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Overview
1.1
1.2
1.3
1.4
1.5
1.6

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

NZ_CP040435.1 (Stenotrophomonas maltophilia)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | RiPP-like | 1,228,561 | 1,239,406 |  |
Region 2 | RiPP-like | 1,515,224 | 1,526,099 |
Region 3 | lanthipeptide-class-ii | 1,847,366 | 1,870,263 |
Region 4 | NRP-metallophore,NRPS | 2,749,835 | 2,798,202 | High | 2,3-dihydroxybenzoylserine | NRPS:Type I
Region 5 | terpene-precursor | 3,473,569 | 3,494,447 |
Region 6 | arylpolyene | 4,665,002 | 4,708,604 | Low | aryl polyenes | other:other

NZ_CP040435.1 - 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: 1,228,561 - 1,239,406 nt. (total: 10,846 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
--- | --- | --- | --- | --- | ---
BGC0000043.5 |  | 0.37 | PKS | curacin A | Moorea producens 19L
BGC0001484.3 |  | 0.33 | other (other) | 2'-chloropentostatin, 2'-amino-2'-deoxyadenosine | Actinomadura sp. ATCC 39365
BGC0002000.4 |  | 0.32 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0000527.5 |  | 0.31 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0002571.2 |  | 0.31 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0001789.3 |  | 0.31 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000453.5 |  | 0.31 | NRPS | valinomycin | Streptomyces tsusimaensis
BGC0000536.3 |  | 0.31 | ribosomal | nisin Q | Lactococcus lactis
BGC0000535.4 |  | 0.31 | ribosomal | nisin A | Lactococcus lactis subsp. lactis
BGC0000537.3 |  | 0.31 | ribosomal | nisin U | Streptococcus uberis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000043.5 |  | 0.37 | PKS | curacin A | Moorea producens 19L
BGC0001484.3 |  | 0.33 | other (other) | 2'-chloropentostatin, 2'-amino-2'-deoxyadenosine | Actinomadura sp. ATCC 39365
BGC0002000.4 |  | 0.32 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0000527.5 |  | 0.31 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0002571.2 |  | 0.31 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0001789.3 |  | 0.31 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000453.5 |  | 0.31 | NRPS | valinomycin | Streptomyces tsusimaensis
BGC0000536.3 |  | 0.31 | ribosomal | nisin Q | Lactococcus lactis
BGC0000535.4 |  | 0.31 | ribosomal | nisin A | Lactococcus lactis subsp. lactis
BGC0000537.3 |  | 0.31 | ribosomal | nisin U | Streptococcus uberis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
Additional weak hits (1):
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.64 out of 32.93
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP040435.1 - Region 2 - 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: 1,515,224 - 1,526,099 nt. (total: 10,876 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
--- | --- | --- | --- | --- | ---
BGC0002133.3 |  | 0.37 | ribosomal | group 1 methanobactin | Methylosinus sp. LW3
BGC0001962.3 |  | 0.27 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0000188.5 |  | 0.23 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0001650.4 |  | 0.23 | NRPS | Le-pyrrolopyrazines | Lysobacter enzymogenes
BGC0000452.5 |  | 0.21 | NRPS | tyrocidine | Brevibacillus brevis NBRC 100599
BGC0000651.5 |  | 0.20 | terpene | KS-505a | Streptomyces argenteolus
BGC0001283.3 |  | 0.18 | PKS | Bisenarsan | Streptomyces lividans 1326

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002133.3 |  | 0.37 | ribosomal | group 1 methanobactin | Methylosinus sp. LW3
BGC0001962.3 |  | 0.27 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0000188.5 |  | 0.23 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0001650.4 |  | 0.23 | NRPS | Le-pyrrolopyrazines | Lysobacter enzymogenes
BGC0000452.5 |  | 0.21 | NRPS | tyrocidine | Brevibacillus brevis NBRC 100599
BGC0000651.5 |  | 0.20 | terpene | KS-505a | Streptomyces argenteolus
BGC0001283.3 |  | 0.18 | PKS | Bisenarsan | Streptomyces lividans 1326

