Select genomic region:
Overview
1.1
1.2
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1.5
1.6
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1.9
1.10
1.11

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

NZ_AP019791.1 (Rubrobacter xylanophilus)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | terpene | 112,942 | 133,886 |
Region 2 | T3PKS | 358,408 | 399,457 |  |
Region 3 | terpene-precursor | 727,942 | 748,838 |
Region 4 | betalactone | 826,343 | 850,587 |  |
Region 5 | betalactone,NRPS-like | 974,130 | 1,039,924 |  |
Region 6 | lanthipeptide-class-i | 1,246,390 | 1,271,026 | Low | geobacillin I | ribosomal:RiPP:Lanthipeptide
Region 7 | betalactone | 1,283,835 | 1,317,041 |
Region 8 | RiPP-like | 2,236,165 | 2,246,461 |
Region 9 | redox-cofactor | 2,384,352 | 2,409,956 |
Region 10 | NI-siderophore | 2,752,266 | 2,785,700 | Medium | schizokinen | NRPS:Type IV
Region 11 | terpene | 2,831,997 | 2,852,971 |

NZ_AP019791.1 - 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: 112,942 - 133,886 nt. (total: 20,945 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase
RxyAA322_RS00575: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

RxyAA322_RS00625: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

RxyAA322_RS00635: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

Transferases: aminotransferase
RxyAA322_RS00570: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

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
--- | --- | --- | --- | --- | ---
BGC0000656.5 |  | 0.48 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000643.3 |  | 0.46 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000634.3 |  | 0.46 | terpene | carotenoid | Brevundimonas sp. SD212
BGC0000645.3 |  | 0.44 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000630.3 |  | 0.42 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000667.3 |  | 0.41 | terpene | PR-toxin | Penicillium roqueforti FM164
BGC0001227.3 |  | 0.41 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000633.3 |  | 0.41 | terpene | carotenoid | Streptomyces avermitilis
BGC0000635.3 |  | 0.41 | terpene | carotenoid | Paracoccus sp. N81106
BGC0000648.3 |  | 0.41 | terpene | carotenoid | Myxococcus xanthus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000656.5 |  | 0.48 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000643.3 |  | 0.46 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000634.3 |  | 0.46 | terpene | carotenoid | Brevundimonas sp. SD212
BGC0000645.3 |  | 0.44 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000630.3 |  | 0.42 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000667.3 |  | 0.41 | terpene | PR-toxin | Penicillium roqueforti FM164
BGC0001227.3 |  | 0.41 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000633.3 |  | 0.41 | terpene | carotenoid | Streptomyces avermitilis
BGC0000635.3 |  | 0.41 | terpene | carotenoid | Paracoccus sp. N81106
BGC0000648.3 |  | 0.41 | terpene | carotenoid | Myxococcus xanthus

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
RxyAA322_RS00620: PT_phytoene_like
Domain 1 (17 - 294): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (7):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.19 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.97 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.22 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.04 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.72 out of 29.38
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.48 out of 33.14
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_AP019791.1 - Region 2 - 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: 358,408 - 399,457 nt. (total: 41,050 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase reductase
RxyAA322_RS01900: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

RxyAA322_RS01910: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

RxyAA322_RS01955: alkyl hydroperoxide reductase/ Thiol specific

smcogs
  SMCOG1196: alkyl hydroperoxide reductase/ Thiol specific

RxyAA322_RS02050: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: kinase methyltransferase
RxyAA322_RS01870: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

RxyAA322_RS01980: isoprenylcysteine carboxyl methyltransferase

smcogs
  SMCOG1150: isoprenylcysteine carboxyl methyltransferase

Ligases: synthase
RxyAA322_RS01960: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RxyAA322_RS01975: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

Translocases: permease
RxyAA322_RS02040: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.69 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001831.3 |  | 0.55 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001268.4 |  | 0.52 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001962.3 |  | 0.50 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0002403.2 |  | 0.48 | PKS | β-Diketones | Hordeum vulgare subsp. vulgare
BGC0002332.2 |  | 0.47 | PKS | 4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A | Candidatus Entotheonella sp.
BGC0002711.2 |  | 0.42 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0002510.2 |  | 0.42 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0001987.2 |  | 0.42 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0000196.4 |  | 0.41 | PKS | AQ-256, AQ-270a, AQ-284a | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.69 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001831.3 |  | 0.55 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001268.4 |  | 0.52 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001962.3 |  | 0.50 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0002403.2 |  | 0.48 | PKS | β-Diketones | Hordeum vulgare subsp. vulgare
BGC0002332.2 |  | 0.47 | PKS | 4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A | Candidatus Entotheonella sp.
BGC0002711.2 |  | 0.42 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0002510.2 |  | 0.42 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0001987.2 |  | 0.42 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0000196.4 |  | 0.41 | PKS | AQ-256, AQ-270a, AQ-284a | 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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.74 out of 23.79
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.75 out of 23.79
Confidence: medium
Additional weak hits (10):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.85 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.35 out of 28.14
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.35 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.01 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.16 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.38 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.07 out of 21.55
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.02 out of 32.93
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_AP019791.1 - 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: 727,942 - 748,838 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
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: formyltransferase
RxyAA322_RS03915: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

Hydrolases: deformylase
RxyAA322_RS03920: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Ligases: synthase synthetase
RxyAA322_RS03865: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

