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Overview
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1.13
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1.23
1.24
1.25
1.26
1.27
1.28
1.29
1.30
1.31
1.32
1.33
1.34

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

NC_019673.1 (Saccharothrix espanaensis DSM 44229)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | redox-cofactor | 762,807 | 784,852 | Low | lankacidin C | NRPS:Type I+PKS
Region 2 | terpene | 1,156,889 | 1,179,105 | High | geosmin | terpene:Sesquiterpene
Region 3 | lanthipeptide-class-iii | 1,610,107 | 1,632,638 | Medium | Ery-9/Ery-6/Ery-8/Ery-7/Ery-5/Ery-4/Ery-3 | ribosomal:RiPP:Lanthipeptide
Region 4 | terpene | 1,696,767 | 1,722,091 | Low | isorenieratene | terpene
Region 5 | RiPP-like | 1,932,882 | 1,943,673 |
Region 6 | furan | 2,219,933 | 2,241,042 | Low | asukamycin | PKS:Type II
Region 7 | RRE-containing | 2,275,187 | 2,296,293 |
Region 8 | NRPS | 2,343,810 | 2,386,878 |
Region 9 | CDPS | 2,512,807 | 2,533,487 |
Region 10 | NRP-metallophore,NRPS | 2,815,306 | 2,883,455 | Medium | myxochelin B/myxochelin A | NRPS:Type I
Region 11 | indole | 3,201,192 | 3,222,301 |  |
Region 12 | thioamide-NRP,HR-T2PKS,NRPS | 3,409,679 | 3,523,585 | Low | colibrimycin | NRPS:Type I+other:other
Region 13 | azole-containing-RiPP | 3,547,227 | 3,569,124 | Low | streptamidine | ribosomal:unmodified
Region 14 | T1PKS,hglE-KS | 3,587,958 | 3,669,961 |  |
Region 15 | NRPS | 3,835,837 | 3,895,826 | Low | oxazolomycin | NRPS:Type I+PKS
Region 16 | NAPAA | 4,053,825 | 4,087,622 | High | ε-Poly-L-lysine | NRPS:Type I
Region 17 | NRPS-like,T1PKS | 4,239,911 | 4,317,336 | Low | kedarcidin | NRPS:Type I+PKS:Iterative type I
Region 18 | lanthipeptide-class-ii | 4,520,676 | 4,543,519 |  |
Region 19 | oligosaccharide | 4,850,224 | 4,873,898 |  |
Region 20 | melanin | 4,911,671 | 4,922,060 |
Region 21 | NRPS,hglE-KS,T1PKS,PKS-like,NRPS-like,transAT-PKS | 4,954,497 | 5,110,155 | Medium | Largimycin A1/Largimycin A2/Largimycin A3 | NRPS:Type I+PKS:Type I
Region 22 | T1PKS,NRPS,NRPS-like | 5,176,387 | 5,418,301 | Low | lavendiol | PKS
Region 23 | terpene | 5,672,303 | 5,698,469 | High | isorenieratene | terpene
Region 24 | NRPS | 5,715,154 | 5,761,384 |  |
Region 25 | amglyccycl | 5,878,506 | 5,899,633 |  |
Region 26 | NRPS-like | 5,909,193 | 5,952,159 |  |
Region 27 | lassopeptide,azole-containing-RiPP,other,RRE-containing | 6,028,417 | 6,089,588 | Medium | ulleungdin | ribosomal:unmodified
Region 28 | T2PKS,terpene,lassopeptide,NRPS,T1PKS | 6,102,782 | 6,189,332 | High | SEK90/pentangumycin | PKS
Region 29 | terpene,NRPS,T1PKS | 6,285,999 | 6,385,448 | Medium | Ficellomycin | NRPS:Type I
Region 30 | oligosaccharide | 6,552,566 | 6,585,668 |  |
Region 31 | terpene | 6,620,360 | 6,641,823 |
Region 32 | terpene-precursor | 6,786,167 | 6,807,207 |  |
Region 33 | terpene | 6,944,768 | 6,965,850 |  |
Region 34 | lanthipeptide-class-ii | 7,144,344 | 7,167,229 |  |

NC_019673.1 - 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: 762,807 - 784,852 nt. (total: 22,046 nt) Show pHMM detection rules used
redox-cofactor: (cds(PF04055 and (TIGR04085 or SPASM)) and (TIGR02111 or TIGR03966) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
BN6_RS03730: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: acetyltransferase
BN6_RS03810: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

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

Reference | redox-cofactor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002318.2 |  | 0.50 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000866.5 |  | 0.42 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.41 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0002316.2 |  | 0.40 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000591.5 |  | 0.39 | ribosomal | marinostatin | Alteromonas sp. B-10-31
BGC0001483.4 |  | 0.38 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000528.5 |  | 0.37 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001561.4 |  | 0.36 | NRPS | curacomycin | Streptomyces curacoi
BGC0001100.5 |  | 0.36 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0001569.4 |  | 0.32 | NRPS | dechlorocuracomycin | Streptomyces noursei ATCC 11455

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002318.2 |  | 0.50 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000866.5 |  | 0.42 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.41 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0002316.2 |  | 0.40 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000591.5 |  | 0.39 | ribosomal | marinostatin | Alteromonas sp. B-10-31
BGC0001483.4 |  | 0.38 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000528.5 |  | 0.37 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001561.4 |  | 0.36 | NRPS | curacomycin | Streptomyces curacoi
BGC0001100.5 |  | 0.36 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0001569.4 |  | 0.32 | NRPS | dechlorocuracomycin | Streptomyces noursei ATCC 11455

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 (3):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.70 out of 30.98
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.35 out of 20.01
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (762806...784852)
BN6_RS03775
  RRE type: PqqD_RRE
  Location: 2 - 85
  Score: 66.3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NC_019673.1 - 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: 1,156,889 - 1,179,105 nt. (total: 22,217 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase
BN6_RS05510: Terpene synthase/cyclase metal-binding domain protein

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.81 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0002531.3 |  | 0.41 | NRPS | cepaciachelin | Burkholderia ambifaria AMMD
BGC0001294.5 |  | 0.40 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002115.3 |  | 0.39 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0002682.2 |  | 0.38 | other (other) | aerobactin | Vibrio mimicus
BGC0001660.3 |  | 0.38 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0001787.3 |  | 0.36 | ribosomal | suicin 3908 | Streptococcus suis
BGC0002683.2 |  | 0.36 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000547.5 |  | 0.36 | ribosomal | salivaricin 9 | Streptococcus salivarius

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.81 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0002531.3 |  | 0.41 | NRPS | cepaciachelin | Burkholderia ambifaria AMMD
BGC0001294.5 |  | 0.40 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002115.3 |  | 0.39 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0002682.2 |  | 0.38 | other (other) | aerobactin | Vibrio mimicus
BGC0001660.3 |  | 0.38 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0001787.3 |  | 0.36 | ribosomal | suicin 3908 | Streptococcus suis
BGC0002683.2 |  | 0.36 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000547.5 |  | 0.36 | ribosomal | salivaricin 9 | Streptococcus salivarius

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 |  | germacradienol | C15 | C1-C10 | OH
sesquiterpene |  | geosmin | C12 | C1-C10 | OH

Genes with terpene domains:
BN6_RS05510: T1TS + T1TS
Domain 1 (1 - 329): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (330 - 700): Type 1 terpene synthase
Subtype: Geosmin synthase, C terminal domain

Reactions:
  germacradienol → geosmin

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: 23.62 out of 29.72
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 32.11 out of 36.53
Confidence: strong
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.81 out of 26.85
Confidence: medium
Additional weak hits (8):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.30 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.99 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.96 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.53 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.30 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.23 out of 27.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.42 out of 26.85
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
DmdR1 | Iron(II)-dependent repressor
NtrC | Nitrogen regulatory protein C
RutR | Regulator of the pyrimidine and purine metabolism

NC_019673.1 - Region 3 - lanthipeptide-class-iii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,610,107 - 1,632,638 nt. (total: 22,532 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
BN6_RS07670: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: acylase
BN6_RS07730: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: synthase
BN6_RS07715: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS07725: 3-oxoacyl-(acyl carrier protein) synthase III

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

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

Reference | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.64 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.63 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000501.3 |  | 0.60 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000496.5 |  | 0.60 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001160.5 |  | 0.59 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002700.2 |  | 0.52 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000518.3 |  | 0.51 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002698.2 |  | 0.51 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.64 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.63 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000501.3 |  | 0.60 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000496.5 |  | 0.60 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001160.5 |  | 0.59 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002700.2 |  | 0.52 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000518.3 |  | 0.51 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002698.2 |  | 0.51 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566

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 BN6_RS07705

BN6_RS44805
Leader:
MEFILDLQDMDTPEVQSNAMAS
Core:
G G S S G G G G S T T A S S V S L L L P C S H S S A S L L L C
Core with dehydrations:
G G Dha Dha G G G G Dha Dhb Dhb A Dha Dha V Dha L L L P Cys Dha H Dha Dha A Dha L L L Cys

