Select genomic region:
Overview
1.1
1.2
1.3
1.4
1.5
1.6
1.7
1.8
2.1
3.1
3.2
4.1

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

NC_009636.1 (Sinorhizobium medicae WSM419 (Ensifer medicae WSM419))

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | T1PKS | 197,291 | 244,793 |
Region 1.2 | terpene | 1,244,252 | 1,265,094 |
Region 1.3 | hserlactone | 1,644,170 | 1,664,814 |
Region 1.4 | arylpolyene | 1,799,350 | 1,840,552 |  |
Region 1.5 | thioamitides | 2,029,871 | 2,051,884 |
Region 1.6 | azole-containing-RiPP | 2,280,220 | 2,307,339 |  |
Region 1.7 | 2dos | 2,638,242 | 2,672,640 |
Region 1.8 | terpene-precursor | 3,260,606 | 3,281,520 | Low | polyhydroxyalkanoate | other:other

NC_009620.1 (Sinorhizobium medicae WSM419 (Ensifer medicae WSM419))

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | redox-cofactor | 356,981 | 379,168 |

NC_009621.1 (Sinorhizobium medicae WSM419 (Ensifer medicae WSM419))

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | hserlactone | 331,930 | 352,550 |
Region 3.2 | lanthipeptide-class-ii,thioamitides | 1,013,923 | 1,051,872 |  |

NC_009622.1 (Sinorhizobium medicae WSM419 (Ensifer medicae WSM419))

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 4.1 | NRPS,hserlactone | 98,254 | 191,847 |  |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | T1PKS | 197,291 | 244,793 |
Region 1.2 | terpene | 1,244,252 | 1,265,094 |
Region 1.3 | hserlactone | 1,644,170 | 1,664,814 |
Region 1.4 | arylpolyene | 1,799,350 | 1,840,552 |  |
Region 1.5 | thioamitides | 2,029,871 | 2,051,884 |
Region 1.6 | azole-containing-RiPP | 2,280,220 | 2,307,339 |  |
Region 1.7 | 2dos | 2,638,242 | 2,672,640 |
Region 1.8 | terpene-precursor | 3,260,606 | 3,281,520 | Low | polyhydroxyalkanoate | other:other
Region 2.1 | redox-cofactor | 356,981 | 379,168 |
Region 3.1 | hserlactone | 331,930 | 352,550 |
Region 3.2 | lanthipeptide-class-ii,thioamitides | 1,013,923 | 1,051,872 |  |
Region 4.1 | NRPS,hserlactone | 98,254 | 191,847 |  |

Compact view
NC_009636.1 - Region 1 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 197,291 - 244,793 nt. (total: 47,503 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
SMED_RS00955: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

SMED_RS00980: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMED_RS00990: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Hydrolases: hydrolase
SMED_RS00930: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Ligases: synthase
SMED_RS00985: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

Translocases: transporter
SMED_RS00935: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  | 0.66 | PKS | asperlactone | Aspergillus ochraceus
BGC0002191.2 |  | 0.62 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000107.3 |  | 0.60 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0002154.2 |  | 0.60 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001257.3 |  | 0.59 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0000037.4 |  | 0.59 | PKS | cichorine | Aspergillus nidulans FGSC A4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  | 0.66 | PKS | asperlactone | Aspergillus ochraceus
BGC0002191.2 |  | 0.62 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000107.3 |  | 0.60 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0002154.2 |  | 0.60 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001257.3 |  | 0.59 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0000037.4 |  | 0.59 | PKS | cichorine | 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:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.79 out of 21.84
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (7):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.57 out of 20.97
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.10 out of 28.14
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.79 out of 26.85
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.48 out of 28.14
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.03 out of 30.12
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.64 out of 29.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.67 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 1, location 197290 - 244793:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (redmal)

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).
SMED_RS00990: mal
PKS_AT (527..824): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  Propionyl-CoA: 62.5%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 87.3
  Methoxymalonyl-CoA: 80.0
  Methylmalonyl-CoA: 79.7
  Ethylmalonyl-CoA: 47.4
  Propionyl-CoA: 37.1
  trans-1,2-CPDA: 35.1
  3-Methylbutyryl-CoA: 29.0
  inactive: 25.9
  Isobutyryl-CoA: 21.1
  2-Methylbutyryl-CoA: 19.4
  fatty_acid: 18.6
  CHC-CoA: 12.9
  Acetyl-CoA: 7.5
  Benzoyl-CoA: 0.0

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
MexT | Global virulence regulator

NC_009636.1 - Region 2 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,244,252 - 1,265,094 nt. (total: 20,843 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002120.3 |  | 0.25 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000698.5 |  | 0.18 | saccharide | hygromycin A | Streptomyces hygroscopicus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002120.3 |  | 0.25 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000698.5 |  | 0.18 | saccharide | hygromycin A | Streptomyces hygroscopicus

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

No significant matches found.

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

No significant matches found.

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 |  | PSPP | C30 | acyclic | PP
triterpene |  | squalene | C30 | acyclic | none
triterpene | C30 carotenoid | diapophytoene | C30 | acyclic | none
tetraterpene | C40 carotenoid | phytoene | C40 | acyclic | none
triterpene |  | hydroxysqualene | C30 | acyclic | OH

Genes with terpene domains:
SMED_RS05875: PT_phytoene_like
Domain 1 (12 - 277): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.52 out of 27.55
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.74 out of 25.88
Confidence: medium
Additional weak hits (1):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.70 out of 31.73
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
--- | ---
GnfM | Regulator of nitrogen-fixation genes
PsrA | Oleic acid responsive regulator

NC_009636.1 - Region 3 - hserlactone
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: 1,644,170 - 1,664,814 nt. (total: 20,645 nt) Show pHMM detection rules used
hserlactone: Autoind_synth

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
SMED_RS07845: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: hydratase
SMED_RS07860: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

Isomerases: racemase
SMED_RS07805: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

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 | hserlactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001555.4 |  | 0.41 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000584.5 |  | 0.40 | ribosomal | colicin V | Escherichia coli
BGC0001660.3 |  | 0.40 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000589.5 |  | 0.39 | ribosomal | microcin M | Escherichia coli Nissle 1917
BGC0000588.5 |  | 0.39 | ribosomal | microcin L | Escherichia coli
BGC0000561.5 |  | 0.39 | ribosomal | thermophilin 1277 | Streptococcus thermophilus
BGC0000587.5 |  | 0.39 | ribosomal | microcin H47 | Escherichia coli
BGC0000498.5 |  | 0.38 | ribosomal | bovicin HJ50 | Streptococcus equinus
BGC0001684.3 |  | 0.38 | other (other) | N-acyloxyacyl glutamine | Klebsiella variicola
BGC0000188.5 |  | 0.38 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001555.4 |  | 0.41 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000584.5 |  | 0.40 | ribosomal | colicin V | Escherichia coli
BGC0001660.3 |  | 0.40 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000589.5 |  | 0.39 | ribosomal | microcin M | Escherichia coli Nissle 1917
BGC0000588.5 |  | 0.39 | ribosomal | microcin L | Escherichia coli
BGC0000561.5 |  | 0.39 | ribosomal | thermophilin 1277 | Streptococcus thermophilus
BGC0000587.5 |  | 0.39 | ribosomal | microcin H47 | Escherichia coli
BGC0000498.5 |  | 0.38 | ribosomal | bovicin HJ50 | Streptococcus equinus
BGC0001684.3 |  | 0.38 | other (other) | N-acyloxyacyl glutamine | Klebsiella variicola
BGC0000188.5 |  | 0.38 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 21.40 out of 23.05
Confidence: strong
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
Additional weak hits (10):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.55 out of 27.78
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.46 out of 32.74
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.58 out of 30.22
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.27 out of 32.74
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.52 out of 18.57
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.75 out of 26.12
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 21.27 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.00 out of 27.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.81 out of 32.93
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.76 out of 32.93
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production

