Select genomic region:
Overview
7.1
7.2
9.1
12.1
14.1

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

NZ_VEDP01000001.1 (Enterococcus casseliflavus)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 7.1 | terpene | 568,204 | 589,127 |
Region 7.2 | terpene-precursor | 628,359 | 649,255 |

NZ_VEDP01000003.1 (Enterococcus casseliflavus)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 9.1 | lanthipeptide-class-i | 255,337 | 279,558 |

NZ_VEDP01000006.1 (Enterococcus casseliflavus)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 12.1 | ranthipeptide | 1 | 20,459 |

NZ_VEDP01000008.1 (Enterococcus casseliflavus)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 14.1 | T3PKS | 1 | 38,901 |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 7.1 | terpene | 568,204 | 589,127 |
Region 7.2 | terpene-precursor | 628,359 | 649,255 |
Region 9.1 | lanthipeptide-class-i | 255,337 | 279,558 |
Region 12.1 | ranthipeptide | 1 | 20,459 |
Region 14.1 | T3PKS | 1 | 38,901 |

No secondary metabolite regions were found in these records:
  NZ_VEDP01000010.1 (Enterococcus casseliflavus)
  NZ_VEDP01000011.1 (Enterococcus casseliflavus)
  NZ_VEDP01000012.1 (Enterococcus casseliflavus)
  NZ_VEDP01000013.1 (Enterococcus casseliflavus)
  NZ_VEDP01000014.1 (Enterococcus casseliflavus)
  NZ_VEDP01000015.1 (Enterococcus casseliflavus)
  NZ_VEDP01000002.1 (Enterococcus casseliflavus)
  NZ_VEDP01000004.1 (Enterococcus casseliflavus)
  NZ_VEDP01000005.1 (Enterococcus casseliflavus)
  NZ_VEDP01000007.1 (Enterococcus casseliflavus)
  NZ_VEDP01000009.1 (Enterococcus casseliflavus)

Compact view
NZ_VEDP01000001.1 - Region 1 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 568,204 - 589,127 nt. (total: 20,924 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
FS693_RS02595: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: kinase phosphotransferase
FS693_RS02575: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

FS693_RS02625: 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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000647.3 |  | 0.76 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000645.3 |  | 0.49 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000664.5 |  | 0.48 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000630.3 |  | 0.48 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0001456.3 |  | 0.48 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000656.5 |  | 0.47 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000635.3 |  | 0.47 | terpene | carotenoid | Paracoccus sp. N81106
BGC0000633.3 |  | 0.46 | terpene | carotenoid | Streptomyces avermitilis
BGC0000642.3 |  | 0.46 | terpene | carotenoid | Enterobacteriaceae bacterium DC413

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000647.3 |  | 0.76 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000645.3 |  | 0.49 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000664.5 |  | 0.48 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000630.3 |  | 0.48 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0001456.3 |  | 0.48 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000656.5 |  | 0.47 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000635.3 |  | 0.47 | terpene | carotenoid | Paracoccus sp. N81106
BGC0000633.3 |  | 0.46 | terpene | carotenoid | Streptomyces avermitilis
BGC0000642.3 |  | 0.46 | terpene | carotenoid | Enterobacteriaceae bacterium DC413

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

No significant matches found.

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
triterpene | C30 carotenoid | diapophytoene | C30 | acyclic | none

Genes with terpene domains:
FS693_RS02590: PT_phytoene_like
Domain 1 (14 - 302): Prenyltransferase; Phytoene synthase like
Subtype: Diapophytoene synthase

Reactions:
  FPP → diapophytoene

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:
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 24.02 out of 30.25
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.08 out of 23.79
Confidence: medium
Additional weak hits (2):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.68 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.04 out of 30.25
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ColR | Phenol-responsive regulator
IolR | Regulator of the inositol catabolism