#### antiSMASH-DB 4.0 matches for BN6_RS44805

100.0%
NC_019673.1:
Lanthipeptides: BN6_RS44805_lanthipeptide
1
G G S S G G G G S T T A S S V S L L L P C S H S S A S L L L C
31
G G S S G G G G S T T A S S V S L L L P C S H S S A S L L L C
1
G G S S G G G G S T T A S S V S L L L P C S H S S A S L L L C
31
67.7%
NZ_PVTF01000018.1:
Lanthipeptides: CLV43_RS41575_lanthipeptide
9
S T T A S S V S L L L P C S H S S A S L L L C
31
S T T A S S S L L L P C S H S S A S L+L C
9
S T T A S S A S L L L P C S H S S A S L V L C
31
61.3%
NZ_CP034550.1:
Lanthipeptides: EKG83_RS07645_lanthipeptide
8
G S T T A S S V S L L L P C S H S S A S L L L C
31
G S T T A S+ S L L L P C S H S+ S L L C
7
G S T T A S N A S L L L P C S H S T V S L L A C
30
with 58 more sequence matches
Only the first 10 are displayed here.
60.6%
NZ_BMRG01000002.1:
Lanthipeptides: IEZ00_RS05680_lanthipeptide
7
G G S T T A S S V S L L L P C S H S S A S L L L C
31
G G S T T A S+ S L L L P C S H S+ S L L+C
9
G G S T T A S N A S L L L P C S H S T V S L L I C
33
59.4%
NZ_JACHJN010000006.1:
Lanthipeptides: FHS29_RS22065_lanthipeptide
10
T T A S S V S L L L P C S H S S A S L L L C
31
T T A S+V S L L L P C S H S+A S L+L C
11
T T A S N V S L L L P C S H S T A S L V L C
32
57.1%
NZ_BMNC01000020.1 and 5 others:
NZ_CP099738.1 Lanthipeptides: ND450_RS23215_lanthipeptide NZ_FOFR01000004.1 Lanthipeptides: BMW88_RS12345_lanthipeptide NZ_FOFV01000016.1 Lanthipeptides: BMY74_RS32885_lanthipeptide NZ_JAAMPJ010000008.1 Lanthipeptides: G7043_RS27905_lanthipeptide NZ_QFWW01000007.1 Lanthipeptides: DI276_RS13535_lanthipeptide
Lanthipeptides: IEY88_RS39185_lanthipeptide
7
G G S T T A S S V S L L L P C S H S S A S L L L C
31
G G S T T A S+ S L L L P C S H S+ S L L C
11
G G S T T A S N A S L L L P C S H S T V S L L A C
35
56.2%
NZ_BBOJ01000004.1 and 8 others:
NZ_BNAR01000026.1 Lanthipeptides: IE307_RS43650_lanthipeptide NZ_FNCC01000020.1 Lanthipeptides: BLT23_RS35745_lanthipeptide NZ_FNET01000005.1 Lanthipeptides: BLR21_RS13720_lanthipeptide NZ_FNIX01000011.1 Lanthipeptides: BLQ91_RS25790_lanthipeptide NZ_FWYC01000011.1 Lanthipeptides: B9C42_RS41415_lanthipeptide NZ_JAJCXE010000046.1 Lanthipeptides: L6E10_RS30695_lanthipeptide NZ_JAPJDL010000024.1 Lanthipeptides: ORI60_RS35805_lanthipeptide NZ_QQAU01000015.1 Lanthipeptides: DFR72_RS35920_lanthipeptide
Lanthipeptides: AOM45_RS50700_lanthipeptide
9
S T T A S S V S L L L P C S H S S A S L L L C
31
S T T A S+ S L L L P C S H S+ S L L C
10
S T T A S N A S L L L P C S H S T V S L L A C
32
53.1%
NZ_CP016793.1 and 2 others:
NZ_QGHB01000016.1 Lanthipeptides: C8D88_RS40205_lanthipeptide NZ_QLTT01000007.1 Lanthipeptides: C8D87_RS29500_lanthipeptide
Lanthipeptides: BBK82_RS02805_lanthipeptide
10
T T A S S V S L L L P C S H S S A S L L L C
31
T T A S+ S L L L P C S H S+ S L L C
11
T T A S N A S L L L P C S H S T V S L L A C
32
52.9%
NZ_JAJHUO010000006.1:
Lanthipeptides: LNK82_RS10890_lanthipeptide
9
S T T A S S V S L L L P C S H S S A S L L L C
31
S T T A S+ S L L L P C S H S+ S L+L C
12
S T T A S N A S L L L P C S H S T V S L V L C
34
52.9%
NZ_LWLC01000002.1:
Lanthipeptides: A6A25_RS42770_lanthipeptide
9
S T T A S S V S L L L P C S H S S A S L L L C
31
S T T A S+ S L L L P C S H S+ S L+L C
12
S T T A S N A S L L L P C S H S T V S L I L C
34
48.4%
NC_021252.1 and 9 others:
NZ_CP008953.1 Lanthipeptides: AJAP_RS43890_lanthipeptide NZ_CP024972.1 Lanthipeptides: CVV72_RS27155_lanthipeptide NZ_CP092497.1 Lanthipeptides: MJQ72_RS39855_lanthipeptide NZ_CP102415.1 Lanthipeptides: NQK81_RS21060_lanthipeptide NZ_CP120210.1 Lanthipeptides: P3102_RS01815_lanthipeptide NZ_JPLW01000001.1 Lanthipeptides: ED92_RS42365_lanthipeptide NZ_LIWC01000002.1 Lanthipeptides: AMK34_RS42700_lanthipeptide NZ_LQMT02000022.1 Lanthipeptides: AVR91_RS42870_lanthipeptide NZ_LT629789.1 Lanthipeptides: BLU53_RS44680_lanthipeptide
Lanthipeptides: AORI_RS83200_lanthipeptide
2
G S S G G G G S T T A S S V S L L L P C S H S S A S L L L C
31
G S G G A S++S L L C++S+ S L L C
1
G S H G G-----A S N L S L L A S C A N S T V S L L T C
25
48.4%
NZ_CP095376.1:
Lanthipeptides: MUY14_RS34840_lanthipeptide
5
G G G G S T T A S S V S L L L P C S H S S A S L L L C
31
G G G T S++S L L C+H S+ S L L C
1
G H G G G T--S N L S L L A A C A H S T L S L L T C
25
48.4%
NZ_FOYL01000007.1:
Lanthipeptides: BM417_RS27140_lanthipeptide
17
L L L P C S H S S A S L L L C
31
L L L P C S H S S A S L L L C
17
L L L P C S H S S A S L L L C
31

#### MIBiG 4.0 matches for BN6_RS44805

38.7%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
11
T A S S V S L L L P C S H S S A S L L L C
31
T S V S L L+ C +S S S++L C
1
T G S Q V S L L V-C E Y S S L S V V L C
20

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.34 out of 23.79
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.72 out of 20.97
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.03 out of 27.04
Confidence: medium
Additional weak hits (16):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.73 out of 25.88
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.44 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.35 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.95 out of 28.19
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.74 out of 25.31
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.35 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.86 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.80 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.75 out of 26.06
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.49 out of 25.88
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.90 out of 31.73
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.06 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.08 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.95 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.64 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.75 out of 28.19
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.

BN6_RS44805 - Class III
  Cleavage pHMM score: 12.60
  RODEO score: 0
  Monoisotopic mass: 2576.3 Da
  Molecular weight: 2577.8 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2595.9 Da N = 1
    2613.9 Da N = 2
    2631.9 Da N = 3
    2649.9 Da N = 4
    2667.9 Da N = 5
    2686.0 Da N = 6
    2704.0 Da N = 7
    2722.0 Da N = 8
    2740.0 Da N = 9
    2758.0 Da N = 10

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NC_019673.1 - Region 4 - 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: 1,696,767 - 1,722,091 nt. (total: 25,325 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
BN6_RS08115: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: acyltransferase
BN6_RS08075: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Lyases: decarboxylase
BN6_RS08130: putative carboxymuconolactone decarboxylase

smcogs
  SMCOG1298: putative carboxymuconolactone decarboxylase

Ligases: synthetase
BN6_RS08120: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.58 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.57 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.55 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.55 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000650.3 |  | 0.54 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000649.3 |  | 0.53 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000648.3 |  | 0.50 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.47 | terpene | β-carotein | uncultured bacterium
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000640.3 |  | 0.45 | terpene | carotenoid | Enterobacteriaceae bacterium DC404

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.58 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.57 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.55 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.55 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000650.3 |  | 0.54 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000649.3 |  | 0.53 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000648.3 |  | 0.50 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.47 | terpene | β-carotein | uncultured bacterium
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000640.3 |  | 0.45 | terpene | carotenoid | Enterobacteriaceae bacterium DC404

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
--- | --- | --- | --- | --- | ---
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:
BN6_RS08105: PT_phytoene_like
Domain 1 (6 - 297): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

BN6_RS08120: PT_FPPS_like
Domain 1 (46 - 333): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

Reactions:
  IPP, DMAPP → FPP
  IPP, DMAPP → GGPP
  IPP, DMAPP → GFPP
  IPP, DMAPP → HPP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 25.27 out of 29.65
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.07 out of 24.78
Confidence: medium
Additional weak hits (5):
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.92 out of 32.93
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.86 out of 24.78
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.69 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.60 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
LexA variant 1 | Repressor of DNA damage response
LexA variant 2 | Repressor of DNA damage response

NC_019673.1 - Region 5 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,932,882 - 1,943,673 nt. (total: 10,792 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: protease
BN6_RS09165: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000595.3 |  | 0.31 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000597.4 |  | 0.29 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0000842.5 |  | 0.26 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000595.3 |  | 0.31 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000597.4 |  | 0.29 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0000842.5 |  | 0.26 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus

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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.89 out of 23.79
Confidence: medium
Additional weak hits (3):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.91 out of 30.22
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.43 out of 32.93
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.39 out of 24.78
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NC_019673.1 - Region 6 - furan
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: 2,219,933 - 2,241,042 nt. (total: 21,110 nt) Show pHMM detection rules used
furan: (mmyO or AvrD)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
BN6_RS10365: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

BN6_RS10370: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: esterase
BN6_RS10440: thioesterase

smcogs
  SMCOG1004: thioesterase

BN6_RS45500: thioesterase superfamily protein

smcogs
  SMCOG1144: thioesterase superfamily protein

Ligases: ligase synthase
BN6_RS10350: 3-oxoacyl-(acyl carrier protein) synthase III

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

BN6_RS10385: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS10390: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

BN6_RS10395: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS10410: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS10435: 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 | furan | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002193.2 |  | 0.63 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0002274.2 |  | 0.63 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0001641.4 |  | 0.61 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002276.2 |  | 0.60 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002164.2 |  | 0.58 | NRPS | peramine | Epichloe festucae
BGC0000187.5 |  | 0.58 | PKS | asukamycin | Streptomyces nodosus subsp. asukaensis
BGC0001160.5 |  | 0.57 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002826.2 |  | 0.52 | other (other) | closoxazole A, closoxazole B | Clostridium cavendishii DSM 21758
BGC0000213.4 |  | 0.52 | PKS | colabomycin E | Streptomyces aureus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002193.2 |  | 0.63 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0002274.2 |  | 0.63 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0001641.4 |  | 0.61 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002276.2 |  | 0.60 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002164.2 |  | 0.58 | NRPS | peramine | Epichloe festucae
BGC0000187.5 |  | 0.58 | PKS | asukamycin | Streptomyces nodosus subsp. asukaensis
BGC0001160.5 |  | 0.57 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002826.2 |  | 0.52 | other (other) | closoxazole A, closoxazole B | Clostridium cavendishii DSM 21758
BGC0000213.4 |  | 0.52 | PKS | colabomycin E | Streptomyces aureus

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.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.75 out of 23.79
Confidence: medium
Additional weak hits (2):
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.27 out of 29.65
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.59 out of 26.85
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NC_019673.1 - Region 7 - RRE-containing
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: 2,275,187 - 2,296,293 nt. (total: 21,107 nt) Show pHMM detection rules used
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
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 | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002317.2 |  | 0.45 | ribosomal | herbicolin O, mcceh252, pantocin A | Pantoea agglomerans
BGC0000585.5 |  | 0.44 | ribosomal | microcin C7 | Escherichia coli
BGC0000393.5 |  | 0.37 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622
BGC0000812.3 |  | 0.35 | other (other) | huperzine A | Shiraia sp. slf14
BGC0002716.2 |  | 0.34 | NRPS | gamexpeptide A, gamexpeptide B, gamexpeptide E, luminmide B, luminmide D, luminmide E, luminmide F, luminmide G | Photorhabdus laumondii subsp. laumondii
BGC0002064.2 |  | 0.30 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0000632.5 |  | 0.30 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0000925.5 |  | 0.28 | other (other) | quinolobactin | Pseudomonas fluorescens
BGC0000821.5 |  | 0.25 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0000709.5 |  | 0.24 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002317.2 |  | 0.45 | ribosomal | herbicolin O, mcceh252, pantocin A | Pantoea agglomerans
BGC0000585.5 |  | 0.44 | ribosomal | microcin C7 | Escherichia coli
BGC0000393.5 |  | 0.37 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622
BGC0000812.3 |  | 0.35 | other (other) | huperzine A | Shiraia sp. slf14
BGC0002716.2 |  | 0.34 | NRPS | gamexpeptide A, gamexpeptide B, gamexpeptide E, luminmide B, luminmide D, luminmide E, luminmide F, luminmide G | Photorhabdus laumondii subsp. laumondii
BGC0002064.2 |  | 0.30 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0000632.5 |  | 0.30 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0000925.5 |  | 0.28 | other (other) | quinolobactin | Pseudomonas fluorescens
BGC0000821.5 |  | 0.25 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0000709.5 |  | 0.24 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063