RxyAA322_RS03880: 3-dehydroquinate synthase

smcogs
  SMCOG1183: 3-dehydroquinate 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
--- | --- | --- | --- | --- | ---
BGC0001641.4 |  | 0.52 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002439.3 |  | 0.42 | other (other) | diastaphenazine, izumiphenazine C | Streptomyces diastaticus
BGC0001605.3 |  | 0.41 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000720.3 |  | 0.37 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0001529.5 |  | 0.37 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0000633.3 |  | 0.37 | terpene | carotenoid | Streptomyces avermitilis
BGC0002309.2 |  | 0.37 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001641.4 |  | 0.52 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002439.3 |  | 0.42 | other (other) | diastaphenazine, izumiphenazine C | Streptomyces diastaticus
BGC0001605.3 |  | 0.41 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000720.3 |  | 0.37 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0001529.5 |  | 0.37 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0000633.3 |  | 0.37 | terpene | carotenoid | Streptomyces avermitilis
BGC0002309.2 |  | 0.37 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
RxyAA322_RS03865: PT_FPPS_like
Domain 1 (35 - 296): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:
  DMAPP, IPP → FPP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.41 out of 29.72
Confidence: medium
Additional weak hits (3):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.92 out of 18.57
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.53 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.30 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
IPP | Isopentenyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_AP019791.1 - Region 4 - 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: 826,343 - 850,587 nt. (total: 24,245 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
RxyAA322_RS04355: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: carboxylase
RxyAA322_RS04395: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Hydrolases: hydrolase
RxyAA322_RS15425: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: lyase
RxyAA322_RS04425: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase
RxyAA322_RS04380: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RxyAA322_RS04390: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate 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 | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000528.5 |  | 0.47 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002573.2 |  | 0.45 | other (other) | phosphoramidon | Streptomyces mozunensis
BGC0002284.3 |  | 0.44 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0002458.3 |  | 0.44 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0000234.5 |  | 0.44 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001440.5 |  | 0.43 | other (other) | cystargolide A, cystargolide B | Kitasatospora cystarginea
BGC0001295.5 |  | 0.43 | other (other) | cremeomycin | Streptomyces cremeus
BGC0002645.3 |  | 0.41 | other (other) | fluopsin C | Pseudomonas aeruginosa PAO1
BGC0002316.2 |  | 0.41 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0001286.3 |  | 0.40 | other (other) | itaconic acid | Ustilago maydis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000528.5 |  | 0.47 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002573.2 |  | 0.45 | other (other) | phosphoramidon | Streptomyces mozunensis
BGC0002284.3 |  | 0.44 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0002458.3 |  | 0.44 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0000234.5 |  | 0.44 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001440.5 |  | 0.43 | other (other) | cystargolide A, cystargolide B | Kitasatospora cystarginea
BGC0001295.5 |  | 0.43 | other (other) | cremeomycin | Streptomyces cremeus
BGC0002645.3 |  | 0.41 | other (other) | fluopsin C | Pseudomonas aeruginosa PAO1
BGC0002316.2 |  | 0.41 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0001286.3 |  | 0.40 | other (other) | itaconic acid | Ustilago maydis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.07 out of 20.47
Confidence: medium
Additional weak hits (9):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.52 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.06 out of 21.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.49 out of 20.97
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.43 out of 32.93
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.77 out of 21.55
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.91 out of 36.54
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.36 out of 27.78
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_AP019791.1 - Region 5 - NRPS-like,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: 974,130 - 1,039,924 nt. (total: 65,795 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase oxidoreductase
RxyAA322_RS05245: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

RxyAA322_RS05280: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

RxyAA322_RS05285: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RxyAA322_RS05305: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

RxyAA322_RS05315: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

RxyAA322_RS05340: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

RxyAA322_RS05350: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

RxyAA322_RS05355: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RxyAA322_RS05360: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

RxyAA322_RS05370: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Transferases: carboxylase kinase transferase
RxyAA322_RS05145: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

RxyAA322_RS05210: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

RxyAA322_RS05215: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

RxyAA322_RS05365: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Hydrolases: amidase esterase hydrolase
RxyAA322_RS05175: isochorismatase

smcogs
  SMCOG1027: isochorismatase

RxyAA322_RS05205: amidase

smcogs
  SMCOG1105: amidase

RxyAA322_RS15640: thioesterase superfamily protein

smcogs
  SMCOG1144: thioesterase superfamily protein

Lyases: dehydratase
RxyAA322_RS05195: L-carnitine dehydratase/bile acid-inducible

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

Ligases: ligase synthase
RxyAA322_RS05160: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RxyAA322_RS05190: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

RxyAA322_RS05220: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RxyAA322_RS05265: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RxyAA322_RS05290: 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 | betalactone | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002276.2 |  |  | 0.54 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001166.5 |  |  | 0.48 | NRPS | HC-toxin | Alternaria jesenskae
BGC0002284.3 |  |  | 0.46 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000131.5 |  |  | 0.41 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0000234.5 |  |  | 0.30 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000207.5 |  |  | 0.30 | PKS | chartreusin | Streptomyces chartreusis
BGC0000253.4 |  |  | 0.29 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002493.3 |  |  | 0.29 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0002706.2 |  |  | 0.28 | NRPS | saframycin Mx1 | Myxococcus xanthus
BGC0001050.5 |  |  | 0.28 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.81 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
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
BGC0001833.4 |  | 0.60 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002174.2 |  | 0.59 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  | 0.59 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.59 | 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.
No hits above weak threshold.
Weak hits (19):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.13 out of 26.85
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.18 out of 18.57
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.82 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.31 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.67 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.84 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.60 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.24 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.96 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.75 out of 30.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.93 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.44 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.95 out of 28.14
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.91 out of 32.93
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.67 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.62 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.68 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.39 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 5, location 974129 - 1039924:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ala)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 996855 - 1039924:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ala)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
RxyAA322_RS05160: X
AMP-binding (61..506): 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:
    LSMA-DIGWYIGFTFLAGERDNYWQTETGILSSM
  Nearest Stachelhaus code(s):
    Aol DIWFVAGIYK (35% 8Å match)
    Val DAWMFAAILK (32% 8Å match)
  Stachelhaus code match:
    60% (weak)