NC_009636.1 - Region 4 - arylpolyene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,799,350 - 1,840,552 nt. (total: 41,203 nt) Show pHMM detection rules used
arylpolyene: (APE_KS1 or APE_KS2)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
SMED_RS08600: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

SMED_RS08605: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

SMED_RS08655: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

SMED_RS08680: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: aminotransferase
SMED_RS08715: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Ligases: synthase
SMED_RS08685: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SMED_RS08690: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

Translocases: transporter
SMED_RS08635: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | arylpolyene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002000.4 |  | 0.44 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0002487.3 |  | 0.44 | other (other) | staphylopine | Staphylococcus aureus subsp. aureus Mu50
BGC0001987.2 |  | 0.44 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0002488.3 |  | 0.44 | other (other) | bacillopaline | Paenibacillus mucilaginosus KNP414
BGC0002656.2 |  | 0.44 | PKS | oryzanaphthopyran A, oryzanaphthopyran B, oryzanaphthopyran C, oryzanthrone A, oryzanthrone B, chlororyzanthrone A, chlororyzanthrone B | Streptacidiphilus oryzae TH49
BGC0000196.4 |  | 0.44 | PKS | AQ-256, AQ-270a, AQ-284a | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002711.2 |  | 0.43 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000254.5 |  | 0.43 | PKS | oxytetracycline | Streptomyces rimosus
BGC0000264.5 |  | 0.43 | PKS | resistomycin, resistoflavine | Streptomyces resistomycificus
BGC0002510.2 |  | 0.43 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002000.4 |  | 0.44 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0002487.3 |  | 0.44 | other (other) | staphylopine | Staphylococcus aureus subsp. aureus Mu50
BGC0001987.2 |  | 0.44 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0002488.3 |  | 0.44 | other (other) | bacillopaline | Paenibacillus mucilaginosus KNP414
BGC0002656.2 |  | 0.44 | PKS | oryzanaphthopyran A, oryzanaphthopyran B, oryzanaphthopyran C, oryzanthrone A, oryzanthrone B, chlororyzanthrone A, chlororyzanthrone B | Streptacidiphilus oryzae TH49
BGC0000196.4 |  | 0.44 | PKS | AQ-256, AQ-270a, AQ-284a | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002711.2 |  | 0.43 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000254.5 |  | 0.43 | PKS | oxytetracycline | Streptomyces rimosus
BGC0000264.5 |  | 0.43 | PKS | resistomycin, resistoflavine | Streptomyces resistomycificus
BGC0002510.2 |  | 0.43 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.71 out of 20.47
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46
Confidence: strong
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 23.22 out of 27.55
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 24.74 out of 26.33
Confidence: strong
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.54 out of 28.19
Confidence: medium
Additional weak hits (9):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.13 out of 26.06
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.90 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.55 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.59 out of 30.97
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.25 out of 36.53
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.70 out of 32.93
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
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
--- | ---
ANR | Anaerobic transcriptional regulator
GnfM | Regulator of nitrogen-fixation genes
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NC_009636.1 - Region 5 - thioamitides
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,029,871 - 2,051,884 nt. (total: 22,014 nt) Show pHMM detection rules used
thioamitides: ((YcaO or TIGR03604) and TfuA)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acyltransferase
SMED_RS09885: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

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

Reference | thioamitides | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001849.4 |  | 0.45 | ribosomal | thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D | Streptomyces varsoviensis
BGC0002560.3 |  | 0.45 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0000625.5 |  | 0.41 | ribosomal | thioviridamide | Streptomyces olivoviridis
BGC0001802.5 |  | 0.40 | ribosomal | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0001696.5 |  | 0.40 | ribosomal | neothioviridamide | Streptomyces sp.
BGC0002669.2 |  | 0.38 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87
BGC0002120.3 |  | 0.31 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000544.4 |  | 0.31 | ribosomal | planosporicin | Planomonospora alba
BGC0001510.5 |  | 0.28 | other (other) | anisomycin | Streptomyces hygrospinosus
BGC0001797.3 |  | 0.27 | ribosomal | telomestatin | Streptomyces anulatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001849.4 |  | 0.45 | ribosomal | thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D | Streptomyces varsoviensis
BGC0002560.3 |  | 0.45 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0000625.5 |  | 0.41 | ribosomal | thioviridamide | Streptomyces olivoviridis
BGC0001802.5 |  | 0.40 | ribosomal | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0001696.5 |  | 0.40 | ribosomal | neothioviridamide | Streptomyces sp.
BGC0002669.2 |  | 0.38 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87
BGC0002120.3 |  | 0.31 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000544.4 |  | 0.31 | ribosomal | planosporicin | Planomonospora alba
BGC0001510.5 |  | 0.28 | other (other) | anisomycin | Streptomyces hygrospinosus
BGC0001797.3 |  | 0.27 | ribosomal | telomestatin | Streptomyces anulatus

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.02 out of 21.84
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31
Confidence: medium
Additional weak hits (7):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.89 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.33 out of 26.06
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.70 out of 20.97
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.23 out of 30.98
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.27 out of 18.57
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.97 out of 30.98
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 23.67 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
MexT | Global virulence regulator

NC_009636.1 - Region 6 - azole-containing-RiPP
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,280,220 - 2,307,339 nt. (total: 27,120 nt) Show pHMM detection rules used
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
SMED_RS11105: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: sulfhydrylase
SMED_RS10985: O-succinylhomoserine sulfhydrylase

smcogs
  SMCOG1168: O-succinylhomoserine sulfhydrylase

Lyases: hydratase
SMED_RS11005: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: synthase
SMED_RS11110: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate 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 | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000948.5 |  | 0.53 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0000706.3 |  | 0.42 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001909.3 |  | 0.39 | PKS | strobilurin A | Strobilurus tenacellus
BGC0000483.5 |  | 0.38 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0000477.3 |  | 0.38 | ribosomal | patellin 2, patellin 3 | uncultured Prochloron sp. 06037A
BGC0000904.5 |  | 0.38 | other (other) | FR-900098 | Streptomyces rubellomurinus
BGC0001215.5 |  | 0.38 | NRPS | conglobatin | Streptomyces conglobatus
BGC0002246.3 |  | 0.37 | terpene | naematolin | Hypholoma sublateritium FD-334 SS-4
BGC0000783.3 |  | 0.37 | saccharide | O-antigen | Xanthomonas oryzae pv. oryzae
BGC0002560.3 |  | 0.36 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000948.5 |  | 0.53 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0000706.3 |  | 0.42 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001909.3 |  | 0.39 | PKS | strobilurin A | Strobilurus tenacellus
BGC0000483.5 |  | 0.38 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0000477.3 |  | 0.38 | ribosomal | patellin 2, patellin 3 | uncultured Prochloron sp. 06037A
BGC0000904.5 |  | 0.38 | other (other) | FR-900098 | Streptomyces rubellomurinus
BGC0001215.5 |  | 0.38 | NRPS | conglobatin | Streptomyces conglobatus
BGC0002246.3 |  | 0.37 | terpene | naematolin | Hypholoma sublateritium FD-334 SS-4
BGC0000783.3 |  | 0.37 | saccharide | O-antigen | Xanthomonas oryzae pv. oryzae
BGC0002560.3 |  | 0.36 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4

