoyl-CoA: 29.7
  trans-1,2-CPDA: 28.9
  fatty_acid: 27.7
  2-Methylbutyryl-CoA: 27.7
  Acetyl-CoA: 25.2
  3-Methylbutyryl-CoA: 18.4

A-OX (5400..6119): X
No predictions made
AMP-binding (6634..7035): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFMCSGEHNLYGPTEAAVDVTS
  Nearest Stachelhaus code(s):
    Ser DVWHMSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (8158..8597): Arg
nrpys: Arg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAMAFDAAIEQQDGSIGGEYNGYGPTEVTVDATT
  Nearest Stachelhaus code(s):
    Arg DADDSGCVDK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (9259..9658): X
nrpys: Orn, Lys, Arg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MAFAFDA-VMDVDCMMGGDFNGYGPTECTVCTAG
  Nearest Stachelhaus code(s):
    Val DAMFTGGVFK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (10313..10713): X
nrpys: Orn, Lys, Arg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSLGFDASVTQLDCFIGGEYNAYGPTEGTVASTT
  Nearest Stachelhaus code(s):
    Leu DALHSGAVAK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

EJ065_RS20305: X - X - X - X
AMP-binding (5..269): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAMAFDVSVGQLDCLLAGEFNLYGPTEATVYATW
  Nearest Stachelhaus code(s):
    Ser DVGYLAAVYK (56% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (928..1328): X
nrpys: bOH-Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGAAFDASTLEGWLLAGGDVNGYGPTENTTFSAT
  Nearest Stachelhaus code(s):
    bOH-Val DALWLGGTFK (88% 8Å match)
    Val DALWLGGTFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1985..2384): X
nrpys: Orn, Lys, Arg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MAFAFDA-VMDVDCMMGGDFNGYGPTECTVCTAG
  Nearest Stachelhaus code(s):
    Val DAMFTGGVFK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (3039..3440): 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:
    LAMAFDASVQQSDTSIGGEFNAYGPTEVTVNTTL
  Nearest Stachelhaus code(s):
    Dpr DAQDLAVVNK (71% 8Å match)
    Gln or Glu DAQDLGVVDK (68% 8Å match)
    Ile DAQDLGVVDK (65% 8Å match)
    Cap DPQDIGIVNK (62% 8Å match)
  Stachelhaus code match:
    70% (weak)

EJ065_RS20315: NH2 - X - mal
CAL_domain (55..502): NH2
minowa: NH2

Prediction, score:
  NH2: 30.0
  AHBA: 27.3
  fatty_acid: 13.9
  shikimic_acid: 7.6
  Acetyl-CoA: -2.7

AMP-binding (1187..1586): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAEAFDGSVMETHLHVAGDINAYGPSECSVAASF
  Nearest Stachelhaus code(s):
    Ala DVMFVAAVYK (59% 8Å match)
    Tyr DAATLAAVAK (56% 8Å match)
  Stachelhaus code match:
    60% (weak)

PKS_AT (2312..2559): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 106.5
  Methoxymalonyl-CoA: 71.9
  Methylmalonyl-CoA: 61.9
  CHC-CoA: 46.0
  Ethylmalonyl-CoA: 43.3
  Propionyl-CoA: 41.9
  inactive: 35.7
  Isobutyryl-CoA: 35.3
  Benzoyl-CoA: 32.8
  2-Methylbutyryl-CoA: 28.7
  fatty_acid: 25.3
  trans-1,2-CPDA: 24.6
  Acetyl-CoA: 21.0
  3-Methylbutyryl-CoA: 16.2

EJ065_RS20370: mal
PKS_AT (527..817): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 103.2
  Methoxymalonyl-CoA: 60.4
  inactive: 49.9
  Methylmalonyl-CoA: 46.4
  Ethylmalonyl-CoA: 34.8
  CHC-CoA: 30.5
  Propionyl-CoA: 27.6
  Benzoyl-CoA: 26.6
  fatty_acid: 25.5
  2-Methylbutyryl-CoA: 24.8
  Acetyl-CoA: 20.9
  trans-1,2-CPDA: 18.1
  Isobutyryl-CoA: 17.8
  3-Methylbutyryl-CoA: 12.3

EJ065_RS20375: Leu - X
Search NORINE for peptide: strict or relaxed
AMP-binding (9..405): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FYHAFDAFVMTPFLLTGGDVNGYGPAECTIYSTS
  Nearest Stachelhaus code(s):
    Ile DAMFLGCTYK (47% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1081..1472): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHYFDPSVAEPDLLAGGDFNQYGPTETTVTATS
  Nearest Stachelhaus code(s):
    Leu DAWFLGQVVK (74% 8Å match)
    Hty DLAFTGCVTK (62% 8Å match)
    Cap DPQDIGIVNK (59% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism
PsrA | Oleic acid responsive regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP034669.1 - Region 22 - 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: 5,170,959 - 5,191,273 nt. (total: 20,315 nt) Show pHMM detection rules used
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: kinase
EJ065_RS20640: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

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

Reference | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002674.2 |  | 0.40 | ribosomal | enterocin F4-9 | Enterococcus faecalis
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0001356.4 |  | 0.39 | ribosomal | paeninodin | Paenibacillus dendritiformis C454
BGC0002575.2 |  | 0.39 | ribosomal | cochonodin I | Streptococcus suis
BGC0001364.3 |  | 0.39 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0002307.3 |  | 0.37 | ribosomal | humidimycin | Streptomyces humidus
BGC0000496.5 |  | 0.37 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001660.3 |  | 0.37 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000563.4 |  | 0.37 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  | 0.36 | ribosomal | streptocollin | Streptomyces collinus Tu 365

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002674.2 |  | 0.40 | ribosomal | enterocin F4-9 | Enterococcus faecalis
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0001356.4 |  | 0.39 | ribosomal | paeninodin | Paenibacillus dendritiformis C454
BGC0002575.2 |  | 0.39 | ribosomal | cochonodin I | Streptococcus suis
BGC0001364.3 |  | 0.39 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0002307.3 |  | 0.37 | ribosomal | humidimycin | Streptomyces humidus
BGC0000496.5 |  | 0.37 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001660.3 |  | 0.37 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000563.4 |  | 0.37 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  | 0.36 | ribosomal | streptocollin | Streptomyces collinus Tu 365

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.79 out of 23.79
Confidence: medium
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (5170958...5191273)
EJ065_RS20605
  RRE type: Stand_Alone_Lasso_RRE
  Location: 19 - 90
  Score: 36.0
  RRE type: PqqD_RRE
  Location: 35 - 90
  Score: 32.0

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_CP034669.1 - Region 23 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,234,225 - 5,255,223 nt. (total: 20,999 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: deaminase glucanase glucosidase
EJ065_RS20885: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

EJ065_RS20895: Pullulanase, type I

smcogs
  SMCOG1297: Pullulanase, type I

EJ065_RS20950: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Ligases: synthetase
EJ065_RS20925: 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 |  | 0.45 | terpene | astallatene | Arabidopsis thaliana
BGC0002285.2 |  | 0.43 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0002400.2 |  | 0.43 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000905.5 |  | 0.40 | other (other) | heme D1 | Heliobacillus mobilis
BGC0001285.5 |  | 0.40 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0000906.3 |  | 0.39 | other (other) | heme D1 | Heliophilum fasciatum
BGC0002007.2 |  | 0.39 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0001529.5 |  | 0.38 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0001510.5 |  | 0.38 | other (other) | anisomycin | Streptomyces hygrospinosus
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.45 | terpene | astallatene | Arabidopsis thaliana
BGC0002285.2 |  | 0.43 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0002400.2 |  | 0.43 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000905.5 |  | 0.40 | other (other) | heme D1 | Heliobacillus mobilis
BGC0001285.5 |  | 0.40 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0000906.3 |  | 0.39 | other (other) | heme D1 | Heliophilum fasciatum
BGC0002007.2 |  | 0.39 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0001529.5 |  | 0.38 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0001510.5 |  | 0.38 | other (other) | anisomycin | Streptomyces hygrospinosus
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576

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

No significant matches found.