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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.19 out of 19.26
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.64 out of 26.85
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47
Confidence: medium
Additional weak hits (4):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.75 out of 39.62
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.95 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP040435.1 - Region 3 - 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: 1,847,366 - 1,870,263 nt. (total: 22,898 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
Lyases: cyclase
FEO92_RS08805: 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
--- | --- | --- | --- | --- | ---
BGC0000528.5 |  | 0.52 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002346.3 |  | 0.47 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000503.5 |  | 0.46 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0001579.4 |  | 0.46 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0002698.2 |  | 0.43 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001576.3 |  | 0.43 | ribosomal | divamide A | Prochloron didemni
BGC0000500.5 |  | 0.41 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0002316.2 |  | 0.41 | ribosomal | cebulantin | Saccharopolyspora cebuensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000528.5 |  | 0.52 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002346.3 |  | 0.47 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000503.5 |  | 0.46 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0001579.4 |  | 0.46 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0002698.2 |  | 0.43 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001576.3 |  | 0.43 | ribosomal | divamide A | Prochloron didemni
BGC0000500.5 |  | 0.41 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0002316.2 |  | 0.41 | ribosomal | cebulantin | Saccharopolyspora cebuensis

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 FEO92_RS08805

FEO92_RS08800
Leader:
MDLNDDVVSGWLNGSDDVDGCANPAGSLFIYGA
Core:
A A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
Core with dehydrations:
A A Dhb E Dha A L Dhb Dha A Dha D Dhb L I Dhb G G G Dhb E Cys Dhb Dhb Dhb M Dha V V N H Cys L Cys Cys