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 (10):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.32 out of 26.12
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.91 out of 31.73
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.49 out of 39.62
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.34 out of 27.78
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.78 out of 20.01
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.12 out of 27.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.43 out of 30.25
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.28 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.66 out of 29.65
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
TFBS Finder
Azole RiPPs
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
NC_009636.1 - Region 7 - 2dos
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: 2,638,242 - 2,672,640 nt. (total: 34,399 nt) Show pHMM detection rules used
2dos: ((DOIS or DHQ_synthase or ValA or salQ) and DegT_DnrJ_EryC1 and (LipV or ADSI-DH or cds(ADH_N and ADH_zinc_N)))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acyltransferase aminotransferase transferase
SMED_RS12750: acyltransferase

smcogs
  SMCOG1141: acyltransferase

SMED_RS12770: aminotransferase

smcogs
  SMCOG1019: aminotransferase

SMED_RS12855: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Hydrolases: hydrolase
SMED_RS12780: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

SMED_RS12880: amidohydrolase

smcogs
  SMCOG1244: amidohydrolase

Ligases: synthase
SMED_RS12840: 3-dehydroquinate synthase

smcogs
  SMCOG1183: 3-dehydroquinate synthase

SMED_RS12870: cobalamin synthesis protein/P47K family protein

smcogs
  SMCOG1178: cobalamin synthesis protein/P47K family protein

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

Reference | 2dos | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002584.2 |  | 0.43 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0001206.5 |  | 0.42 | other (other) | indolmycin | Streptomyces griseus subsp. griseus
BGC0001485.4 |  | 0.42 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000558.5 |  | 0.42 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0002116.3 |  | 0.42 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0001534.3 |  | 0.41 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0001267.3 |  | 0.41 | terpene | elymoclavine, Agroclavine I | Claviceps fusiformis
BGC0001229.4 |  | 0.41 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0000925.5 |  | 0.41 | other (other) | quinolobactin | Pseudomonas fluorescens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002584.2 |  | 0.43 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0001206.5 |  | 0.42 | other (other) | indolmycin | Streptomyces griseus subsp. griseus
BGC0001485.4 |  | 0.42 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000558.5 |  | 0.42 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0002116.3 |  | 0.42 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0001534.3 |  | 0.41 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0001267.3 |  | 0.41 | terpene | elymoclavine, Agroclavine I | Claviceps fusiformis
BGC0001229.4 |  | 0.41 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0000925.5 |  | 0.41 | other (other) | quinolobactin | Pseudomonas fluorescens

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:
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.41 out of 27.55
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.59 out of 18.57
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.82 out of 21.84
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.29 out of 25.31
Confidence: medium
Additional weak hits (6):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.46 out of 21.55
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.79 out of 20.01
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.48 out of 32.74
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.09 out of 20.01
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.66 out of 29.25
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.90 out of 24.78
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
GnfM | Regulator of nitrogen-fixation genes
MexT | Global virulence regulator
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NC_009636.1 - Region 8 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,260,606 - 3,281,520 nt. (total: 20,915 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
SMED_RS15640: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SMED_RS15680: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase aminotransferase kinase sulfotransferase transketolase
SMED_RS15645: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

SMED_RS15660: glutathione S-transferase

smcogs
  SMCOG1193: glutathione S-transferase

SMED_RS15675: aminotransferase

smcogs
  SMCOG1019: aminotransferase

SMED_RS15700: transketolase

smcogs
  SMCOG1204: transketolase

SMED_RS15710: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

Ligases: synthase synthetase
SMED_RS15670: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

SMED_RS15705: 1-deoxy-D-xylulose-5-phosphate synthase

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

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000866.5 |  | 0.58 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000867.3 |  | 0.50 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0001361.3 |  | 0.48 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.48 | terpene | sodorifen | Serratia plymuthica
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0001184.4 |  | 0.45 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0000894.4 |  | 0.45 | other (other) | citrinin | Monascus aurantiacus
BGC0000888.5 |  | 0.44 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001605.3 |  | 0.44 | terpene | gibberellin | Sinorhizobium fredii NGR234

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000866.5 |  | 0.58 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000867.3 |  | 0.50 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0001361.3 |  | 0.48 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.48 | terpene | sodorifen | Serratia plymuthica
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0001184.4 |  | 0.45 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0000894.4 |  | 0.45 | other (other) | citrinin | Monascus aurantiacus
BGC0000888.5 |  | 0.44 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001605.3 |  | 0.44 | terpene | gibberellin | Sinorhizobium fredii NGR234

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

No significant matches found.

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

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

Genes with terpene domains:
SMED_RS15670: PT_FPPS_like
Domain 1 (42 - 303): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:
  IPP, DMAPP → 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: 25.77 out of 29.72
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 23.11 out of 27.18
Confidence: medium
Additional weak hits (10):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.24 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.74 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.62 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.74 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.88 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.49 out of 30.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.40 out of 26.12
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.76 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.27 out of 29.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.42 out of 35.63
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
--- | ---
NrdR | Represses ribonucleotide reductase encoding genes
NtrC | Nitrogen regulatory protein C

NC_009620.1 - Region 1 - 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: 356,981 - 379,168 nt. (total: 22,188 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
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
SMED_RS19620: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: transketolase
SMED_RS19670: transketolase

smcogs
  SMCOG1204: transketolase

Hydrolases: hydrolase
SMED_RS19605: 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
--- | --- | --- | --- | --- | ---
BGC0002571.2 |  | 0.43 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0002404.2 |  | 0.41 | other (other) | falcarindiol | Solanum lycopersicum
BGC0002575.2 |  | 0.41 | ribosomal | cochonodin I | Streptococcus suis
BGC0000043.5 |  | 0.39 | PKS | curacin A | Moorea producens 19L
BGC0002514.3 |  | 0.38 | PKS | julichrome Q6.6 | Streptomyces sampsonii
BGC0002012.4 |  | 0.37 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772
BGC0002181.3 |  | 0.37 | terpene | pleuromutilin | Rhodocybe pseudopiperita
BGC0000252.5 |  | 0.37 | PKS | nonactin | Streptomyces griseus subsp. griseus
BGC0001605.3 |  | 0.37 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0002000.4 |  | 0.37 | PKS | setomimycin | Streptomyces aurantiacus JA 4570

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002571.2 |  | 0.43 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0002404.2 |  | 0.41 | other (other) | falcarindiol | Solanum lycopersicum
BGC0002575.2 |  | 0.41 | ribosomal | cochonodin I | Streptococcus suis
BGC0000043.5 |  | 0.39 | PKS | curacin A | Moorea producens 19L
BGC0002514.3 |  | 0.38 | PKS | julichrome Q6.6 | Streptomyces sampsonii
BGC0002012.4 |  | 0.37 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772
BGC0002181.3 |  | 0.37 | terpene | pleuromutilin | Rhodocybe pseudopiperita
BGC0000252.5 |  | 0.37 | PKS | nonactin | Streptomyces griseus subsp. griseus
BGC0001605.3 |  | 0.37 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0002000.4 |  | 0.37 | PKS | setomimycin | Streptomyces aurantiacus JA 4570

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.19 out of 20.47
Confidence: strong
Additional weak hits (4):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.53 out of 23.43
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.10 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.98 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.38 out of 31.73
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (356980...379168)
SMED_RS19635
  RRE type: PqqD_RRE
  Location: 7 - 95
  Score: 93.9
  RRE type: Thurincin_rSAM_RRE
  Location: 34 - 89
  Score: 27.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NC_009621.1 - Region 1 - hserlactone
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: 331,930 - 352,550 nt. (total: 20,621 nt) Show pHMM detection rules used
hserlactone: Autoind_synth