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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.70 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.52 out of 28.19
Confidence: medium
Additional weak hits (18):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.55 out of 26.12
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.79 out of 26.85
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.57 out of 20.97
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.55 out of 30.22
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.34 out of 27.78
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.42 out of 27.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.42 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.54 out of 29.38
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.52 out of 24.78
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.32 out of 30.98
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.96 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.92 out of 24.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.90 out of 26.85
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.38 out of 29.25
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (2275186...2296293)
BN6_RS10580
  RRE type: Pantocin_Microcin_RRE
  Location: 0 - 92
  Score: 61.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NC_019673.1 - Region 8 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,343,810 - 2,386,878 nt. (total: 43,069 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
BN6_RS10905: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

BN6_RS10915: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

Hydrolases: hydrolase
BN6_RS10980: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase
BN6_RS10880: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS10885: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN6_RS10910: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS10920: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN6_RS10935: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Translocases: transport
BN6_RS11005: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002164.2 |  | 0.67 | NRPS | peramine | Epichloe festucae
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001240.4 |  | 0.64 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001250.4 |  | 0.63 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.63 | NRPS | epichloenin A | Epichloe festucae
BGC0000357.5 |  | 0.63 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0002135.2 |  | 0.62 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001166.5 |  | 0.62 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002164.2 |  | 0.67 | NRPS | peramine | Epichloe festucae
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001240.4 |  | 0.64 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001250.4 |  | 0.63 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.63 | NRPS | epichloenin A | Epichloe festucae
BGC0000357.5 |  | 0.63 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0002135.2 |  | 0.62 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001166.5 |  | 0.62 | NRPS | HC-toxin | Alternaria jesenskae

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (3):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.21 out of 36.54
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.92 out of 30.22
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
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 8, location 2343809 - 2386878:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BN6_RS10880: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (17..402): Ser
nrpys: Ser

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFALSGEVNMYGPTECAIDVSH
  Nearest Stachelhaus code(s):
    Ser DVWHFSLIDK (85% 8Å match)
  Stachelhaus code match:
    80% (moderate)

BN6_RS10910: Asn
Search NORINE for peptide: strict or relaxed
AMP-binding (15..401): 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:
    YWSTFDLTVTSGKLVVGGEVNEYGPSEAAVGCCR
  Nearest Stachelhaus code(s):
    Asn DLTKVGEVGK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

BN6_RS10935: X
AMP-binding (51..423): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    YQFAYDAHHCQAETMCSGEHNEFGPTECVLATWH
  Nearest Stachelhaus code(s):
    aza-bTyr DACELALLAK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---

NC_019673.1 - Region 9 - CDPS
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: 2,512,807 - 2,533,487 nt. (total: 20,681 nt) Show pHMM detection rules used
CDPS: CDPS

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: deformylase
BN6_RS11615: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

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 | CDPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000528.5 |  | 0.47 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002346.3 |  | 0.45 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000503.5 |  | 0.44 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0001210.5 |  | 0.40 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000600.3 |  | 0.39 | ribosomal | thurincin H | Bacillus thuringiensis
BGC0000498.5 |  | 0.39 | ribosomal | bovicin HJ50 | Streptococcus equinus
BGC0000561.5 |  | 0.38 | ribosomal | thermophilin 1277 | Streptococcus thermophilus
BGC0001684.3 |  | 0.38 | other (other) | N-acyloxyacyl glutamine | Klebsiella variicola
BGC0002316.2 |  | 0.38 | ribosomal | cebulantin | Saccharopolyspora cebuensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000528.5 |  | 0.47 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002346.3 |  | 0.45 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000503.5 |  | 0.44 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0001210.5 |  | 0.40 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000600.3 |  | 0.39 | ribosomal | thurincin H | Bacillus thuringiensis
BGC0000498.5 |  | 0.39 | ribosomal | bovicin HJ50 | Streptococcus equinus
BGC0000561.5 |  | 0.38 | ribosomal | thermophilin 1277 | Streptococcus thermophilus
BGC0001684.3 |  | 0.38 | other (other) | N-acyloxyacyl glutamine | Klebsiella variicola
BGC0002316.2 |  | 0.38 | ribosomal | cebulantin | Saccharopolyspora cebuensis

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

No significant matches found.

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

No significant matches found.

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: 19.35 out of 20.47
Confidence: strong
Additional weak hits (2):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.92 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.90 out of 36.54
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NC_019673.1 - Region 10 - NRP-metallophore,NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,815,306 - 2,883,455 nt. (total: 68,150 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
BN6_RS13085: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase
BN6_RS13100: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Isomerases: isomerase
BN6_RS13090: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase
BN6_RS13050: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN6_RS13060: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN6_RS13095: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter
BN6_RS13125: 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 | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001825.4 |  |  | 0.80 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000343.5 |  |  | 0.79 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0000401.5 |  |  | 0.77 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0001833.4 |  |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001185.5 |  |  | 0.74 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0000357.5 |  |  | 0.73 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001758.4 |  |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000309.5 |  |  | 0.71 | NRPS | bacillibactin | Bacillus subtilis subsp. subtilis str. 168

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000343.5 |  | 0.71 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0000401.5 |  | 0.71 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001185.5 |  | 0.69 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0000357.5 |  | 0.69 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000309.5 |  | 0.68 | NRPS | bacillibactin | Bacillus subtilis subsp. subtilis str. 168

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.50 out of 20.47
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.16 out of 26.33
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 34.36 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 33.07 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.36 out of 36.53
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.38 out of 25.88
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (14):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.76 out of 32.74
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.45 out of 21.55
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.57 out of 30.98
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.37 out of 29.65
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.32 out of 26.85
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.98 out of 27.18
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 26.16 out of 36.53
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.22 out of 26.85
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.55 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.65 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.65 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.46 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 10, location 2815305 - 2883455:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser - D-X - D-Arg - D-X - Ac-OH-Orn)

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).
BN6_RS13050: Ser - X - Arg - X - Ac-OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (738..1129): Ser
nrpys: Ser

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFICSGEHNLYGPTEASVDVTS
  Nearest Stachelhaus code(s):
    Ser DVWHISLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1757..2120): X
nrpys: (unknown)

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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAHAFDASWDPWDFAVGGELNLYGPTECTVDTYW
  Nearest Stachelhaus code(s):
    Arg DADDVGLVDK (79% 8Å match)
    Lys DADDAGTVDK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (3134..3496): Arg
nrpys: Arg

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGHAFDAAWDPWDFCVGGEVDLYGPTEYTVDAYL
  Nearest Stachelhaus code(s):
    Arg DADDVGLVDK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (4523..4884): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSHAFDAAWDPWDFCVGGEYDCYGPTEYTVDAYV
  Nearest Stachelhaus code(s):
    Arg DADDSGCVDK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (5902..6293): Ac-OH-Orn
nrpys: Ac-OH-Orn

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LTAAFDLAFFEMALLCGTENDAYGPTEATVNSTL
  Nearest Stachelhaus code(s):
    Ac-OH-Orn DVFALGAVNK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

BN6_RS13060: Gln
Search NORINE for peptide: strict or relaxed
AMP-binding (442..716): Gln
nrpys: Gln

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 with H-bond donor (Asp, Asn, Glu, Gln, Aad)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAAAFDASVEEVDLVIGGEINTYGPTEATVVATA
  Nearest Stachelhaus code(s):
    Lys DAEDIGTVVK (85% 8Å match)
    Gln or Tyr DAESVGTVVK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

BN6_RS13095: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (31..433): diOH-Bz
nrpys: diOH-Bz

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
  Small clusters prediction:
    Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
  Single AA prediction:
    dhb (diOH-Bz)

Stachelhaus prediction details:
  Stachelhaus sequence:
    SESLFPMSSPGGGVQVGGAQQVFGMAEGLVNYTR
  Nearest Stachelhaus code(s):
    diOH-Bz PMPAQGVVNK (94% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AfsR | Pleiotropic regulatory for antibiotic production
DmdR1 | Iron(II)-dependent repressor
PsrA | Oleic acid responsive regulator
VqsM | Regulator of quorum-sensing signalling systems

NC_019673.1 - Region 11 - indole
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: 3,201,192 - 3,222,301 nt. (total: 21,110 nt) Show pHMM detection rules used
indole: (indsynth or dmat or indole_PTase)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
BN6_RS14670: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

BN6_RS14690: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

BN6_RS14695: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Translocases: permease
BN6_RS14675: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | indole | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002128.3 |  | 0.48 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001483.4 |  | 0.48 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001197.5 |  | 0.45 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001924.3 |  | 0.42 | terpene | ascofuranone | Acremonium egyptiacum
BGC0000667.3 |  | 0.42 | terpene | PR-toxin | Penicillium roqueforti FM164
BGC0002404.2 |  | 0.41 | other (other) | falcarindiol | Solanum lycopersicum
BGC0000706.3 |  | 0.40 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001267.3 |  | 0.39 | terpene | elymoclavine, Agroclavine I | Claviceps fusiformis
BGC0001910.4 |  | 0.38 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001605.3 |  | 0.38 | terpene | gibberellin | Sinorhizobium fredii NGR234

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002128.3 |  | 0.48 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001483.4 |  | 0.48 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001197.5 |  | 0.45 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001924.3 |  | 0.42 | terpene | ascofuranone | Acremonium egyptiacum
BGC0000667.3 |  | 0.42 | terpene | PR-toxin | Penicillium roqueforti FM164
BGC0002404.2 |  | 0.41 | other (other) | falcarindiol | Solanum lycopersicum
BGC0000706.3 |  | 0.40 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001267.3 |  | 0.39 | terpene | elymoclavine, Agroclavine I | Claviceps fusiformis
BGC0001910.4 |  | 0.38 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001605.3 |  | 0.38 | 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.

