Select genomic region:
Overview
7.1
7.2
8.1
9.1
10.1
11.1
11.2
11.3
11.4
11.5
11.6
11.7
11.8
11.9
11.10

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

NZ_LN884295.1 (Paenibacillus ihumii)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 7.1 | RiPP-like | 101,901 | 117,768 |
Region 7.2 | lanthipeptide-class-iii | 165,176 | 187,782 | Medium | andalusicin A/andalusicin B | ribosomal:RiPP:Lanthipeptide

NZ_LN884296.1 (Paenibacillus ihumii)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 8.1 | NRPS-like | 23,725 | 67,465 |  |

NZ_LN884297.1 (Paenibacillus ihumii)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 9.1 | proteusin | 268,851 | 289,096 |

NZ_LN884298.1 (Paenibacillus ihumii)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 10.1 | NRPS,T1PKS | 561,587 | 619,458 |  |

NZ_LN884299.1 (Paenibacillus ihumii)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 11.1 | lanthipeptide-class-ii | 157,797 | 180,850 |
Region 11.2 | NRPS | 988,532 | 1,031,687 |
Region 11.3 | terpene-precursor | 1,617,329 | 1,638,183 |  |
Region 11.4 | cyclic-lactone-autoinducer | 1,847,769 | 1,868,409 |
Region 11.5 | NRPS,T3PKS | 2,125,276 | 2,215,578 | Low | octapeptin C4 | NRPS:Type I
Region 11.6 | NRPS | 2,315,911 | 2,426,579 |
Region 11.7 | NRP-metallophore,NRPS | 2,749,140 | 2,801,501 | High | bacillibactin | NRPS:Type I
Region 11.8 | ranthipeptide | 2,821,946 | 2,843,364 |
Region 11.9 | NRPS,betalactone | 2,903,119 | 2,967,574 |
Region 11.10 | terpene-precursor | 3,686,768 | 3,709,158 |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 7.1 | RiPP-like | 101,901 | 117,768 |
Region 7.2 | lanthipeptide-class-iii | 165,176 | 187,782 | Medium | andalusicin A/andalusicin B | ribosomal:RiPP:Lanthipeptide
Region 8.1 | NRPS-like | 23,725 | 67,465 |  |
Region 9.1 | proteusin | 268,851 | 289,096 |
Region 10.1 | NRPS,T1PKS | 561,587 | 619,458 |  |
Region 11.1 | lanthipeptide-class-ii | 157,797 | 180,850 |
Region 11.2 | NRPS | 988,532 | 1,031,687 |
Region 11.3 | terpene-precursor | 1,617,329 | 1,638,183 |  |
Region 11.4 | cyclic-lactone-autoinducer | 1,847,769 | 1,868,409 |
Region 11.5 | NRPS,T3PKS | 2,125,276 | 2,215,578 | Low | octapeptin C4 | NRPS:Type I
Region 11.6 | NRPS | 2,315,911 | 2,426,579 |
Region 11.7 | NRP-metallophore,NRPS | 2,749,140 | 2,801,501 | High | bacillibactin | NRPS:Type I
Region 11.8 | ranthipeptide | 2,821,946 | 2,843,364 |
Region 11.9 | NRPS,betalactone | 2,903,119 | 2,967,574 |
Region 11.10 | terpene-precursor | 3,686,768 | 3,709,158 |

No secondary metabolite regions were found in these records:
  NZ_LN884288.1 (Paenibacillus ihumii)
  NZ_LN884290.1 (Paenibacillus ihumii)
  NZ_LN884291.1 (Paenibacillus ihumii)
  NZ_LN884292.1 (Paenibacillus ihumii)
  NZ_LN884293.1 (Paenibacillus ihumii)
  NZ_LN884294.1 (Paenibacillus ihumii)

Compact view
NZ_LN884295.1 - 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: 101,901 - 117,768 nt. (total: 15,868 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
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: hydrolase
BN2762_RS01470: hydrolase

smcogs
  SMCOG1179: hydrolase

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
--- | --- | --- | --- | --- | ---
BGC0000617.5 |  | 0.49 | ribosomal | coagulin | Bacillus coagulans
BGC0000558.5 |  | 0.49 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0002579.2 |  | 0.48 | ribosomal | carnobacteriocin XY | Carnobacterium maltaromaticum
BGC0000624.3 |  | 0.46 | ribosomal | salivaricin CRL1328 α peptide, salivaricin CRL1328 β peptide | Lactobacillus salivarius
BGC0000619.3 |  | 0.45 | ribosomal | gassericin T | Lactobacillus gasseri
BGC0001602.3 |  | 0.45 | ribosomal | gassericin-T | Lactobacillus gasseri
BGC0001388.3 |  | 0.45 | ribosomal | gassericin E | Lactobacillus gasseri
BGC0001862.4 |  | 0.45 | ribosomal | pallidocin | Aeribacillus pallidus
BGC0002577.2 |  | 0.44 | ribosomal | lactococcin G | Lactococcus lactis
BGC0000589.5 |  | 0.44 | ribosomal | microcin M | Escherichia coli Nissle 1917

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000617.5 |  | 0.49 | ribosomal | coagulin | Bacillus coagulans
BGC0000558.5 |  | 0.49 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0002579.2 |  | 0.48 | ribosomal | carnobacteriocin XY | Carnobacterium maltaromaticum
BGC0000624.3 |  | 0.46 | ribosomal | salivaricin CRL1328 α peptide, salivaricin CRL1328 β peptide | Lactobacillus salivarius
BGC0000619.3 |  | 0.45 | ribosomal | gassericin T | Lactobacillus gasseri
BGC0001602.3 |  | 0.45 | ribosomal | gassericin-T | Lactobacillus gasseri
BGC0001388.3 |  | 0.45 | ribosomal | gassericin E | Lactobacillus gasseri
BGC0001862.4 |  | 0.45 | ribosomal | pallidocin | Aeribacillus pallidus
BGC0002577.2 |  | 0.44 | ribosomal | lactococcin G | Lactococcus lactis
BGC0000589.5 |  | 0.44 | ribosomal | microcin M | Escherichia coli Nissle 1917

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:
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 28.84 out of 29.38
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.40 out of 29.38
Confidence: medium
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 28.83 out of 32.74
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.17 out of 29.38
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.61 out of 27.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.70 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.06 out of 28.19
Confidence: medium
Additional weak hits (12):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.80 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 26.03 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.90 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.89 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.63 out of 26.06
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.35 out of 26.33
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.81 out of 39.62
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 25.38 out of 31.73
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.75 out of 30.98
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.24 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 23.26 out of 35.63
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.38 out of 23.43
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1 | Ferric Uptake Regulator
FuR variant 2 | Ferric Uptake Regulator
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_LN884295.1 - Region 2 - lanthipeptide-class-iii
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: 165,176 - 187,782 nt. (total: 22,607 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
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 | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002700.2 |  | 0.57 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000551.5 |  | 0.51 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000519.4 |  | 0.50 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000496.5 |  | 0.50 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002111.3 |  | 0.49 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000513.3 |  | 0.49 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000553.3 |  | 0.49 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0002701.2 |  | 0.45 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0000518.3 |  | 0.44 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000528.5 |  | 0.43 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002700.2 |  | 0.57 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000551.5 |  | 0.51 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000519.4 |  | 0.50 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000496.5 |  | 0.50 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002111.3 |  | 0.49 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000513.3 |  | 0.49 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000553.3 |  | 0.49 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0002701.2 |  | 0.45 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0000518.3 |  | 0.44 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000528.5 |  | 0.43 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

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

No significant matches found.