#### Legend:

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

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

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

Reference | hserlactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001992.3 |  | 0.35 | other (other) | thioguanine | Erwinia amylovora CFBP1430
BGC0002713.2 |  | 0.23 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0000495.5 |  | 0.22 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0000446.5 |  | 0.20 | NRPS | tilivalline, 9-deoxy tilivalline, dihydroxy tilivalline, dehydro tilivalline, dihydroxy-dehydro tilivalline | Klebsiella oxytoca
BGC0000344.5 |  | 0.20 | NRPS | entolysin | Pseudomonas entomophila L48
BGC0002336.2 |  | 0.18 | NRPS | bolagladin A, bolagladin B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001992.3 |  | 0.35 | other (other) | thioguanine | Erwinia amylovora CFBP1430
BGC0002713.2 |  | 0.23 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0000495.5 |  | 0.22 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0000446.5 |  | 0.20 | NRPS | tilivalline, 9-deoxy tilivalline, dihydroxy tilivalline, dehydro tilivalline, dihydroxy-dehydro tilivalline | Klebsiella oxytoca
BGC0000344.5 |  | 0.20 | NRPS | entolysin | Pseudomonas entomophila L48
BGC0002336.2 |  | 0.18 | NRPS | bolagladin A, bolagladin B | Burkholderia gladioli

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.65 out of 18.46
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.13 out of 20.97
Confidence: medium
Additional weak hits (5):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.37 out of 29.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.62 out of 30.22
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.02 out of 32.93
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.31 out of 29.65
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.68 out of 27.18
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
RpoN | Regulator of nitrogen assimilation and virulence

NC_009621.1 - Region 2 - lanthipeptide-class-ii,thioamitides
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,013,923 - 1,051,872 nt. (total: 37,950 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)
thioamitides: ((YcaO or TIGR03604) and TfuA)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: methyltransferase
SMED_RS30005: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: cyclase
SMED_RS29965: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

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

Reference | lanthipeptide-class-ii | thioamitides | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000917.3 |  |  | 0.36 | other (other) | molybdenum cofactor | Rhodobacter capsulatus
BGC0001687.3 |  |  | 0.24 | other (other) | N-tetradecanoyl tyrosine | uncultured bacterium CSL12
BGC0002560.3 |  |  | 0.23 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0000925.5 |  |  | 0.20 | other (other) | quinolobactin | Pseudomonas fluorescens
BGC0000297.5 |  |  | 0.16 | NRPS, PKS, saccharide | aeruginoside 126B, aeruginoside 126A | Planktothrix agardhii NIVA-CYA 126
BGC0000320.5 |  |  | 0.16 | NRPS | cereulide | Bacillus cereus
BGC0000651.5 |  |  | 0.15 | terpene | KS-505a | Streptomyces argenteolus
BGC0001802.5 |  |  | 0.15 | ribosomal | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0001696.5 |  |  | 0.15 | ribosomal | neothioviridamide | Streptomyces sp.
BGC0001212.4 |  |  | 0.14 | NRPS, PKS | nannocystin a | Nannocystis sp. MB1016

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002560.3 |  | 0.50 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0000917.3 |  | 0.49 | other (other) | molybdenum cofactor | Rhodobacter capsulatus
BGC0001867.2 |  | 0.47 | ribosomal | prochlorosins | Prochlorococcus marinus str. MIT 9313
BGC0001802.5 |  | 0.47 | ribosomal | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0001696.5 |  | 0.47 | ribosomal | neothioviridamide | Streptomyces sp.
BGC0000625.5 |  | 0.43 | ribosomal | thioviridamide | Streptomyces olivoviridis
BGC0000554.4 |  | 0.42 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000772.5 |  | 0.42 | saccharide | lipopolysaccharide | Brucella melitensis
BGC0002699.2 |  | 0.41 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0002120.3 |  | 0.41 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706

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 SMED_RS29965

allorf_1014954_1015118
Leader:
MRSHRSRGEHPGIRSRERGA
Core:
A R C P G C S S D A P K M R R S G R F M C W L Q A W E S R P V F R G
Core with dehydrations:
A R Cys P G Cys Dha Dha D A P K M R R Dha G R F M Cys W L Q A W E Dha R P V F R G

#### antiSMASH-DB 4.0 matches for allorf_1014954_1015118

100.0%
NC_009621.1 and 2 others:
NZ_CP088111.1 Lanthipeptides: allorf_0781198_0781362_lanthipeptide NZ_VITA01000039.1 Lanthipeptides: allorf_12218_12382_lanthipeptide
Lanthipeptides: allorf_1014954_1015118_lanthipeptide
1
A R C P G C S S D A P K M R R S G R F M C W L Q A W E S R P V F R G
34
A R C P G C S S D A P K M R R S G R F M C W L Q A W E S R P V F R G
1
A R C P G C S S D A P K M R R S G R F M C W L Q A W E S R P V F R G
34
20.6%
NZ_CP119804.1:
Lanthipeptides: allorf_1910563_1910769_lanthipeptide
5
G C S S D A P K M R R S G R F M C W L Q A W
26
G C S D P++ R + L +
6
G C E S D P P R I Y E I V R K I I T L M L Y
27
20.6%
NZ_JPLW01000002.1 and 1 other:
NZ_LIWC01000001.1 Lanthipeptides: allorf_1205972_1206109_lanthipeptide
Lanthipeptides: allorf_1074773_1074940_lanthipeptide
21
C W L Q A W E S R P
30
C L Q+ E S R P
4
C G L Q S R E S R P
13
with 4 more sequence matches
20.5%
NZ_CP035758.1:
Lanthipeptides: allorf_03482707_03482883_lanthipeptide
6
C S S D A P K M R R S G R F M C W L Q A W E
27
C S+++ K+R R +C++ W E
21
C S A E S H K I R R Q---I C F V T R W E
39
17.6%
NZ_NUFU01000017.1 and 1 other:
NZ_VEAZ01000013.1 Lanthipeptides: allorf_70472_70657_lanthipeptide
Lanthipeptides: allorf_1190_1375_lanthipeptide
11
P K M R R S G R F M C W
22
P M S F C W
1
P A M S T S S A F A C W
12
14.7%
NZ_CP063989.1:
Lanthipeptides: allorf_0180638_0180811_lanthipeptide
2
R C P G C S S
8
R C P G C +
2
R C P G C D T
8
11.8%
NZ_AKXV01000031.1 and 1 other:
NZ_LMEI01000006.1 Lanthipeptides: ASC82_RS06200_lanthipeptide
Lanthipeptides: Y19_RS0109830_lanthipeptide
21
C W L Q A W E S R P
30
C W+ W+ +P
8
C W V N G W Q E K P
17
allorf_1015605_1015727
Leader:
MSRDDRFATILAS
Core:
A S H S C E R R R G F M L S K V E R R R I F C L K P S
Core with dehydrations:
A Dha H Dha Cys E R R R G F M L Dha K V E R R R I F Cys L K P Dha

#### antiSMASH-DB 4.0 matches for allorf_1015605_1015727

100.0%
NC_009621.1 and 2 others:
NZ_CP088111.1 Lanthipeptides: allorf_0781849_0781971_lanthipeptide NZ_VITA01000039.1 Lanthipeptides: allorf_11609_11731_lanthipeptide
Lanthipeptides: allorf_1015605_1015727_lanthipeptide
1
A S H S C E R R R G F M L S K V E R R R I F C L K P S
27
A S H S C E R R R G F M L S K V E R R R I F C L K P S
1
A S H S C E R R R G F M L S K V E R R R I F C L K P S
27
22.2%
NZ_CP059997.1:
Lanthipeptides: allorf_02572182_02572382_lanthipeptide
1
A S H S C E R R R G F M L S K
15
A C R R G F+ +
8
A Y S P C A R R P G F L T G Q
22
22.2%
NZ_QGTL01000006.1:
Lanthipeptides: allorf_313739_313885_lanthipeptide
1
A S H S C E R R R G
10
A+ +C R R R G
12
A A Q A C A R R R G
21
with 1 more sequence matches
12.3%
NZ_CP059318.1:
Lanthipeptides: allorf_0101772_0101999_lanthipeptide
4
S C E R R R G F M L S K V E R R R
20
S + R G F+ +V R R+
19
S A D G S R G F L P V R V G R R Q
35