NZ_VEDP01000001.1 - Region 2 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 628,359 - 649,255 nt. (total: 20,897 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
Hydrolases: peptidase
FS693_RS02895: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Ligases: synthetase
FS693_RS02925: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000558.5 |  | 0.43 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0001962.3 |  | 0.40 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0001743.3 |  | 0.39 | ribosomal | plantaricyclin | Lactobacillus plantarum
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000639.3 |  | 0.38 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000641.3 |  | 0.38 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000634.3 |  | 0.37 | terpene | carotenoid | Brevundimonas sp. SD212

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000558.5 |  | 0.43 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0001962.3 |  | 0.40 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0001743.3 |  | 0.39 | ribosomal | plantaricyclin | Lactobacillus plantarum
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000639.3 |  | 0.38 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000641.3 |  | 0.38 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000634.3 |  | 0.37 | terpene | carotenoid | Brevundimonas sp. SD212

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
FS693_RS02925: PT_FPPS_like
Domain 1 (32 - 276): 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:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 23.90 out of 29.25
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 24.77 out of 27.78
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.31 out of 27.78
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.38 out of 25.88
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.76 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.94 out of 27.78
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.84 out of 29.38
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.02 out of 21.55
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.42 out of 25.88
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.38 out of 28.19
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.37 out of 24.78
Confidence: medium
Additional weak hits (3):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.83 out of 26.12
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.13 out of 25.88
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.62 out of 29.25
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
--- | ---
ArcA | Repressor of carbon oxidation
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1 | Ferric Uptake Regulator
LexA variant 2 | Repressor of DNA damage response
PsrA | Oleic acid responsive regulator
RpoN | Regulator of nitrogen assimilation and virulence
SypG | Regulator of biofilm formation and host colonization
ZuR variant 1 | Zinc-responsive repressor

NZ_VEDP01000003.1 - Region 1 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 255,337 - 279,558 nt. (total: 24,222 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase dehydratase
FS693_RS10075: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

FS693_RS10080: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

Ligases: synthase
FS693_RS10100: 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 | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001289.5 |  | 0.50 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000538.3 |  | 0.48 | ribosomal | nisin Z | Lactococcus lactis
BGC0000542.3 |  | 0.46 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.46 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000556.5 |  | 0.46 | ribosomal | streptin | Streptococcus pyogenes
BGC0000515.4 |  | 0.45 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0000506.4 |  | 0.45 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0001727.3 |  | 0.44 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000559.4 |  | 0.44 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000535.4 |  | 0.43 | ribosomal | nisin A | Lactococcus lactis subsp. lactis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001289.5 |  | 0.50 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000538.3 |  | 0.48 | ribosomal | nisin Z | Lactococcus lactis
BGC0000542.3 |  | 0.46 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.46 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000556.5 |  | 0.46 | ribosomal | streptin | Streptococcus pyogenes
BGC0000515.4 |  | 0.45 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0000506.4 |  | 0.45 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0001727.3 |  | 0.44 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000559.4 |  | 0.44 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000535.4 |  | 0.43 | ribosomal | nisin A | Lactococcus lactis subsp. lactis

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 FS693_RS10075

FS693_RS10090
Leader:
MDKLFDLDVEVVKTNTQARSG
Core:
I G T L G V Y C F T T G Q G V M C S S G A G S H S C M T S A T R C T G T Q S A C A I L P S S L K K
Core with dehydrations:
I G Dhb L G V Y Cys F Dhb Dhb G Q G V M Cys Dha Dha G A G Dha H Dha Cys M Dhb Dha A Dhb R Cys Dhb G Dhb Q Dha A Cys A I L P Dha Dha L K K