#### antiSMASH-DB 4.0 matches for FEO92_RS08800

100.0%
NZ_CP015612.1 and 17 others:
NZ_CP027562.1 Lanthipeptides: C6Y55_RS08375_lanthipeptide NZ_CP028358.1 Lanthipeptides: C9J74_RS08630_lanthipeptide NZ_CP040435.1 Lanthipeptides: FEO92_RS08800_lanthipeptide NZ_CP040438.1 Lanthipeptides: FEO89_RS08350_lanthipeptide NZ_CP040439.1 Lanthipeptides: FEO88_RS08780_lanthipeptide NZ_CP056088.1 Lanthipeptides: HUZ96_RS08220_lanthipeptide NZ_CP090418.1 Lanthipeptides: LYZ64_RS08310_lanthipeptide NZ_CP109812.1 Lanthipeptides: FQS62_RS08595_lanthipeptide NZ_DS999412.1 Lanthipeptides: SSKA14_RS15505_lanthipeptide NZ_JAEDUZ010000008.1 Lanthipeptides: JAK52_RS03215_lanthipeptide NZ_JAEDWK010000010.1 Lanthipeptides: JAK51_RS04155_lanthipeptide NZ_JAJNMF010000022.1 Lanthipeptides: LQ423_RS11465_lanthipeptide NZ_JVUI01000059.1 Lanthipeptides: ADG58_RS15825_lanthipeptide NZ_LR134301.1 Lanthipeptides: EL200_RS07985_lanthipeptide NZ_OBEE01000002.1 Lanthipeptides: CRO53_RS02030_lanthipeptide NZ_RHQE01000015.1 Lanthipeptides: EGJ89_RS13150_lanthipeptide NZ_SOCO01000001.1 Lanthipeptides: N440_RS05690_lanthipeptide
Lanthipeptides: A7326_RS08120_lanthipeptide
1
A A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
A A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
1
A A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
97.1%
NZ_CP011010.1:
Lanthipeptides: VN11_RS08230_lanthipeptide
1
A A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
A A T E S A L T+A S D T L I T G G G T E C T T T M S V V N H C L C C
1
A A T E S A L T A A S D T L I T G G G T E C T T T M S V V N H C L C C
35
97.1%
NZ_CP043578.1 and 3 others:
NZ_CP067993.1 Lanthipeptides: JJL50_RS07700_lanthipeptide NZ_JVHP01000063.1 Lanthipeptides: ADI44_RS21105_lanthipeptide NZ_OU943334.1 Lanthipeptides: LNN95_RS09005_lanthipeptide
Lanthipeptides: F0Q13_RS08255_lanthipeptide
1
A A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
1
G A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
with 16 more sequence matches
Only the first 10 are displayed here.
72.3%
NZ_CP047310.1 and 4 others:
NZ_CP104169.1 Lanthipeptides: NDR96_RS06465_lanthipeptide NZ_JABDRV010000001.1 Lanthipeptides: HRL60_RS01085_lanthipeptide NZ_JAEDVS010000025.1 Lanthipeptides: JAK50_RS15965_lanthipeptide NZ_JVPM01000038.1 Lanthipeptides: ADH50_RS19075_lanthipeptide
Lanthipeptides: GS396_RS07720_lanthipeptide
2
A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
14
A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
47
37.1%
NZ_CP011305.1 and 19 others:
NZ_CP031058.1 Lanthipeptides: DUW70_RS15590_lanthipeptide NZ_CP031167.1 Lanthipeptides: MG068_RS07815_lanthipeptide NZ_CP040436.1 Lanthipeptides: FEO91_RS08085_lanthipeptide NZ_CP046588.1 Lanthipeptides: GOC52_RS08100_lanthipeptide NZ_CP060259.1 Lanthipeptides: H7F32_RS08235_lanthipeptide NZ_CP071784.1 Lanthipeptides: J3U96_RS13765_lanthipeptide NZ_CP077679.1 Lanthipeptides: KS456_RS07940_lanthipeptide NZ_CP096975.1 Lanthipeptides: M1L61_RS08375_lanthipeptide NZ_CP104071.1 Lanthipeptides: K7565_RS07800_lanthipeptide NZ_CP104287.1 Lanthipeptides: K7567_RS07875_lanthipeptide NZ_CP104324.1 Lanthipeptides: K7569_RS08320_lanthipeptide NZ_JACLBK010000002.1 Lanthipeptides: ID844_RS05155_lanthipeptide NZ_JAEDVP010000027.1 Lanthipeptides: JAK38_RS15550_lanthipeptide NZ_JAEDVW010000007.1 Lanthipeptides: JAK53_RS03160_lanthipeptide NZ_JAEDWD010000009.1 Lanthipeptides: JAK45_RS02000_lanthipeptide NZ_JAFLWT010000006.1 Lanthipeptides: J1F00_RS06425_lanthipeptide NZ_JAQQGI010000014.1 Lanthipeptides: PQS91_RS16925_lanthipeptide NZ_KB907502.1 Lanthipeptides: G370_RS0114170_lanthipeptide NZ_RHPZ01000014.1 Lanthipeptides: EGJ03_RS16365_lanthipeptide
Lanthipeptides: YH67_RS07965_lanthipeptide
21
E C T T T M S V V N H C L C C
35
E C T T T+S V+N H C L C C
3
E C T T T V S V I N H C L C C
17
36.2%
NZ_CP007597.1:
Lanthipeptides: DX03_RS09815_lanthipeptide
2
A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
A T++A L T+ + T++T G G C T T T M S V+N H C+C C
25
A T D A A L T A M A P T M V T G G T G N C T T T M S V I N H C M C C
58
29.3%
NZ_CP069396.1:
Lanthipeptides: JRI60_RS03735_lanthipeptide
1
A A T E S A L T S A S D T L I T
16
A A T E+A L T A S D L+T
12
A A T E N A L T D A S D A L V T
27
28.8%
NZ_CP069338.1:
Lanthipeptides: JQX13_RS07220_lanthipeptide
2
A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
A T E+A L T+++D L T G + C T ++ H C C
24
A T E A A L T N S T D A L Y T-G C S S C T G S L----H S Y C C
52
26.4%
NZ_CP093340.1:
Lanthipeptides: MNO14_RS04685_lanthipeptide
1
A A T E S A L T S A S D T L I T G G G T E C T T-T M S V V N H C
32
A A T E+A+T S L+ T+C++ T S+ H C
24
A A T E A A M T D K S F L L L----T Q C S S C T A S I P A H C
52
24.4%
NZ_CP029194.1 and 1 other:
NZ_CP059991.1 Lanthipeptides: H4W23_RS35675_lanthipeptide
Lanthipeptides: DEJ46_RS04155_lanthipeptide
1
A A T E S A L T S A S D T L I T G
17
A A E+A L T A++ L+T G
12
A A G E A A L T D A T E A L L T G
28
24.4%
NZ_JH941044.1:
Lanthipeptides: Y19_RS0126875_lanthipeptide
1
A A T E S A L T S A S D T L I T G
17
A A E+A L T A++ L T G
12
A A G E A A L T D A T E A L F T G
28
22.9%
NZ_CP089924.1:
Lanthipeptides: LVB77_RS02735_lanthipeptide
16
T G G G T E C T T T M S V V N H C
32
+G C T+ S V N H C
2
S G A S V N C T S G S S V S N H C
18
22.0%
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
1
A A T E S A L T S A S D T L I T G
17
A A E+A L T ++ L+T G
12
A A G E A A L T D G T E A L L T G
28
allorf_1850191_1850412
Leader:
MAPSMAPTVLERAACPLLTVSWCVRMRRSAGRLLPQLAGNRPESVGS
Core:
P R A G P L A P R M A S S S P H G W V H G V S C P G
Core with dehydrations:
P R A G P L A P R M A Dha Dha Dha P H G W V H G V Dha Cys P G