#### MIBiG 4.0 matches for allorf_1015605_1015727

18.5%
BGC0001155.5 (AGY49587.1):
Thiopeptide: GE2270
4
S C E R R R G F M L S
14
S C G F S
1
S C N C V C G F C C S
11
allorf_1016269_1016397
Leader:
MRRRLSTRSAA
Core:
D P G Q L Q A R R G L L R R C F R G S A D E C F K R C H A E G
Core with dehydrations:
D P G Q L Q A R R G L L R R Cys F R G Dha A D E Cys F K R Cys H A E G

#### antiSMASH-DB 4.0 matches for allorf_1016269_1016397

100.0%
NC_009621.1:
Lanthipeptides: allorf_1016269_1016397_lanthipeptide
1
D P G Q L Q A R R G L L R R C F R G S A D E C F K R C H A E G
31
D P G Q L Q A R R G L L R R C F R G S A D E C F K R C H A E G
1
D P G Q L Q A R R G L L R R C F R G S A D E C F K R C H A E G
31
19.4%
NZ_LNZF01000002.1:
Lanthipeptides: allorf_0849351_0849530_lanthipeptide
16
F R G S A D E C F K R C
27
F S C F R C
3
F S S S H S T C F H R C
14

#### MIBiG 4.0 matches for allorf_1016269_1016397

8.1%
BGC0001229.4 (SBI_06989):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
21
D E C F K R C
27
+C R C
31
T K C T S R C
37
allorf_1016557_1016634
Leader:
MGICLTRPHRGQIAAT
Core:
E L A L S C E E C
Core with dehydrations:
E L A L Dha Cys E E Cys

#### antiSMASH-DB 4.0 matches for allorf_1016557_1016634

100.0%
NC_009621.1 and 1 other:
NZ_CP088111.1 Lanthipeptides: allorf_0782801_0782878_lanthipeptide
Lanthipeptides: allorf_1016557_1016634_lanthipeptide
1
E L A L S C E E C
9
E L A L S C E E C
1
E L A L S C E E C
9
allorf_1019318_1019422
Leader:
MRYMYEATYARLCPSSSTISKIYLKQITGS
Core:
N C T I
Core with dehydrations:
N Cys Dhb I
allorf_1019406_1019552
Leader:
MQPTSLGG
Core:
P R P L H F I L V D C A P V A N P T Y V E A D L R A T M K H D Q F M C F A I H V
Core with dehydrations:
P R P L H F I L V D Cys A P V A N P Dhb Y V E A D L R A Dhb M K H D Q F M Cys F A I H V

#### antiSMASH-DB 4.0 matches for allorf_1019406_1019552

100.0%
NC_009621.1 and 4 others:
NZ_CP088111.1 Lanthipeptides: allorf_0785650_0785796_lanthipeptide NZ_NBUK01000063.1 Lanthipeptides: allorf_7824_7970_lanthipeptide NZ_VISX01000063.1 Lanthipeptides: allorf_0786_0932_lanthipeptide NZ_VITA01000039.1 Lanthipeptides: allorf_07780_07926_lanthipeptide
Lanthipeptides: allorf_1019406_1019552_lanthipeptide
1
P R P L H F I L V D C A P V A N P T Y V E A D L R A T M K H D Q F M C F A I H V
40
P R P L H F I L V D C A P V A N P T Y V E A D L R A T M K H D Q F M C F A I H V
1
P R P L H F I L V D C A P V A N P T Y V E A D L R A T M K H D Q F M C F A I H V
40
97.5%
NC_017327.1 and 1 other:
NZ_CP021217.1 Lanthipeptides: allorf_1159245_1159391_lanthipeptide
Lanthipeptides: allorf_0124716_0124862_lanthipeptide
1
P R P L H F I L V D C A P V A N P T Y V E A D L R A T M K H D Q F M C F A I H V
40
P R P L H F I L V D C A P V A N P T Y V+A D L R A T M K H D Q F M C F A I H V
1
P R P L H F I L V D C A P V A N P T Y V D A D L R A T M K H D Q F M C F A I H V
40
20.0%
NZ_CP015591.1 and 15 others:
NZ_CP078085.1 Lanthipeptides: KU891_RS29355_lanthipeptide NZ_CP078085.1 Lanthipeptides: KU891_RS29350_lanthipeptide NZ_CP078085.1 Lanthipeptides: KU891_RS29345_lanthipeptide NZ_CP078085.1 Lanthipeptides: KU891_RS29340_lanthipeptide NZ_CP078085.1 Lanthipeptides: KU891_RS29335_lanthipeptide NZ_CP085411.1 Lanthipeptides: LIT28_RS29930_lanthipeptide NZ_CP085411.1 Lanthipeptides: LIT28_RS29925_lanthipeptide NZ_CP085411.1 Lanthipeptides: LIT28_RS29920_lanthipeptide NZ_CP085411.1 Lanthipeptides: LIT28_RS29910_lanthipeptide NZ_CP085411.1 Lanthipeptides: LIT28_RS29930_lanthipeptide NZ_CP085411.1 Lanthipeptides: LIT28_RS29925_lanthipeptide NZ_CP085411.1 Lanthipeptides: LIT28_RS29920_lanthipeptide NZ_CP085411.1 Lanthipeptides: LIT28_RS29910_lanthipeptide NZ_QNUC01000031.1 Lanthipeptides: DN396_RS23050_lanthipeptide NZ_QNUC01000031.1 Lanthipeptides: DN396_RS23050_lanthipeptide
Lanthipeptides: A7A70_RS27550_lanthipeptide
15
A N P T Y V E A D L R A T M K
29
A P T V E A + A T+
10
A T P T I V E A T I A A T V S
24
with 4 more sequence matches
20.0%
NZ_CP059734.1:
Lanthipeptides: allorf_0384683_0384871_lanthipeptide
4
L H F I L V D C A P V A N P
17
L H + C P V A N P
1
L H I Y F L T C Q P V A N P
14
17.5%
NZ_CP012109.1:
Lanthipeptides: allorf_7979331_7979543_lanthipeptide
1
P R P L H F I L V D C A P
13
P R P +L D C P
14
P R P A R A L L R D C R P
26
17.5%
NZ_FONG01000023.1:
Lanthipeptides: allorf_088862_088996_lanthipeptide
10
D C A P V A N P T Y V E A D L R A
26
D A P P T +L R
7
D A A P P T Q P T R R R P E L R G
23
12.5%
NZ_VIKW01000003.1:
Lanthipeptides: FJR04_RS03310_lanthipeptide
3
P L H F I L V D C A P V A
15
P H + V C P+
7
P F H T L W V G C K P I G
19
allorf_1019555_1019737
Leader:
MLNCAQRAFSKAPLPTGVIWRCSVIPTLRVVGTIPGA
Core:
P S A A A T A S I P V D T W P F S T K D S D C
Core with dehydrations:
P Dha A A A Dhb A Dha I P V D Dhb W P F Dha Dhb K D Dha D Cys