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene 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:
EJ065_RS20925: PT_FPPS_like
Domain 1 (43 - 320): 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:
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 25.32 out of 29.65
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.85 out of 24.78
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (14):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.65 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.78 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.17 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.95 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.86 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.00 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.00 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.13 out of 21.55
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.25 out of 36.54
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.15 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.89 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.24 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.77 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.80 out of 20.01
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
--- | ---
AbrC3 | Antibiotic production activator
LexA variant 1 | Repressor of DNA damage response
LexA variant 2 | Repressor of DNA damage response

NZ_CP034669.1 - Region 24 - NRP-metallophore,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: 5,257,423 - 5,364,319 nt. (total: 106,897 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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 electron transfer
EJ065_RS21050: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

EJ065_RS21115: flavodoxin

smcogs
  SMCOG1134: flavodoxin

Transferases: acylase aminotransferase
EJ065_RS21045: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

EJ065_RS21180: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase
EJ065_RS21065: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Isomerases: isomerase
EJ065_RS21055: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase
EJ065_RS21060: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

EJ065_RS21070: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

EJ065_RS21185: 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 | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  |  |  | 1.53 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  |  |  |  | 1.40 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  |  |  |  | 1.39 | NRPS | AM-toxin | Alternaria alternata
BGC0001833.4 |  |  |  |  | 1.38 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000342.4 |  |  |  |  | 1.35 | NRPS | enniatin | Fusarium equiseti
BGC0000307.4 |  |  |  |  | 1.35 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001128.4 |  |  |  |  | 1.35 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  |  | 1.32 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  |  | 1.31 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001641.4 |  |  |  |  | 1.27 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002492.3 |  | 0.77 | NRPS | myxochelin B, myxochelin A | Myxococcus xanthus DK 1622
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000343.5 |  | 0.77 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001345.5 |  | 0.75 | NRPS | myxochelin A, myxochelin B | Stigmatella aurantiaca Sg a15
BGC0001185.5 |  | 0.74 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0001758.4 |  | 0.73 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001166.5 |  | 0.73 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001833.4 |  | 0.72 | 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:
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.88 out of 29.38
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.14 out of 29.38
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.88 out of 29.38
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.40 out of 27.78
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.74 out of 23.79
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.06 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.44 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.44 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.70 out of 28.19
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 21.40 out of 23.05
Confidence: strong
Additional weak hits (35):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.07 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.62 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.43 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 24.78 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.71 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.38 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.51 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.39 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.89 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.76 out of 29.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.42 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.67 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.91 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 26.20 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.87 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.80 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.13 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.74 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.96 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.25 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.39 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.10 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.44 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.93 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.80 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.73 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.08 out of 29.38
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.13 out of 32.93
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.84 out of 28.14
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.77 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.40 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.67 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.44 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 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.75 out of 29.65
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 29, location 5257422 - 5364319:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (AHBA - Asp - D-Tyr - Thr - Phe) + (ohmal) + (Phe - Phe) + (Lys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 30, location 5257422 - 5306529:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Lys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 31, location 5295867 - 5364319:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (AHBA - Asp - D-Tyr - Thr - Phe) + (ohmal) + (Phe - Phe)

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).
EJ065_RS21060: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (37..444): 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:
    SASLFPMSSPGGALQVGGAQQVFGMAEGLVNYTR
  Nearest Stachelhaus code(s):
    diOH-Bz PMPAQGVVNK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

EJ065_RS21070: Lys
Search NORINE for peptide: strict or relaxed
AMP-binding (454..879): Lys
nrpys: Lys

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 with H-bond donor (Asp, Asn, Glu, Gln, Aad)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FGAAFDASVEEVDLIIGGELNTYGPTEATVVATV
  Nearest Stachelhaus code(s):
    Lys DAEDIGTVVK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

EJ065_RS21175: Phe - Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (507..898): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MAVAFDASVAESTLISAGELNGYGPTEVTVCASV
  Nearest Stachelhaus code(s):
    Phe DAWTIAGVCK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1558..1945): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MAVAFDASVAESTLISAGELNGYGPTEVTVCASV
  Nearest Stachelhaus code(s):
    Phe DAWTIAGVCK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

EJ065_RS21180: mal
PKS_AT (535..828): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 83.3%
  2-Methylbutyryl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 181.5
  inactive: 112.1
  Methoxymalonyl-CoA: 73.3
  Methylmalonyl-CoA: 72.1
  Propionyl-CoA: 45.4
  Ethylmalonyl-CoA: 35.8
  Isobutyryl-CoA: 34.7
  2-Methylbutyryl-CoA: 30.1
  CHC-CoA: 29.9
  Benzoyl-CoA: 24.3
  trans-1,2-CPDA: 17.2
  fatty_acid: 11.4
  Acetyl-CoA: 10.3
  3-Methylbutyryl-CoA: 8.8

EJ065_RS21185: AHBA - Asp - Tyr - Thr - Phe
Search NORINE for peptide: strict or relaxed
CAL_domain (30..477): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 27.6
  fatty_acid: 18.6
  NH2: 12.2
  shikimic_acid: 11.0
  Acetyl-CoA: 2.7

AMP-binding (1142..1547): Asp
nrpys: Asp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YGLSADLGHTAPKIVLGGEFNHYGPTETTVGVLT
  Nearest Stachelhaus code(s):
    Asp DLTKVGHVGK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2207..2599): Tyr
nrpys: Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TAVAFDAGVCESTLISAGEINAYGPTEITVCATL
  Nearest Stachelhaus code(s):
    Tyr DASTIAAVCK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (3722..4129): 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:
    LATHFDFSVWEGNQIFGGEVNMYGITETTVHVTF
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4794..5185): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MAVAFDASVAESTLISAGELNGYGPTEVTVCASV
  Nearest Stachelhaus code(s):
    Phe DAWTIAGVCK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1 | Ferric Uptake Regulator
IolR | Regulator of the inositol catabolism
ZuR variant 1 | Zinc-responsive repressor

NZ_CP034669.1 - Region 25 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,414,952 - 5,425,824 nt. (total: 10,873 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001838.4 |  | 0.29 | NRPS | WLIP | Pseudomonas putida
BGC0001588.3 |  | 0.23 | saccharide | exopolysaccharides | Burkholderia pseudomallei 1026b
BGC0000714.5 |  | 0.22 | saccharide | sisomicin | Micromonospora inyonensis
BGC0001603.3 |  | 0.22 | saccharide | gentamicin | Micromonospora echinospora
BGC0001589.3 |  | 0.22 | saccharide | exopolysaccharides | Burkholderia cenocepacia J2315
BGC0002025.4 |  | 0.21 | NRPS, PKS | thaxteramide C | Jahnella sp. MSr9139
BGC0001093.3 |  | 0.21 | NRPS, PKS | disorazol A | Sorangium cellulosum
BGC0000080.5 |  | 0.21 | PKS | jerangolid A, jerangolid D | Sorangium cellulosum
BGC0000696.5 |  | 0.20 | saccharide | gentamicin | Micromonospora echinospora

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001838.4 |  | 0.29 | NRPS | WLIP | Pseudomonas putida
BGC0001588.3 |  | 0.23 | saccharide | exopolysaccharides | Burkholderia pseudomallei 1026b
BGC0000714.5 |  | 0.22 | saccharide | sisomicin | Micromonospora inyonensis
BGC0001603.3 |  | 0.22 | saccharide | gentamicin | Micromonospora echinospora
BGC0001589.3 |  | 0.22 | saccharide | exopolysaccharides | Burkholderia cenocepacia J2315
BGC0002025.4 |  | 0.21 | NRPS, PKS | thaxteramide C | Jahnella sp. MSr9139
BGC0001093.3 |  | 0.21 | NRPS, PKS | disorazol A | Sorangium cellulosum
BGC0000080.5 |  | 0.21 | PKS | jerangolid A, jerangolid D | Sorangium cellulosum
BGC0000696.5 |  | 0.20 | saccharide | gentamicin | Micromonospora echinospora

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (1):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.98 out of 29.25
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP034669.1 - Region 26 - 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: 5,540,042 - 5,566,759 nt. (total: 26,718 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
Hydrolases: back translocase
EJ065_RS22160: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

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

Reference | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002584.2 |  | 0.50 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0000483.5 |  | 0.50 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0002551.2 |  | 0.48 | other (other), ribosomal, terpene | muscoride A, muscoride B | Nostoc sp. UHCC-0398
BGC0002485.2 |  | 0.48 | other (other), ribosomal | muscoride A, muscoride B | Desmonostoc sp. PCC 7906
BGC0000565.5 |  | 0.47 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0000475.5 |  | 0.46 | ribosomal | patellamide A, patellamide C | Prochloron didemni
BGC0000480.5 |  | 0.46 | ribosomal | tenuecyclamide A, tenuecyclamide C | Nostoc spongiaeforme var. tenue str. Carmeli
BGC0000471.4 |  | 0.45 | ribosomal | viridisamide A | Oscillatoria nigro-viridis PCC 7112
BGC0000477.3 |  | 0.45 | ribosomal | patellin 2, patellin 3 | uncultured Prochloron sp. 06037A
BGC0002311.3 |  | 0.44 | ribosomal | cutimycin | Cutibacterium acnes KPA171202