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

#### Lanthipeptide(s) for BN2762_RS01745

BN2762_RS27185
Leader:
MNAVLELQKLEHDTDDKD
Core:
Q A M I G L V S T V G P I K T I I T F T S T I K C
Core with dehydrations:
Q A M I G L V Dha Dhb V G P I K Dhb I I Dhb F Dhb Dha Dhb I K Cys

#### antiSMASH-DB 4.0 matches for BN2762_RS27185

100.0%
NZ_LN884295.1:
Lanthipeptides: BN2762_RS27185_lanthipeptide
1
Q A M I G L V S T V G P I K T I I T F T S T I K C
25
Q A M I G L V S T V G P I K T I I T F T S T I K C
1
Q A M I G L V S T V G P I K T I I T F T S T I K C
25
23.7%
NZ_CP084237.1:
Lanthipeptides: RES5_RS11640_lanthipeptide
4
I G L V S T V G P I K T I I T F T S T I K C
25
I G+ S V I T T ++ K C
11
I G I A S F V A T I P T G Y T A S A A F K C
32
15.2%
NZ_CP096019.1:
Lanthipeptides: MW046_RS07480_lanthipeptide
5
G L V S T V G P I K T I I T F T S T I K C
25
G V +V G + +++ F + K C
15
G P V V S V G Y M P S V M E F V T G Y K C
35

#### 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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.18 out of 27.78
Confidence: medium
Additional weak hits (1):
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.48 out of 29.65
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.

BN2762_RS27185 - Class III
  Cleavage pHMM score: -0.00
  RODEO score: 0
  Monoisotopic mass: 2495.5 Da
  Molecular weight: 2497.0 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2515.1 Da N = 1
    2533.1 Da N = 2
    2551.1 Da N = 3
    2569.1 Da N = 4
    2587.1 Da N = 5
    2605.2 Da N = 6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
ToxT | Regulator of MSHA biosynthesis

NZ_LN884296.1 - Region 1 - 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: 23,725 - 67,465 nt. (total: 43,741 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
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
Isomerases: isomerase
BN2762_RS02190: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
BN2762_RS02130: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN2762_RS02185: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

BN2762_RS02195: carbamoyl phosphate synthase small subunit

smcogs
  SMCOG1249: carbamoyl phosphate synthase small subunit

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

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002164.2 |  | 0.61 | NRPS | peramine | Epichloe festucae
BGC0001135.5 |  | 0.60 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0000357.5 |  | 0.60 | 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
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001240.4 |  | 0.60 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001261.3 |  | 0.60 | NRPS | AM-toxin | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002164.2 |  | 0.61 | NRPS | peramine | Epichloe festucae
BGC0001135.5 |  | 0.60 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0000357.5 |  | 0.60 | 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
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001240.4 |  | 0.60 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001261.3 |  | 0.60 | 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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.22 out of 18.57
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.87 out of 29.72
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.86 out of 18.57
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.94 out of 21.55
Confidence: medium
Additional weak hits (16):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.41 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.46 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.95 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.73 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.90 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.64 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.92 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.79 out of 31.73
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 21.88 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.72 out of 35.63
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.50 out of 24.78
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.47 out of 30.98
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.65 out of 22.40
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 21.39 out of 33.14
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 1, location 23724 - 67465:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BN2762_RS02130: Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (244..657): 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAASFDASVYDSILVIGGEVNAYGPTEATVVTTV
  Nearest Stachelhaus code(s):
    Leu DAWIVGAIVK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
NtrC | Nitrogen regulatory protein C
ToxT | Regulator of MSHA biosynthesis

NZ_LN884297.1 - Region 1 - proteusin
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: 268,851 - 289,096 nt. (total: 20,246 nt) Show pHMM detection rules used
proteusin: (PoyD or TIGR03793)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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: phosphotransferase
BN2762_RS04055: Glucose-specific phosphotransferase enzyme IIA

smcogs
  SMCOG1145: Glucose-specific phosphotransferase enzyme IIA

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 | proteusin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000908.3 |  | 0.39 | other (other) | melanin | Streptomyces avermitilis
BGC0001778.5 |  | 0.31 | other (other) | showdomycin | Streptomyces showdoensis
BGC0002496.3 |  | 0.30 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0001047.4 |  | 0.30 | NRPS, PKS | syringolin A | Pseudomonas syringae
BGC0000436.5 |  | 0.29 | NRPS | syringolin A | Rhizobium sp. AP16
BGC0002713.2 |  | 0.26 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0002443.3 |  | 0.26 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0001392.5 |  | 0.25 | ribosomal | pinensins | Chitinophaga pinensis DSM 2588
BGC0002122.2 |  | 0.24 | NRPS | gramicidin S | Aneurinibacillus migulanus
BGC0000905.5 |  | 0.23 | other (other) | heme D1 | Heliobacillus mobilis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000908.3 |  | 0.39 | other (other) | melanin | Streptomyces avermitilis
BGC0001778.5 |  | 0.31 | other (other) | showdomycin | Streptomyces showdoensis
BGC0002496.3 |  | 0.30 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0001047.4 |  | 0.30 | NRPS, PKS | syringolin A | Pseudomonas syringae
BGC0000436.5 |  | 0.29 | NRPS | syringolin A | Rhizobium sp. AP16
BGC0002713.2 |  | 0.26 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0002443.3 |  | 0.26 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0001392.5 |  | 0.25 | ribosomal | pinensins | Chitinophaga pinensis DSM 2588
BGC0002122.2 |  | 0.24 | NRPS | gramicidin S | Aneurinibacillus migulanus
BGC0000905.5 |  | 0.23 | other (other) | heme D1 | Heliobacillus mobilis

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

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:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 26.06 out of 26.06
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.56 out of 26.06
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 19.12 out of 20.97
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
Additional weak hits (5):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.54 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.49 out of 26.06
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.59 out of 39.62
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.98 out of 29.25
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
MogR | Repressor of flagellar motility genes

NZ_LN884298.1 - Region 1 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 561,587 - 619,458 nt. (total: 57,872 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
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
BN2762_RS07520: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

BN2762_RS07540: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BN2762_RS28135: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Hydrolases: hydrolase
BN2762_RS07515: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

BN2762_RS07550: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: cyclase
BN2762_RS07415: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Ligases: ligase synthase
BN2762_RS07475: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN2762_RS07480: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

BN2762_RS07490: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN2762_RS07495: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002075.3 |  |  | 0.85 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000426.5 |  |  | 0.81 | NRPS | sevadicin | Paenibacillus larvae
BGC0001833.4 |  |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  | 0.75 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4 |  |  | 0.72 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  |  | 0.72 | NRPS | enniatin | Fusarium equiseti
BGC0002286.3 |  |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000426.5 |  | 0.72 | NRPS | sevadicin | Paenibacillus larvae
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4 |  | 0.69 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.90 out of 26.06
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.55 out of 21.55
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.22 out of 18.57
Confidence: strong
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.56 out of 27.55
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.67 out of 32.93
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.69 out of 26.06
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.42 out of 25.88
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.82 out of 21.84
Confidence: medium
Additional weak hits (10):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.65 out of 29.38
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.05 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.08 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.08 out of 39.62
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.51 out of 30.25
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.26 out of 26.06
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.07 out of 32.93
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.81 out of 32.93
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 561586 - 619458:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (ohmal) + (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).
BN2762_RS07475: X
AMP-binding (470..871): 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:
    LAMSFDASVVEPISVSVGEINAYGPTEATVWVTD
  Nearest Stachelhaus code(s):
    S-bohPhe or Phe DALIVAAVCK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

BN2762_RS07480: mal
PKS_AT (546..836): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 175.2
  inactive: 128.6
  Methoxymalonyl-CoA: 68.4
  Methylmalonyl-CoA: 47.1
  Propionyl-CoA: 34.6
  Isobutyryl-CoA: 33.4
  Ethylmalonyl-CoA: 22.0
  CHC-CoA: 18.2
  Benzoyl-CoA: 15.8
  2-Methylbutyryl-CoA: 14.6
  fatty_acid: 11.9
  Acetyl-CoA: 5.2
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