#### antiSMASH-DB 4.0 matches for allorf_1019555_1019737

100.0%
NC_009621.1 and 3 others:
NZ_CP088111.1 Lanthipeptides: allorf_0785799_0785981_lanthipeptide NZ_NBUK01000063.1 Lanthipeptides: allorf_7639_7821_lanthipeptide NZ_VISX01000063.1 Lanthipeptides: allorf_0935_1117_lanthipeptide
Lanthipeptides: allorf_1019555_1019737_lanthipeptide
1
P S A A A T A S I P V D T W P F S T K D S D C
23
P S A A A T A S I P V D T W P F S T K D S D C
1
P S A A A T A S I P V D T W P F S T K D S D C
23
22.6%
NZ_QLLX01000002.1 and 1 other:
NZ_QLLX01000002.1 Lanthipeptides: allorf_335035_335211_lanthipeptide
Lanthipeptides: allorf_335035_335211_lanthipeptide
2
S A A A T A S I P V D T W P F
16
+A A A S+P T P+
10
T A A A H R S V P T R T C P Y
24
17.9%
NZ_NTWJ01000043.1 and 1 other:
NZ_NTWJ01000043.1 Lanthipeptides: CN427_RS29340_lanthipeptide
Lanthipeptides: CN427_RS29340_lanthipeptide
5
A T A S I P V D T W P F S T K D S D C
23
A ++ V T W F T + C
12
A G L T V A V G T W V F Q T S E K T C
30
with 1 more sequence matches
17.9%
NZ_NTWJ01000043.1 and 1 other:
NZ_NTWJ01000043.1 Lanthipeptides: CN427_RS31525_lanthipeptide
Lanthipeptides: CN427_RS31525_lanthipeptide
8
S I P V D T W P F S T K D S D C
23
++ V T W F T D C
15
T V A V G T W V F Q T S D K T C
30
allorf_1019980_1020051
Leader:
MVASAGG
Core:
F P A P A R S A E P A D V H N C
Core with dehydrations:
F P A P A R Dha A E P A D V H N Cys

#### antiSMASH-DB 4.0 matches for allorf_1019980_1020051

100.0%
NC_009621.1 and 6 others:
NC_017327.1 Lanthipeptides: allorf_0124171_0124311_lanthipeptide NZ_CP021217.1 Lanthipeptides: allorf_1159796_1159936_lanthipeptide NZ_CP088111.1 Lanthipeptides: allorf_0786224_0786295_lanthipeptide NZ_NBUK01000063.1 Lanthipeptides: allorf_7325_7396_lanthipeptide NZ_VISX01000063.1 Lanthipeptides: allorf_1360_1431_lanthipeptide NZ_VITA01000039.1 Lanthipeptides: allorf_07280_07351_lanthipeptide
Lanthipeptides: allorf_1019980_1020051_lanthipeptide
1
F P A P A R S A E P A D V H N C
16
F P A P A R S A E P A D V H N C
1
F P A P A R S A E P A D V H N C
16
43.8%
NZ_CP077072.1:
Lanthipeptides: allorf_2549811_2549951_lanthipeptide
3
A P A R S A E P A D
12
A P R A E P D
6
A P P R H A E P H D
15
allorf_1020482_1020715
Leader:
MMVVYLRASPSAAYQRINSCQPIRDNESAIS
Core:
Y L S E V A E R L N K Q L I K V Q G E N M V T K S L I K R L M M L V C P P S R R V P P G L G
Core with dehydrations:
Y L Dha E V A E R L N K Q L I K V Q G E N M V Dhb K Dha L I K R L M M L V Cys P P Dha R R V P P G L G

#### antiSMASH-DB 4.0 matches for allorf_1020482_1020715

100.0%
NC_009621.1 and 4 others:
NZ_CP088111.1 Lanthipeptides: allorf_0786726_0786959_lanthipeptide NZ_NBUK01000063.1 Lanthipeptides: allorf_6661_6894_lanthipeptide NZ_VISX01000063.1 Lanthipeptides: allorf_1862_2095_lanthipeptide NZ_VITA01000039.1 Lanthipeptides: allorf_06616_06849_lanthipeptide
Lanthipeptides: allorf_1020482_1020715_lanthipeptide
1
Y L S E V A E R L N K Q L I K V Q G E N M V T K S L I K R L M M L V C P P S R R V P P G L G
46
Y L S E V A E R L N K Q L I K V Q G E N M V T K S L I K R L M M L V C P P S R R V P P G L G
1
Y L S E V A E R L N K Q L I K V Q G E N M V T K S L I K R L M M L V C P P S R R V P P G L G
46
19.6%
NZ_FMHJ01000003.1:
Lanthipeptides: allorf_516193_516348_lanthipeptide
23
T K S L I K R L M M L V C P--P S R R V P P G
44
++ K R L +C P R R P G
5
S R G R G K R L R N A L C G G W P G R R A P Q G
28
17.4%
NZ_BLIS01000009.1 and 5 others:
NZ_BLIS01000009.1 Lanthipeptides: GVO03_RS04860_lanthipeptide NZ_QRWZ01000002.1 Lanthipeptides: DWX18_RS02665_lanthipeptide NZ_QRWZ01000002.1 Lanthipeptides: DWX18_RS02665_lanthipeptide NZ_SPGD01000003.1 Lanthipeptides: FGQ50_RS01890_lanthipeptide NZ_SPGD01000003.1 Lanthipeptides: FGQ50_RS01890_lanthipeptide
Lanthipeptides: GVO03_RS04860_lanthipeptide
17
Q G E N M V T K S L I K R L M M L V C
35
+G E N+ T L+K + L C
10
K G E N V T T D I L L K I C I A L D C
28
with 1 more sequence matches
12.5%
NZ_CP086102.1 and 1 other:
NZ_KZ195572.1 Lanthipeptides: allorf_6138327_6138542_lanthipeptide
Lanthipeptides: allorf_6127439_6127654_lanthipeptide
27
I K R L M M L V C P P S R
39
+R L M +C P R
21
A R R L F M C L C P H C R
33
allorf_1031644_1031781
Leader:
MSRTQAFTRNCRNQAPDAKGEAQAEQTA
Core:
R R E Y R C R R L G R T D P Y E R
Core with dehydrations:
R R E Y R Cys R R L G R Dhb D P Y E R

#### antiSMASH-DB 4.0 matches for allorf_1031644_1031781

100.0%
NC_009621.1:
Lanthipeptides: allorf_1031644_1031781_lanthipeptide
1
R R E Y R C R R L G R T D P Y E R
17
R R E Y R C R R L G R T D P Y E R
1
R R E Y R C R R L G R T D P Y E R
17
11.1%
NZ_CP008953.1:
Lanthipeptides: allorf_3865033_3865224_lanthipeptide
5
R C R R L G R T D P Y E
16
R C R+G P Y
21
R C P R M G A G T P Y S
32
allorf_1031905_1032045
Leader:
MALRDRLSGA
Core:
G L K P V R A A A V K S R G G E R R M K S S D E I R A G A C P K D E R K
Core with dehydrations:
G L K P V R A A A V K Dha R G G E R R M K Dha Dha D E I R A G A Cys P K D E R K

#### antiSMASH-DB 4.0 matches for allorf_1031905_1032045

100.0%
NC_009621.1:
Lanthipeptides: allorf_1031905_1032045_lanthipeptide
1
G L K P V R A A A V K S R G G E R R M K S S D E I R A G A C P K D E R K
36
G L K P V R A A A V K S R G G E R R M K S S D E I R A G A C P K D E R K
1
G L K P V R A A A V K S R G G E R R M K S S D E I R A G A C P K D E R K
36
27.0%
NZ_PNGD01000001.1 and 1 other:
NZ_PNGD01000001.1 Lanthipeptides: CJ239_RS00165_lanthipeptide
Lanthipeptides: CJ239_RS00165_lanthipeptide
2
L K P V R A A A V K S R G G E R R M K S S D E I R A G A C P K D
33
+ P A A S G + + + A G A C P
1
I T P T I I A A T I S F A G---V T F T V T L N A G A C P T S
29
19.4%
NZ_CP045920.1 and 1 other:
NZ_WHMT01000001.1 Lassopeptides: GCG21_RS00575_lassopeptide
Lassopeptides: GCE65_RS02520_lassopeptide
14
G G E R R M K S S D E I R
26
G G S D E I R
1
G G H N L Q D W S D E I R
13
allorf_1033917_1034090
Leader:
MARAPNPRCGGELGTSAQS
Core:
I R H P V I A F E L S D G C T G K C C L A A C R R A P Q A I I A K F S P K R
Core with dehydrations:
I R H P V I A F E L Dha D G Cys Dhb G K Cys Cys L A A Cys R R A P Q A I I A K F Dha P K R