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002584.2 |  | 0.50 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0000483.5 |  | 0.50 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0002551.2 |  | 0.48 | other (other), ribosomal, terpene | muscoride A, muscoride B | Nostoc sp. UHCC-0398
BGC0002485.2 |  | 0.48 | other (other), ribosomal | muscoride A, muscoride B | Desmonostoc sp. PCC 7906
BGC0000565.5 |  | 0.47 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0000475.5 |  | 0.46 | ribosomal | patellamide A, patellamide C | Prochloron didemni
BGC0000480.5 |  | 0.46 | ribosomal | tenuecyclamide A, tenuecyclamide C | Nostoc spongiaeforme var. tenue str. Carmeli
BGC0000471.4 |  | 0.45 | ribosomal | viridisamide A | Oscillatoria nigro-viridis PCC 7112
BGC0000477.3 |  | 0.45 | ribosomal | patellin 2, patellin 3 | uncultured Prochloron sp. 06037A
BGC0002311.3 |  | 0.44 | ribosomal | cutimycin | Cutibacterium acnes KPA171202

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.98 out of 23.79
Confidence: medium
Additional weak hits (3):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.52 out of 29.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.60 out of 30.22
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.70 out of 36.53
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 (5540041...5566759)
EJ065_RS22120
  RRE type: Cyanobactin_D_RRE
  Location: 1 - 79
  Score: 79.8
  RRE type: NHLP_CD_RRE
  Location: 1 - 95
  Score: 71.3
  RRE type: Goadsporin_CD_RRE
  Location: 0 - 98
  Score: 61.6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

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_CP034669.1 - Region 27 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,837,886 - 5,858,779 nt. (total: 20,894 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
Ligases: synthase synthetase
EJ065_RS23300: 1-deoxy-D-xylulose-5-phosphate synthase

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

EJ065_RS23305: 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
--- | --- | --- | --- | --- | ---
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000639.3 |  | 0.38 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000642.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000665.5 |  | 0.37 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000668.5 |  | 0.36 | other (other), terpene | 12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole | Hapalosiphon welwitschii UTEX B 1830
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000639.3 |  | 0.38 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000642.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000665.5 |  | 0.37 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000668.5 |  | 0.36 | other (other), terpene | 12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole | Hapalosiphon welwitschii UTEX B 1830
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488

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

No significant matches found.

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP

Genes with terpene domains:
EJ065_RS23305: PT_FPPS_like
Domain 1 (37 - 296): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:
  DMAPP, IPP → FPP

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:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.86 out of 21.84
Confidence: medium
Additional weak hits (6):
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.67 out of 29.72
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.06 out of 32.93
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.35 out of 31.73
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.82 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.87 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.01 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MexT | Global virulence regulator

NZ_CP034669.1 - Region 28 - 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: 6,217,742 - 6,268,242 nt. (total: 50,501 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
EJ065_RS24885: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Hydrolases: esterase
EJ065_RS24915: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase
EJ065_RS24910: 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
--- | --- | --- | --- | --- | ---
BGC0001261.3 |  | 0.74 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.72 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001261.3 |  | 0.74 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.72 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
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.

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.21 out of 20.47
Confidence: medium
Additional weak hits (14):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.32 out of 30.22
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.85 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.62 out of 27.78
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
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.95 out of 30.25
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 32.93
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.22 out of 26.12
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.00 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.30 out of 24.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.16 out of 25.88
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.74 out of 28.14
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.54 out of 26.85
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.45 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 35, location 6217741 - 6268242:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu - X) + (Asp)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
EJ065_RS24910: Leu - X
Search NORINE for peptide: strict or relaxed
AMP-binding (18..409): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAFAFDASVLEPFLLTGGEFNCYGPTETTAIVTR
  Nearest Stachelhaus code(s):
    Ile DALFLGCTFK (53% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1061..1462): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAKVFDVSVSDMVLIAGGEINAYGPTETTICTTM
  Nearest Stachelhaus code(s):
    Trp DVSQIGAVCK (68% 8Å match)
  Stachelhaus code match:
    80% (moderate)

EJ065_RS24915: Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (502..907): Asp
nrpys: Asp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YGISADLGTTMGKLVFAGEQNHYGPTETSVATLT
  Nearest Stachelhaus code(s):
    Asp DLTKVGHVGK (74% 8Å match)
  Stachelhaus code match:
    80% (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_CP034669.1 - Region 29 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,606,232 - 6,627,203 nt. (total: 20,972 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
Ligases: ligase
EJ065_RS26485: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001909.3 |  | 0.36 | PKS | strobilurin A | Strobilurus tenacellus
BGC0002259.2 |  | 0.33 | NRPS, PKS | beauveriolide I, beauveriolide III | Cordyceps militaris CM01
BGC0002711.2 |  | 0.33 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0001290.4 |  | 0.33 | NRPS | emericellamide A, emericellamide B | Aspergillus nidulans FGSC A4
BGC0001463.4 |  | 0.31 | other (other) | 2,3,4,5-tetrabromopyrrole | Pseudoalteromonas piscicida
BGC0001464.3 |  | 0.31 | other (other) | tetrabromopyrrole | Pseudoalteromonas sp. PS5
BGC0001937.4 |  | 0.31 | other (other) | tubercidin | Streptomyces tubercidicus
BGC0002056.3 |  | 0.30 | NRPS, PKS | peloruside A | sponge metagenome
BGC0002188.3 |  | 0.30 | NRPS, PKS | W493 B, W493 A | Fusarium pseudograminearum CS3096
BGC0001504.4 |  | 0.30 | PKS | amycomicin | Amycolatopsis sp. AA4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001909.3 |  | 0.36 | PKS | strobilurin A | Strobilurus tenacellus
BGC0002259.2 |  | 0.33 | NRPS, PKS | beauveriolide I, beauveriolide III | Cordyceps militaris CM01
BGC0002711.2 |  | 0.33 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0001290.4 |  | 0.33 | NRPS | emericellamide A, emericellamide B | Aspergillus nidulans FGSC A4
BGC0001463.4 |  | 0.31 | other (other) | 2,3,4,5-tetrabromopyrrole | Pseudoalteromonas piscicida
BGC0001464.3 |  | 0.31 | other (other) | tetrabromopyrrole | Pseudoalteromonas sp. PS5
BGC0001937.4 |  | 0.31 | other (other) | tubercidin | Streptomyces tubercidicus
BGC0002056.3 |  | 0.30 | NRPS, PKS | peloruside A | sponge metagenome
BGC0002188.3 |  | 0.30 | NRPS, PKS | W493 B, W493 A | Fusarium pseudograminearum CS3096
BGC0001504.4 |  | 0.30 | PKS | amycomicin | Amycolatopsis sp. AA4

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
EJ065_RS26475: PT_phytoene_like
Domain 1 (21 - 226): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.18 out of 23.79
Confidence: medium
Additional weak hits (7):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.75 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.05 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.52 out of 26.06
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.44 out of 26.85
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.93 out of 28.19
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.43 out of 27.18
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.27 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP034669.1 - Region 30 - thioamitides
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,786,164 - 6,808,562 nt. (total: 22,399 nt) Show pHMM detection rules used
thioamitides: ((YcaO or TIGR03604) and TfuA)

#### 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: reductase
EJ065_RS27240: alkyl hydroperoxide reductase/ Thiol specific

smcogs
  SMCOG1196: alkyl hydroperoxide reductase/ Thiol specific

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 | thioamitides | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000625.5 |  | 0.36 | ribosomal | thioviridamide | Streptomyces olivoviridis
BGC0002339.3 |  | 0.35 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0002120.3 |  | 0.31 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0002284.3 |  | 0.30 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0002326.2 |  | 0.29 | NRPS | endopyrrole B, endopyrrole C, endopyrrole A | Mycetohabitans rhizoxinica
BGC0001430.4 |  | 0.28 | NRPS, PKS | myxochromide S | Stigmatella aurantiaca Sg a15
BGC0001127.5 |  | 0.27 | NRPS | jagaricin | Janthinobacterium agaricidamnosum
BGC0001964.2 |  | 0.26 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0000135.5 |  | 0.21 | PKS | reveromycin A | Streptomyces sp. SN-593
BGC0002100.2 |  | 0.20 | NRPS, other (other) | colibrimycin | Streptomyces sp. CS147