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: 19.46 out of 20.47
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.31 out of 23.43
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.98 out of 23.43
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (6):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.29 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.03 out of 27.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.65 out of 27.04
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.30 out of 28.14
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
VqsM | Regulator of quorum-sensing signalling systems

NC_019673.1 - Region 12 - HR-T2PKS,NRPS,thioamide-NRP
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: 3,409,679 - 3,523,585 nt. (total: 113,907 nt) Show pHMM detection rules used
thioamide-NRP: (ATP-grasp and AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC))
HR-T2PKS: (hr-t2pks-ksa and (t2fas or APE_KS2 or ketoacyl-synt))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
BN6_RS15715: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BN6_RS15725: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

BN6_RS15775: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

BN6_RS15810: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BN6_RS15830: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

Transferases: halogenase
BN6_RS15785: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
MITE
  MITE0000130Halogenation (identity: 66.30%)
smcogs
  SMCOG1119: halogenase

Hydrolases: deaminase hydrolase peptidase
BN6_RS15605: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

BN6_RS15655: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

BN6_RS15690: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

BN6_RS15790: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

BN6_RS15860: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: decarboxylase
BN6_RS15650: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

BN6_RS15755: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase
BN6_RS15685: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS15700: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS15745: 3-oxoacyl-(acyl carrier protein) synthase III

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

BN6_RS15795: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

BN6_RS15800: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN6_RS15850: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS15855: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS15930: 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 | thioamide-NRP | HR-T2PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001833.4 |  |  |  | 0.85 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  |  | 0.84 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  |  | 0.84 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  |  |  | 0.84 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  |  | 0.81 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  |  |  | 0.81 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  |  | 0.79 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  |  |  | 0.79 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  |  |  | 0.73 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001641.4 |  |  |  | 0.71 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.75 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  | 0.74 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.74 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0002071.2 |  | 0.73 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027

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.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.23 out of 27.78
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.19 out of 24.78
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (18):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.55 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.84 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.49 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.77 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.79 out of 30.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.22 out of 21.55
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.09 out of 27.04
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.91 out of 20.01
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.10 out of 27.78
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.34 out of 27.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.88 out of 29.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.24 out of 35.63
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.32 out of 30.98
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.49 out of 27.04
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.11 out of 28.14
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.99 out of 27.04
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 12, location 3409678 - >3523585:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - Thr) + (D-Orn - X - D-Orn - Thr - D-Leu) + (D-X - Trp - X - X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BN6_RS15800: X - Trp - X - X
Search NORINE for peptide: strict or relaxed
AMP-binding (453..841): X
nrpys: Dpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HAKAFDISVWQAEVVVTGEVNAYGPTECSDDVTH
  Nearest Stachelhaus code(s):
    Dpr DIWEVTADDK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1964..2356): Trp
nrpys: Trp

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    MSLAFDATVWELALVVAGEFNGYGPTESVLASTV
  Nearest Stachelhaus code(s):
    Trp DAWAFAGVAK (56% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (3022..3413): X
nrpys: Dpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HCKAFDISVWQTEVVVTGEVNAYGPTECSDDVTH
  Nearest Stachelhaus code(s):
    Dpr DIWEVTADDK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4071..4424): X
nrpys: Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDLT---FALEVRAVLAGEVEGGGP----VDTKV
  Nearest Stachelhaus code(s):
    Pro DVLLVAGVLK (32% 8Å match)
  Stachelhaus code match:
    60% (weak)

BN6_RS15850: Orn - X - Orn - Thr - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (478..849): Orn
nrpys: Orn

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNHAFDTSWECLDLMVGGEYNFYGPTETTVDAAS
  Nearest Stachelhaus code(s):
    Orn DTEDMGFVDK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1875..2244): 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LANAFDTSWEGFDLLVGGEFNYYGPTETTVDAVS
  Nearest Stachelhaus code(s):
    Orn DTEDMGYVDK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2852..3223): Orn
nrpys: Orn

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNHAFDTSWEGLDLMLGGEYNFYGPTETAVDAVS
  Nearest Stachelhaus code(s):
    Orn DTEDMGFVDK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4261..4625): 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 (5239..5605): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAESFDASVLEMLIVVGGDINAYGPTESTVVTSW
  Nearest Stachelhaus code(s):
    Leu DALLVGAVVK (74% 8Å match)
  Stachelhaus code match:
    100% (strong)

BN6_RS15855: X - Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (8..374): X
nrpys: Leu, 3OH-Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAESFDASVLEMLIIVGGDINAYGPTESTVVTSW
  Nearest Stachelhaus code(s):
    Leu or 3OH-Leu DALLIGAVVK (82% 8Å match)
    Leu DALLIGAVVK (68% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1967..2331): 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)

BN6_RS15930: X
AMP-binding (39..440): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    GSTSWAKHAWSACAVGAGERDGFGQTETTVQIAN
  Nearest Stachelhaus code(s):
    Phe or Tyr DAACVAGVAK (32% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
LexA variant 2 | Repressor of DNA damage response

NC_019673.1 - Region 13 - 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: 3,547,227 - 3,569,124 nt. (total: 21,898 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
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
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
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 | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002115.3 |  | 0.66 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0002531.3 |  | 0.43 | NRPS | cepaciachelin | Burkholderia ambifaria AMMD
BGC0000947.5 |  | 0.43 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0001870.3 |  | 0.42 | other (other) | putrebactin, avaroferrin | Xenorhabdus budapestensis
BGC0000565.5 |  | 0.41 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0002490.2 |  | 0.40 | other (other) | yersinopine | Yersinia pestis CO92
BGC0002073.3 |  | 0.40 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0000569.5 |  | 0.38 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0001173.5 |  | 0.38 | ribosomal | plantazolicin | Bacillus pumilus ATCC 7061
BGC0002494.3 |  | 0.38 | NRPS | vibriobactin | Vibrio cholerae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002115.3 |  | 0.66 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0002531.3 |  | 0.43 | NRPS | cepaciachelin | Burkholderia ambifaria AMMD
BGC0000947.5 |  | 0.43 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0001870.3 |  | 0.42 | other (other) | putrebactin, avaroferrin | Xenorhabdus budapestensis
BGC0000565.5 |  | 0.41 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0002490.2 |  | 0.40 | other (other) | yersinopine | Yersinia pestis CO92
BGC0002073.3 |  | 0.40 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0000569.5 |  | 0.38 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0001173.5 |  | 0.38 | ribosomal | plantazolicin | Bacillus pumilus ATCC 7061
BGC0002494.3 |  | 0.38 | NRPS | vibriobactin | Vibrio cholerae

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: 17.80 out of 20.47
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.83 out of 28.19
Confidence: medium
Additional weak hits (18):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.59 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.75 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.67 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.37 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.80 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.27 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.46 out of 29.38
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.60 out of 32.93
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.05 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.51 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.92 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.53 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.34 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.01 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.95 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.50 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.80 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.19 out of 28.19
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
--- | ---
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

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_019673.1 - Region 14 - T1PKS,hglE-KS
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: 3,587,958 - 3,669,961 nt. (total: 82,004 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))
hglE-KS: (hglE or hglD)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
BN6_RS16270: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

BN6_RS16285: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BN6_RS49620: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: acylase
BN6_RS16240: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

BN6_RS16255: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

BN6_RS16310: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: dehalogenase hydrolase
BN6_RS16330: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

BN6_RS41995: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Ligases: synthase
BN6_RS16235: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS16315: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS16340: 3-oxoacyl-(acyl carrier protein) synthase III

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

BN6_RS16345: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl 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 | T1PKS | hglE-KS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  |  | 0.96 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  |  | 0.95 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  |  | 0.95 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001160.5 |  |  |  | 0.89 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  |  | 0.88 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002192.3 |  |  |  | 0.82 | PKS | FR901512 | fungal sp. No.14919
BGC0002154.2 |  |  |  | 0.79 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001268.4 |  |  |  | 0.74 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0000041.3 |  |  |  | 0.63 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001284.4 |  |  |  | 0.57 | PKS | alternariol | Parastagonospora nodorum SN15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.66 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000037.4 |  | 0.62 | PKS | cichorine | Aspergillus nidulans FGSC A4
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0000041.3 |  | 0.61 | PKS | oronofacic acid | Pseudomonas syringae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.27 out of 23.79
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.94 out of 26.85
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.56 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.22 out of 23.79
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.70 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.49 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.75 out of 23.79
Confidence: medium
Additional weak hits (23):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.35 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.00 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.38 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.33 out of 32.74
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.11 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.90 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.33 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.76 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.57 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.87 out of 24.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.39 out of 25.75
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.56 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.68 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.59 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.15 out of 29.65
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.81 out of 21.84
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.17 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.59 out of 24.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.02 out of 25.88
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.89 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 14, location 3587957 - 3669961:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-pk) + (Me-redmal) + (mal)
Non-colinear ordering:
  BN6_RS16345 + BN6_RS16255 + BN6_RS16315

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 15, location 3587957 - 3634350:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-redmal) + (mal)
Non-colinear ordering:
  BN6_RS16255 + BN6_RS16315

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 16, location 3609150 - 3655033:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-pk) + (Me-redmal) + (mal)
Non-colinear ordering:
  BN6_RS16345 + BN6_RS16255 + BN6_RS16315

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 17, location 3622698 - 3669961:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (Me-pk)
Non-colinear ordering:
  BN6_RS16315 + BN6_RS16345

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).
BN6_RS16240: mal
PKS_AT (19..314): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 42.5
  Methoxymalonyl-CoA: 38.9
  Methylmalonyl-CoA: 34.6
  fatty_acid: 15.8
  Ethylmalonyl-CoA: 15.6
  inactive: 12.2
  Benzoyl-CoA: 8.4
  trans-1,2-CPDA: 6.5
  CHC-CoA: 6.5
  Isobutyryl-CoA: 2.2
  Propionyl-CoA: 1.3
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: -0.4

BN6_RS16255: mmal
PKS_AT (551..847): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 79.2%
  Malonyl-CoA: 70.8%
  Ethylmalonyl-CoA: 70.8%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 146.6
  Ethylmalonyl-CoA: 125.1
  Methoxymalonyl-CoA: 120.6
  Malonyl-CoA: 103.1
  2-Methylbutyryl-CoA: 77.1
  trans-1,2-CPDA: 76.5
  Propionyl-CoA: 74.4
  Isobutyryl-CoA: 74.1
  Acetyl-CoA: 51.9
  fatty_acid: 50.5
  Benzoyl-CoA: 49.4
  inactive: 46.6
  CHC-CoA: 45.8
  3-Methylbutyryl-CoA: 40.0

BN6_RS16315: mal
PKS_AT (579..876): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 119.5
  Methoxymalonyl-CoA: 51.9
  inactive: 49.1
  Methylmalonyl-CoA: 38.8
  Isobutyryl-CoA: 27.1
  Propionyl-CoA: 16.6
  Ethylmalonyl-CoA: 15.6
  fatty_acid: 10.3
  CHC-CoA: 7.0
  trans-1,2-CPDA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

BN6_RS16345: pk
PKS_AT (531..808): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  Methylmalonyl-CoA: 66.7%
  CE-Malonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 109.7
  Malonyl-CoA: 109.1
  Methoxymalonyl-CoA: 97.1
  Ethylmalonyl-CoA: 75.8
  Isobutyryl-CoA: 64.6
  Propionyl-CoA: 60.9
  2-Methylbutyryl-CoA: 55.3
  trans-1,2-CPDA: 33.0
  CHC-CoA: 31.5
  inactive: 31.3
  fatty_acid: 28.7
  3-Methylbutyryl-CoA: 23.2
  Benzoyl-CoA: 22.2
  Acetyl-CoA: 18.9

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism
RutR | Regulator of the pyrimidine and purine metabolism

NC_019673.1 - Region 15 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,835,837 - 3,895,826 nt. (total: 59,990 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
BN6_RS17170: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: methyltransferase
BN6_RS17230: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: phosphatase
BN6_RS17180: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Lyases: decarboxylase
BN6_RS17290: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: ligase synthase
BN6_RS17175: 3-oxoacyl-(acyl carrier protein) synthase III

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

BN6_RS17185: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS17200: 3-oxoacyl-(acyl carrier protein) synthase III

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

BN6_RS17235: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS17245: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN6_RS17260: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN6_RS42060: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: permease
BN6_RS17320: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.71 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.71 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
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:
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 25.83 out of 30.22
Confidence: medium
Additional weak hits (12):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.15 out of 26.85
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.63 out of 21.55
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.01 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.14 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.40 out of 36.54
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.10 out of 32.74
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.61 out of 39.62
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 30.98
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.19 out of 29.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.00 out of 18.57
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.76 out of 29.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.40 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 18, location 3835836 - 3895826:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (X) + (Gly) + (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BN6_RS17185: X
AMP-binding (7..419): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YHNFFDPSVFDVFSVFIGEDNVYGPTELTVACTE
  Nearest Stachelhaus code(s):
    Ala DVFFVGLVAK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