#### antiSMASH-DB 4.0 matches for allorf_1850191_1850412

100.0%
NZ_CP040435.1:
Lanthipeptides: allorf_1850191_1850412_lanthipeptide
1
P R A G P L A P R M A S S S P H G W V H G V S C P G
26
P R A G P L A P R M A S S S P H G W V H G V S C P G
1
P R A G P L A P R M A S S S P H G W V H G V S C P G
26
96.2%
NZ_CP046588.1 and 6 others:
NZ_CP056088.1 Lanthipeptides: allorf_1820746_1820967_lanthipeptide NZ_CP060259.1 Lanthipeptides: allorf_1747353_1747574_lanthipeptide NZ_CP104071.1 Lanthipeptides: allorf_1665125_1665346_lanthipeptide NZ_CP109812.1 Lanthipeptides: allorf_1794166_1794387_lanthipeptide NZ_JVPM01000038.1 Lanthipeptides: allorf_457583_457804_lanthipeptide NZ_OU943334.1 Lanthipeptides: allorf_1870884_1871105_lanthipeptide
Lanthipeptides: allorf_1742372_1742593_lanthipeptide
1
P R A G P L A P R M A S S S P H G W V H G V S C P G
26
P R A G P L A P R M A S S P H G W V H G V S C P G
1
P R A G P L A P R M A P S S P H G W V H G V S C P G
26
92.3%
NZ_RHPZ01000014.1:
Lanthipeptides: allorf_009576_009797_lanthipeptide
1
P R A G P L A P R M A S S S P H G W V H G V S C P G
26
P R A G P L A P M A S S P H G W V H G V S C P G
1
P R A G P L A P W M A P S S P H G W V H G V S C P G
26
with 4 more sequence matches
80.8%
NZ_SOCO01000001.1:
Lanthipeptides: allorf_1178234_1178455_lanthipeptide
4
G P L A P R M A S S S P H G W V H G V S C P G
26
G P L A P M A S S P H G W V H G V S C P G
1
G P L A P W M A P S S P H G W V H G V S C P G
23
28.8%
NZ_JABDRV010000001.1:
Lanthipeptides: allorf_0223350_0223580_lanthipeptide
11
A S S S P H G W V H G V S C P G
26
A S S P H G W V H G V S C P G
37
A P S S P H G W V H G V S C P G
52
17.5%
NZ_PUPX01000001.1:
Lanthipeptides: allorf_1103640_1103849_lanthipeptide
14
S P H G W V H G V S
23
S H G +H G V S
6
S L H G R I H G V S
15
16.7%
NZ_AZVD01000036.1 and 1 other:
NZ_KB913036.1 Lanthipeptides: A39M_RS1000000128680_lanthipeptide
Lanthipeptides: K389_RS1000000128010_lanthipeptide
1
P R A G P L A P R M A S S
13
P R+G P L A A S
8
P R S G P L A T E C A D S
20
allorf_1856776_1856916
Leader:
MPAPAGHPMSLRLPSIRSRMNGA
Core:
R P R I P C R L R A A H A A H P R A C R S A A
Core with dehydrations:
R P R I P Cys R L R A A H A A H P R A Cys R Dha A A