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000625.5 |  | 0.36 | ribosomal | thioviridamide | Streptomyces olivoviridis
BGC0002339.3 |  | 0.35 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0002120.3 |  | 0.31 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0002284.3 |  | 0.30 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0002326.2 |  | 0.29 | NRPS | endopyrrole B, endopyrrole C, endopyrrole A | Mycetohabitans rhizoxinica
BGC0001430.4 |  | 0.28 | NRPS, PKS | myxochromide S | Stigmatella aurantiaca Sg a15
BGC0001127.5 |  | 0.27 | NRPS | jagaricin | Janthinobacterium agaricidamnosum
BGC0001964.2 |  | 0.26 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0000135.5 |  | 0.21 | PKS | reveromycin A | Streptomyces sp. SN-593
BGC0002100.2 |  | 0.20 | NRPS, other (other) | colibrimycin | Streptomyces sp. CS147

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.44 out of 23.79
Confidence: medium
Additional weak hits (7):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.08 out of 30.22
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.17 out of 25.88
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.80 out of 23.43
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.68 out of 20.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.46 out of 26.06
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.42 out of 30.22
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.60 out of 20.97
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP034669.1 - Region 31 - NRPS,T1PKS,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: 6,845,891 - 6,923,698 nt. (total: 77,808 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))
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
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
EJ065_RS27475: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

Transferases: aminotransferase synthase
EJ065_RS27515: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain
smcogs
  SMCOG1093: Beta-ketoacyl synthase

EJ065_RS27625: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Hydrolases: amidase
EJ065_RS27570: amidase

smcogs
  SMCOG1105: amidase

Ligases: ligase synthase
EJ065_RS27505: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

EJ065_RS27510: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

EJ065_RS27515: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain
smcogs
  SMCOG1093: Beta-ketoacyl synthase

EJ065_RS27520: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

EJ065_RS27525: 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 | NRPS | T1PKS | linaridin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  |  | 0.90 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  |  | 0.82 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  |  |  | 0.82 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  |  |  | 0.80 | NRPS | enniatin | Fusarium equiseti
BGC0001833.4 |  |  |  | 0.78 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  |  | 0.78 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  |  | 0.77 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  |  |  | 0.76 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  |  |  | 0.75 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001758.4 |  |  |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  | 0.72 | NRPS | enniatin | Fusarium equiseti
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.71 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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: 19.17 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.31 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26
Confidence: strong
Additional weak hits (17):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.21 out of 20.01
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.90 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.59 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.72 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.26 out of 26.06
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.22 out of 26.12
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.37 out of 30.25
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
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.56 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.52 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.28 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.25 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.36 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.56 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.87 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 38, location 6845890 - 6923698:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2 - X) + (ohmal) + (ohmal) + (Ser) + (ohmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 39, location 6845890 - 6909836:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2 - X) + (ohmal) + (ohmal) + (Ser) + (ohmal)

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).
EJ065_RS27505: NH2 - X
CAL_domain (146..478): NH2
minowa: NH2

Prediction, score:
  NH2: 158.9
  Acetyl-CoA: 18.3
  fatty_acid: 3.8
  shikimic_acid: 0.0
  AHBA: 0.0

AMP-binding (1186..1580): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSFTSASFVGEPSTLSGGEVNGYGLTETTVCSTY
  Nearest Stachelhaus code(s):
    Sam ASGSLGGICK (88% 8Å match)
  Stachelhaus code match:
    90% (moderate)

EJ065_RS27510: mal
PKS_AT (535..831): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 190.7
  inactive: 131.8
  Methoxymalonyl-CoA: 72.4
  Methylmalonyl-CoA: 57.9
  Propionyl-CoA: 51.2
  Isobutyryl-CoA: 34.3
  trans-1,2-CPDA: 31.0
  Ethylmalonyl-CoA: 28.5
  Acetyl-CoA: 27.1
  CHC-CoA: 26.4
  Benzoyl-CoA: 24.6
  2-Methylbutyryl-CoA: 22.2
  fatty_acid: 20.3
  3-Methylbutyryl-CoA: 10.4

EJ065_RS27515: mal
PKS_AT (540..833): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 193.6
  inactive: 117.3
  Methoxymalonyl-CoA: 81.4
  Methylmalonyl-CoA: 76.6
  Propionyl-CoA: 53.6
  Ethylmalonyl-CoA: 51.9
  2-Methylbutyryl-CoA: 37.0
  CHC-CoA: 35.7
  trans-1,2-CPDA: 28.2
  Isobutyryl-CoA: 26.4
  Benzoyl-CoA: 20.9
  Acetyl-CoA: 19.9
  fatty_acid: 13.8
  3-Methylbutyryl-CoA: 0.0

EJ065_RS27520: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (488..888): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFVCSGEHNLYGPTEAAVDVTF
  Nearest Stachelhaus code(s):
    Ser DVWHVSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

EJ065_RS27525: mal
PKS_AT (534..828): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 188.5
  inactive: 119.9
  Methoxymalonyl-CoA: 80.2
  Methylmalonyl-CoA: 63.9
  Propionyl-CoA: 61.9
  Ethylmalonyl-CoA: 45.6
  Isobutyryl-CoA: 36.6
  2-Methylbutyryl-CoA: 36.5
  Benzoyl-CoA: 29.4
  trans-1,2-CPDA: 27.9
  Acetyl-CoA: 27.4
  CHC-CoA: 23.6
  fatty_acid: 15.3
  3-Methylbutyryl-CoA: 5.7

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

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

NZ_CP034669.1 - Region 32 - NRPS,arylpolyene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,008,013 - 7,090,853 nt. (total: 82,841 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
arylpolyene: (APE_KS1 or APE_KS2)

#### 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
EJ065_RS27985: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

EJ065_RS28190: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acyltransferase glycosyltransferase halogenase
EJ065_RS28115: acyltransferase

smcogs
  SMCOG1141: acyltransferase

EJ065_RS28170: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

EJ065_RS28265: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: glucosidase peptidase protease
EJ065_RS27980: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

EJ065_RS28225: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

EJ065_RS28260: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Ligases: ligase synthase
EJ065_RS28045: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

EJ065_RS28135: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

EJ065_RS28140: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

EJ065_RS28180: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

EJ065_RS28195: 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 | arylpolyene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002608.2 |  |  | 0.45 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0002008.3 |  |  | 0.45 | other (other) | aryl polyenes | Xenorhabdus doucetiae
BGC0002341.2 |  |  | 0.44 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0000836.5 |  |  | 0.43 | other (other) | APE Ec | Escherichia coli CFT073
BGC0001833.4 |  |  | 0.42 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.41 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  | 0.41 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  |  | 0.40 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  | 0.40 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  |  | 0.39 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002608.2 |  | 0.75 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0002341.2 |  | 0.75 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.72 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.71 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.37 out of 30.12
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.46 out of 25.88
Confidence: medium
Additional weak hits (19):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.80 out of 20.01
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.36 out of 27.78
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.67 out of 29.72
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.04 out of 27.78
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
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.54 out of 39.62
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.87 out of 30.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.52 out of 28.14
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.11 out of 25.88
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.83 out of 31.73
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.83 out of 32.74
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.22 out of 23.43
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.42 out of 20.97
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.79 out of 29.25
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.85 out of 39.62
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.09 out of 35.63
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.03 out of 29.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.20 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 41, location 7008012 - 7090853:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Pro - Val - Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 42, location 7008012 - 7058320:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Pro - Val - Pro)

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).
EJ065_RS28045: Pro - Val - Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (487..887): Pro
nrpys: Pro

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQSFDVCFQEPFLNTAGEDNHYGPTETHAATAH
  Nearest Stachelhaus code(s):
    Pro DVQFIAHAVK (71% 8Å match)
    4Me-Pro DVQFIAHVAK (68% 8Å match)
    pPro DVQFSAHGAK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1545..1941): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGAAFDAATLEGFLLTGGDVNAYGPTENTTLSTA
  Nearest Stachelhaus code(s):
    Val DALFLGGTFK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2590..2993): Pro
nrpys: Pro

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQSFDVSFQEAFMMVAGEHNHYGPSEAHAVTSL
  Nearest Stachelhaus code(s):
    Pro DVQFIAHAVK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

EJ065_RS28135: X
AMP-binding (48..304): 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:
    ETLVYGLLFR-WVAFSSGGVEVYGSSETGGVAWR
  Nearest Stachelhaus code(s):
    Ant GIILFGVGVK (26% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
OsdR | Development and stress management regulator
PsrA | Oleic acid responsive regulator

NZ_CP034669.1 - Region 33 - lanthipeptide-class-ii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,152,898 - 7,176,119 nt. (total: 23,222 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### 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
Hydrolases: dehalogenase protease
EJ065_RS28520: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

EJ065_RS28530: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

Lyases: cyclase
EJ065_RS28560: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Ligases: synthase
EJ065_RS28545: pseudouridine synthase

smcogs
  SMCOG1279: pseudouridine 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 | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000525.5 |  | 0.51 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0002704.2 |  | 0.46 | ribosomal | archalan β | Halorussus salinus
BGC0001210.5 |  | 0.44 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0001407.5 |  | 0.44 | ribosomal | bicereucin | Bacillus cereus SJ1
BGC0001576.3 |  | 0.43 | ribosomal | divamide A | Prochloron didemni
BGC0000554.4 |  | 0.43 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001660.3 |  | 0.43 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000527.5 |  | 0.42 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000595.3 |  | 0.42 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000516.4 |  | 0.41 | ribosomal | geobacillin II | Geobacillus thermodenitrificans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000525.5 |  | 0.51 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0002704.2 |  | 0.46 | ribosomal | archalan β | Halorussus salinus
BGC0001210.5 |  | 0.44 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0001407.5 |  | 0.44 | ribosomal | bicereucin | Bacillus cereus SJ1
BGC0001576.3 |  | 0.43 | ribosomal | divamide A | Prochloron didemni
BGC0000554.4 |  | 0.43 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001660.3 |  | 0.43 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000527.5 |  | 0.42 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000595.3 |  | 0.42 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000516.4 |  | 0.41 | ribosomal | geobacillin II | Geobacillus thermodenitrificans

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

No significant matches found.