#### antiSMASH-DB 4.0 matches for allorf_1033917_1034090

100.0%
NC_009621.1 and 1 other:
NZ_CP088111.1 Lanthipeptides: allorf_0798277_0798450_lanthipeptide
Lanthipeptides: allorf_1033917_1034090_lanthipeptide
1
I R H P V I A F E L S D G C T G K C C L A A C R R A P Q A I I A K F S P K R
38
I R H P V I A F E L S D G C T G K C C L A A C R R A P Q A I I A K F S P K R
1
I R H P V I A F E L S D G C T G K C C L A A C R R A P Q A I I A K F S P K R
38
26.3%
NC_007777.1 and 1 other:
NC_007777.1 Lanthipeptides: FRANCCI3_RS24210_lanthipeptide
Lanthipeptides: FRANCCI3_RS24210_lanthipeptide
4
P V I A F E L S D G C T G K C C L A A C R R A P Q
28
P + S D C G K C +A C Q
2
P E L L R S T S D N C-G K T C S S A C T S C K Q
25
23.7%
NZ_CP058322.1 and 3 others:
NZ_CP058322.1 Lanthipeptides: HXZ27_RS15425_lanthipeptide NZ_FMCW01000048.1 Lanthipeptides: GA0070558_RS30485_lanthipeptide NZ_FMCW01000048.1 Lanthipeptides: GA0070558_RS30485_lanthipeptide
Lanthipeptides: HXZ27_RS15425_lanthipeptide
5
V I A F E L S D G C T G K C C L A A C R R A
26
V+A S D G C C +A C +
2
V M A C S T S D G C G S T C S T S A C N T S
23
with 17 more sequence matches
Only the first 10 are displayed here.
21.1%
NC_014391.1 and 1 other:
NC_014391.1 Lanthipeptides: MICAU_RS30575_lanthipeptide
Lanthipeptides: MICAU_RS30575_lanthipeptide
5
V I A F E L S D G C T G K C C L A A C R R A
26
++A S D G C C +A C +
2
I M A C S T S D G C G S T C N T S A C A T S
23
21.1%
NZ_CP022752.1 and 3 others:
NZ_CP022752.1 Lanthipeptides: CDG81_RS17720_lanthipeptide NZ_FOMZ01000022.1 Lanthipeptides: BM150_RS23220_lanthipeptide NZ_FOMZ01000022.1 Lanthipeptides: BM150_RS23220_lanthipeptide
Lanthipeptides: CDG81_RS17720_lanthipeptide
6
I A F E L S D G C T G K C C L A A C R R
25
++ + S D G C G C +A C
1
M S C D T S D G C G G T T C G S A C T S
20
21.1%
NZ_KB895870.1 and 1 other:
NZ_KB895870.1 Lanthipeptides: C569_RS0127950_lanthipeptide
Lanthipeptides: C569_RS0127950_lanthipeptide
5
V I A F E L S D G C T G K C C L A A C R R
25
V+ S D G C C +A C
2
V M M C S T S D G C G S S C S T S A C T T
22
21.1%
NZ_SNXZ01000002.1 and 1 other:
NZ_SNXZ01000002.1 Lanthipeptides: EV186_RS12145_lanthipeptide
Lanthipeptides: EV186_RS12145_lanthipeptide
6
I A F E L S D G C T G K C C L A A C R R
25
+A S D C G C +A C
1
M A C S T S D N C G G S T C G S A C T S
20
21.1%
NZ_VEHK01000015.1 and 1 other:
NZ_VEHK01000015.1 Lanthipeptides: FS984_RS32600_lanthipeptide
Lanthipeptides: FS984_RS32600_lanthipeptide
9
E L S D G C T G K C C L A A C R R A P
27
+ S D G C T C +A C +
3
D T S D G C T S T-C Q S A C S N S T
20
21.1%
NZ_VLLL01000010.1 and 1 other:
NZ_VLLL01000010.1 Lanthipeptides: LX16_RS23985_lanthipeptide
Lanthipeptides: LX16_RS23985_lanthipeptide
9
E L S D G C T G K C C L A A C R R A P Q
28
+ S D G C C +A C A
4
D T S D G C G S T C A T S A C N S A T N
23
20.0%
NZ_LT607413.1 and 1 other:
NZ_LT607413.1 Lanthipeptides: GA0070618_RS10945_lanthipeptide
Lanthipeptides: GA0070618_RS10945_lanthipeptide
6
I A F E L S D G C T G K C C L A A C R R A
26
+ + +D G C G K C +A C
18
L I Y M T N D G C-G K T C Q S A C S T T
37
18.4%
NZ_ATYW01000025.1 and 1 other:
NZ_ATYW01000025.1 Lanthipeptides: YWW_RS32370_lanthipeptide
Lanthipeptides: YWW_RS32370_lanthipeptide
9
E L S D G C T G K C C L A A C
23
+ S D G C C +A C
4
D T S D G C G N T C Q T S A C
18
18.4%
NZ_BCBX01000066.1 and 1 other:
NZ_BCBX01000066.1 Lanthipeptides: AP234_RS33370_lanthipeptide
Lanthipeptides: AP234_RS33370_lanthipeptide
5
V I A F E L S D G C T G K C C L A A C R R A P Q
28
++ + S D G C C +A C +
2
I M M C D T S D G C G N S C S T S A C A T S S N
25
18.4%
NZ_CM001439.1 and 5 others:
NZ_CM001439.1 Lanthipeptides: SACMADRAFT_RS20585_lanthipeptide NZ_CP059997.1 Lanthipeptides: HUW46_RS22770_lanthipeptide NZ_CP059997.1 Lanthipeptides: HUW46_RS22770_lanthipeptide NZ_CP090063.1 Lanthipeptides: LWP59_RS37700_lanthipeptide NZ_CP090063.1 Lanthipeptides: LWP59_RS37700_lanthipeptide
Lanthipeptides: SACMADRAFT_RS20585_lanthipeptide
6
I A F E L S D G C T G K C C L A A C R R
25
++ + S D C G C +A C
1
M S C D T S D N C G G T T C G S A C T S
20

#### MIBiG 4.0 matches for allorf_1033917_1034090

13.2%
BGC0001229.4 (SBI_06989):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
7
A F E L S D G C T G K C
18
A F + C T +C
26
A F C P T T K C T S R C
37
10.5%
BGC0002110.3 (QKV49894.1):
Lanthipeptide: birimositide
14
C T G K C
18
C T K C
22
C T S K C
26