#### antiSMASH-DB 4.0 matches for allorf_1856776_1856916

100.0%
NZ_CP028358.1 and 5 others:
NZ_CP040435.1 Lanthipeptides: allorf_1856776_1856916_lanthipeptide NZ_CP056088.1 Lanthipeptides: allorf_1814243_1814383_lanthipeptide NZ_CP109812.1 Lanthipeptides: allorf_1800751_1800891_lanthipeptide NZ_JAEDUZ010000008.1 Lanthipeptides: allorf_126406_126546_lanthipeptide NZ_LR134301.1 Lanthipeptides: allorf_1747066_1747206_lanthipeptide
Lanthipeptides: allorf_1803368_1803508_lanthipeptide
1
R P R I P C R L R A A H A A H P R A C R S A A
23
R P R I P C R L R A A H A A H P R A C R S A A
1
R P R I P C R L R A A H A A H P R A C R S A A
23
87.0%
NZ_CP047310.1:
Lanthipeptides: allorf_1658784_1658924_lanthipeptide
1
R P R I P C R L R A A H A A H P R A C R S A A
23
R P R I P R R A A H A A P R A C R S A A
1
R P R I P S R F R A A H A A L P R A C R S A A
23
78.3%
NZ_CP011305.1 and 4 others:
NZ_CP046588.1 Lanthipeptides: allorf_1748975_1749091_lanthipeptide NZ_CP096975.1 Lanthipeptides: allorf_1778660_1778776_lanthipeptide NZ_JAEDVP010000027.1 Lanthipeptides: allorf_23874_23990_lanthipeptide NZ_RHPZ01000014.1 Lanthipeptides: allorf_016179_016295_lanthipeptide
Lanthipeptides: allorf_1722617_1722733_lanthipeptide
1
R P R I P C R L R A A H A A H P R A C R S A A
23
R P I P R A A H A A P R A C R S A A
1
R P L I P S C F R A A H A A L P R A C R S A A
23
with 4 more sequence matches
39.1%
NZ_OBEE01000002.1 and 1 other:
NZ_RHQE01000015.1 Lanthipeptides: allorf_094530_094610_lanthipeptide
Lanthipeptides: allorf_016795_016875_lanthipeptide
15
H P R A C R S A A
23
H P R A C R S A A
1
H P R A C R S A A
9
30.4%
NZ_LMEQ01000012.1:
Lanthipeptides: allorf_0970902_0971075_lanthipeptide
3
R I P C R L R A A H A A H P R A C R S A
22
R+P C + + A + R S A
1
R V P C S V G G S G A Y T A D S A R S A
20
20.0%
NZ_CP095742.1:
Lanthipeptides: allorf_0682536_0682703_lanthipeptide
1
R P R I P C R L R A A H A A H P R A
18
R P I C+ R A A P A
5
R P S I R C K G R A M V T A Q P A A
22
12.5%
NZ_JALBFU010000003.1:
Lanthipeptides: MD221_RS10145_lanthipeptide
1
R P R I P C--R L R A A H A A H P R A
18
R P I P C L+ A P +
15
R P T I P C T P E L Q G T I V A T P T S
34

#### 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:
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 27.95 out of 32.74
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.47 out of 28.19
Confidence: medium
Additional weak hits (5):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.61 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.79 out of 29.65
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.77 out of 23.43
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.18 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.00 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.

FEO92_RS08800 - Class II
  Cleavage pHMM score: -6.70
  RODEO score: 0
  Monoisotopic mass: 3231.5 Da
  Molecular weight: 3233.6 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3251.6 Da N = 1
    3269.6 Da N = 2
    3287.7 Da N = 3
    3305.7 Da N = 4
    3323.7 Da N = 5
    3341.7 Da N = 6
    3359.7 Da N = 7
    3377.8 Da N = 8
allorf_1850191_1850412 - Class II
  Cleavage pHMM score: -5.70
  RODEO score: 0
  Monoisotopic mass: 2538.3 Da
  Molecular weight: 2539.9 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2557.9 Da N = 1
    2575.9 Da N = 2
    2593.9 Da N = 3
allorf_1856776_1856916 - Class II
  Cleavage pHMM score: -1.60
  RODEO score: 0
  Monoisotopic mass: 2518.4 Da
  Molecular weight: 2520.0 Da
  Number of bridges: 1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
FuR variant 2 | Ferric Uptake Regulator
ZuR variant 1 | Zinc-responsive repressor

NZ_CP040435.1 - Region 4 - NRP-metallophore,NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,749,835 - 2,798,202 nt. (total: 48,368 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
FEO92_RS12940: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

FEO92_RS12980: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

FEO92_RS13000: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

Hydrolases: hydrolase
FEO92_RS12955: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Isomerases: isomerase
FEO92_RS12965: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase
FEO92_RS12945: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

FEO92_RS12960: 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 | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002689.2 |  |  | 1.36 | NRPS | 2,3-dihydroxybenzoylserine | Stenotrophomonas maltophilia K279a
BGC0001132.4 |  |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  | 0.63 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000343.5 |  |  | 0.62 | NRPS | enterobactin | Pseudomonas sp. J465

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002689.2 |  | 0.88 | NRPS | 2,3-dihydroxybenzoylserine | Stenotrophomonas maltophilia K279a
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000343.5 |  | 0.65 | NRPS | enterobactin | Pseudomonas sp. J465