RxyAA322_RS05220: Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (44..451): 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:
    HGVTWIGGLFDFFLACGGENEFYGQTENLVLSNC
  Nearest Stachelhaus code(s):
    Val DGFFAGGVFK (38% 8Å match)
  Stachelhaus code match:
    70% (weak)

RxyAA322_RS05265: X
AMP-binding (99..529): 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:
    LTYAWTFPIWSGFTSLVGENNTYGQTETATGWTS
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

RxyAA322_RS05290: Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (13..413): 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:
    ala (Ala)

Stachelhaus prediction details:
  Stachelhaus sequence:
    SWRV---FVWERLVWLNGELNVYSVSETHEVAAG
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

Regulator | Description
--- | ---

NZ_AP019791.1 - Region 6 - 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: 1,246,390 - 1,271,026 nt. (total: 24,637 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
RxyAA322_RS06490: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RxyAA322_RS06495: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: methyltransferase
RxyAA322_RS06500: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Lyases: cyclase dehydratase
RxyAA322_RS06450: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

RxyAA322_RS06455: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

Ligases: synthase
RxyAA322_RS06505: 3-oxoacyl-(acyl carrier protein) synthase III

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

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.76 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002635.2 |  | 0.63 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0001289.5 |  | 0.56 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000508.3 |  | 0.56 | ribosomal | epidermin | Staphylococcus epidermidis
BGC0000560.5 |  | 0.56 | ribosomal | subtilomycin | Bacillus subtilis
BGC0000541.5 |  | 0.53 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000533.3 |  | 0.53 | ribosomal | mutacin III | Streptococcus mutans
BGC0000542.3 |  | 0.52 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000530.5 |  | 0.52 | ribosomal | mutacin B-Ny266 | Streptococcus mutans N66
BGC0000514.5 |  | 0.52 | ribosomal | gallidermin | Staphylococcus gallinarum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.76 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002635.2 |  | 0.63 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0001289.5 |  | 0.56 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000508.3 |  | 0.56 | ribosomal | epidermin | Staphylococcus epidermidis
BGC0000560.5 |  | 0.56 | ribosomal | subtilomycin | Bacillus subtilis
BGC0000541.5 |  | 0.53 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000533.3 |  | 0.53 | ribosomal | mutacin III | Streptococcus mutans
BGC0000542.3 |  | 0.52 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000530.5 |  | 0.52 | ribosomal | mutacin B-Ny266 | Streptococcus mutans N66
BGC0000514.5 |  | 0.52 | ribosomal | gallidermin | Staphylococcus gallinarum

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 RxyAA322_RS06455

RxyAA322_RS06460
Leader:
MTVAYESKALNRDTAGSADAGELFDLDIQVSKGSGDVEPQ
Core:
I T S Y S L C T P G C A K T G S F N S Y C C
Core with dehydrations:
I Dhb Dha Y Dha L Cys Dhb P G Cys A K Dhb G Dha F N Dha Y Cys Cys