#### antiSMASH-DB 4.0 matches for FS693_RS10090

100.0%
NZ_KE350253.1 and 1 other:
NZ_VEDP01000003.1 Lanthipeptides: FS693_RS10090_lanthipeptide
Lanthipeptides: D932_RS16685_lanthipeptide
1
I G T L G V Y C F T T G Q G V M C S S G A G S H S C M T S A T R C T G T Q S A C A I L P S S L K K
49
I G T L G V Y C F T T G Q G V M C S S G A G S H S C M T S A T R C T G T Q S A C A I L P S S L K K
1
I G T L G V Y C F T T G Q G V M C S S G A G S H S C M T S A T R C T G T Q S A C A I L P S S L K K
49
18.4%
NC_005071.1:
Lanthipeptides: AKG35_RS01305_lanthipeptide
12
G Q G V M C S S G A G S H S C M T S A T R C T G T Q S A C A I
42
G G V+C +G +T + T A I
5
G N G V L C F T G T E E I D A I T D G R K K T D F M K A K R I
35
17.6%
NZ_KB903814.1:
Lanthipeptides: allorf_854978_855211_lanthipeptide
8
C F T T G Q G V M C S S G A G S H S C M T S
29
C F G C S S G C++S
4
C F P R N H G Q R C S S G H S M P K C L S S
25
with 1 more sequence matches
13.0%
NZ_CABY01000005.1:
Lanthipeptides: SZBHS5_RS06435_lanthipeptide
2
G T L G V Y C F T T G Q
13
G G V Y C+ T G+
9
G G T G V Y C W N T G K
20

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 25.42 out of 26.06
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.58 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.11 out of 26.06
Confidence: medium
Additional weak hits (4):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.18 out of 29.25
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.14 out of 22.40
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.52 out of 19.52
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.15 out of 25.88
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

FS693_RS10090 - Class I
  Cleavage pHMM score: 3.20
  RODEO score: 22
  Monoisotopic mass: 4588.2 Da
  Molecular weight: 4591.3 Da
  Number of bridges: 5
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4609.3 Da N = 1
    4627.3 Da N = 2
    4645.3 Da N = 3
    4663.4 Da N = 4
    4681.4 Da N = 5
    4699.4 Da N = 6
    4717.4 Da N = 7
    4735.4 Da N = 8
    4753.5 Da N = 9
    4771.5 Da N = 10

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (255336...279558)
FS693_RS10075
  RRE type: Lanthipeptide_LanB_RRE
  Location: 160 - 228
  Score: 25.5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis

NZ_VEDP01000006.1 - Region 1 - 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: 1 - 20,459 nt. (total: 20,459 nt) Show pHMM detection rules used
Region on contig edge.
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
Translocases: transporter
FS693_RS14225: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

FS693_RS14270: 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 | ranthipeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002285.2 |  | 0.41 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000916.5 |  | 0.40 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0001364.3 |  | 0.36 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0000495.5 |  | 0.36 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0002754.2 |  | 0.29 | NRPS | hectoramide B | Moorena producens JHB
BGC0000268.5 |  | 0.28 | PKS | Sch-47554, Sch-47555 | Streptomyces sp. SCC 2136
BGC0001011.5 |  | 0.27 | NRPS, PKS | meridamycin | Streptomyces sp. NRRL 30748
BGC0001093.3 |  | 0.26 | NRPS, PKS | disorazol A | Sorangium cellulosum
BGC0002657.2 |  | 0.26 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis
BGC0000388.5 |  | 0.26 | NRPS | mannopeptimycin | Streptomyces hygroscopicus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002285.2 |  | 0.41 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000916.5 |  | 0.40 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0001364.3 |  | 0.36 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0000495.5 |  | 0.36 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0002754.2 |  | 0.29 | NRPS | hectoramide B | Moorena producens JHB
BGC0000268.5 |  | 0.28 | PKS | Sch-47554, Sch-47555 | Streptomyces sp. SCC 2136
BGC0001011.5 |  | 0.27 | NRPS, PKS | meridamycin | Streptomyces sp. NRRL 30748
BGC0001093.3 |  | 0.26 | NRPS, PKS | disorazol A | Sorangium cellulosum
BGC0002657.2 |  | 0.26 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis
BGC0000388.5 |  | 0.26 | NRPS | mannopeptimycin | Streptomyces hygroscopicus