BN6_RS17235: X
AMP-binding (484..891): X
nrpys: Val, Leu, Ile, Abu, Ival

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAFPFDASVGDPDGMIGGEVNHYGPTEATVCATA
  Nearest Stachelhaus code(s):
    CysA DATKMGHVGK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

BN6_RS17245: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (510..889): 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:
    LTFTFDISVLELQAISGGEWNVYGPTETTVWSAA
  Nearest Stachelhaus code(s):
    Gly DILQLGVVWK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

BN6_RS17260: X
AMP-binding (448..823): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAMSFDVSTVEVQGVTGGEVDGYGPTETTVYSAA
  Nearest Stachelhaus code(s):
    Trp DVSQVGAVAK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

BN6_RS42060: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (485..881): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNPSFDLTTLEGWLLAGGDVNGYGPTENTTFTSC
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (79% 8Å match)
    bOH-Val DALWLGGTFK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
ClgR | Caseinolytic protease gene regulator

NC_019673.1 - Region 16 - NAPAA
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,053,825 - 4,087,622 nt. (total: 33,798 nt) Show pHMM detection rules used
NAPAA: (AMP-binding and TIGR02353)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidase oxidoreductase
BN6_RS18055: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

BN6_RS18085: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

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 | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.78 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.59 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.78 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.59 | NRPS | icosalide A, icosalide 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.
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
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (8):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.00 out of 21.55
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.67 out of 26.33
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.88 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.21 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.85 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.91 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 19, location 4053824 - 4087622:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BN6_RS18080: X
AMP-binding (30..401): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAELFDASCEELSTIFGGEWNTYGPTEATVVACA
  Nearest Stachelhaus code(s):
    Lys DAEDIGTVVK (71% 8Å match)
    Gln or Tyr DAESVGTVVK (65% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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
VqsM | Regulator of quorum-sensing signalling systems

NC_019673.1 - Region 17 - NRPS-like,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: 4,239,911 - 4,317,336 nt. (total: 77,426 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
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
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
BN6_RS18855: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

BN6_RS18860: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BN6_RS18925: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BN6_RS18930: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

BN6_RS18935: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BN6_RS18985: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

BN6_RS19025: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

Hydrolases: amidase hydrolase
BN6_RS18900: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

BN6_RS19045: amidase

smcogs
  SMCOG1105: amidase

Lyases: dehydratase
BN6_RS19030: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
BN6_RS18885: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN6_RS18890: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS18920: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS18945: 1-deoxy-D-xylulose-5-phosphate synthase

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

BN6_RS19015: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl 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 | NRPS-like | T1PKS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001534.3 |  |  |  | 1.17 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0001535.3 |  |  |  | 0.90 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0001275.3 |  |  |  | 0.88 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  |  |  | 0.88 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  |  | 0.86 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001249.5 |  |  |  | 0.82 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002192.3 |  |  |  | 0.78 | PKS | FR901512 | fungal sp. No.14919
BGC0002154.2 |  |  |  | 0.76 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001254.3 |  |  |  | 0.72 | PKS | ACT-Toxin II | Alternaria alternata
BGC0000056.3 |  |  |  | 0.72 | PKS | esperamicin | Actinomadura verrucosospora

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  | 0.75 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001534.3 |  | 0.71 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0002164.2 |  | 0.69 | NRPS | peramine | Epichloe festucae
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
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: 19.35 out of 20.47
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.74 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.11 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.76 out of 23.79
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.20 out of 26.85
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.50 out of 20.47
Confidence: medium
Additional weak hits (22):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.77 out of 27.55
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.82 out of 30.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.41 out of 32.93
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.62 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.21 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.11 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.18 out of 26.06
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.37 out of 26.12
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.29 out of 35.63
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.30 out of 27.04
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.21 out of 20.01
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.00 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.79 out of 27.78
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.29 out of 33.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.38 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.36 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.36 out of 27.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.45 out of 24.78
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.81 out of 35.63
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 20, location 4239910 - 4317336:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk) + (Hpg)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 21, location 4239910 - 4281665:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk) + (Hpg)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 22, location 4246471 - 4291322:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk) + (Hpg)

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).
BN6_RS18890: Hpg
Search NORINE for peptide: strict or relaxed
AMP-binding (9..405): Hpg
nrpys: Hpg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDPSFSMSTFEVHIMTGGDRVMYGATETNLFVTN
  Nearest Stachelhaus code(s):
    Hpg NVYHLGMLFK (65% 8Å match)
  Stachelhaus code match:
    60% (weak)

BN6_RS18920: pk
PKS_AT (548..829): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  Methylmalonyl-CoA: 66.7%
  Propionyl-CoA: 58.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 110.6
  Methoxymalonyl-CoA: 89.1
  Ethylmalonyl-CoA: 87.7
  Malonyl-CoA: 84.4
  Isobutyryl-CoA: 75.3
  2-Methylbutyryl-CoA: 54.3
  Propionyl-CoA: 47.3
  inactive: 40.7
  Acetyl-CoA: 37.3
  trans-1,2-CPDA: 36.2
  Benzoyl-CoA: 35.5
  3-Methylbutyryl-CoA: 34.1
  fatty_acid: 31.3
  CHC-CoA: 23.4

BN6_RS19015: mal
PKS_AT (618..846): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 58.3%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 71.8
  Methoxymalonyl-CoA: 51.3
  Methylmalonyl-CoA: 45.7
  Propionyl-CoA: 28.9
  Ethylmalonyl-CoA: 23.2
  fatty_acid: 22.4
  inactive: 21.9
  Isobutyryl-CoA: 21.0
  trans-1,2-CPDA: 12.0
  2-Methylbutyryl-CoA: 11.5
  CHC-CoA: 7.7
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems

NC_019673.1 - Region 18 - lanthipeptide-class-ii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,520,676 - 4,543,519 nt. (total: 22,844 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase
BN6_RS19950: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

BN6_RS20020: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

Transferases: glycosyltransferase methyltransferase
BN6_RS19970: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

BN6_RS20025: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: cyclase
BN6_RS20010: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

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

Reference | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000554.4 |  | 0.53 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000659.3 |  | 0.49 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000658.3 |  | 0.48 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000528.5 |  | 0.48 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002704.2 |  | 0.47 | ribosomal | archalan β | Halorussus salinus
BGC0000504.5 |  | 0.46 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0001576.3 |  | 0.46 | ribosomal | divamide A | Prochloron didemni
BGC0000500.5 |  | 0.46 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0000657.5 |  | 0.45 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000554.4 |  | 0.53 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000659.3 |  | 0.49 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000658.3 |  | 0.48 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000528.5 |  | 0.48 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002704.2 |  | 0.47 | ribosomal | archalan β | Halorussus salinus
BGC0000504.5 |  | 0.46 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0001576.3 |  | 0.46 | ribosomal | divamide A | Prochloron didemni
BGC0000500.5 |  | 0.46 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0000657.5 |  | 0.45 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15

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 BN6_RS20010

allorf_4537799_4537888
Leader:
MPARRPEQAAGS
Core:
A H R L T H S G D C T R S N S R C
Core with dehydrations:
A H R L Dhb H Dha G D Cys Dhb R Dha N Dha R Cys

#### antiSMASH-DB 4.0 matches for allorf_4537799_4537888

100.0%
NC_019673.1:
Lanthipeptides: allorf_4537799_4537888_lanthipeptide
1
A H R L T H S G D C T R S N S R C
17
A H R L T H S G D C T R S N S R C
1
A H R L T H S G D C T R S N S R C
17
42.1%
NZ_CP006910.1:
Lanthipeptides: W903_RS05315_lanthipeptide
4
L T H S G D C T R S N S R C
17
L T S +C T N R C
5
L T Q S Y E C T T P N V R C
18
25.0%
NZ_CP031248.1 and 2 others:
NZ_CP040803.1 Lanthipeptides: FHI56_RS00850_lanthipeptide NZ_CP090008.1 Lanthipeptides: LV497_RS10140_lanthipeptide
Lanthipeptides: DV130_RS02025_lanthipeptide
4
L T H S G D C T R S N S R C
17
T H S +C T N R C
18
F T H S Y E C T S P N V R C
31
with 5 more sequence matches
21.9%
NZ_AP023392.1 and 4 others:
NZ_CP015557.1 Lanthipeptides: A6M16_RS04830_lanthipeptide NZ_CP065430.1 Lanthipeptides: I5V48_RS05980_lanthipeptide NZ_CP100430.1 Lanthipeptides: NLY76_RS04570_lanthipeptide NZ_JAEUXF010000003.1 Lanthipeptides: JNE40_RS02515_lanthipeptide
Lanthipeptides: H7679_RS04985_lanthipeptide
4
L T H S G D C T R S N S R C
17
T S +C T N R C
18
F T F S Y E C T S P N V R C
31
21.9%
NZ_CGZJ01000010.1 and 13 others:
NZ_CP028436.1 Lanthipeptides: DA395_RS05855_lanthipeptide NZ_CP113267.1 Lanthipeptides: OTB22_RS04705_lanthipeptide NZ_CRIA01000002.1 Lanthipeptides: AKS83_RS03035_lanthipeptide NZ_FHPK02000016.1 Lanthipeptides: AZ518_RS08960_lanthipeptide NZ_FNJT01000001.1 Lanthipeptides: BLS46_RS10015_lanthipeptide NZ_FZCI01000021.1 Lanthipeptides: CFV25_RS09690_lanthipeptide NZ_JALDWE010000003.1 Lanthipeptides: M1F86_RS04905_lanthipeptide NZ_JFJA01000026.1 Lanthipeptides: BM49_RS12025_lanthipeptide NZ_JUQX01000059.1 Lanthipeptides: ADI74_RS08850_lanthipeptide NZ_LR699783.1 Lanthipeptides: F1569_RS10835_lanthipeptide NZ_NANQ01000004.1 Lanthipeptides: B5K28_RS02505_lanthipeptide NZ_NANU01000009.1 Lanthipeptides: B5K23_RS03050_lanthipeptide NZ_NCUW01000030.1 Lanthipeptides: B7709_RS10285_lanthipeptide
Lanthipeptides: AQF97_RS08520_lanthipeptide
4
L T H S G D C T R S N S R C
17
T S +C T +N R C
19
F T C S Y E C T T N N V R C
32
21.9%
NZ_CGZJ01000010.1 and 13 others:
NZ_CP028436.1 Lanthipeptides: DA395_RS05860_lanthipeptide NZ_CP113267.1 Lanthipeptides: OTB22_RS04710_lanthipeptide NZ_CRIA01000002.1 Lanthipeptides: AKS83_RS03040_lanthipeptide NZ_FHPK02000016.1 Lanthipeptides: AZ518_RS08955_lanthipeptide NZ_FNJT01000001.1 Lanthipeptides: BLS46_RS03540_lanthipeptide NZ_FZCI01000021.1 Lanthipeptides: CFV25_RS09695_lanthipeptide NZ_JALDWE010000003.1 Lanthipeptides: M1F86_RS04900_lanthipeptide NZ_JFJA01000026.1 Lanthipeptides: BM49_RS09505_lanthipeptide NZ_JUQX01000059.1 Lanthipeptides: ADI74_RS08855_lanthipeptide NZ_LR699783.1 Lanthipeptides: F1569_RS03105_lanthipeptide NZ_NANQ01000004.1 Lanthipeptides: B5K28_RS02500_lanthipeptide NZ_NANU01000009.1 Lanthipeptides: B5K23_RS03045_lanthipeptide NZ_NCUW01000030.1 Lanthipeptides: B7709_RS09410_lanthipeptide
Lanthipeptides: AQF97_RS08525_lanthipeptide
1
A H R L T H S G D C T R S N S R C
17
T+S +C T N R C
15
G W W F T Y S Y E C T S P N V R C
31
21.9%
NZ_CP006910.1:
Lanthipeptides: W903_RS05320_lanthipeptide
4
L T H S G D C T R S N S R C
17
T S +C T +N R C
19
F T C S S E C T S N N V R C
32
19.4%
NZ_VMLD01000009.1 and 3 others:
NZ_VMLI01000004.1 Lanthipeptides: HT696_RS02300_lanthipeptide NZ_VMMD01000015.1 Lanthipeptides: HT711_RS05565_lanthipeptide NZ_VMMI01000027.1 Lanthipeptides: HT721_RS06685_lanthipeptide
Lanthipeptides: HT679_RS04550_lanthipeptide
4
L T H S G D C T R S N S R C
17
T S +C T N R C
22
F T L S Y E C T S P N V R C
35
allorf_4537901_4538068
Leader:
MVLPAPATPSRGRYSWSPPARPSGRHRARSAAAA
Core:
A S R G P P G P G R T N T V R P R N A A C
Core with dehydrations:
A Dha R G P P G P G R Dhb N Dhb V R P R N A A Cys