#### antiSMASH-DB 4.0 matches for RxyAA322_RS06460

100.0%
NZ_AP019791.1:
Lanthipeptides: RxyAA322_RS06460_lanthipeptide
1
I T S Y S L C T P G C A K T G S F N S Y C C
22
I T S Y S L C T P G C A K T G S F N S Y C C
1
I T S Y S L C T P G C A K T G S F N S Y C C
22
87.5%
NZ_VKCY01000012.1:
Lanthipeptides: FNK43_RS09020_lanthipeptide
1
I T S Y S L C T P G C A K T G S F N S Y C C
22
I T S+S L C T P G C A K T G S F N S Y C C
3
I T S F S L C T P G C A K T G S F N S Y C C
24
87.0%
NC_003923.1 and 9 others:
NC_009641.1 Lanthipeptides: NWMN_RS09635_lanthipeptide NZ_CP023076.1 Lanthipeptides: CJ017_RS08945_lanthipeptide NZ_CP054876.1 Lanthipeptides: HUW54_RS09150_lanthipeptide NZ_CP077098.1 Lanthipeptides: KSF82_RS09475_lanthipeptide NZ_CP092781.1 Lanthipeptides: ML436_RS08940_lanthipeptide NZ_CP102959.1 Lanthipeptides: NW979_RS08780_lanthipeptide NZ_CP102962.1 Lanthipeptides: NW971_RS09555_lanthipeptide NZ_LR133917.1 Lanthipeptides: ELZ45_RS09155_lanthipeptide NZ_LS483317.1 Lanthipeptides: DQL75_RS09700_lanthipeptide
Lanthipeptides: MW_RS09420_lanthipeptide
1
I T S Y S L C T P G C A K T G S F N S Y C C
22
I T S+S L C T P G C A K T G S F N S+C C
2
I T S H S L C T P G C A K T G S F N S F C C
23
with 112 more sequence matches
Only the first 10 are displayed here.
86.4%
NZ_CP094805.1:
Lanthipeptides: MUA37_RS13310_lanthipeptide
1
I T S Y S L C T P G C A K T G S F N S Y C C
22
I S L C T P G C A K T G S F N S Y C C
1
I A S K F L C T P G C A K T G S F N S Y C C
22
86.4%
NZ_FNNQ01000006.1 and 2 others:
NZ_FNNQ01000006.1 Lanthipeptides: BLV90_RS07685_lanthipeptide NZ_FNNQ01000006.1 Lanthipeptides: BLV90_RS07680_lanthipeptide
Lanthipeptides: BLV90_RS07690_lanthipeptide
1
I T S Y S L C T P G C A K T G S F N S Y C C
22
I T S S L C T P G C +T G S F N S Y C C
1
I T S V S L C T P G C G E T G S F N S Y C C
22
86.4%
NZ_FPAA01000016.1 and 3 others:
NZ_FPAA01000016.1 Lanthipeptides: CHX35_RS15995_lanthipeptide NZ_FPAA01000016.1 Lanthipeptides: CHX35_RS15990_lanthipeptide NZ_FPAA01000016.1 Lanthipeptides: CHX35_RS15985_lanthipeptide
Lanthipeptides: CHX35_RS16000_lanthipeptide
1
I T S Y S L C T P G C A K T G S F N S Y C C
22
I T S S L C T P G C T G S F N S Y C C
1
I T S V S L C T P G C G D T G S F N S Y C C
22
86.4%
NZ_LELK01000004.1:
Lanthipeptides: AB986_RS12540_lanthipeptide
1
I T S Y S L C T P G C A K T G S F N S Y C C
22
I T S Y S C T P G C +T G S F N S Y C C
1
I T S Y S F C T P G C G E T G S F N S Y C C
22
82.6%
NZ_CP047792.1 and 1 other:
NZ_JAGSAY010000004.1 Lanthipeptides: KC186_RS06745_lanthipeptide
Lanthipeptides: E3S88_RS07345_lanthipeptide
1
I T S Y S L C T P G C A K T G S F N S Y C C
22
I T S+S L C T P G C A T G S F N S+C C
2
I T S H S L C T P G C A N T G S F N S F C C
23
81.8%
NZ_CP023477.1:
Lanthipeptides: CO204_RS07210_lanthipeptide
1
I T S Y S L C T P G C A K T G S F N S Y C C
22
S+S L C T P G C A+T G S F N S Y C C
1
F K S W S L C T P G C A R T G S F N S Y C C
22
81.8%
NZ_CP090942.1:
Lanthipeptides: LZT96_RS12010_lanthipeptide
1
I T S Y S L C T P G C A K T G S F N S Y C C
22
I S +C T P G C A K T G S F N S Y C C
1
I A S K F I C T P G C A K T G S F N S Y C C
22
77.3%
NC_014023.1 and 36 others:
NC_014023.1 Lanthipeptides: BMQ_RS27575_lanthipeptide NZ_CP018875.1 Lanthipeptides: BUW91_RS26425_lanthipeptide NZ_CP018875.1 Lanthipeptides: BUW91_RS26420_lanthipeptide NZ_CP028091.1 Lanthipeptides: C1N54_RS28075_lanthipeptide NZ_CP028091.1 Lanthipeptides: C1N54_RS28070_lanthipeptide NZ_CP028091.1 Lanthipeptides: C1N54_RS28065_lanthipeptide NZ_CP031776.1 Lanthipeptides: D0441_RS30140_lanthipeptide NZ_CP041065.1 Lanthipeptides: FJM50_RS01185_lanthipeptide NZ_CP041065.1 Lanthipeptides: FJM50_RS01180_lanthipeptide NZ_CP041065.1 Lanthipeptides: FJM50_RS01175_lanthipeptide NZ_CP048884.1 Lanthipeptides: BMG_RS27510_lanthipeptide NZ_CP058263.1 Lanthipeptides: HW576_RS26980_lanthipeptide