BN2762_RS07490: X
AMP-binding (512..906): 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:
    AAAAFDASVLEAVLGSGGELNMYGPTEATIFATA
  Nearest Stachelhaus code(s):
    Val DALWMGGTFK (62% 8Å match)
    aIle DALVFGVVLK (56% 8Å match)
  Stachelhaus code match:
    60% (weak)

BN2762_RS07495: X
AMP-binding (481..874): X
nrpys: Tyr, bOH-Tyr

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    Polar aromatic ring (Tyr, bOH-Tyr)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    TARYFDAFLSCTDCTLGGEVDEYGPTENSIVTTL
  Nearest Stachelhaus code(s):
    Tyr DALTTGEVVK (59% 8Å match)
  Stachelhaus code match:
    70% (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
ArcA | Repressor of carbon oxidation
GnfM | Regulator of nitrogen-fixation genes
LexA variant 3 | Repressor of DNA damage response
MexT | Global virulence regulator
MogR | Repressor of flagellar motility genes
PsrA | Oleic acid responsive regulator
ToxT | Regulator of MSHA biosynthesis

NZ_LN884299.1 - Region 1 - 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: 157,797 - 180,850 nt. (total: 23,054 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
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lanthipeptides
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
BN2762_RS08695: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: protease
BN2762_RS08690: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

Lyases: cyclase
BN2762_RS08670: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Translocases: transporter
BN2762_RS08610: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000504.5 |  | 0.63 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000500.5 |  | 0.56 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0001210.5 |  | 0.55 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000527.5 |  | 0.52 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001555.4 |  | 0.52 | ribosomal | colicin V | Escherichia coli chi7122
BGC0002005.2 |  | 0.51 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0002698.2 |  | 0.50 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000502.5 |  | 0.50 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001407.5 |  | 0.50 | ribosomal | bicereucin | Bacillus cereus SJ1
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000504.5 |  | 0.63 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000500.5 |  | 0.56 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0001210.5 |  | 0.55 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000527.5 |  | 0.52 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001555.4 |  | 0.52 | ribosomal | colicin V | Escherichia coli chi7122
BGC0002005.2 |  | 0.51 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0002698.2 |  | 0.50 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000502.5 |  | 0.50 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001407.5 |  | 0.50 | ribosomal | bicereucin | Bacillus cereus SJ1
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli

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 BN2762_RS08670

BN2762_RS08660
Leader:
MTHEEIKLMNQSCGSGLKSLSMEEMQNIYGA
Core:
S D V D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
Core with dehydrations:
Dha D V D P R A Dhb P Dhb I V A Dha I I R Dha V A Q Dha Dha K V Cys I Dha A V G Dha A I Dha G I V Dha N N K N Cys L G

#### antiSMASH-DB 4.0 matches for BN2762_RS08660

100.0%
NZ_LN884299.1:
Lanthipeptides: BN2762_RS08660_lanthipeptide
1
S D V D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
46
S D V D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
1
S D V D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
46
71.7%
NZ_LWAG01000079.1:
Lanthipeptides: A4R27_RS25230_lanthipeptide
1
S D V D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
46
S D V D P R T P A+I S A+S S K+C I S A V G S A I G I V S N K N C G
1
S D V D P R W T P I A S A A I-N S A A R S S K I C I S A V G S A I G G I V S Y N K N C A G
45
65.2%
NZ_CP041405.1:
Lanthipeptides: FLT43_RS14400_lanthipeptide
1
S D V D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
46
S D V+P R A T P T I V +I +V S S K V C+S V S A I G I S+N +C L G
1
S D V E P R A T P T I V P A I S A A V R T S S K V C L S L V A S A I G G I A S H N N D C L G
46
with 59 more sequence matches
Only the first 10 are displayed here.
65.2%
NZ_CP094446.1:
Lanthipeptides: L3476_RS23825_lanthipeptide
1
S D V D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
46
S D V+P R T P A+I+ +V +S S K C I S A+G S A I S G I+S+N K+C L G
1
S D V E P R G T P---A T I V S A V T R S S K P C I S A I G S A I S G I I S H N K D C L G
43
60.9%
NZ_JACSNF010000005.1 and 1 other:
NZ_LMPR01000013.1 Lanthipeptides: ASF99_RS16390_lanthipeptide
Lanthipeptides: KNQ12_RS14665_lanthipeptide
1
S D V D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
46
S D V D P R T P +++ + R S+ +S+K C I A S A I S G I V S+N K+C L G
1
S D V D P R W T P-V I S L V A R S I V K S T K A C I G A G A S A I S G I V S H N K D C L G
45
56.5%
NZ_CP026035.1:
Lanthipeptides: C2H96_RS00305_lanthipeptide
1
S D V D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
46
+D D P R T P V++++ +V +S+++C I S +G S A I S G I V S+N K+C L G
1
A D A D P R W T P A-V S A V L S A V G R S T R L C I S G I G S A I S G I V S H N K D C L G
45
56.5%
NZ_JAMYJM010000002.1:
Lanthipeptides: NKE69_RS04880_lanthipeptide
4
D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
46
+P R T P T I++S S S K V C I S A V S I G I V S N +C L G
5
E P R W T P T P F--I L K S A T A S S K V C I S A V V S G I G G I V S Y N N D C L G
45
54.3%
NC_003028.3 and 39 others:
NC_003098.1 Lanthipeptides: SPR_RS08860_lanthipeptide NC_011900.1 Lanthipeptides: SPN23F_RS10045_lanthipeptide NC_012466.1 Lanthipeptides: SPJ_RS09630_lanthipeptide NZ_CFDV01000030.1 Lanthipeptides: AQB43_RS08315_lanthipeptide NZ_CFVJ01000005.1 Lanthipeptides: AP598_RS03270_lanthipeptide NZ_CGGJ01000006.1 Lanthipeptides: AP607_RS03210_lanthipeptide NZ_CHVQ01000007.1 Lanthipeptides: AQF85_RS04280_lanthipeptide NZ_CJZM01000008.1 Lanthipeptides: AEE29_RS04150_lanthipeptide NZ_CLHL01000007.1 Lanthipeptides: AE723_RS05755_lanthipeptide NZ_CMIW01000004.1 Lanthipeptides: AD046_RS04070_lanthipeptide NZ_CP035253.1 Lanthipeptides: EQH27_RS09735_lanthipeptide NZ_CP082820.1 Lanthipeptides: K8B76_RS08860_lanthipeptide NZ_CPRX01000013.1 Lanthipeptides: AEE77_RS05815_lanthipeptide NZ_CPTT01000011.1 Lanthipeptides: AEH42_RS06005_lanthipeptide NZ_CRAW01000006.1 Lanthipeptides: AK725_RS04390_lanthipeptide NZ_CRXO01000010.1 Lanthipeptides: AKU38_RS05255_lanthipeptide NZ_FCRW01000008.1 Lanthipeptides: A1N73_RS07430_lanthipeptide NZ_FDDE01000015.1 Lanthipeptides: A1A23_RS09710_lanthipeptide NZ_FDFR01000008.1 Lanthipeptides: A1O50_RS09315_lanthipeptide NZ_FDGF01000009.1 Lanthipeptides: A0899_RS06590_lanthipeptide NZ_FDQP01000009.1 Lanthipeptides: A1S42_RS08045_lanthipeptide NZ_FECM01000008.1 Lanthipeptides: A1930_RS06470_lanthipeptide NZ_FEEQ01000001.1 Lanthipeptides: A1T31_RS01150_lanthipeptide NZ_FEOS01000003.1 Lanthipeptides: A1178_RS03090_lanthipeptide NZ_FFTU01000009.1 Lanthipeptides: A1K37_RS06340_lanthipeptide NZ_FHRS02000028.1 Lanthipeptides: A1898_RS09825_lanthipeptide NZ_FIXQ01000010.1 Lanthipeptides: AZ721_RS04795_lanthipeptide NZ_FZDX01000018.1 Lanthipeptides: CFW91_RS09485_lanthipeptide NZ_FZEI01000008.1 Lanthipeptides: CFW58_RS06405_lanthipeptide NZ_JACVHZ010000010.1 Lanthipeptides: ICJ99_RS03885_lanthipeptide NZ_JAGFAE010000038.1 Lanthipeptides: J5E60_RS09010_lanthipeptide NZ_LR216014.1 Lanthipeptides: E0F05_RS09380_lanthipeptide NZ_LR216019.1 Lanthipeptides: E0E94_RS09630_lanthipeptide NZ_LR216027.1 Lanthipeptides: E0E81_RS09200_lanthipeptide NZ_LR216049.1 Lanthipeptides: E0E96_RS09535_lanthipeptide NZ_LR216064.1 Lanthipeptides: E0F31_RS09520_lanthipeptide NZ_LR536843.1 Lanthipeptides: E0F34_RS09595_lanthipeptide NZ_NANQ01000003.1 Lanthipeptides: B5K28_RS01930_lanthipeptide NZ_NAOJ01000022.1 Lanthipeptides: B5K31_RS08010_lanthipeptide
Lanthipeptides: SP_RS09790_lanthipeptide
4
D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
46
+P R T P T + I++S A S S K V C I S A S I G+V S N +C L G
5
E P R W T P T P I--I L K S A A A S S K V C I S A A V S G I G G L V S Y N N D C L G
45
54.3%
NZ_JALDUX010000010.1:
Lanthipeptides: M1F92_RS09530_lanthipeptide
4
D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
46
+P R T P T + I++S A S S K V C I S A+ S I G+V S N +C L G
5
E P R W T P T P L--I L K S A A A S S K V C I S A L V S G I G G L V S Y N N D C L G
45
54.3%
NZ_KB976303.1 and 1 other:
NZ_KB976303.1 Lanthipeptides: IGY_RS26035_lanthipeptide
Lanthipeptides: IGY_RS26045_lanthipeptide
1
S D V D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
46
S V D R P T+ I+ S A S S K C+S V S A I S G++S N K+C+G
1
S G V D T R T H P T V---I V V S R A-S S K A C M S G V-S A I S G L L S Y N K D C I G
41
52.2%
NZ_CP035244.1 and 3 others:
NZ_CPPE01000023.1 Lanthipeptides: AD654_RS06870_lanthipeptide NZ_FHJP02000011.1 Lanthipeptides: A1O79_RS07380_lanthipeptide NZ_LR216016.1 Lanthipeptides: E0F10_RS10155_lanthipeptide
Lanthipeptides: EQH36_RS09100_lanthipeptide
4
D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
46
+P R T P T + I++S A S S K+C I S A S I G+V S N +C L G
5
E P R W T P T P I--I L K S A A A S S K I C I S A A V S G I G G L V S Y N N D C L G
45
52.2%
NZ_KN125582.1:
Lanthipeptides: DJ91_RS27550_lanthipeptide
1
S D V D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
46
S V D R P T+ I+ S S+K C S + S A I S G+V S N K+C L G
1
S G V D T R T H P T V---I V V S R I S S A K-C A S T I-S A I S G L V S Y N K D C L G
41
52.2%
NZ_MRXY01000010.1:
Lanthipeptides: BTU63_RS06300_lanthipeptide
4
D P R A T P T I V A S I I R S V A Q S S K V C I S A V G S A I S G I V S N N K N C L G
46
+P T P T +I++S A+S S K V C I S A+ S I G I S N +C L G
5
E P L W T P T--P T I L K S A A R S S K V C I S A I I S G I G G I F S Y N N D C L G
45
BN2762_RS08665
Leader:
MNNSLEQSPVGKSLKSLPKEEMAAIFGG
Core:
T G M D A E V R S T L L C G M G I S F V A S Y L A S A A F K C G K D N K N
Core with dehydrations:
Dhb G M D A E V R Dha Dhb L L Cys G M G I Dha F V A Dha Y L A Dha A A F K Cys G K D N K N