#### antiSMASH-DB 4.0 matches for allorf_4537901_4538068

100.0%
NC_019673.1:
Lanthipeptides: allorf_4537901_4538068_lanthipeptide
1
A S R G P P G P G R T N T V R P R N A A C
21
A S R G P P G P G R T N T V R P R N A A C
1
A S R G P P G P G R T N T V R P R N A A C
21
27.6%
NZ_RYYV01000004.1:
Lanthipeptides: allorf_104369_104572_lanthipeptide
2
S R G P P G P G R T N T V R P R N A A C
21
S R G G R +R + A C
10
S R S T A G K G R N T C L R R Q V H A C
29

#### 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.
No hits above weak threshold.
Weak hits (7):
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.46 out of 29.65
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.11 out of 39.62
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.04 out of 26.85
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.48 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.01 out of 28.19
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_4537799_4537888 - Class II
  Cleavage pHMM score: -5.70
  RODEO score: 0
  Monoisotopic mass: 1809.9 Da
  Molecular weight: 1811.0 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1829.0 Da N = 1
    1847.0 Da N = 2
    1865.0 Da N = 3
allorf_4537901_4538068 - Class II
  Cleavage pHMM score: -4.50
  RODEO score: 0
  Monoisotopic mass: 2080.1 Da
  Molecular weight: 2081.3 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2099.3 Da N = 1
    2117.4 Da N = 2

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NC_019673.1 - Region 19 - oligosaccharide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,850,224 - 4,873,898 nt. (total: 23,675 nt) Show pHMM detection rules used
oligosaccharide: (repeatable(3, [DUF1205, Glyco_transf_28, Glycos_transf_1, Glycos_transf_2, MGT]) and minscore(MGT, 150))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase reductase
BN6_RS21495: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

BN6_RS21505: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase glycosyltransferase methyltransferase
BN6_RS21545: glycosyltransferase

smcogs
  SMCOG1102: glycosyltransferase

BN6_RS21550: methyltransferase

smcogs
  SMCOG1089: methyltransferase

BN6_RS21560: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

BN6_RS21595: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Translocases: permease
BN6_RS21605: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | oligosaccharide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002573.2 |  | 0.45 | other (other) | phosphoramidon | Streptomyces mozunensis
BGC0001782.3 |  | 0.44 | other (other) | spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G | Streptomyces sp. SCSIO 03032
BGC0000902.4 |  | 0.42 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000277.5 |  | 0.42 | PKS | urdamycin | Streptomyces fradiae
BGC0000903.3 |  | 0.40 | other (other) | fluorometabolite | Streptomyces cattleya
BGC0000285.5 |  | 0.40 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000219.4 |  | 0.38 | PKS, saccharide | elloramycin | Streptomyces olivaceus
BGC0002387.2 |  | 0.38 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0000925.5 |  | 0.38 | other (other) | quinolobactin | Pseudomonas fluorescens
BGC0000875.4 |  | 0.38 | other (nucleoside), saccharide | caprazamycin, caprazamycin aglycon | Streptomyces sp. MK730-62F2

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002573.2 |  | 0.45 | other (other) | phosphoramidon | Streptomyces mozunensis
BGC0001782.3 |  | 0.44 | other (other) | spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G | Streptomyces sp. SCSIO 03032
BGC0000902.4 |  | 0.42 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000277.5 |  | 0.42 | PKS | urdamycin | Streptomyces fradiae
BGC0000903.3 |  | 0.40 | other (other) | fluorometabolite | Streptomyces cattleya
BGC0000285.5 |  | 0.40 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000219.4 |  | 0.38 | PKS, saccharide | elloramycin | Streptomyces olivaceus
BGC0002387.2 |  | 0.38 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0000925.5 |  | 0.38 | other (other) | quinolobactin | Pseudomonas fluorescens
BGC0000875.4 |  | 0.38 | other (nucleoside), saccharide | caprazamycin, caprazamycin aglycon | Streptomyces sp. MK730-62F2

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:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.82 out of 26.85
Confidence: medium
Additional weak hits (14):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.91 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.29 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.40 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.05 out of 36.54
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.09 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.26 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.90 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.27 out of 27.78
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.77 out of 32.74
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.77 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.70 out of 26.12
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.74 out of 26.33
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.27 out of 36.54
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
RutR | Regulator of the pyrimidine and purine metabolism

NC_019673.1 - Region 20 - melanin
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,911,671 - 4,922,060 nt. (total: 10,390 nt) Show pHMM detection rules used
melanin: melC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: protease
BN6_RS47975: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

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 | melanin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000912.3 |  | 0.60 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  | 0.59 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000911.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000909.3 |  | 0.53 | other (other) | melanin | Streptomyces avermitilis
BGC0000908.3 |  | 0.49 | other (other) | melanin | Streptomyces avermitilis
BGC0000662.5 |  | 0.37 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.37 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.36 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.35 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001624.3 |  | 0.35 | other (other) | iso-A82775C | Pestalotiopsis fici

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000912.3 |  | 0.60 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  | 0.59 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000911.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000909.3 |  | 0.53 | other (other) | melanin | Streptomyces avermitilis
BGC0000908.3 |  | 0.49 | other (other) | melanin | Streptomyces avermitilis
BGC0000662.5 |  | 0.37 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.37 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.36 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.35 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001624.3 |  | 0.35 | other (other) | iso-A82775C | Pestalotiopsis fici

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.50 out of 26.85
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (8):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.51 out of 30.22
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.78 out of 30.22
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.09 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.76 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.52 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.30 out of 26.06
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.69 out of 27.04
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
RutR | Regulator of the pyrimidine and purine metabolism

NC_019673.1 - Region 21 - NRPS,NRPS-like,PKS-like,T1PKS,hglE-KS,transAT-PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,954,497 - 5,110,155 nt. (total: 155,659 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
hglE-KS: (hglE or hglD)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
PKS-like: (t2pks2 or ksIII)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
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: oxygenase
BN6_RS22310: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acylase aminotransferase glycosyltransferase halogenase kinase methyltransferase
BN6_RS22060: methyltransferase

smcogs
  SMCOG1089: methyltransferase

BN6_RS22215: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

BN6_RS22235: methyltransferase

smcogs
  SMCOG1248: methyltransferase

BN6_RS22260: halogenase

smcogs
  SMCOG1119: halogenase

BN6_RS22290: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

BN6_RS22305: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

BN6_RS22375: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

BN6_RS22425: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Hydrolases: esterase hydrolase
BN6_RS21990: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

BN6_RS22150: isochorismatase

smcogs
  SMCOG1027: isochorismatase

BN6_RS22210: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

BN6_RS22300: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: decarboxylase hydratase
BN6_RS22350: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

BN6_RS22370: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

BN6_RS22410: putative carboxymuconolactone decarboxylase

smcogs
  SMCOG1298: putative carboxymuconolactone decarboxylase

Ligases: ligase synthase
BN6_RS22075: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS22195: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS22200: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS22265: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS22280: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS22295: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN6_RS22335: hydroxymethylglutaryl-CoA synthase

smcogs
  SMCOG1043: hydroxymethylglutaryl-CoA synthase

BN6_RS22365: hydroxymethylglutaryl-CoA synthase

smcogs
  SMCOG1043: hydroxymethylglutaryl-CoA synthase

BN6_RS22385: 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 | hglE-KS | T1PKS | PKS-like | NRPS-like | transAT-PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001758.4 |  |  |  |  |  |  |  | 1.86 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  |  |  |  |  |  |  | 1.85 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  |  |  |  |  | 1.85 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  |  |  |  |  |  | 1.84 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  |  |  |  |  |  | 1.84 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  |  |  |  |  |  | 1.81 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  |  |  |  |  |  |  | 1.81 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  |  |  |  |  |  |  | 1.79 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  |  |  |  |  |  | 1.77 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  |  |  |  |  |  |  | 1.76 | NRPS | enniatin | Fusarium equiseti

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002164.2 |  | 0.70 | NRPS | peramine | Epichloe festucae
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001273.3 |  | 0.66 | PKS | asperlactone | Aspergillus ochraceus
BGC0001758.4 |  | 0.66 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.76 out of 26.85
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.52 out of 29.72
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.80 out of 26.85
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.01 out of 23.43
Confidence: medium
Additional weak hits (24):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.16 out of 26.85
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.02 out of 30.22
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.45 out of 32.74
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.88 out of 27.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.61 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.89 out of 30.25
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.62 out of 32.93
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.37 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.46 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.39 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 21.14 out of 36.54
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.70 out of 26.33
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.91 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.25 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.94 out of 29.65
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 26.15 out of 36.53
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.04 out of 29.65
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.00 out of 32.38
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.39 out of 25.88
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.46 out of 39.62
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 27, location 4954496 - 5110155:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - ccmal) + (mal - Me-ccmal - ccmal - mal) + (Cys) + (Thr) + (mxmal) + (mal) + (Val - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 28, location 4954496 - 5000718:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 29, location 4988349 - 5039259:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (mxmal) + (Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 30, location 5013700 - 5054930:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (mxmal) + (Thr) + (Cys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 31, location 5016111 - 5057914:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mxmal) + (Thr) + (Cys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 32, location 5018917 - 5110155:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mxmal) + (Thr) + (Cys) + (mal - Me-ccmal - ccmal - mal) + (ccmal - ccmal)