NZ_CP058263.1 Lanthipeptides: HW576_RS26975_lanthipeptide NZ_CP058263.1 Lanthipeptides: HW576_RS26970_lanthipeptide NZ_CP085427.1 Lanthipeptides: LIT30_RS26985_lanthipeptide NZ_CP085427.1 Lanthipeptides: LIT30_RS26980_lanthipeptide NZ_CP085427.1 Lanthipeptides: LIT30_RS26975_lanthipeptide NZ_CP085432.1 Lanthipeptides: LIT34_RS27820_lanthipeptide NZ_CP085432.1 Lanthipeptides: LIT34_RS27815_lanthipeptide NZ_CP085432.1 Lanthipeptides: LIT34_RS27810_lanthipeptide NZ_JACJHT010000009.1 Lanthipeptides: HNP21_RS25635_lanthipeptide NZ_JACJHT010000009.1 Lanthipeptides: HNP21_RS25630_lanthipeptide NZ_JACJHT010000009.1 Lanthipeptides: HNP21_RS25625_lanthipeptide NZ_JAHHYI010000015.1 Lanthipeptides: KM925_RS26245_lanthipeptide NZ_JANIOE010000010.1 Lanthipeptides: NQ109_RS28075_lanthipeptide NZ_JANIOE010000010.1 Lanthipeptides: NQ109_RS28070_lanthipeptide NZ_JANIOE010000010.1 Lanthipeptides: NQ109_RS28065_lanthipeptide NZ_NKAQ01000005.1 Lanthipeptides: CE057_RS19640_lanthipeptide NZ_NKAQ01000005.1 Lanthipeptides: CE057_RS19635_lanthipeptide NZ_NTZG01000054.1 Lanthipeptides: CN510_RS18265_lanthipeptide NZ_NUIN01000020.1 Lanthipeptides: CN973_RS26930_lanthipeptide NZ_NUOI01000090.1 Lanthipeptides: COE08_RS30285_lanthipeptide NZ_NUOI01000090.1 Lanthipeptides: COE08_RS30280_lanthipeptide NZ_NUOQ01000009.1 Lanthipeptides: COE31_RS05925_lanthipeptide NZ_NUXL01000007.1 Lanthipeptides: COJ36_RS20885_lanthipeptide NZ_NUZS01000089.1 Lanthipeptides: COJ90_RS28785_lanthipeptide
Lanthipeptides: BMQ_RS27580_lanthipeptide
1
I T S Y S L C T P G C A K T G S F N S Y C C
22
I T S S L C T P G C T G S+N S+C C
1
I T S V S L C T P G C G D T G S W N S F C C
22
77.3%
NC_022873.1 and 92 others:
NZ_CM000742.1 Lanthipeptides: BMYCO0001_RS26515_lanthipeptide NZ_CP011151.1 Lanthipeptides: WR47_RS18180_lanthipeptide NZ_CP011151.1 Lanthipeptides: WR47_RS18175_lanthipeptide NZ_CP011151.1 Lanthipeptides: WR47_RS18170_lanthipeptide NZ_CP011151.1 Lanthipeptides: WR47_RS18165_lanthipeptide NZ_CP015350.1 Lanthipeptides: BT246_RS19775_lanthipeptide NZ_CP015350.1 Lanthipeptides: BT246_RS19770_lanthipeptide NZ_CP015350.1 Lanthipeptides: BT246_RS19765_lanthipeptide NZ_CP017060.1 Lanthipeptides: FORC47_RS18710_lanthipeptide NZ_CP017060.1 Lanthipeptides: FORC47_RS18705_lanthipeptide NZ_CP017060.1 Lanthipeptides: FORC47_RS18700_lanthipeptide NZ_CP026678.1 Lanthipeptides: C2I25_RS21370_lanthipeptide NZ_CP026678.1 Lanthipeptides: C2I25_RS21365_lanthipeptide NZ_CP026678.1 Lanthipeptides: C2I25_RS21360_lanthipeptide NZ_CP035965.1 Lanthipeptides: EXW35_RS16385_lanthipeptide NZ_CP035965.1 Lanthipeptides: EXW35_RS16380_lanthipeptide NZ_CP035994.1 Lanthipeptides: EXW32_RS16155_lanthipeptide NZ_CP035994.1 Lanthipeptides: EXW32_RS16150_lanthipeptide NZ_CP035994.1 Lanthipeptides: EXW32_RS16145_lanthipeptide NZ_CP035994.1 Lanthipeptides: EXW32_RS16140_lanthipeptide NZ_CP035999.1 Lanthipeptides: EXW27_RS26195_lanthipeptide NZ_CP035999.1 Lanthipeptides: EXW27_RS26190_lanthipeptide NZ_CP035999.1 Lanthipeptides: EXW27_RS26185_lanthipeptide NZ_CP035999.1 Lanthipeptides: EXW27_RS26180_lanthipeptide NZ_CP036099.1 Lanthipeptides: EXW47_RS16265_lanthipeptide NZ_CP036099.1 Lanthipeptides: EXW47_RS16260_lanthipeptide NZ_CP036099.1 Lanthipeptides: EXW47_RS16255_lanthipeptide NZ_CP036099.1 Lanthipeptides: EXW47_RS16250_lanthipeptide NZ_CP036117.1 Lanthipeptides: EXW43_RS16620_lanthipeptide NZ_CP036117.1 Lanthipeptides: EXW43_RS16615_lanthipeptide NZ_CP036117.1 Lanthipeptides: EXW43_RS16610_lanthipeptide NZ_CP036117.1 Lanthipeptides: EXW43_RS16605_lanthipeptide NZ_CP036145.1 Lanthipeptides: EXW57_RS16110_lanthipeptide NZ_CP036145.1 Lanthipeptides: EXW57_RS16105_lanthipeptide NZ_CP036145.1 Lanthipeptides: EXW57_RS16100_lanthipeptide NZ_CP036145.1 Lanthipeptides: EXW57_RS16095_lanthipeptide NZ_CP040334.1 Lanthipeptides: EUC39_RS14125_lanthipeptide NZ_CP040334.1 Lanthipeptides: EUC39_RS14120_lanthipeptide NZ_CP040334.1 Lanthipeptides: EUC39_RS14115_lanthipeptide NZ_CP045606.2 Lanthipeptides: GE376_RS18355_lanthipeptide NZ_CP045606.2 Lanthipeptides: GE376_RS18350_lanthipeptide NZ_CP045606.2 Lanthipeptides: GE376_RS18345_lanthipeptide NZ_CP047366.1 Lanthipeptides: GSN03_RS15835_lanthipeptide NZ_CP047366.1 Lanthipeptides: GSN03_RS15830_lanthipeptide NZ_CP071811.1 Lanthipeptides: EXW36_RS16415_lanthipeptide NZ_CP071811.1 Lanthipeptides: EXW36_RS16410_lanthipeptide NZ_CP071811.1 Lanthipeptides: EXW36_RS16405_lanthipeptide NZ_CP072061.1 Lanthipeptides: J5V93_RS15130_lanthipeptide NZ_CP072061.1 Lanthipeptides: J5V93_RS15125_lanthipeptide NZ_CP072061.1 Lanthipeptides: J5V93_RS15120_lanthipeptide NZ_CP084035.1 Lanthipeptides: LCF45_RS15990_lanthipeptide NZ_CP084035.1 Lanthipeptides: LCF45_RS15985_lanthipeptide NZ_CP084035.1 Lanthipeptides: LCF45_RS15980_lanthipeptide NZ_CP084035.1 Lanthipeptides: LCF45_RS15975_lanthipeptide NZ_CP093291.1 Lanthipeptides: MN093_RS25975_lanthipeptide NZ_CP093291.1 Lanthipeptides: MN093_RS25970_lanthipeptide NZ_CP093291.1 Lanthipeptides: MN093_RS25965_lanthipeptide NZ_CP093291.1 Lanthipeptides: MN093_RS25960_lanthipeptide NZ_CP093835.1 Lanthipeptides: MN034_RS15810_lanthipeptide NZ_CP093835.1 Lanthipeptides: MN034_RS15805_lanthipeptide NZ_CP093835.1 Lanthipeptides: MN034_RS15800_lanthipeptide NZ_CP093835.1 Lanthipeptides: MN034_RS15795_lanthipeptide NZ_JAIPUK010000008.1 Lanthipeptides: K9P71_RS24265_lanthipeptide NZ_JAIPUK010000008.1 Lanthipeptides: K9P71_RS24260_lanthipeptide NZ_JANCTB010000001.1 Lanthipeptides: NMG90_RS06155_lanthipeptide NZ_JANCTB010000001.1 Lanthipeptides: NMG90_RS06150_lanthipeptide NZ_JANCTB010000001.1 Lanthipeptides: NMG90_RS06145_lanthipeptide NZ_JANCTB010000001.1 Lanthipeptides: NMG90_RS06140_lanthipeptide NZ_JH792114.1 Lanthipeptides: II3_RS21535_lanthipeptide NZ_JH792114.1 Lanthipeptides: II3_RS21530_lanthipeptide NZ_JH792114.1 Lanthipeptides: II3_RS21525_lanthipeptide NZ_JH792251.1 Lanthipeptides: III_RS11095_lanthipeptide NZ_JH792251.1 Lanthipeptides: III_RS11090_lanthipeptide NZ_JH792251.1 Lanthipeptides: III_RS11085_lanthipeptide NZ_JH792251.1 Lanthipeptides: III_RS11080_lanthipeptide NZ_JH792251.1 Lanthipeptides: III_RS11075_lanthipeptide NZ_LDGT01000041.1 Lanthipeptides: ABE17_RS18900_lanthipeptide NZ_LDGT01000041.1 Lanthipeptides: ABE17_RS18895_lanthipeptide NZ_LDGT01000041.1 Lanthipeptides: ABE17_RS18890_lanthipeptide NZ_LDGT01000041.1 Lanthipeptides: ABE17_RS18885_lanthipeptide NZ_LDHL01000037.1 Lanthipeptides: ABD98_RS26430_lanthipeptide NZ_LDHL01000037.1 Lanthipeptides: ABD98_RS26425_lanthipeptide NZ_MOOL01000076.1 Lanthipeptides: BK733_RS27280_lanthipeptide NZ_MOOL01000076.1 Lanthipeptides: BK733_RS27275_lanthipeptide NZ_MOOL01000076.1 Lanthipeptides: BK733_RS27270_lanthipeptide NZ_MSTN01000016.1 Lanthipeptides: BVF97_RS28620_lanthipeptide NZ_NIUP01000011.1 Lanthipeptides: CEU84_RS08145_lanthipeptide NZ_NIUP01000011.1 Lanthipeptides: CEU84_RS08140_lanthipeptide NZ_NKAX01000026.1 Lanthipeptides: CE086_RS26165_lanthipeptide NZ_NKAX01000026.1 Lanthipeptides: CE086_RS26160_lanthipeptide NZ_NVGU01000011.1 Lanthipeptides: COL71_RS14760_lanthipeptide NZ_NVGU01000011.1 Lanthipeptides: COL71_RS14755_lanthipeptide
Lanthipeptides: YBT1518_RS19670_lanthipeptide
1
I T S Y S L C T P G C A K T G S F N S Y C C
22
I T S S C T P G C T G S F N S+C C
1
I T S I S A C T P G C G N T G S F N S F C C
22
73.9%
NZ_CP047792.1 and 2 others:
NZ_GG730342.1 Lanthipeptides: SAUG_RS17380_lanthipeptide NZ_JAGSAY010000004.1 Lanthipeptides: KC186_RS06750_lanthipeptide
Lanthipeptides: E3S88_RS07350_lanthipeptide
1
I T S Y S L C T P G C A K T G S F N S Y C C
22
+T S Y S L C+ G C K T G S F N S+C C
2
L T S Y S L C S F G C G K T G S F N S F C C
23