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

No significant matches found.

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

#### Lanthipeptide(s) for EJ065_RS28560

EJ065_RS28555
Leader:
MMTPDLIIRAWKDPSFRESLTAEQRAQLPANPSGTTVNEMSETELMDVVGG
Core:
K I D I G F T A T N S C E Y I C T N M T F V C
Core with dehydrations:
K I D I G F Dhb A Dhb N Dha Cys E Y I Cys Dhb N M Dhb F V Cys

#### antiSMASH-DB 4.0 matches for EJ065_RS28555

100.0%
NZ_CP034669.1:
Lanthipeptides: EJ065_RS28555_lanthipeptide
1
K I D I G F T A T N S C E Y I C T N M T F V C
23
K I D I G F T A T N S C E Y I C T N M T F V C
1
K I D I G F T A T N S C E Y I C T N M T F V C
23
79.2%
NC_017030.1 and 1 other:
NZ_CP114039.1 Lanthipeptides: O0N60_RS37970_lanthipeptide
Lanthipeptides: COCOR_RS29830_lanthipeptide
1
K I D I G F T A T N S C E Y I C T N M T F
21
+I D I G F T A T N S C E Y I C T N+T F
1
R I D I G F T A T N S C E Y I C T N L T F
21
76.0%
NZ_CP079946.1:
Lanthipeptides: KYK13_RS28915_lanthipeptide
3
D I G--F T A T N S C E Y I C T N M T F V C
23
D+G F T A T N S C E Y I C T N+T F V C
3
D V G D F F T A T N S C E Y I C T N L T F V C
25
with 9 more sequence matches
34.8%
NZ_CP104318.1 and 1 other:
NZ_CP104318.1 Lanthipeptides: NW605_RS33555_lanthipeptide
Lanthipeptides: NW605_RS33555_lanthipeptide
3
D I G F T A T N S C E Y I C T N M T
20
D G T +C E C+N T
3
D T G D G C T A T C E S A C S N S T
20
30.4%
NZ_BBUZ01000023.1 and 5 others:
NZ_BBUZ01000023.1 Lanthipeptides: ASC60_RS09240_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS29940_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS29940_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS29795_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS29795_lanthipeptide
Lanthipeptides: ASC60_RS09240_lanthipeptide
3
D I G F T A T N S C E Y I C T N M T
20
D G T +C+ C+N T
4
D T G D G C T A T C Q S A C S N S T
21
30.4%
NZ_BBYG01000008.1 and 3 others:
NZ_BBYG01000008.1 Lanthipeptides: AOQ37_RS04295_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS17875_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS17875_lanthipeptide
Lanthipeptides: AOQ37_RS04295_lanthipeptide
3
D I G F T A T N S C E Y I C T N M T
20
D G T++C+ C+N T
3
D T G D G C T S T C Q S A C S N S T
20
30.4%
NZ_CP086322.1 and 1 other:
NZ_CP086322.1 Lanthipeptides: K9S39_RS30905_lanthipeptide
Lanthipeptides: K9S39_RS30905_lanthipeptide
3
D I G F T A T N S C E Y I C T N M T
20
D G +C E C+N T
3
D T G D G C G Q T C E S A C S N S T
20
26.1%
NZ_CP034669.1:
Lanthipeptides: EJ065_RS32040_lanthipeptide
10
N S C E Y I C T
17
N S C Y+C T
8
N S C G Y V C T
15
25.0%
NZ_CP084541.1 and 1 other:
NZ_CP084541.1 Lanthipeptides: LC193_RS13810_lanthipeptide
Lanthipeptides: LC193_RS13810_lanthipeptide
3
D I G F T A T N S C E Y I C T N M T F V
22
D G T++C+ C+N T +
7
D T G D G C T S T C Q S A C S N S T C I
26
20.8%
NZ_CP072611.1:
Lassopeptides: J7654_RS03615_lassopeptide
2
I D I G F T A T N S C E Y I
15
+D+G F T A + +
8
L D V G F T A G T P L D Q L
21
16.3%
NZ_CP114039.1:
Lanthipeptides: allorf_9368264_9368425_lanthipeptide
8
A T N S C E Y I C T N M T F V C
23
A N+C Y I + V C
28
A L N A C A Y I D V R L W T V C
43
15.6%
NZ_CP047936.1:
Lanthipeptides: allorf_0851538_0851693_lanthipeptide
1
K I D I G F T A T N S C E Y
14
K+D+ T N C +
13
K V D L S T T I R N R C R H
26
EJ065_RS40790
Leader:
MRDDGLLGQ
Core:
C E L D A S C N P T C W G V E S A Y P V Y S D Y F Y C T H C P
Core with dehydrations:
Cys E L D A Dha Cys N P Dhb Cys W G V E Dha A Y P V Y Dha D Y F Y Cys Dhb H Cys P

#### antiSMASH-DB 4.0 matches for EJ065_RS40790

25.8%
NZ_AQRJ01000038.1 and 1 other:
NZ_AQRJ01000038.1 Lanthipeptides: YW7_RS06850_lanthipeptide
Lanthipeptides: YW7_RS06850_lanthipeptide
1
C E L D A S C N P T C W G V E S A
17
C C P T C G S A
5
C S T G D G C G P T C Q G G A S A
21
19.4%
NZ_CP036016.1:
Lanthipeptides: allorf_075467_075682_lanthipeptide
1
C E L D A S C N P T C W
12
C L C P C W
18
C T L S V E C R P A C W
29
19.4%
NZ_CP090100.1 and 3 others:
NZ_SIJR01000001.1 Lanthipeptides: allorf_2037526_2037627_lanthipeptide NZ_SIKP01000006.1 Lanthipeptides: allorf_316621_316722_lanthipeptide NZ_SIMU01000019.1 Lanthipeptides: allorf_15718_15819_lanthipeptide
Lanthipeptides: allorf_353644_353745_lanthipeptide
8
N P T C W G V E S A Y P
19
N T C W G + P
3
N E T C W G R L R S A P
14
with 2 more sequence matches
19.4%
NZ_NTSF01000026.1 and 1 other:
NZ_NTSF01000026.1 Lanthipeptides: CN325_RS21835_lanthipeptide
Lanthipeptides: CN325_RS21835_lanthipeptide
1
C E L D A S C N P T C W
12
C L C P C W
18
C T L T K E C R P A C W
29
11.1%
NZ_CP031598.1:
Lanthipeptides: allorf_1753918_1754139_lanthipeptide
7
C N P T C W G V E S A Y P V
20
N P W G S A+P+
34
T N P G S W G R T S A F P I
47

#### MIBiG 4.0 matches for EJ065_RS40790

16.1%
BGC0000517.4 (BAB04173.1):
Lanthipeptide: haloduracin β or haloduracin α
1
C E L D A S C N P T C
11
C L C P+C
17
C T L T V E C M P S C
27
16.1%
BGC0002110.3 (QKV49893.1):
Lanthipeptide: birimositide
1
C E L D A S C N P T C
11
C L C P C
19
C T L T K E C Q P N C
29
12.8%
BGC0001229.4 (SBI_06990):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
1
C E L D A S C N P T C
11
C L C P C
28
C T L S K E C Q P N C
38
allorf_7162463_7162558
Leader:
MWGRLLLDGAPRLARELRLLQTSAA
Core:
F S C I T G
Core with dehydrations:
F Dha Cys I Dhb G