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: 19.12 out of 23.79
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.67 out of 20.01
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.55 out of 19.26
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.86 out of 25.31
Confidence: medium
Additional weak hits (23):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.44 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.65 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.56 out of 29.38
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.92 out of 25.88
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.81 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.35 out of 30.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.98 out of 32.74
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.13 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.08 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.16 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.59 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 26.18 out of 32.74
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.91 out of 30.97
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.81 out of 31.73
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 28.19 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.50 out of 39.62
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.58 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.91 out of 29.38
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.73 out of 24.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.56 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.92 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 27.05 out of 39.62
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 26.35 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 4, location 2749834 - 2798202:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser)

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).
FEO92_RS12945: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (457..845): 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:
    RWMTFDVSVWELHFFTSGEHNLYGPTEAAVDVSY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

FEO92_RS12960: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (39..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:
    SASLFPMSSPGGGLQVGGAQQVFGMAEGLVNYTR
  Nearest Stachelhaus code(s):
    diOH-Bz PMPAQGVVNK (94% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
ArgR | Regulator of arginine biosynthesis genes
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor
IolR | Regulator of the inositol catabolism

NZ_CP040435.1 - Region 5 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,473,569 - 3,494,447 nt. (total: 20,879 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: synthetase
FEO92_RS16350: 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 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000643.3 |  | 0.33 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000634.3 |  | 0.32 | terpene | carotenoid | Brevundimonas sp. SD212
BGC0000640.3 |  | 0.32 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000630.3 |  | 0.31 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0002219.2 |  | 0.31 | terpene | (-)-(R)-nephthenol | Stereum hirsutum FP-91666 SS1
BGC0000641.3 |  | 0.30 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000639.3 |  | 0.30 | terpene | carotenoid | Enterobacteriaceae bacterium DC260

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
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
BGC0000643.3 |  | 0.33 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000634.3 |  | 0.32 | terpene | carotenoid | Brevundimonas sp. SD212
BGC0000640.3 |  | 0.32 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000630.3 |  | 0.31 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0002219.2 |  | 0.31 | terpene | (-)-(R)-nephthenol | Stereum hirsutum FP-91666 SS1
BGC0000641.3 |  | 0.30 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000639.3 |  | 0.30 | terpene | carotenoid | Enterobacteriaceae bacterium DC260

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:
FEO92_RS16350: PT_FPPS_like
Domain 1 (32 - 292): 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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
Additional weak hits (2):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.63 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.42 out of 18.57
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
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein

NZ_CP040435.1 - Region 6 - 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: 4,665,002 - 4,708,604 nt. (total: 43,603 nt) Show pHMM detection rules used
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 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 reductase
FEO92_RS21730: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

FEO92_RS21755: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

FEO92_RS21800: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acyltransferase
FEO92_RS21870: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Hydrolases: hydrolase
FEO92_RS21760: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase synthase
FEO92_RS21795: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

FEO92_RS21810: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

FEO92_RS21845: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

FEO92_RS21850: 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 | arylpolyene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000837.4 |  | 0.65 | other (other) | APE Vf | Aliivibrio fischeri ES114
BGC0002008.3 |  | 0.63 | other (other) | aryl polyenes | Xenorhabdus doucetiae
BGC0000836.5 |  | 0.62 | other (other) | APE Ec | Escherichia coli CFT073
BGC0002276.2 |  | 0.60 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001164.3 |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002000.4 |  | 0.49 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0001723.5 |  | 0.49 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001895.4 |  | 0.49 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001
BGC0002047.2 |  | 0.49 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0002510.2 |  | 0.48 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000837.4 |  | 0.65 | other (other) | APE Vf | Aliivibrio fischeri ES114
BGC0002008.3 |  | 0.63 | other (other) | aryl polyenes | Xenorhabdus doucetiae
BGC0000836.5 |  | 0.62 | other (other) | APE Ec | Escherichia coli CFT073
BGC0002276.2 |  | 0.60 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001164.3 |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002000.4 |  | 0.49 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0001723.5 |  | 0.49 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001895.4 |  | 0.49 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001
BGC0002047.2 |  | 0.49 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0002510.2 |  | 0.48 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | 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.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.99 out of 20.47
Confidence: medium
Additional weak hits (4):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.18 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.50 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.63 out of 33.14
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
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).
FEO92_RS21850: X
AMP-binding (124..344): 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:
    THQ-----LFRWVAFSSGGTEVYGSSETGGIAWR
  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
--- | ---
VqsM | Regulator of quorum-sensing signalling systems