#### antiSMASH-DB 4.0 matches for BN2762_RS08665

100.0%
NZ_LN884299.1:
Lanthipeptides: BN2762_RS08665_lanthipeptide
1
T G M D A E V R S T L L C G M G I S F V A S Y L A S A A F K C G K D N K N
37
T G M D A E V R S T L L C G M G I S F V A S Y L A S A A F K C G K D N K N
1
T G M D A E V R S T L L C G M G I S F V A S Y L A S A A F K C G K D N K N
37
81.1%
NZ_CP041405.1:
Lanthipeptides: FLT43_RS14405_lanthipeptide
1
T G M D A E V R S T L L C G M G I S F V A S Y L A S A A F K C G K D N K N
37
G M D E V R S+L+C G G I S+V A S Y L A S A A F K C G K N K N
1
N G M D V E V R S S L V C G A G I S Y V A S Y L A S A A F K C G K K N K N
37
76.3%
NZ_LWAG01000079.1:
Lanthipeptides: A4R27_RS25235_lanthipeptide
1
T G M D A E V R S T L L C G M G I S F V A S Y L A S A A F K C G K D N K
36
+G M D A E R S T L+C G G I S + S Y L A S A A F K C G K D N K
1
S G M D A E A R S T L I C G A G I S L I G S Y L A S A A F K C G K D N K
36
with 22 more sequence matches
Only the first 10 are displayed here.
75.7%
NZ_CP094446.1:
Lanthipeptides: L3476_RS23820_lanthipeptide
2
G M D A E V R S T L L C G M G I S F V A S Y L A S A A F K C G K D N K N
37
G M D E V R S T L+C G+G S F+ S Y L A S A A F K C G K N K
2
G M D V E V R S T L I C G V G A S F I G S Y L A S A A F K C G K K N K K
37
64.9%
NZ_CP026035.1:
Lanthipeptides: C2H96_RS00310_lanthipeptide
2
G M D A E V R S T L L C G M G I S F V A S Y L A S A A F K C G K D N K
36
G D A+V R S T +C G I S F+A+Y L S A A C G K D N K
2
G A D A D V R S T P I C S A G I S F I A T Y L G S A A T N C G K D N K
36
59.5%
NZ_JACSNF010000005.1 and 1 other:
NZ_LMPR01000013.1 Lanthipeptides: ASF99_RS16385_lanthipeptide
Lanthipeptides: KNQ12_RS14670_lanthipeptide
4
D A E V R S T L L C G M G I S F V A S Y L A S A A F K C G K D N K
36
D +V R S+L+C +S F V S Y L A S A K C G K D N K
3
D V D V R S S L V C S A L L S F V G S Y L A S A G L K C G K D N K
35
55.3%
NZ_CP084237.1:
Lanthipeptides: RES5_RS11640_lanthipeptide
4
D A E V R S T L L C G M G I S F V A S----Y L A S A A F K C G K D N K N
37
+ E+R T G+ S F V A+ Y A S A A F K C G K D N K
2
E V E L R G T P T I G I A-S F V A T I P T G Y T A S A A F K C G K D N K K
38
54.1%
NZ_JACSPZ010000014.1:
Lanthipeptides: H9635_RS18395_lanthipeptide
1
T G M D A E V R S T L L C G M G I S F V A S Y L A S A A F K C G K D N K
36
T G + + +S T L C S F+A S Y+ S A F K C G D N K
1
T G S E I Q P Q S T P L C----S F L A S Y I I S A Q F K C G G D N K
32
54.1%
NZ_NVMQ01000017.1:
Lanthipeptides: CON32_RS17790_lanthipeptide
1
T G M D A E V R S T L L C G M G I S F V A S Y L A S A A F K C G K D N K
36
+G+D + L S F V A S Y+A S A F K C G K D N K
1
S G V D P R T T P S P L L A---S F V A S Y I A S A E F K C G K D N K
33
51.4%
NC_003028.3 and 45 others:
NC_003098.1 Lanthipeptides: SPR_RS08865_lanthipeptide NC_011900.1 Lanthipeptides: SPN23F_RS10050_lanthipeptide NC_012466.1 Lanthipeptides: SPJ_RS09635_lanthipeptide NZ_CFDV01000030.1 Lanthipeptides: AQB43_RS08320_lanthipeptide NZ_CFVJ01000005.1 Lanthipeptides: AP598_RS03265_lanthipeptide NZ_CGGJ01000006.1 Lanthipeptides: AP607_RS03205_lanthipeptide NZ_CHVQ01000007.1 Lanthipeptides: AQF85_RS04285_lanthipeptide NZ_CJZM01000008.1 Lanthipeptides: AEE29_RS04155_lanthipeptide NZ_CLHL01000007.1 Lanthipeptides: AE723_RS05750_lanthipeptide NZ_CMIW01000004.1 Lanthipeptides: AD046_RS04075_lanthipeptide NZ_CMKL01000017.1 Lanthipeptides: AD734_RS09110_lanthipeptide NZ_CP035244.1 Lanthipeptides: EQH36_RS09105_lanthipeptide NZ_CP035253.1 Lanthipeptides: EQH27_RS09740_lanthipeptide NZ_CP082820.1 Lanthipeptides: K8B76_RS08865_lanthipeptide NZ_CPPE01000023.1 Lanthipeptides: AD654_RS06875_lanthipeptide NZ_CPRX01000013.1 Lanthipeptides: AEE77_RS05820_lanthipeptide NZ_CPTT01000011.1 Lanthipeptides: AEH42_RS06000_lanthipeptide NZ_CRAW01000006.1 Lanthipeptides: AK725_RS04395_lanthipeptide NZ_CRXO01000010.1 Lanthipeptides: AKU38_RS05260_lanthipeptide NZ_FCRW01000008.1 Lanthipeptides: A1N73_RS07425_lanthipeptide NZ_FDDE01000015.1 Lanthipeptides: A1A23_RS09705_lanthipeptide NZ_FDFR01000008.1 Lanthipeptides: A1O50_RS09320_lanthipeptide NZ_FDGF01000009.1 Lanthipeptides: A0899_RS06595_lanthipeptide NZ_FDQP01000009.1 Lanthipeptides: A1S42_RS08050_lanthipeptide NZ_FECM01000008.1 Lanthipeptides: A1930_RS06475_lanthipeptide NZ_FEEQ01000001.1 Lanthipeptides: A1T31_RS01145_lanthipeptide NZ_FEOS01000003.1 Lanthipeptides: A1178_RS03085_lanthipeptide NZ_FFTU01000009.1 Lanthipeptides: A1K37_RS06335_lanthipeptide NZ_FHJP02000011.1 Lanthipeptides: A1O79_RS07375_lanthipeptide NZ_FHRS02000028.1 Lanthipeptides: A1898_RS09820_lanthipeptide NZ_FIXQ01000010.1 Lanthipeptides: AZ721_RS04790_lanthipeptide NZ_FZDX01000018.1 Lanthipeptides: CFW91_RS09480_lanthipeptide NZ_FZEI01000008.1 Lanthipeptides: CFW58_RS06410_lanthipeptide NZ_JACVHZ010000010.1 Lanthipeptides: ICJ99_RS03880_lanthipeptide NZ_JAGFAE010000038.1 Lanthipeptides: J5E60_RS09005_lanthipeptide NZ_JALDUX010000010.1 Lanthipeptides: M1F92_RS09535_lanthipeptide NZ_JAMYJM010000002.1 Lanthipeptides: NKE69_RS04885_lanthipeptide NZ_LR216014.1 Lanthipeptides: E0F05_RS09385_lanthipeptide NZ_LR216016.1 Lanthipeptides: E0F10_RS10160_lanthipeptide NZ_LR216019.1 Lanthipeptides: E0E94_RS09635_lanthipeptide NZ_LR216027.1 Lanthipeptides: E0E81_RS09205_lanthipeptide NZ_LR216049.1 Lanthipeptides: E0E96_RS09540_lanthipeptide NZ_LR216064.1 Lanthipeptides: E0F31_RS09525_lanthipeptide NZ_LR536843.1 Lanthipeptides: E0F34_RS09600_lanthipeptide NZ_NANQ01000003.1 Lanthipeptides: B5K28_RS01935_lanthipeptide
Lanthipeptides: SP_RS09795_lanthipeptide
5
A E V R S T L L C G M G I S F V A S Y L A S A A F K C G K D N K