#### antiSMASH-DB 4.0 matches for allorf_7162463_7162558

100.0%
NZ_CP034669.1:
Lanthipeptides: allorf_7162463_7162558_lanthipeptide
1
F S C I T G
6
F S C I T G
1
F S C I T G
6
allorf_7167087_7167263
Leader:
MRLGAKITSGRSFLQGRHLVERVIRRAGQGM
Core:
Q R W T R G S R S A A R A R G L V R A R R P E C P G S
Core with dehydrations:
Q R W Dhb R G Dha R Dha A A R A R G L V R A R R P E Cys P G Dha

#### antiSMASH-DB 4.0 matches for allorf_7167087_7167263

100.0%
NZ_CP034669.1:
Lanthipeptides: allorf_7167087_7167263_lanthipeptide
1
Q R W T R G S R S A A R A R G L V R A R R P E C P G S
27
Q R W T R G S R S A A R A R G L V R A R R P E C P G S
1
Q R W T R G S R S A A R A R G L V R A R R P E C P G S
27
25.9%
NZ_CP030771.1:
Lanthipeptides: allorf_09779504_09779617_lanthipeptide
19
A R R P E C P G
26
A R R P C P G
11
A R R P I C P G
18
18.2%
NZ_AQQB01000068.1 and 6 others:
NZ_BCEY01000024.1 Lanthipeptides: GOZ53_RS05100_lanthipeptide NZ_BCEZ01000067.1 Lanthipeptides: GOZ55_RS11230_lanthipeptide NZ_BCFC01000053.1 Lanthipeptides: GOZ35_RS07920_lanthipeptide NZ_BCFG01000017.1 Lanthipeptides: GOZ50_RS03220_lanthipeptide NZ_BCFI01000009.1 Lanthipeptides: GOZ54_RS02495_lanthipeptide NZ_CP019557.1 Lanthipeptides: BZG42_RS05725_lanthipeptide
Lanthipeptides: K738_RS01000000110290_lanthipeptide
15
G L V R A R R P E C P G
26
G L V+ +C P G
4
G L V K T L T K D C P G
15
with 1 more sequence matches
14.7%
NZ_CP040409.1 and 4 others:
NZ_CP040414.1 Lanthipeptides: FE331_RS04020_lanthipeptide NZ_CP040415.1 Lanthipeptides: allorf_0721024_0721203_lanthipeptide NZ_CP040417.1 Lanthipeptides: FE328_RS00745_lanthipeptide NZ_CP040424.1 Lanthipeptides: FE321_RS03445_lanthipeptide
Lanthipeptides: FE336_RS03450_lanthipeptide
15
G L V R A R R P E C P G S
27
G L++ +C P G+
4
G L L K T L T K D C P G T
16

#### MIBiG 4.0 matches for allorf_7167087_7167263

14.8%
BGC0000563.4 (AEA03263.1):
Lanthipeptide: venezuelin
9
S A A R A R G L V R A R R P E C P G
26
+ G L+ C G
1
A T C E C V G L L T L L N T V C I G
18

#### 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.
No hits above weak threshold.
Weak hits (7):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.86 out of 30.25
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.47 out of 26.85
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.57 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.35 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.99 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.27 out of 29.65
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.61 out of 20.01
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.

EJ065_RS28555 - Class II
  Cleavage pHMM score: 3.40
  RODEO score: 0
  Monoisotopic mass: 2483.1 Da
  Molecular weight: 2484.9 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2502.9 Da N = 1
    2520.9 Da N = 2
EJ065_RS40790 - Class II
  Cleavage pHMM score: -6.70
  RODEO score: 0
  Monoisotopic mass: 3432.4 Da
  Molecular weight: 3434.8 Da
  Number of bridges: 5
allorf_7162463_7162558 - Class II
  Cleavage pHMM score: -7.20
  RODEO score: 0
  Monoisotopic mass: 590.3 Da
  Molecular weight: 590.7 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    608.7 Da N = 1
allorf_7167087_7167263 - Class II
  Cleavage pHMM score: -5.40
  RODEO score: 0
  Monoisotopic mass: 2964.6 Da
  Molecular weight: 2966.3 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2984.4 Da N = 1
    3002.4 Da N = 2
    3020.4 Da N = 3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP034669.1 - Region 34 - butyrolactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,817,796 - 7,828,620 nt. (total: 10,825 nt) Show pHMM detection rules used
butyrolactone: AfsA

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: dehydratase
EJ065_RS31295: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

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

Reference | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001458.4 |  | 0.38 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0000260.3 |  | 0.26 | PKS | prodigiosin | Hahella chejuensis KCTC 2396
BGC0002381.3 |  | 0.24 | PKS, other (other) | tambjamine BE-18591 | Streptomyces albus subsp. albus
BGC0000262.5 |  | 0.21 | PKS, saccharide | prejadomycin, rabelomycin, gaudimycin C, gaudimycin D, UWM6, gaudimycin A | Streptomyces sp. PGA64
BGC0000112.5 |  | 0.20 | PKS | neocarzinostatin | Streptomyces carzinostaticus subsp. neocarzinostaticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001458.4 |  | 0.38 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0000260.3 |  | 0.26 | PKS | prodigiosin | Hahella chejuensis KCTC 2396
BGC0002381.3 |  | 0.24 | PKS, other (other) | tambjamine BE-18591 | Streptomyces albus subsp. albus
BGC0000262.5 |  | 0.21 | PKS, saccharide | prejadomycin, rabelomycin, gaudimycin C, gaudimycin D, UWM6, gaudimycin A | Streptomyces sp. PGA64
BGC0000112.5 |  | 0.20 | PKS | neocarzinostatin | Streptomyces carzinostaticus subsp. neocarzinostaticus

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (2):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.10 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.34 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP034669.1 - Region 35 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,947,709 - 7,990,723 nt. (total: 43,015 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
EJ065_RS31895: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Lyases: dehydratase
EJ065_RS31905: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

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

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.71 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.60 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001641.4 |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001249.5 |  | 0.60 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002286.3 |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.71 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.60 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001641.4 |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001249.5 |  | 0.60 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002286.3 |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.31 out of 23.79
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 19.14 out of 20.97
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
Additional weak hits (5):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.41 out of 33.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.50 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.78 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.97 out of 27.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.29 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 46, location 7947708 - 7990723:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Phe)

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).
EJ065_RS31905: Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (24..399): Phe
nrpys: Phe

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:
    Unpolar aromatic ring (Phe, Trp)
  Single AA prediction:
    phe (Phe)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGVAFDASVWEPCLVMAGEFNAYGPTEGTVCATA
  Nearest Stachelhaus code(s):
    Leu or Met DAWCIAAVCK (79% 8Å match)
    Phe DAWTVAAVCK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
IolR | Regulator of the inositol catabolism

NZ_CP034669.1 - Region 36 - lanthipeptide-class-ii,phenazine
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,992,849 - 8,032,695 nt. (total: 39,847 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)
phenazine: phzB

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
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Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
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
EJ065_RS32005: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

EJ065_RS32050: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: sulfotransferase
EJ065_RS32045: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain

Lyases: cyclase
EJ065_RS32035: lanthionine synthetase C family protein

smcogs
  SMCOG1070: 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-ii | phenazine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000554.4 |  |  | 0.24 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001210.5 |  |  | 0.22 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0001555.4 |  |  | 0.20 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  |  | 0.19 | ribosomal | microcin N | Escherichia coli
BGC0000525.5 |  |  | 0.19 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000527.5 |  |  | 0.18 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0002698.2 |  |  | 0.18 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000588.5 |  |  | 0.18 | ribosomal | microcin L | Escherichia coli
BGC0001407.5 |  |  | 0.17 | ribosomal | bicereucin | Bacillus cereus SJ1
BGC0000516.4 |  |  | 0.17 | ribosomal | geobacillin II | Geobacillus thermodenitrificans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000554.4 |  | 0.57 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001210.5 |  | 0.55 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000516.4 |  | 0.54 | ribosomal | geobacillin II | Geobacillus thermodenitrificans
BGC0000527.5 |  | 0.53 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001555.4 |  | 0.52 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  | 0.51 | ribosomal | microcin N | Escherichia coli
BGC0000525.5 |  | 0.51 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0002698.2 |  | 0.50 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli
BGC0001407.5 |  | 0.49 | ribosomal | bicereucin | Bacillus cereus SJ1

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

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 EJ065_RS32035

EJ065_RS32040
Leader:
MMTQDMIIRAWKDPSFRATLTVEQLAELPASPSGPTMNELNEGDLMDVVGG
Core:
I Q A V S H R N S C G Y V C T L T T E C G C
Core with dehydrations:
I Q A V Dha H R N Dha Cys G Y V Cys Dhb L Dhb Dhb E Cys G Cys