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).
BN6_RS22075: Val - X
Search NORINE for peptide: strict or relaxed
AMP-binding (9..416): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRSFDASTYEVFVLVGGDHNGYGPTETTTFATR
  Nearest Stachelhaus code(s):
    Val DAYFLGGTFK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1070..1474): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FDSSFDASTYEVFLWTGGEVDGYGPTEATVFITC
  Nearest Stachelhaus code(s):
    Cyc-D-Gly DAYLWGGVFK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

BN6_RS22195: mal
PKS_AT (1205..1496): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 66.7%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 90.2
  inactive: 38.7
  Methoxymalonyl-CoA: 35.9
  Methylmalonyl-CoA: 25.4
  Propionyl-CoA: 15.4
  2-Methylbutyryl-CoA: 14.3
  fatty_acid: 8.7
  Isobutyryl-CoA: 8.4
  Ethylmalonyl-CoA: 7.3
  CHC-CoA: 6.6
  trans-1,2-CPDA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

BN6_RS22200: mxmal
PKS_AT (595..813): mxmal
ATSignature: (unknown)
No matches above 50%
minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 9.6
  Propionyl-CoA: 5.7
  Malonyl-CoA: 4.8
  Methylmalonyl-CoA: 3.1
  inactive: 1.0
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

BN6_RS22280: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (10..411): 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:
    LRAHFDFSVWEGSQVFGGEVNMYGITEITVHATH
  Nearest Stachelhaus code(s):
    Thr DFWSVGMVHK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

BN6_RS22290: mal
PKS_AT (8..282): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 100.8
  Methoxymalonyl-CoA: 32.9
  Methylmalonyl-CoA: 26.0
  inactive: 25.1
  Propionyl-CoA: 16.1
  Isobutyryl-CoA: 13.8
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

BN6_RS22295: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (933..1333): Cys
nrpys: Cys

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:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Small clusters prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Single AA prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWTTFDLSVFDGNSFLSGDISLGGATEATVWSNW
  Nearest Stachelhaus code(s):
    Cys DLFNFSLVWK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

BN6_RS22375: mal
PKS_AT (5..277): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 66.7%
  inactive: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 94.9
  inactive: 42.0
  Methylmalonyl-CoA: 35.0
  Methoxymalonyl-CoA: 34.4
  Propionyl-CoA: 29.3
  Isobutyryl-CoA: 17.4
  Benzoyl-CoA: 17.3
  fatty_acid: 13.1
  Ethylmalonyl-CoA: 10.8
  2-Methylbutyryl-CoA: 2.1
  CHC-CoA: 1.6
  trans-1,2-CPDA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

BN6_RS22385: X
AMP-binding (16..398): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDTS---STTVLILGNASANSAYAQSEAVPAIML
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
BldD | Development and antibiotic global regulator
NtrC | Nitrogen regulatory protein C
RutR | Regulator of the pyrimidine and purine metabolism

NC_019673.1 - Region 22 - NRPS,NRPS-like,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: 5,176,387 - 5,418,301 nt. (total: 241,915 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))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
BN6_RS22835: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BN6_RS22845: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

BN6_RS22855: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

BN6_RS22920: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BN6_RS22945: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

BN6_RS22980: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

BN6_RS23050: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BN6_RS23075: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BN6_RS23080: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BN6_RS23300: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

BN6_RS23315: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

BN6_RS23380: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

BN6_RS23425: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

BN6_RS23440: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

BN6_RS23445: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BN6_RS23450: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: acylase acyltransferase aminotransferase carboxylase glycosyltransferase methyltransferase transferase
BN6_RS22870: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

BN6_RS23040: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

BN6_RS23045: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

BN6_RS23170: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

BN6_RS23180: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

BN6_RS23325: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

BN6_RS23350: methyltransferase

smcogs
  SMCOG1248: methyltransferase

BN6_RS23385: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

BN6_RS23395: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

BN6_RS23420: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

BN6_RS42270: methyltransferase

smcogs
  SMCOG1089: methyltransferase

BN6_RS49715: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: dehalogenase esterase glucosidase hydrolase protease
BN6_RS22805: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

BN6_RS22830: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

BN6_RS23140: HAD-superfamily hydrolase, subfamily IA, variant

smcogs
  SMCOG1115: HAD-superfamily hydrolase, subfamily IA, variant

BN6_RS23200: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

BN6_RS23295: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

BN6_RS23320: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: hydratase lyase
BN6_RS23145: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

BN6_RS23155: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
BN6_RS22860: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS22865: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS22925: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS22930: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

BN6_RS22935: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS23060: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS23070: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN6_RS23150: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS23160: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS23185: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS23365: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

BN6_RS23375: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS48030: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS48035: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS49005: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl 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 | T1PKS | NRPS | NRPS | T1PKS | NRPS-like | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  |  |  |  |  | 1.75 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  |  |  |  |  |  | 1.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  |  |  |  |  |  | 1.72 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0002075.3 |  |  |  |  |  |  | 1.72 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001244.3 |  |  |  |  |  |  | 1.71 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001132.4 |  |  |  |  |  |  | 1.61 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  |  |  |  | 1.58 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  |  |  |  | 1.57 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001249.5 |  |  |  |  |  |  | 1.54 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001833.4 |  |  |  |  |  |  | 1.54 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001132.4 |  | 0.77 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001273.3 |  | 0.77 | PKS | asperlactone | Aspergillus ochraceus
BGC0001128.4 |  | 0.76 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001275.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002286.3 |  | 0.76 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  | 0.76 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001249.5 |  | 0.75 | NRPS | dimethylcoprogen | Alternaria alternata

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.72 out of 20.47
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.40 out of 20.97
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.91 out of 26.33
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.04 out of 27.04
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.13 out of 23.79
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.56 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.07 out of 20.47
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.52 out of 29.72
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
Additional weak hits (32):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.11 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.52 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.97 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.74 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.93 out of 21.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.09 out of 20.97
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.66 out of 36.54
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.07 out of 26.85
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.36 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
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.00 out of 21.55
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.98 out of 24.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.13 out of 28.19
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.92 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.60 out of 30.22
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.72 out of 31.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.43 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.98 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.34 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.07 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.37 out of 27.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.54 out of 27.04
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.47 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.22 out of 32.93
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.36 out of 21.84
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.14 out of 35.63
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.05 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.54 out of 28.19
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.77 out of 27.18
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 33, location 5176386 - 5282840:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - ccmal) + (ohmal) + (ccmal - ccmal - ccmal) + (ohmal) + (ccmal - Me-mal) + (ccmal) + (ohmal)
Non-colinear ordering:
  BN6_RS22935 + BN6_RS22865 + BN6_RS49005 + BN6_RS49715 + BN6_RS22930 + BN6_RS22925 + BN6_RS22860

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 34, location 5270796 - 5418301:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal - ccmal - ccmal) + (ccmal - mal) + (pk) + (Ser) + (ohmal) + (Gly) + (X) + (Ser - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 35, location 5270796 - 5317711:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 36, location 5299709 - 5347767:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser) + (ohmal) + (Gly) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 37, location 5308943 - 5354828:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser) + (ohmal) + (Gly) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 38, location 5349900 - 5418301:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal - ccmal - ccmal) + (ccmal - mal) + (pk)
Non-colinear ordering:
  BN6_RS23375 + BN6_RS48030 + BN6_RS23365

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).
BN6_RS22860: mal
PKS_AT (557..835): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 66.7%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 192.8
  inactive: 90.0
  Methoxymalonyl-CoA: 78.7
  Methylmalonyl-CoA: 69.9
  Isobutyryl-CoA: 50.5
  Acetyl-CoA: 33.2
  Propionyl-CoA: 30.5
  Ethylmalonyl-CoA: 23.6
  Benzoyl-CoA: 21.4
  trans-1,2-CPDA: 14.6
  3-Methylbutyryl-CoA: 12.2
  CHC-CoA: 11.7
  fatty_acid: 11.5
  2-Methylbutyryl-CoA: 8.0

BN6_RS22865: mal
PKS_AT (563..851): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 62.5%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 148.1
  inactive: 74.6
  Methoxymalonyl-CoA: 65.3
  Methylmalonyl-CoA: 60.4
  Isobutyryl-CoA: 31.1
  Propionyl-CoA: 29.4
  Benzoyl-CoA: 28.1
  Ethylmalonyl-CoA: 20.8
  Acetyl-CoA: 15.7
  2-Methylbutyryl-CoA: 13.1
  CHC-CoA: 10.9
  3-Methylbutyryl-CoA: 9.8
  fatty_acid: 9.5
  trans-1,2-CPDA: 6.8

BN6_RS49005: mal - mal - mal
PKS_AT (1116..1393): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 187.4
  inactive: 90.0
  Methoxymalonyl-CoA: 69.1
  Methylmalonyl-CoA: 58.1
  Isobutyryl-CoA: 29.5
  Propionyl-CoA: 23.2
  Acetyl-CoA: 20.3
  Ethylmalonyl-CoA: 17.2
  Benzoyl-CoA: 16.7
  fatty_acid: 9.9
  CHC-CoA: 6.3
  2-Methylbutyryl-CoA: 5.0
  trans-1,2-CPDA: 4.0
  3-Methylbutyryl-CoA: 1.8

PKS_AT (2763..3058): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 91.7%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 190.6
  inactive: 103.9
  Methoxymalonyl-CoA: 41.0
  Methylmalonyl-CoA: 40.3
  Propionyl-CoA: 23.8
  2-Methylbutyryl-CoA: 14.2
  Isobutyryl-CoA: 12.8
  Benzoyl-CoA: 9.8
  Acetyl-CoA: 7.8
  CHC-CoA: 3.8
  trans-1,2-CPDA: 2.5
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0
  Ethylmalonyl-CoA: -0.6

PKS_AT (4388..4667): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 178.3
  inactive: 89.8
  Methoxymalonyl-CoA: 64.6
  Methylmalonyl-CoA: 57.2
  Propionyl-CoA: 34.1
  Ethylmalonyl-CoA: 26.5
  Acetyl-CoA: 22.4
  Isobutyryl-CoA: 17.6
  Benzoyl-CoA: 17.5
  2-Methylbutyryl-CoA: 16.9
  fatty_acid: 12.4
  trans-1,2-CPDA: 11.6
  CHC-CoA: 9.9
  3-Methylbutyryl-CoA: 0.0

BN6_RS22925: mal
PKS_AT (567..865): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 202.3
  inactive: 89.3
  Methoxymalonyl-CoA: 61.5
  Methylmalonyl-CoA: 57.9
  Propionyl-CoA: 42.6
  Ethylmalonyl-CoA: 29.3
  Benzoyl-CoA: 29.1
  Isobutyryl-CoA: 23.3
  Acetyl-CoA: 22.5
  2-Methylbutyryl-CoA: 20.9
  CHC-CoA: 16.5
  fatty_acid: 11.3
  trans-1,2-CPDA: 11.0
  3-Methylbutyryl-CoA: 0.0

BN6_RS22930: mal - mmal
PKS_AT (560..848): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 79.2%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 187.0
  inactive: 92.9
  Methoxymalonyl-CoA: 56.4
  Methylmalonyl-CoA: 52.6
  Propionyl-CoA: 37.1
  Isobutyryl-CoA: 29.3
  Ethylmalonyl-CoA: 23.9
  Acetyl-CoA: 13.7
  fatty_acid: 13.5
  Benzoyl-CoA: 13.4
  2-Methylbutyryl-CoA: 6.0
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0
  CHC-CoA: -0.7