36
A+ R S T++C +S F+A S Y L S A +C G K D N K
4
A D P R S T I I C S A T L S F I A S Y L G S A Q T R C G K D N K
35
51.4%
NZ_FNYB01000021.1:
Lanthipeptides: BMZ34_RS24355_lanthipeptide
1
T G M D A E V R S T L L C G M G I S F V A S Y L A S A A F K C G K D N K
36
+G+D + L S F V A S Y+A S A F+C G K D N K
1
S G V D P R T T P S P L L A---S F V A S Y I A S A E F R C G K D N K
33
51.4%
NZ_KB976303.1:
Lanthipeptides: IGY_RS26050_lanthipeptide
1
T G M D A E V R S T L L C G M G I S F V A S Y L A S A A F K C G K D N K
36
+G+D + L S F V A S Y+A S A F+C G K D N K
1
S G V D P R T T P S P L L A---S F V A S Y I A S A Q F R C G K D N K
33
51.4%
NZ_NAOJ01000022.1:
Lanthipeptides: B5K31_RS08015_lanthipeptide
5
A E V R S T L L C G M G I S F V A S Y L A S A A F K C G K D N K
36
A+ R S T +C +S F+A S Y L S A +C G K D N K
4
A D P R S T T I C S A T L S F I A S Y L G S A Q T R C G K D N K
35

#### 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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.08 out of 23.79
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.01 out of 26.06
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.46 out of 24.78
Confidence: medium
Additional weak hits (2):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.76 out of 23.43
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.

BN2762_RS08660 - Class II
  Cleavage pHMM score: 3.00
  RODEO score: 0
  Monoisotopic mass: 4386.4 Da
  Molecular weight: 4389.0 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4407.0 Da N = 1
    4425.0 Da N = 2
    4443.0 Da N = 3
    4461.1 Da N = 4
    4479.1 Da N = 5
    4497.1 Da N = 6
    4515.1 Da N = 7
    4533.1 Da N = 8
    4551.2 Da N = 9
BN2762_RS08665 - Class II
  Cleavage pHMM score: 2.50
  RODEO score: 0
  Monoisotopic mass: 3746.8 Da
  Molecular weight: 3749.3 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3767.3 Da N = 1
    3785.3 Da N = 2
    3803.4 Da N = 3
    3821.4 Da N = 4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
LexA variant 2 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes

NZ_LN884299.1 - Region 2 - 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: 988,532 - 1,031,687 nt. (total: 43,156 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
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
Ligases: ligase
BN2762_RS12155: 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
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.65 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.64 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.65 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.64 | 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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
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
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.67 out of 20.97
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 22.16 out of 24.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.83 out of 28.19
Confidence: medium
Additional weak hits (9):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.06 out of 31.73
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 20.61 out of 30.11
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.34 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.34 out of 29.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.22 out of 28.14
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.70 out of 33.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.88 out of 29.65
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.68 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.95 out of 29.25
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 2, location 988531 - 1031687:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ile)

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).
BN2762_RS12155: Ile
Search NORINE for peptide: strict or relaxed
AMP-binding (468..863): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGASFDGSTFDNFMFFGGEYHIYGPTECTVYAAY
  Nearest Stachelhaus code(s):
    Ile DGFFFGVVYK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
LexA variant 2 | Repressor of DNA damage response
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_LN884299.1 - Region 3 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,617,329 - 1,638,183 nt. (total: 20,855 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
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: carboxylase
BN2762_RS14690: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Ligases: synthase synthetase
BN2762_RS14730: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

BN2762_RS14735: 1-deoxy-D-xylulose-5-phosphate synthase

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

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002284.3 |  | 0.38 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0001594.3 |  | 0.37 | other (other) | fischerindole L | Fischerella muscicola UTEX 1829
BGC0001501.5 |  | 0.36 | other (other) | ambiguine P | Fischerella sp. TAU
BGC0000666.5 |  | 0.36 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002284.3 |  | 0.38 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0001594.3 |  | 0.37 | other (other) | fischerindole L | Fischerella muscicola UTEX 1829
BGC0001501.5 |  | 0.36 | other (other) | ambiguine P | Fischerella sp. TAU
BGC0000666.5 |  | 0.36 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999

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

No significant matches found.