#### antiSMASH-DB 4.0 matches for EJ065_RS32040

100.0%
NZ_CP034669.1:
Lanthipeptides: EJ065_RS32040_lanthipeptide
1
I Q A V S H R N S C G Y V C T L T T E C G C
22
I Q A V S H R N S C G Y V C T L T T E C G C
1
I Q A V S H R N S C G Y V C T L T T E C G C
22
45.5%
NZ_CP036455.1 and 4 others:
NZ_JAGPXN010000019.1 Lanthipeptides: KBX06_RS22045_lanthipeptide NZ_JAODUN010000003.1 Lanthipeptides: BXY51_RS10560_lanthipeptide NZ_KB895893.1 Lanthipeptides: C569_RS0129325_lanthipeptide NZ_KB900614.1 Lanthipeptides: SALPAC6_RS0114155_lanthipeptide
Lanthipeptides: EKD16_RS25235_lanthipeptide
9
S C G Y V C T L T T E C G
21
S G+V C T L T E C G
1
S S G W V C T L T I E C G
13
45.5%
NZ_JALMDK010000017.1:
Lanthipeptides: allorf_059288_059443_lanthipeptide
9
S C G Y V C T L T T E C G C
22
S G Y+C T L T E C C
2
S G G Y I C T L T W E C N C
15
with 107 more sequence matches
Only the first 10 are displayed here.
45.5%
NZ_LWKZ01000001.1:
Lanthipeptides: A6A06_RS41385_lanthipeptide
9
S C G Y V C T L T T E C G C
22
S G Y C T+T T E C C
2
S S G Y F C T I T T E C F C
15
40.9%
NC_009480.1 and 10 others:
NZ_CP033724.1 Lanthipeptides: EFE39_RS10220_lanthipeptide NZ_CP047051.1 Lanthipeptides: GRD74_RS10365_lanthipeptide NZ_CP047054.1 Lanthipeptides: GRD61_RS10460_lanthipeptide NZ_CP053860.1 Lanthipeptides: DQP62_RS10825_lanthipeptide NZ_CP076352.1 Lanthipeptides: KN218_RS09900_lanthipeptide NZ_CP085137.1 Lanthipeptides: LHJ48_RS10290_lanthipeptide NZ_CP085140.1 Lanthipeptides: LHJ47_RS10305_lanthipeptide NZ_CP095274.1 Lanthipeptides: MU580_RS10460_lanthipeptide NZ_PSTW01000024.1 Lanthipeptides: C5C03_RS09675_lanthipeptide NZ_SISU01000002.1 Lanthipeptides: EOG37_RS09890_lanthipeptide
Lanthipeptides: CMM_RS10575_lanthipeptide
8
N S C G Y V C T L T T E C G
21
+S G++C T L T E C G
1
S S S G W L C T L T I E C G
14
40.9%
NZ_AUBN01000022.1:
Lanthipeptides: G448_RS16025_lanthipeptide
9
S C G Y V C T L T T E C G
21
S G+ C T L T E C G
2
S S G W F C T L T I E C G
14
40.9%
NZ_CP015515.1 and 2 others:
NZ_CP028130.1 Lanthipeptides: C7V51_RS14690_lanthipeptide NZ_PSUO01000011.1 Lanthipeptides: C5C18_RS08595_lanthipeptide
Lanthipeptides: A6122_RS12855_lanthipeptide
8
N S C G Y V C T L T T E C G
21
S G++C T L T E C G
1
G S S G W M C T L T I E C G
14
40.9%
NZ_CP061274.1 and 1 other:
NZ_JADKRR010000001.1 Lanthipeptides: ITJ40_RS10085_lanthipeptide
Lanthipeptides: H9X71_RS09850_lanthipeptide
9
S C G Y V C T L T T E C G
21
S G++C T L T E C G
2
S S G W L C T L T I E C G
14
38.7%
NZ_KQ040792.1 and 1 other:
NZ_KQ040792.1 Lanthipeptides: WH45_RS23330_lanthipeptide
Lanthipeptides: WH45_RS23330_lanthipeptide
1
I Q A V S H R N S C G Y V C T L T T E C G
21
+Q +S N G V C T L T E C G
3
V Q G L S Q G N D-G K V C T L T W E C G
22
36.4%
NZ_CP086242.1 and 1 other:
NZ_CP086245.1 Lanthipeptides: LL037_RS25615_lanthipeptide
Lanthipeptides: LL038_RS25355_lanthipeptide
9
S C G Y V C T L T T E C
20
S G +C T T T E C
2
S S G A I C T A T T E C
13
35.7%
NZ_QRHZ01000008.1 and 2 others:
NZ_QSRF01000021.1 Lanthipeptides: DXC87_RS15310_lanthipeptide NZ_QUEQ01000033.1 Lanthipeptides: DXA48_RS19000_lanthipeptide
Lanthipeptides: DW272_RS13830_lanthipeptide
3
A V S H R N S C G Y V C T L T T E C
20
A R N S G C T T E C
1
A G E P R N S G G M F C T S T G E C
18
35.3%
NZ_CP040417.1 and 7 others:
NZ_CP040417.1 Lanthipeptides: FE328_RS09040_lanthipeptide NZ_CP040419.1 Lanthipeptides: FE326_RS02895_lanthipeptide NZ_CP040419.1 Lanthipeptides: FE326_RS02895_lanthipeptide NZ_CP040421.1 Lanthipeptides: FE324_RS02835_lanthipeptide NZ_CP040421.1 Lanthipeptides: FE324_RS02835_lanthipeptide NZ_CP040422.1 Lanthipeptides: FE323_RS02870_lanthipeptide NZ_CP040422.1 Lanthipeptides: FE323_RS02870_lanthipeptide
Lanthipeptides: FE328_RS09040_lanthipeptide
1
I Q A V S H R N S C G Y V C T L T T E C G
21
I+ +S N+ G V C T L T E C G
6
I R K L S K G N T-G K V C T L T W E C G
25
34.6%
NC_017912.1 and 15 others:
NZ_BORO01000007.1 Lanthipeptides: KI343_RS07745_lanthipeptide NZ_CP007242.1 Lanthipeptides: KHU1_RS17410_lanthipeptide NZ_CP031424.1 Lanthipeptides: DXX91_RS18935_lanthipeptide NZ_CP032855.1 Lanthipeptides: D9C11_RS10440_lanthipeptide NZ_CP043809.1 Lanthipeptides: ETZ92_RS14260_lanthipeptide NZ_CP049904.1 Lanthipeptides: V753_RS18470_lanthipeptide NZ_CP053764.1 Lanthipeptides: HPQ66_RS18325_lanthipeptide NZ_CP061938.1 Lanthipeptides: IEN91_RS19800_lanthipeptide NZ_CP063768.1 Lanthipeptides: IM712_RS05205_lanthipeptide NZ_CP087137.1 Lanthipeptides: LOK79_RS18580_lanthipeptide NZ_CP092383.1 Lanthipeptides: MID02_RS19390_lanthipeptide NZ_JAEACM010000001.1 Lanthipeptides: I5F15_RS04355_lanthipeptide NZ_JAJNPN010000015.1 Lanthipeptides: LQ568_RS13285_lanthipeptide NZ_SDKF01000002.1 Lanthipeptides: EUA41_RS09950_lanthipeptide NZ_VDUT01000007.1 Lanthipeptides: FS412_RS14545_lanthipeptide
Lanthipeptides: MUS_RS20065_lanthipeptide
11
G Y V C T L T T E C G C
22
G V C T L T+E C C
15
G G V C T L T S E C I C
26

#### MIBiG 4.0 matches for EJ065_RS32040

25.0%
BGC0000517.4 (BAB04173.1):
Lanthipeptide: haloduracin β or haloduracin α
11
G Y V C T L T T E C
20
G C T L T E C
14
G A Y C T L T V E C
23
23.3%
BGC0002110.3 (QKV49893.1):
Lanthipeptide: birimositide
11
G Y V C T L T T E C
20
G C T L T E C
16
G G W C T L T K E C
25
22.7%
BGC0001155.5 (AGY49587.1):
Thiopeptide: GE2270
9
S C G Y V C T L T T E C
20
S C V C C
1
S C N C V C G F C C S C
12
with 1 more sequence matches
12.8%
BGC0001229.4 (SBI_06990):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
14
C T L T T E C
20
C T L+ E C
28
C T L S K E C
34
allorf_8006470_8006631
Leader:
MAEARPRRPGLSATHPPPASRMFQVEYM
Core:
H E P L S L Y C G M P A L S W R S R Q K G G G P P
Core with dehydrations:
H E P L Dha L Y Cys G M P A L Dha W R Dha R Q K G G G P P