#### MIBiG 4.0 matches for RxyAA322_RS06460

38.2%
BGC0000535.4 (ADJ56352.1):
Lanthipeptide: nisin A
1
I T S Y S L C T P G C A K T G S F
17
I T S S L C T P G C K T G+
1
I T S I S L C T P G C-K T G A L
16

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.19 out of 20.47
Confidence: strong
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 24.01 out of 29.25
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.12 out of 23.79
Confidence: medium
Additional weak hits (1):
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.10 out of 24.78
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.

RxyAA322_RS06460 - Class I
  Cleavage pHMM score: 7.20
  RODEO score: 34
  Monoisotopic mass: 2133.0 Da
  Molecular weight: 2134.5 Da
  Number of bridges: 3
  Additional modifications: AviCys
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2152.5 Da N = 1
    2170.5 Da N = 2
    2188.5 Da N = 3

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (1246389...1271026)
RxyAA322_RS06455
  RRE type: Lanthipeptide_LanB_RRE
  Location: 182 - 274
  Score: 58.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
SypG | Regulator of biofilm formation and host colonization
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP019791.1 - Region 7 - 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: 1,283,835 - 1,317,041 nt. (total: 33,207 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
RxyAA322_RS06660: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

RxyAA322_RS06700: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Transferases: acetyltransferase carboxylase
RxyAA322_RS06630: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

RxyAA322_RS06695: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Lyases: hydratase
RxyAA322_RS06680: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase
RxyAA322_RS06670: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RxyAA322_RS06715: 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 | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002274.2 |  | 0.56 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0001160.5 |  | 0.52 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002405.2 |  | 0.47 | saccharide | mid-chain acyl sugars | Solanum lycopersicum
BGC0000866.5 |  | 0.47 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.45 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0000234.5 |  | 0.44 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001137.5 |  | 0.41 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0002284.3 |  | 0.40 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0002474.2 |  | 0.40 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0002711.2 |  | 0.39 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002274.2 |  | 0.56 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0001160.5 |  | 0.52 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002405.2 |  | 0.47 | saccharide | mid-chain acyl sugars | Solanum lycopersicum
BGC0000866.5 |  | 0.47 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.45 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0000234.5 |  | 0.44 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001137.5 |  | 0.41 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0002284.3 |  | 0.40 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0002474.2 |  | 0.40 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0002711.2 |  | 0.39 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102

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:
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.44 out of 25.88
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.33 out of 20.97
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
Additional weak hits (4):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.25 out of 26.06
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.74 out of 25.88
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.38 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 19.15 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
PsrA | Oleic acid responsive regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP019791.1 - Region 8 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,236,165 - 2,246,461 nt. (total: 10,297 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
RxyAA322_RS11450: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000616.4 |  | 0.57 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0002447.3 |  | 0.47 | ribosomal | cerecyclin | Bacillus cereus
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0001210.5 |  | 0.41 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002700.2 |  | 0.41 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000539.5 |  | 0.41 | ribosomal | nukacin ISK-1 | Staphylococcus warneri
BGC0000626.3 |  | 0.41 | ribosomal | thuricin | Bacillus thuringiensis
BGC0000486.4 |  | 0.40 | ribosomal | butyrivibriocin AR10 | Butyrivibrio fibrisolvens
BGC0000521.3 |  | 0.40 | ribosomal | lacticin 481 | Lactococcus lactis subsp. lactis
BGC0002005.2 |  | 0.40 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000616.4 |  | 0.57 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0002447.3 |  | 0.47 | ribosomal | cerecyclin | Bacillus cereus
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0001210.5 |  | 0.41 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002700.2 |  | 0.41 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000539.5 |  | 0.41 | ribosomal | nukacin ISK-1 | Staphylococcus warneri
BGC0000626.3 |  | 0.41 | ribosomal | thuricin | Bacillus thuringiensis
BGC0000486.4 |  | 0.40 | ribosomal | butyrivibriocin AR10 | Butyrivibrio fibrisolvens
BGC0000521.3 |  | 0.40 | ribosomal | lacticin 481 | Lactococcus lactis subsp. lactis
BGC0002005.2 |  | 0.40 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (2):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.25 out of 30.97
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_AP019791.1 - Region 9 - redox-cofactor
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: 2,384,352 - 2,409,956 nt. (total: 25,605 nt) Show pHMM detection rules used
redox-cofactor: (cds(PF04055 and (TIGR04085 or SPASM)) and (TIGR02111 or TIGR03966) 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]))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
RxyAA322_RS12230: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RxyAA322_RS12245: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: methyltransferase
RxyAA322_RS12265: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
RxyAA322_RS12210: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

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

Reference | redox-cofactor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000905.5 |  | 0.43 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000906.3 |  | 0.43 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000189.4 |  | 0.42 | PKS | 3-(2'-hydroxy-3'-oxo-4'-methylpentyl)-indole, 3-(2'-hydroxy-3'-oxo-4'-methylhexyl)-indole, 3-(2'-acetoxy-3'-oxo-4'-methylpentyl)-indole, 3-(2'-acetoxy-3'-oxo-4'-methylhexyl)-indole | Xenorhabdus bovienii SS-2004
BGC0001937.4 |  | 0.40 | other (other) | tubercidin | Streptomyces tubercidicus
BGC0000205.3 |  | 0.40 | PKS | bryostatin | Candidatus Endobugula sertula
BGC0002234.3 |  | 0.38 | PKS | flavoglaucin | Aspergillus ruber CBS 135680
BGC0001565.4 |  | 0.36 | NRPS | cyclosporin C | Beauveria felina
BGC0000334.4 |  | 0.35 | NRPS | cyclosporin A | Tolypocladium inflatum NRRL 8044
BGC0001987.2 |  | 0.35 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0000101.5 |  | 0.35 | PKS | emodin, monodictyphenone, shamixanthone | Aspergillus nidulans FGSC A4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000905.5 |  | 0.43 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000906.3 |  | 0.43 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000189.4 |  | 0.42 | PKS | 3-(2'-hydroxy-3'-oxo-4'-methylpentyl)-indole, 3-(2'-hydroxy-3'-oxo-4'-methylhexyl)-indole, 3-(2'-acetoxy-3'-oxo-4'-methylpentyl)-indole, 3-(2'-acetoxy-3'-oxo-4'-methylhexyl)-indole | Xenorhabdus bovienii SS-2004
BGC0001937.4 |  | 0.40 | other (other) | tubercidin | Streptomyces tubercidicus
BGC0000205.3 |  | 0.40 | PKS | bryostatin | Candidatus Endobugula sertula
BGC0002234.3 |  | 0.38 | PKS | flavoglaucin | Aspergillus ruber CBS 135680
BGC0001565.4 |  | 0.36 | NRPS | cyclosporin C | Beauveria felina
BGC0000334.4 |  | 0.35 | NRPS | cyclosporin A | Tolypocladium inflatum NRRL 8044
BGC0001987.2 |  | 0.35 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0000101.5 |  | 0.35 | PKS | emodin, monodictyphenone, shamixanthone | Aspergillus nidulans FGSC A4