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

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

Genes with terpene domains:
BN2762_RS14730: PT_FPPS_like
Domain 1 (19 - 283): 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:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 23.25 out of 25.31
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.17 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.49 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.55 out of 27.78
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.50 out of 24.78
Confidence: medium
Additional weak hits (10):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.93 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.04 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.15 out of 21.55
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.88 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.28 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.53 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.78 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.84 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.21 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.73 out of 29.65
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
--- | ---
CatR | H2O2-responsive repressor
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
LexA variant 2 | Repressor of DNA damage response
RpoN | Regulator of nitrogen assimilation and virulence
ToxT | Regulator of MSHA biosynthesis

NZ_LN884299.1 - Region 4 - cyclic-lactone-autoinducer
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: 1,847,769 - 1,868,409 nt. (total: 20,641 nt) Show pHMM detection rules used
cyclic-lactone-autoinducer: (TIGR04223 or AgrB)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase oxygenase
BN2762_RS15840: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

BN2762_RS15845: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

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 | cyclic-lactone-autoinducer | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000558.5 |  | 0.42 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0000846.5 |  | 0.41 | other (other) | tabtoxin | Pseudomonas syringae
BGC0001940.3 |  | 0.39 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0001864.3 |  | 0.39 | ribosomal | listeriocytocin | Listeria monocytogenes SLCC2540
BGC0001684.3 |  | 0.37 | other (other) | N-acyloxyacyl glutamine | Klebsiella variicola
BGC0002289.2 |  | 0.37 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0002509.3 |  | 0.36 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | Streptomyces sp.
BGC0000632.5 |  | 0.36 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0002470.2 |  | 0.34 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000558.5 |  | 0.42 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0000846.5 |  | 0.41 | other (other) | tabtoxin | Pseudomonas syringae
BGC0001940.3 |  | 0.39 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0001864.3 |  | 0.39 | ribosomal | listeriocytocin | Listeria monocytogenes SLCC2540
BGC0001684.3 |  | 0.37 | other (other) | N-acyloxyacyl glutamine | Klebsiella variicola
BGC0002289.2 |  | 0.37 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0002509.3 |  | 0.36 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | Streptomyces sp.
BGC0000632.5 |  | 0.36 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0002470.2 |  | 0.34 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002

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: 18.57 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.54 out of 27.78
Confidence: medium
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 24.83 out of 28.14
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.06 out of 27.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.67 out of 28.19
Confidence: medium
Additional weak hits (13):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.25 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.78 out of 30.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 22.79 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.82 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.61 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.04 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.00 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.47 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.34 out of 26.06
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.43 out of 39.62
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 21.35 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 21.09 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 24.42 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
PerR | Peroxide regulator
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_LN884299.1 - Region 5 - NRPS,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: 2,125,276 - 2,215,578 nt. (total: 90,303 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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
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
BN2762_RS17110: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BN2762_RS17125: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BN2762_RS17295: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

BN2762_RS17360: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

BN2762_RS17395: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase kinase methyltransferase phosphotransferase
BN2762_RS17100: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

BN2762_RS17105: Glucose-specific phosphotransferase enzyme IIA

smcogs
  SMCOG1145: Glucose-specific phosphotransferase enzyme IIA

BN2762_RS17215: methyltransferase

smcogs
  SMCOG1089: methyltransferase

BN2762_RS17350: methyltransferase

smcogs
  SMCOG1089: methyltransferase

BN2762_RS17370: Chloramphenicol acetyltransferase

smcogs
  SMCOG1156: Chloramphenicol acetyltransferase

Hydrolases: peptidase
BN2762_RS17340: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Lyases: dehydratase
BN2762_RS17380: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
BN2762_RS17135: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN2762_RS17305: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

BN2762_RS17310: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN2762_RS17320: 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 | T3PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001132.4 |  |  |  | 1.08 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  | 1.04 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  |  | 1.04 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  |  | 1.03 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  |  |  | 1.02 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  |  | 1.00 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  |  |  | 0.99 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000342.4 |  |  |  | 0.99 | NRPS | enniatin | Fusarium equiseti
BGC0002075.3 |  |  |  | 0.98 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001758.4 |  |  |  | 0.97 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001132.4 |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
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 |  | 0.71 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0002135.2 |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.70 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.21 out of 27.78
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.63 out of 18.46
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.68 out of 27.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.30 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.48 out of 28.19
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.15 out of 24.78
Confidence: medium
Additional weak hits (20):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.99 out of 20.01
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.23 out of 33.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.04 out of 31.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.19 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.32 out of 29.38
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.71 out of 33.73
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.96 out of 30.22
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.17 out of 32.74
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 28.27 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.06 out of 29.38
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.66 out of 25.75
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.40 out of 31.73
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.64 out of 24.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.73 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.96 out of 29.25
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.50 out of 32.93
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 25.24 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.41 out of 29.65
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.58 out of 28.14
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.33 out of 27.18
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 5, location 2125275 - 2215578:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 2125275 - 2169544:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Asp)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 2161391 - 2202546:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 8, location 2162732 - 2215578:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-X - Val) + (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).
BN2762_RS17135: Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (568..968): 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:
    YGVQVDSCQTVPKIILGGEYNHYGPTETTVGIST
  Nearest Stachelhaus code(s):
    Asp DLTKIGHVGK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

BN2762_RS17310: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (25..418): 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:
    LNCGFDASTFEGFLLVGGEMNGYGPTENTTFSTV
  Nearest Stachelhaus code(s):
    Ile DAFFLGITFK (88% 8Å match)
    Val DAFWLGGTFK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

BN2762_RS17320: X - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (254..663): 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:
    LYLAFDASVYEGMLVSAGELNAYGPTEVTIICSV
  Nearest Stachelhaus code(s):
    Phe DAWTVAAICK (65% 8Å match)
    Ph-Ser or Phe DAFTVAAIWK (62% 8Å match)
    Val DAWMFAAILK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1782..2190): 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:
    LHTGFDASTFEGWLLVGGELNVYGPTENTTFSTS
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (85% 8Å match)
    Ile DAFFLGVTFK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
LexA variant 2 | Repressor of DNA damage response
RpoN | Regulator of nitrogen assimilation and virulence
ZuR variant 1 | Zinc-responsive repressor

NZ_LN884299.1 - Region 6 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,315,911 - 2,426,579 nt. (total: 110,669 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
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: synthase
BN2762_RS17860: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

Hydrolases: esterase synthase
BN2762_RS17860: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

BN2762_RS17950: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: cyclase
BN2762_RS17855: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Ligases: ligase
BN2762_RS17915: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN2762_RS17920: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN2762_RS17925: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN2762_RS17935: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN2762_RS17940: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN2762_RS17945: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001133.4 |  | 0.73 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001641.4 |  | 0.73 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001133.4 |  | 0.73 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001641.4 |  | 0.73 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