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:
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 25.37 out of 28.14
Confidence: medium
Additional weak hits (2):
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.58 out of 32.93
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 19.93 out of 30.11
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

ranthipeptide protocluster (0...20459)
FS693_RS14250
  RRE type: Thurincin_rSAM_RRE
  Location: 31 - 81
  Score: 30.6
  RRE type: PqqD_RRE
  Location: 28 - 87
  Score: 30.3
  RRE type: Subtilosin_rSAM_RRE
  Location: 32 - 85
  Score: 26.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
PerR | Peroxide regulator

NZ_VEDP01000008.1 - Region 1 - T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 38,901 nt. (total: 38,901 nt) Show pHMM detection rules used
Region on contig edge.
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
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
FS693_RS15925: hydroxymethylglutaryl-CoA reductase

smcogs
  SMCOG1187: hydroxymethylglutaryl-CoA reductase

FS693_RS15940: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Hydrolases: back translocase
FS693_RS15955: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

Ligases: synthase
FS693_RS15920: hydroxymethylglutaryl-CoA synthase

smcogs
  SMCOG1043: hydroxymethylglutaryl-CoA synthase

FS693_RS16020: Pseudouridine synthase

smcogs
  SMCOG1154: Pseudouridine synthase

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000866.5 |  | 0.43 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0002707.2 |  | 0.42 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0000867.3 |  | 0.41 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0002561.3 |  | 0.40 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0000255.5 |  | 0.40 | PKS | pederin | Uncultured bacterium
BGC0000501.3 |  | 0.40 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000205.3 |  | 0.40 | PKS | bryostatin | Candidatus Endobugula sertula
BGC0000548.4 |  | 0.37 | ribosomal | salivaricin A | Streptococcus salivarius
BGC0000934.4 |  | 0.37 | other (phenazine) | 5-acetyl-5,10-dihydrophenazine-1-carboxylic acid, 5-(2-hydroxyacetyl)-5,10-dihydrophenazine-1-carboxylic acid, endophenazine A1, endophenazine F, endophenazine G | Kitasatospora sp. HKI 714
BGC0001080.5 |  | 0.37 | other (phenazine) | endophenazine A, endophenazine B | Streptomyces anulatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000866.5 |  | 0.43 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0002707.2 |  | 0.42 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0000867.3 |  | 0.41 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0002561.3 |  | 0.40 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0000255.5 |  | 0.40 | PKS | pederin | Uncultured bacterium
BGC0000501.3 |  | 0.40 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000205.3 |  | 0.40 | PKS | bryostatin | Candidatus Endobugula sertula
BGC0000548.4 |  | 0.37 | ribosomal | salivaricin A | Streptococcus salivarius
BGC0000934.4 |  | 0.37 | other (phenazine) | 5-acetyl-5,10-dihydrophenazine-1-carboxylic acid, 5-(2-hydroxyacetyl)-5,10-dihydrophenazine-1-carboxylic acid, endophenazine A1, endophenazine F, endophenazine G | Kitasatospora sp. HKI 714
BGC0001080.5 |  | 0.37 | other (phenazine) | endophenazine A, endophenazine B | Streptomyces anulatus

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: 18.31 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
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.25 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.87 out of 26.06
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 26.40 out of 27.78
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.05 out of 20.97
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.94 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.95 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.34 out of 26.06
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.62 out of 23.79
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.86 out of 25.88
Confidence: medium
Additional weak hits (7):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.86 out of 30.25
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.75 out of 33.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.82 out of 26.06
Confidence: weak
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.08 out of 20.47
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.05 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.68 out of 28.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.00 out of 24.78
Confidence: weak
TFBS Finder
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
IolR | Regulator of the inositol catabolism
MogR | Repressor of flagellar motility genes
PsrA | Oleic acid responsive regulator
ToxT | Regulator of MSHA biosynthesis