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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.97 out of 20.97
Confidence: medium
Additional weak hits (9):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.36 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.57 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.53 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.49 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.94 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.03 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.86 out of 35.63
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (2384351...2409956)
RxyAA322_RS12235
  RRE type: Mycofactocin_RRE
  Location: 6 - 89
  Score: 54.6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A

NZ_AP019791.1 - Region 10 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,752,266 - 2,785,700 nt. (total: 33,435 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
RxyAA322_RS13985: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Transferases: aminotransferase
RxyAA322_RS14005: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Lyases: decarboxylase hydratase
RxyAA322_RS13910: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

RxyAA322_RS14000: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001572.3 |  | 0.68 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002633.2 |  | 0.67 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002692.2 |  | 0.66 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0002469.2 |  | 0.63 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0001478.5 |  | 0.62 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002683.2 |  | 0.61 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000941.3 |  | 0.61 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.59 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001499.5 |  | 0.59 | other (other) | aerobactin | Pantoea ananatis
BGC0002682.2 |  | 0.59 | other (other) | aerobactin | Vibrio mimicus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001572.3 |  | 0.68 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002633.2 |  | 0.67 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002692.2 |  | 0.66 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0002469.2 |  | 0.63 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0001478.5 |  | 0.62 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002683.2 |  | 0.61 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000941.3 |  | 0.61 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.59 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001499.5 |  | 0.59 | other (other) | aerobactin | Pantoea ananatis
BGC0002682.2 |  | 0.59 | other (other) | aerobactin | Vibrio mimicus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 18.25 out of 18.46
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.77 out of 23.79
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 21.55
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.86 out of 18.57
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.81 out of 29.38
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 24.08 out of 28.19
Confidence: medium
Additional weak hits (14):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.18 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.55 out of 28.14
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.36 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.03 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.84 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 25.04 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.92 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.05 out of 20.97
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.93 out of 19.26
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.50 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.00 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
ArcA | Repressor of carbon oxidation
FuR variant 1 | Ferric Uptake Regulator
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_AP019791.1 - Region 11 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,831,997 - 2,852,971 nt. (total: 20,975 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
RxyAA322_RS14335: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

RxyAA322_RS14385: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: kinase
RxyAA322_RS14370: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Hydrolases: dehalogenase
RxyAA322_RS14390: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: cyclase
RxyAA322_RS14375: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

RxyAA322_RS14380: Terpene synthase/cyclase metal-binding domain protein

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002707.2 |  | 0.51 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0002700.2 |  | 0.46 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000496.5 |  | 0.45 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000843.5 |  | 0.43 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0002111.3 |  | 0.43 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0001521.3 |  | 0.40 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0000626.3 |  | 0.40 | ribosomal | thuricin | Bacillus thuringiensis
BGC0001778.5 |  | 0.40 | other (other) | showdomycin | Streptomyces showdoensis
BGC0001909.3 |  | 0.39 | PKS | strobilurin A | Strobilurus tenacellus
BGC0000916.5 |  | 0.39 | other (other) | molybdenum cofactor | Staphylococcus carnosus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002707.2 |  | 0.51 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0002700.2 |  | 0.46 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000496.5 |  | 0.45 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000843.5 |  | 0.43 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0002111.3 |  | 0.43 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0001521.3 |  | 0.40 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0000626.3 |  | 0.40 | ribosomal | thuricin | Bacillus thuringiensis
BGC0001778.5 |  | 0.40 | other (other) | showdomycin | Streptomyces showdoensis
BGC0001909.3 |  | 0.39 | PKS | strobilurin A | Strobilurus tenacellus
BGC0000916.5 |  | 0.39 | other (other) | molybdenum cofactor | Staphylococcus carnosus

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
--- | --- | --- | --- | --- | ---
monoterpene |  |  | C10 | C1-C10 | none
sesquiterpene |  |  | C15 | C1-C10 | none

Genes with terpene domains:
RxyAA322_RS14380: T1TS
Domain 1 (7 - 317): Type 1 terpene synthase
Subtype: Germacrene A synthase type

Reactions:
  GPP → monoterpene_C1-C10
  FPP → sesquiterpene_C1-C10

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (2):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.98 out of 29.38
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.61 out of 33.14
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate
GPP | Geranyl diphoshate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---