#### antiSMASH-DB 4.0 matches for allorf_8006470_8006631

100.0%
NZ_CP034669.1:
Lanthipeptides: allorf_8006470_8006631_lanthipeptide
1
H E P L S L Y C G M P A L S W R S R Q K G G G P P
25
H E P L S L Y C G M P A L S W R S R Q K G G G P P
1
H E P L S L Y C G M P A L S W R S R Q K G G G P P
25
23.5%
NZ_KB235948.1 and 1 other:
NZ_KB235948.1 Lanthipeptides: allorf_4821767_4821901_lanthipeptide
Lanthipeptides: allorf_4821767_4821901_lanthipeptide
2
E P L S L Y C G M P A L S W R S R Q K G G
22
E P C G +L W R+ G
5
E P S G S T C G G K S L F W A Q R R A Q G
25
15.4%
NC_018499.1 and 2 others:
NZ_JAOPQW010000026.1 Lanthipeptides: allorf_25942_26136_lanthipeptide NZ_MLKL01000042.1 Lanthipeptides: allorf_27650_27844_lanthipeptide
Lanthipeptides: allorf_26272_26466_lanthipeptide
1
H E P L S L Y C
8
H E P+ ++C
6
H E P I M V F C
13

#### 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:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.59 out of 26.85
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.95 out of 29.38
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.70 out of 28.19
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):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.47 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.71 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.34 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.48 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.22 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.76 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.76 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.39 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.79 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.74 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.69 out of 29.38
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.15 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.38 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.85 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.24 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.90 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
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.

EJ065_RS32040 - Class II
  Cleavage pHMM score: -0.50
  RODEO score: 0
  Monoisotopic mass: 2254.0 Da
  Molecular weight: 2255.6 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2273.6 Da N = 1
allorf_8006470_8006631 - Class II
  Cleavage pHMM score: -4.80
  RODEO score: 0
  Monoisotopic mass: 2669.3 Da
  Molecular weight: 2671.1 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2689.1 Da N = 1
    2707.1 Da N = 2

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
FuR variant 1 | Ferric Uptake Regulator
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NZ_CP034669.1 - Region 37 - 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: 8,594,093 - 8,635,178 nt. (total: 41,086 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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: oxidoreductase reductase
EJ065_RS34430: alkyl hydroperoxide reductase/ Thiol specific

smcogs
  SMCOG1196: alkyl hydroperoxide reductase/ Thiol specific

EJ065_RS34510: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

Transferases: aminotransferase methyltransferase
EJ065_RS34455: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

EJ065_RS34485: aminotransferase

smcogs
  SMCOG1019: aminotransferase

EJ065_RS34525: isoprenylcysteine carboxyl methyltransferase

smcogs
  SMCOG1150: isoprenylcysteine carboxyl methyltransferase

Hydrolases: glucanase
EJ065_RS34595: Pullulanase, type I

smcogs
  SMCOG1297: Pullulanase, type I

Ligases: ligase synthase
EJ065_RS34515: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

EJ065_RS34530: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001831.3 |  | 0.79 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0000282.3 |  | 0.68 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001964.2 |  | 0.64 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0001641.4 |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001164.3 |  | 0.58 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.58 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002458.3 |  | 0.49 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0000513.3 |  | 0.46 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000551.5 |  | 0.46 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0001962.3 |  | 0.46 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001831.3 |  | 0.79 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0000282.3 |  | 0.68 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001964.2 |  | 0.64 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0001641.4 |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001164.3 |  | 0.58 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.58 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002458.3 |  | 0.49 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0000513.3 |  | 0.46 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000551.5 |  | 0.46 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0001962.3 |  | 0.46 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113

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 (7):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.02 out of 21.55
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.41 out of 31.73
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.62 out of 26.12
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.06 out of 27.55
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.85 out of 32.74
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.27 out of 35.63
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.79 out of 29.65
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
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).
EJ065_RS34515: NH2
CAL_domain (41..476): NH2
minowa: NH2

Prediction, score:
  NH2: 90.5
  Acetyl-CoA: 35.3
  AHBA: 16.8
  shikimic_acid: 5.3
  fatty_acid: -1.9

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

Regulator | Description
--- | ---

NZ_CP034669.1 - Region 38 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,772,940 - 8,795,198 nt. (total: 22,259 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
Hydrolases: deacetylase
EJ065_RS35290: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

Lyases: cyclase decarboxylase
EJ065_RS35285: Terpene synthase/cyclase metal-binding domain protein

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

EJ065_RS35310: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: synthase
EJ065_RS35315: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.80 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002708.2 |  | 0.75 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0000657.5 |  | 0.58 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002620.2 |  | 0.37 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002382.3 |  | 0.36 | ribosomal | grimoviridin | Grimontia marina
BGC0000597.4 |  | 0.32 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0002633.2 |  | 0.31 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0000595.3 |  | 0.30 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0001654.5 |  | 0.27 | saccharide | lipooligosaccharide | Bacteroides thetaiotaomicron VPI-5482
BGC0000938.5 |  | 0.27 | other (aminocoumarin) | fosfomycin | Streptomyces fradiae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.80 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002708.2 |  | 0.75 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0000657.5 |  | 0.58 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002620.2 |  | 0.37 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002382.3 |  | 0.36 | ribosomal | grimoviridin | Grimontia marina
BGC0000597.4 |  | 0.32 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0002633.2 |  | 0.31 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0000595.3 |  | 0.30 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0001654.5 |  | 0.27 | saccharide | lipooligosaccharide | Bacteroides thetaiotaomicron VPI-5482
BGC0000938.5 |  | 0.27 | other (aminocoumarin) | fosfomycin | Streptomyces fradiae

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

No significant matches found.

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

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

Genes with terpene domains:
EJ065_RS35285: T1TS + T1TS
Domain 1 (3 - 335): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (348 - 715): Type 1 terpene synthase
Subtype: Geosmin synthase, C terminal domain

Reactions:
  germacradienol → geosmin

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.56 out of 29.51
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.76 out of 23.79
Confidence: medium
Additional weak hits (8):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.06 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.05 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.42 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.22 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.35 out of 26.06
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.37 out of 30.98
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 25.56 out of 30.98
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.52 out of 24.78
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism

NZ_CP034669.1 - Region 39 - RRE-containing,RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 9,018,680 - 9,040,279 nt. (total: 21,600 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))
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
Transferases: aminotransferase methyltransferase
EJ065_RS36335: methyltransferase

smcogs
  SMCOG1089: methyltransferase

EJ065_RS36375: 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 | RiPP-like | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002665.2 |  |  | 0.22 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0001486.4 |  |  | 0.20 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0000858.3 |  |  | 0.16 | other (other) | ectoine | Methylobacter marinus
BGC0000395.5 |  |  | 0.12 | NRPS | nocardicin A | Nocardia uniformis subsp. tsuyamanensis
BGC0000841.5 |  |  | 0.12 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate, clavulanic acid | Streptomyces clavuligerus ATCC 27064
BGC0002535.2 |  |  | 0.10 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0002339.3 |  |  | 0.10 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0002713.2 |  |  | 0.09 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0000402.4 |  |  | 0.09 | NRPS | paenilarvin A, paenilarvin B, paenilarvin C | Paenibacillus larvae subsp. larvae DSM 25430
BGC0002623.2 |  |  | 0.09 | NRPS, PKS | microginin 755, microginin 721, microginin 773, microginin 739, microginin 705, microginin 803, microginin 769, microginin 735, microginin 626, microginin 592, microginin 558, microginin 789 | Microcystis aeruginosa LEGE 91341

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000858.3 |  | 0.47 | other (other) | ectoine | Methylobacter marinus
BGC0002665.2 |  | 0.39 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0000841.5 |  | 0.39 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate, clavulanic acid | Streptomyces clavuligerus ATCC 27064
BGC0001486.4 |  | 0.37 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0002535.2 |  | 0.36 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0002339.3 |  | 0.36 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0002713.2 |  | 0.34 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0000402.4 |  | 0.34 | NRPS | paenilarvin A, paenilarvin B, paenilarvin C | Paenibacillus larvae subsp. larvae DSM 25430
BGC0002623.2 |  | 0.33 | NRPS, PKS | microginin 755, microginin 721, microginin 773, microginin 739, microginin 705, microginin 803, microginin 769, microginin 735, microginin 626, microginin 592, microginin 558, microginin 789 | Microcystis aeruginosa LEGE 91341
BGC0001510.5 |  | 0.33 | other (other) | anisomycin | Streptomyces hygrospinosus

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.61 out of 28.19
Confidence: medium
Additional weak hits (4):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.44 out of 29.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.22 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.84 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.45 out of 29.38
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (9020000...9040279)
EJ065_RS36355
  RRE type: Stand_Alone_Lasso_RRE
  Location: 6 - 86
  Score: 35.9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
ZuR variant 1 | Zinc-responsive repressor