#### 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:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.79 out of 25.31
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.64 out of 25.31
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.64 out of 25.31
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.77 out of 28.19
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.64 out of 25.31
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.64 out of 25.31
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.77 out of 28.19
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.64 out of 25.31
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.64 out of 25.31
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.72 out of 23.79
Confidence: medium
Additional weak hits (6):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.88 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.25 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.72 out of 21.55
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.18 out of 29.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.64 out of 29.25
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 23.29 out of 35.63
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

allorf_1014954_1015118 - Class II
  Cleavage pHMM score: -5.70
  RODEO score: 0
  Monoisotopic mass: 3855.9 Da
  Molecular weight: 3858.5 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3876.5 Da N = 1
allorf_1015605_1015727 - Class II
  Cleavage pHMM score: -5.70
  RODEO score: 0
  Monoisotopic mass: 3176.7 Da
  Molecular weight: 3178.7 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3196.8 Da N = 1
    3214.8 Da N = 2
allorf_1016269_1016397 - Class II
  Cleavage pHMM score: -7.00
  RODEO score: 0
  Monoisotopic mass: 3513.7 Da
  Molecular weight: 3516.0 Da
  Number of bridges: 1
allorf_1016557_1016634 - Class II
  Cleavage pHMM score: -7.30
  RODEO score: 0
  Monoisotopic mass: 977.4 Da
  Molecular weight: 978.1 Da
  Number of bridges: 1
allorf_1019318_1019422 - Class II
  Cleavage pHMM score: -4.20
  RODEO score: 0
  Monoisotopic mass: 431.2 Da
  Molecular weight: 431.5 Da
  Number of bridges: 1
allorf_1019406_1019552 - Class II
  Cleavage pHMM score: -5.30
  RODEO score: 0
  Monoisotopic mass: 4529.3 Da
  Molecular weight: 4532.3 Da
  Number of bridges: 2
allorf_1019555_1019737 - Class II
  Cleavage pHMM score: -4.20
  RODEO score: 0
  Monoisotopic mass: 2240.1 Da
  Molecular weight: 2241.4 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2259.4 Da N = 1
    2277.4 Da N = 2
    2295.5 Da N = 3
    2313.5 Da N = 4
    2331.5 Da N = 5
    2349.5 Da N = 6
allorf_1019980_1020051 - Class II
  Cleavage pHMM score: -5.40
  RODEO score: 0
  Monoisotopic mass: 1662.8 Da
  Molecular weight: 1663.8 Da
  Number of bridges: 1
allorf_1020482_1020715 - Class II
  Cleavage pHMM score: -7.30
  RODEO score: 0
  Monoisotopic mass: 5118.9 Da
  Molecular weight: 5122.2 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    5140.2 Da N = 1
    5158.2 Da N = 2
    5176.2 Da N = 3
allorf_1031644_1031781 - Class II
  Cleavage pHMM score: -5.90
  RODEO score: 0
  Monoisotopic mass: 2263.2 Da
  Molecular weight: 2264.5 Da
  Number of bridges: 1
allorf_1031905_1032045 - Class II
  Cleavage pHMM score: -6.00
  RODEO score: 0
  Monoisotopic mass: 3855.1 Da
  Molecular weight: 3857.4 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3875.4 Da N = 1
    3893.5 Da N = 2
allorf_1033917_1034090 - Class II
  Cleavage pHMM score: -5.00
  RODEO score: 0
  Monoisotopic mass: 4072.2 Da
  Molecular weight: 4074.9 Da
  Number of bridges: 3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CatR | H2O2-responsive repressor
IolR | Regulator of the inositol catabolism
ZuR variant 1 | Zinc-responsive repressor

NC_009622.1 - Region 1 - NRPS,hserlactone
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: 98,254 - 191,847 nt. (total: 93,594 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
hserlactone: Autoind_synth

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: PPTase acyltransferase
SMED_RS31685: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

SMED_RS31710: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Ligases: ligase
SMED_RS33235: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | hserlactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001758.4 |  |  | 0.49 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  |  | 0.48 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.47 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  | 0.46 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002071.2 |  |  | 0.46 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0002135.2 |  |  | 0.46 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.46 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  |  | 0.45 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  |  | 0.45 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  | 0.40 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.78 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.77 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.77 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.76 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002071.2 |  | 0.76 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0002135.2 |  | 0.76 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.76 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.16 out of 20.01
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.74 out of 26.85
Confidence: medium
Additional weak hits (27):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.66 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.39 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.23 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.02 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.88 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.39 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 20.67 out of 31.73
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.00 out of 27.78
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.89 out of 33.73
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.94 out of 29.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.94 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.07 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.10 out of 21.55
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.41 out of 39.62
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.07 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.16 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.08 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.71 out of 27.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.72 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.07 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.13 out of 24.78
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 19.17 out of 33.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.38 out of 23.43
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.50 out of 35.63
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.69 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.22 out of 24.78
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 98253 - 191847:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Asn - Asn - Asn - X - Ala - Ala - Gly - Ala) + (Ala - Asn - Thr - Asn - Asn - Asn - Leu - Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 98253 - 191742:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Asn - Asn - Asn - X - Ala - Ala - Gly - Ala) + (Ala - Asn - Thr - Asn - Asn - Asn - Leu - Gly)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
SMED_RS31710: Ala - Asn - Thr - Asn - Asn - Asn - Leu - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (509..905): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWSTFDLSVYELNTNLAGECNLYAPSETTTYSTW
  Nearest Stachelhaus code(s):
    Ala DLYNNALTYK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1573..1976): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWASFDATVNSANVVIGGEVNEYGPTEAVVGCAF
  Nearest Stachelhaus code(s):
    OH-Asn or Asn DATKVGEVGK (76% 8Å match)
    Asn DATKVGEVGK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2644..3054): Thr
nrpys: Thr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LATHFDFSVWEGNQIFGGEINMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3722..4125): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWASFDATITSAKIVIGGEVNEYGPTEAVVGCAF
  Nearest Stachelhaus code(s):
    Asn DATKVGEVGK (85% 8Å match)
    OH-Asn or Asn DATKVGEVGK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4793..5196): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWASFDATVNSANVVIGGEVNEYGPTEAVVGCAF
  Nearest Stachelhaus code(s):
    OH-Asn or Asn DATKVGEVGK (76% 8Å match)
    Asn DATKVGEVGK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (5864..6267): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWASFDATVNSANVVIGGEVNEYGPTEAVVGCAF
  Nearest Stachelhaus code(s):
    OH-Asn or Asn DATKVGEVGK (76% 8Å match)
    Asn DATKVGEVGK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (6956..7353): 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:
    LWHAFDASAWESFLLIGGDINNYGPTEVTVVATS
  Nearest Stachelhaus code(s):
    Leu DAWFLGNVVK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (8042..8443): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VALTFDIAGLELQALCGGERNLYGPTETTIWATT
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

SMED_RS33235: Asn - Asn - Asn - X - Ala - Ala - Gly - Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (682..1085): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWASFDATVNSANVVIGGEVNEYGPTEAVVGCAF
  Nearest Stachelhaus code(s):
    OH-Asn or Asn DATKVGEVGK (76% 8Å match)
    Asn DATKVGEVGK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1774..2177): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWASFDATVNSANVVIGGEVNEYGPTEAVVGCAF
  Nearest Stachelhaus code(s):
    OH-Asn or Asn DATKVGEVGK (76% 8Å match)
    Asn DATKVGEVGK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2866..3269): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWASFDATVNSANVVIGGEVNEYGPTEAVVGCAF
  Nearest Stachelhaus code(s):
    OH-Asn or Asn DATKVGEVGK (76% 8Å match)
    Asn DATKVGEVGK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (3958..4364): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWSHFDGIVTTGKVMVGGEINHFGPTEATVGCAA
  Nearest Stachelhaus code(s):
    Asp DATKMGHVGK (68% 8Å match)
    CysA DATKMGHVGK (65% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (5053..5449): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWSTFDLSVYELNTNLAGECNLYAPSETTTYSTW
  Nearest Stachelhaus code(s):
    Ala DLYNNALTYK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (6138..6534): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWSTFDLSVYELNTNLAGECNLYAPSETTTYSTW
  Nearest Stachelhaus code(s):
    Ala DLYNNALTYK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (7223..7624): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VALTFDIAGLELQALCGGERNLYGPTETTIWATT
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (8313..8709): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWSTFDLSVYELNTNLAGECNLYAPSETTTYSTW
  Nearest Stachelhaus code(s):
    Ala DLYNNALTYK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
ArgR | Regulator of arginine biosynthesis genes
MexT | Global virulence regulator
RutR | Regulator of the pyrimidine and purine metabolism