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

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:
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 26.99 out of 29.38
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.22 out of 18.57
Confidence: strong
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.19 out of 29.38
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.95 out of 29.38
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.84 out of 29.38
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.86 out of 29.38
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.59 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.46 out of 27.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 24.23 out of 28.19
Confidence: medium
Additional weak hits (20):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 25.99 out of 32.74
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.35 out of 29.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.02 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.21 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.55 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.51 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.42 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.88 out of 28.14
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 25.77 out of 36.54
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.61 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.41 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.88 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.12 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.74 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.31 out of 31.73
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 24.73 out of 30.97
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.13 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 22.52 out of 36.54
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 24.24 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.70 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 9, location 2315910 - 2426579:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid - Thr - D-Ala) + (Val - Leu - Tyr - D-Leu) + (Leu - Val - D-X) + (Leu - Ala - D-Thr) + (Val - X - D-Ala) + (Orn - Ala - 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).
BN2762_RS17915: Orn - Ala - X
Search NORINE for peptide: strict or relaxed
AMP-binding (469..871): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AAWAFDVFAGDRESILGSDINSYGVTEACIDSSY
  Nearest Stachelhaus code(s):
    Orn DVGEIGSIDK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1518..1913): 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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    VSLTFDVSVTEGNFLIAGEENIYGPTEGTIYATK
  Nearest Stachelhaus code(s):
    Ala DVANFAIIYK (82% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2559..2950): X
nrpys: Asp, Asn, Glu, Gln, Aad

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:
    LWFTFDVSVLEVQFISGGDFNHYGPTETTVDVLH
  Nearest Stachelhaus code(s):
    Orn DVGEIGSVDK (38% 8Å match)
  Stachelhaus code match:
    70% (weak)

BN2762_RS17920: Val - X - Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (473..869): 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:
    LNTGFDASTLEGFLMVGGDVNGYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Val DALWMGGTFK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1521..1923): X
nrpys: Ile, Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNTGFDASTLEGFLMVGGDLNVYGPTENTTFSTS
  Nearest Stachelhaus code(s):
    Leu or Ile DALFMGATFK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2575..2970): 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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    IALTFDVSVSEGNFFVAGEENIYGPTEGTIYATR
  Nearest Stachelhaus code(s):
    Ala DVANFAIIYK (88% 8Å match)
  Stachelhaus code match:
    90% (moderate)

BN2762_RS17925: Leu - Ala - Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (470..858): 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:
    LWHAFDASVWEPFLLTGGEVNNYGPTESTVVATS
  Nearest Stachelhaus code(s):
    Leu DAWFLGNVVK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1502..1897): 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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    IALTFDVSVSEGNFFVAGEENIYGPTEGTIYATR
  Nearest Stachelhaus code(s):
    Ala DVANFAIIYK (88% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2541..2940): 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:
    LASHFDFSVWEGNIIFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

BN2762_RS17935: Leu - Val - X
Search NORINE for peptide: strict or relaxed
AMP-binding (465..885): 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:
    LWHAFDASVWEPFLLTGGDVNNYGPTENTVVTTS
  Nearest Stachelhaus code(s):
    Leu DAWFLGNVVK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1549..1942): 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:
    LATGFDASTFEGWLIVGGEVNGYGPTENTTFSTY
  Nearest Stachelhaus code(s):
    Val DAFWIGGTFK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2604..2993): X
nrpys: Asp, Asn, Glu, Gln, Aad

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:
    LWFTFDVVIEEGQFICGGEFNHYGPTETTVDALR
  Nearest Stachelhaus code(s):
    Trp DVSQIGAVCK (59% 8Å match)
    Lys or Arg DVEDIGSVAK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

BN2762_RS17940: Val - Leu - Tyr - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (472..865): 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:
    LATGFDASTFEGWLIVGGEVNGYGPTENTTFSTY
  Nearest Stachelhaus code(s):
    Val DAFWIGGTFK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1533..1953): 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:
    LWHAFDASVWEPFLLTGGDVNNYGPTENTVVTTS
  Nearest Stachelhaus code(s):
    Leu DAWFLGNVVK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2622..3028): 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:
    tyr (Tyr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    AWRFFDGFVLSTICTLAGDVNEYGPTENSVVASC
  Nearest Stachelhaus code(s):
    Tyr DGTITAEVAK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (3674..4094): 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:
    LWHAFDASVWEPFLLTGGDVNNYGPTENTVVTTS
  Nearest Stachelhaus code(s):
    Leu DAWFLGNVVK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

BN2762_RS17945: fatty_acid - Thr - Ala
Search NORINE for peptide: strict or relaxed
CAL_domain (256..564): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 29.4
  AHBA: 14.8
  Acetyl-CoA: 9.3
  shikimic_acid: 0.0
  NH2: 0.0

AMP-binding (1792..2191): 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:
    LNDHFDFSVWEGNQIFGGEINMYGITETAVHVTF
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2865..3263): 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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LALTFDVSVTEGNFFVAGEENIYGPTEVTVYATK
  Nearest Stachelhaus code(s):
    Ala DVANFAIIYK (85% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1 | Ferric Uptake Regulator
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_LN884299.1 - Region 7 - 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: 2,749,140 - 2,801,501 nt. (total: 52,362 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
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
BN2762_RS19645: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase methyltransferase
BN2762_RS19670: methyltransferase

smcogs
  SMCOG1248: methyltransferase

BN2762_RS19675: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: dehalogenase hydrolase
BN2762_RS19585: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

BN2762_RS19630: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Isomerases: isomerase
BN2762_RS19640: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase
BN2762_RS19625: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN2762_RS26240: 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
--- | --- | --- | --- | --- | --- | ---
BGC0000401.5 |  |  | 1.06 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0001185.5 |  |  | 1.01 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0000309.5 |  |  | 1.01 | NRPS | bacillibactin | Bacillus subtilis subsp. subtilis str. 168
BGC0002075.3 |  |  | 0.87 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000343.5 |  |  | 0.87 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001132.4 |  |  | 0.78 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  | 0.75 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000401.5 |  | 0.80 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0001185.5 |  | 0.79 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0000309.5 |  | 0.79 | NRPS | bacillibactin | Bacillus subtilis subsp. subtilis str. 168
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000343.5 |  | 0.74 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.69 | 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.
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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.59 out of 18.57
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.13 out of 23.79
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 29.38 out of 29.38
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.84 out of 27.78
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.22 out of 29.38
Confidence: medium
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 28.01 out of 32.74
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.99 out of 29.38
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.86 out of 18.57
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 25.16 out of 28.19
Confidence: strong
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 28.19
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.79 out of 25.31
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (33):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.22 out of 26.06
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 25.12 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.15 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 20.68 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.72 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.83 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.96 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.72 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.93 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.00 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.46 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.27 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.80 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.80 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.01 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.71 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.52 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.07 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.54 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.31 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.89 out of 30.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.71 out of 29.65
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.19 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.45 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.86 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.24 out of 26.06
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.60 out of 30.98
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.22 out of 28.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 25.52 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.99 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 10, location 2749139 - 2801501:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ala - 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).
BN2762_RS19625: Ala - Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (466..868): Ala
nrpys: Ala

SVM prediction details:
  Predicted physicochemical class:
    N/A
  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:
    LDMTFDISVLELQAIAGGENNQYGPTETTIYSTA
  Nearest Stachelhaus code(s):
    Ala DILQIGQIYK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1556..1972): 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:
    LATHFDFSVWEGNQIFGGEINMYGITETTVHVSY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

BN2762_RS26240: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (31..526): 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:
    SLSLYPLSSPGGALQVGGAQQVFGMAEGLVNYTR
  Nearest Stachelhaus code(s):
    diOH-Bz PLPAQGVVNK (97% 8Å match)
    diOH-Bz or Sal PLPAQGVVNK (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
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CatR | H2O2-responsive repressor
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1 | Ferric Uptake Regulator
FuR variant 2 | Ferric Uptake Regulator
IolR | Regulator of the inositol catabolism
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_LN884299.1 - Region 8 - ranthipeptide
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: 2,821,946 - 2,843,364 nt. (total: 21,419 nt) Show pHMM detection rules used
ranthipeptide: (TIGR03973 or SCIFF or (cds(PF04055 and (TIGR04085 or SPASM)) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]) and not (TIGR01716 or subtilosin or TIGR02111 or TIGR03966 or TIGR04103 or (YcaO or TIGR03604))))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acetyltransferase methyltransferase
BN2762_RS19835: methyltransferase

smcogs
  SMCOG1089: methyltransferase

BN2762_RS19885: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

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

Reference | ranthipeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002306.2 |  | 0.50 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000521.3 |  | 0.44 | ribosomal | lacticin 481 | Lactococcus lactis subsp. lactis
BGC0000539.5 |  | 0.44 | ribosomal | nukacin ISK-1 | Staphylococcus warneri
BGC0001787.3 |  | 0.42 | ribosomal | suicin 3908 | Streptococcus suis
BGC0000563.4 |  | 0.42 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001210.5 |  | 0.41 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000547.5 |  | 0.41 | ribosomal | salivaricin 9 | Streptococcus salivarius
BGC0002700.2 |  | 0.41 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0002005.2 |  | 0.40 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0000626.3 |  | 0.40 | ribosomal | thuricin | Bacillus thuringiensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002306.2 |  | 0.50 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000521.3 |  | 0.44 | ribosomal | lacticin 481 | Lactococcus lactis subsp. lactis
BGC0000539.5 |  | 0.44 | ribosomal | nukacin ISK-1 | Staphylococcus warneri
BGC0001787.3 |  | 0.42 | ribosomal | suicin 3908 | Streptococcus suis
BGC0000563.4 |  | 0.42 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001210.5 |  | 0.41 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000547.5 |  | 0.41 | ribosomal | salivaricin 9 | Streptococcus salivarius
BGC0002700.2 |  | 0.41 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0002005.2 |  | 0.40 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0000626.3 |  | 0.40 | ribosomal | thuricin | Bacillus thuringiensis

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: 18.15 out of 18.46
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.91 out of 26.06
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.16 out of 20.97
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.10 out of 27.78
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.82 out of 21.84
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.53 out of 28.19
Confidence: medium
Additional weak hits (2):
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 19.59 out of 30.12
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 19.72 out of 30.11
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

ranthipeptide protocluster (2821945...2843364)
BN2762_RS19855
  RRE type: Other_Sactipeptide_rSAM_RRE
  Location: 4 - 110
  Score: 37.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
MexT | Global virulence regulator
MogR | Repressor of flagellar motility genes
RpoN | Regulator of nitrogen assimilation and virulence
ZuR variant 1 | Zinc-responsive repressor

NZ_LN884299.1 - Region 9 - NRPS,betalactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,903,119 - 2,967,574 nt. (total: 64,456 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
betalactone: (HMGL-like and AMP-binding)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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 reductase
BN2762_RS20345: alkyl hydroperoxide reductase/ Thiol specific

smcogs
  SMCOG1196: alkyl hydroperoxide reductase/ Thiol specific

BN2762_RS20400: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

Transferases: aminotransferase
BN2762_RS20330: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: hydrolase
BN2762_RS20210: hydrolase

smcogs
  SMCOG1179: hydrolase

Ligases: ligase synthase
BN2762_RS20215: Pseudouridine synthase

smcogs
  SMCOG1154: Pseudouridine synthase

BN2762_RS20255: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

BN2762_RS20305: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN2762_RS20310: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN2762_RS20315: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN2762_RS20320: 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 | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000342.4 |  |  | 0.70 | NRPS | enniatin | Fusarium equiseti
BGC0001261.3 |  |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  |  | 0.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  |  | 0.64 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000307.4 |  |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2 |  | 0.66 | NRPS | peramine | Epichloe festucae
BGC0000307.4 |  | 0.66 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001240.4 |  | 0.66 | 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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.14 out of 29.38
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.70 out of 29.38
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.33 out of 24.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.38 out of 26.06
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.59 out of 28.19
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.24 out of 26.06
Confidence: medium
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 26.71 out of 33.14
Confidence: medium
Additional weak hits (20):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.60 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.15 out of 26.06
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.38 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.04 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.39 out of 28.14
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.48 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.83 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.77 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 27.14 out of 31.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.00 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.05 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.28 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.29 out of 28.14
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.80 out of 30.97
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.56 out of 36.53
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 22.49 out of 36.54
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.68 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.22 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 21.22 out of 33.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.97 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 12, location 2903118 - 2967574:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ile - D-X) + (D-Ser) + (Thr - D-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).
BN2762_RS20305: Thr - Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (468..866): 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:
    LNSHFDFSVWEGNQIFGGEINMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1510..1896): 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:
    LVSSFDASVWEMTLVTGGEINAYGPTEATVCSTL
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

BN2762_RS20310: Dab - X - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (261..671): Dab
nrpys: Dab

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TGYAFDVFVGDRESITSSDINSYGVTEAAIDSSL
  Nearest Stachelhaus code(s):
    Dab DVGEISSIDK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (792..1011): 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:
    SALDMDASCQELHLTTNSRSVLYGAAGALIHAYY
  Nearest Stachelhaus code(s):
    Thr DAYNTGLIHK (32% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1580..1982): 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:
    RWMTFDVSVWEMHFFTSGEYNLYGPTEATIDVSY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLIDK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

BN2762_RS20320: Ile - X
Search NORINE for peptide: strict or relaxed
AMP-binding (252..648): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TNCSFDGSTFDGFILFGGEIHVYGPTETTVFATY
  Nearest Stachelhaus code(s):
    Ile DGFFLGVVFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1291..1674): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FIAAFDASVCEHILVTAGEVNGYGPTEATVGATL
  Nearest Stachelhaus code(s):
    Tyr DASTVAGVCK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
FuR variant 1 | Ferric Uptake Regulator
LexA variant 2 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor
ZuR variant 2 | Zinc-responsive repressor

NZ_LN884299.1 - Region 10 - 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: 3,686,768 - 3,709,158 nt. (total: 22,391 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
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
BN2762_RS23835: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Ligases: synthetase
BN2762_RS23805: 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
--- | --- | --- | --- | --- | ---
BGC0000643.3 |  | 0.35 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000664.5 |  | 0.31 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000452.5 |  | 0.29 | NRPS | tyrocidine | Brevibacillus brevis NBRC 100599
BGC0000864.3 |  | 0.22 | other (other) | eicosapentaenoic acid-like compound | Moritella marina ATCC 15381
BGC0000106.5 |  | 0.21 | PKS | naphthomycin A | Streptomyces sp. CS
BGC0001287.5 |  | 0.20 | PKS | chaxamycin A, chaxamycin B, chaxamycin C, chaxamycin D | Streptomyces leeuwenhoekii
BGC0001785.5 |  | 0.19 | PKS | streptovaricin | Streptomyces spectabilis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000643.3 |  | 0.35 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000664.5 |  | 0.31 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000452.5 |  | 0.29 | NRPS | tyrocidine | Brevibacillus brevis NBRC 100599
BGC0000864.3 |  | 0.22 | other (other) | eicosapentaenoic acid-like compound | Moritella marina ATCC 15381
BGC0000106.5 |  | 0.21 | PKS | naphthomycin A | Streptomyces sp. CS
BGC0001287.5 |  | 0.20 | PKS | chaxamycin A, chaxamycin B, chaxamycin C, chaxamycin D | Streptomyces leeuwenhoekii
BGC0001785.5 |  | 0.19 | PKS | streptovaricin | Streptomyces spectabilis

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:
BN2762_RS23805: PT_FPPS_like
Domain 1 (538 - 758): 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:
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.53 out of 28.19
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
Additional weak hits (5):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.58 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.42 out of 28.14
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.24 out of 36.54
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.13 out of 30.97
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.37 out of 33.14
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
ZuR variant 1 | Zinc-responsive repressor