PKS_AT (2213..2508): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 215.7
  Ethylmalonyl-CoA: 208.2
  Methoxymalonyl-CoA: 182.9
  2-Methylbutyryl-CoA: 164.8
  trans-1,2-CPDA: 145.5
  Propionyl-CoA: 119.1
  Malonyl-CoA: 98.3
  CHC-CoA: 95.1
  Isobutyryl-CoA: 84.4
  Benzoyl-CoA: 57.7
  Acetyl-CoA: 57.1
  3-Methylbutyryl-CoA: 57.1
  fatty_acid: 43.9
  inactive: 39.9

BN6_RS49715: mal
PKS_AT (556..865): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 211.0
  inactive: 107.6
  Methoxymalonyl-CoA: 61.1
  Methylmalonyl-CoA: 57.0
  Propionyl-CoA: 32.2
  Isobutyryl-CoA: 24.7
  Acetyl-CoA: 16.9
  Ethylmalonyl-CoA: 15.5
  Benzoyl-CoA: 9.9
  fatty_acid: 8.5
  CHC-CoA: 6.4
  2-Methylbutyryl-CoA: 6.4
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

BN6_RS22935: mmal - mal
PKS_AT (532..832): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 194.3
  Ethylmalonyl-CoA: 190.5
  Methoxymalonyl-CoA: 152.8
  2-Methylbutyryl-CoA: 119.3
  trans-1,2-CPDA: 105.7
  Propionyl-CoA: 91.7
  Malonyl-CoA: 84.8
  Isobutyryl-CoA: 77.7
  CHC-CoA: 76.4
  Benzoyl-CoA: 51.2
  Acetyl-CoA: 33.8
  3-Methylbutyryl-CoA: 32.1
  fatty_acid: 24.2
  inactive: 18.6

PKS_AT (1513..1805): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 205.7
  inactive: 95.0
  Methoxymalonyl-CoA: 71.7
  Methylmalonyl-CoA: 61.1
  Ethylmalonyl-CoA: 33.6
  Propionyl-CoA: 27.8
  Benzoyl-CoA: 25.7
  Isobutyryl-CoA: 25.0
  trans-1,2-CPDA: 17.2
  fatty_acid: 16.7
  Acetyl-CoA: 16.7
  CHC-CoA: 15.4
  2-Methylbutyryl-CoA: 11.2
  3-Methylbutyryl-CoA: 0.0

BN6_RS23060: Ser - X
Search NORINE for peptide: strict or relaxed
AMP-binding (455..841): Ser
nrpys: Ser

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFFSSGEVNLYGPTEATVDVSF
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1481..1852): X
nrpys: (unknown)

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:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    pro (Pro)
  Single AA prediction:
    pro (Pro)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LHGAFDVSFQESFLISSGEENQYGPTETHVATSY
  Nearest Stachelhaus code(s):
    Aze DVQFISQIAK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

BN6_RS23150: X
AMP-binding (6..412): X
nrpys: Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YYNFFDASTFDVFSLFGAEHNLYGPTEVTITCTE
  Nearest Stachelhaus code(s):
    foGly DLFFLCLIAK (62% 8Å match)
    Ala DCFFFALITK (59% 8Å match)
    Ile DAWFLGNIIK (53% 8Å match)
    Hpg DAFHLGLLCK (47% 8Å match)
  Stachelhaus code match:
    70% (weak)

BN6_RS23160: X
AMP-binding (427..763): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    SWKGWAATVFEAFGVTTGGVDLYATAETSVALVD
  Nearest Stachelhaus code(s):
    Ala DVFFVGLVAK (38% 8Å match)
    Val DALFVGLVAK (35% 8Å match)
  Stachelhaus code match:
    70% (weak)

BN6_RS23170: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (505..872): 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:
    LAMTFDIAGLEGQAVVGGEWNVYGPTETTIWSTT
  Nearest Stachelhaus code(s):
    Gly DILQVGVIWK (71% 8Å match)
  Stachelhaus code match:
    100% (strong)

BN6_RS23180: mal
PKS_AT (511..798): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 75.0%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 135.6
  inactive: 91.3
  Methoxymalonyl-CoA: 73.3
  Methylmalonyl-CoA: 63.1
  Propionyl-CoA: 39.7
  Ethylmalonyl-CoA: 33.6
  2-Methylbutyryl-CoA: 29.0
  Isobutyryl-CoA: 28.8
  trans-1,2-CPDA: 21.3
  CHC-CoA: 16.1
  Benzoyl-CoA: 12.3
  fatty_acid: 11.9
  Acetyl-CoA: 9.3
  3-Methylbutyryl-CoA: 0.0

BN6_RS23185: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (11..392): Ser
nrpys: Ser

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LATAFDVSVWEGNQVFAGEVNMYGITETTVHSTF
  Nearest Stachelhaus code(s):
    Ser DVWNVAMVHK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

BN6_RS23365: pk
PKS_AT (559..853): pk
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 87.5%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 209.9
  Methylmalonyl-CoA: 196.7
  Methoxymalonyl-CoA: 175.1
  2-Methylbutyryl-CoA: 126.1
  trans-1,2-CPDA: 113.8
  Propionyl-CoA: 103.9
  Malonyl-CoA: 81.4
  CHC-CoA: 80.4
  Isobutyryl-CoA: 76.3
  Benzoyl-CoA: 67.5
  3-Methylbutyryl-CoA: 45.5
  Acetyl-CoA: 35.5
  inactive: 25.7
  fatty_acid: 23.4

BN6_RS48030: mal - mal
PKS_AT (549..818): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 66.7%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 161.5
  inactive: 65.2
  Methoxymalonyl-CoA: 53.9
  Methylmalonyl-CoA: 49.5
  Ethylmalonyl-CoA: 27.5
  Propionyl-CoA: 23.3
  fatty_acid: 20.5
  Isobutyryl-CoA: 17.9
  Benzoyl-CoA: 16.0
  Acetyl-CoA: 11.5
  CHC-CoA: 8.6
  2-Methylbutyryl-CoA: 6.3
  trans-1,2-CPDA: 5.3
  3-Methylbutyryl-CoA: 3.0

PKS_AT (2161..2432): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 66.7%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 160.7
  inactive: 57.6
  Methylmalonyl-CoA: 56.2
  Methoxymalonyl-CoA: 55.1
  Propionyl-CoA: 29.8
  Acetyl-CoA: 25.7
  Isobutyryl-CoA: 25.6
  Ethylmalonyl-CoA: 24.1
  fatty_acid: 21.2
  Benzoyl-CoA: 20.1
  CHC-CoA: 10.9
  2-Methylbutyryl-CoA: 10.8
  trans-1,2-CPDA: 9.8
  3-Methylbutyryl-CoA: 4.8

BN6_RS23375: mal - mal - mal
PKS_AT (503..774): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  Propionyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 181.6
  inactive: 79.3
  Methylmalonyl-CoA: 63.9
  Methoxymalonyl-CoA: 63.7
  Ethylmalonyl-CoA: 41.8
  Propionyl-CoA: 36.3
  Isobutyryl-CoA: 31.2
  Acetyl-CoA: 25.3
  2-Methylbutyryl-CoA: 18.8
  Benzoyl-CoA: 18.3
  fatty_acid: 17.9
  trans-1,2-CPDA: 15.5
  CHC-CoA: 11.8
  3-Methylbutyryl-CoA: 6.2

PKS_AT (1474..1744): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 70.8%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 153.6
  Methylmalonyl-CoA: 69.0
  Methoxymalonyl-CoA: 67.4
  inactive: 54.4
  Isobutyryl-CoA: 49.1
  fatty_acid: 36.4
  Ethylmalonyl-CoA: 33.7
  CHC-CoA: 33.4
  Propionyl-CoA: 30.0
  Acetyl-CoA: 26.5
  2-Methylbutyryl-CoA: 19.7
  trans-1,2-CPDA: 19.0
  Benzoyl-CoA: 14.1
  3-Methylbutyryl-CoA: 11.8

PKS_AT (3086..3373): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 158.1
  inactive: 80.9
  Methoxymalonyl-CoA: 53.8
  Methylmalonyl-CoA: 45.3
  Benzoyl-CoA: 23.3
  fatty_acid: 22.1
  Propionyl-CoA: 21.8
  Isobutyryl-CoA: 21.6
  Acetyl-CoA: 17.9
  Ethylmalonyl-CoA: 15.6
  2-Methylbutyryl-CoA: 9.0
  CHC-CoA: 8.0
  trans-1,2-CPDA: 7.2
  3-Methylbutyryl-CoA: -4.0

BN6_RS48035: Acetyl-CoA
CAL_domain (45..507): Acetyl-CoA
minowa: Acetyl-CoA

Prediction, score:
  Acetyl-CoA: 37.2
  fatty_acid: 34.5
  AHBA: 11.2
  shikimic_acid: 0.0
  NH2: -1.1

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AbrC3 | Antibiotic production activator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
CcpA | Catabolite control protein A
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NC_019673.1 - Region 23 - 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: 5,672,303 - 5,698,469 nt. (total: 26,167 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase
BN6_RS24575: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

BN6_RS24590: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

BN6_RS24610: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

BN6_RS24670: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: glycosyltransferase methyltransferase
BN6_RS24555: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

BN6_RS24615: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: synthetase
BN6_RS24595: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Translocases: permease
BN6_RS24650: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.68 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.63 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.57 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.57 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0001456.3 |  | 0.56 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000648.3 |  | 0.53 | terpene | carotenoid | Myxococcus xanthus
BGC0000636.3 |  | 0.52 | terpene | carotenoid | Brevibacterium linens
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000637.3 |  | 0.49 | terpene | carotenoid | Corynebacterium glutamicum
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.68 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.63 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.57 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.57 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0001456.3 |  | 0.56 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000648.3 |  | 0.53 | terpene | carotenoid | Myxococcus xanthus
BGC0000636.3 |  | 0.52 | terpene | carotenoid | Brevibacterium linens
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000637.3 |  | 0.49 | terpene | carotenoid | Corynebacterium glutamicum
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404

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
--- | --- | --- | --- | --- | ---
tetraterpene | C40 carotenoid |  | C40 | unknown | unknown

Genes with terpene domains:
BN6_RS24595: PT_FPPS_like
Domain 1 (41 - 357): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

Reactions:
  IPP, DMAPP → FPP
  IPP, DMAPP → GGPP
  IPP, DMAPP → GFPP
  IPP, DMAPP → HPP

BN6_RS24600: PT_phytoene_like
Domain 1 (18 - 306): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

BN6_RS24620: Lycopene_cycl
Domain 1 (3 - 94): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

BN6_RS24625: Lycopene_cycl
Domain 1 (4 - 92): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

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 (4):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.54 out of 23.43
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.59 out of 36.54
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.41 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.90 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NC_019673.1 - Region 24 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,715,154 - 5,761,384 nt. (total: 46,231 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: electron transfer oxidoreductase oxygenase
BN6_RS24760: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

BN6_RS24795: flavodoxin

smcogs
  SMCOG1134: flavodoxin

BN6_RS24845: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

BN6_RS24860: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

BN6_RS24875: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Transferases: methyltransferase
BN6_RS24900: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Hydrolases: hydrolase
BN6_RS24820: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: dehydratase
BN6_RS24870: L-carnitine dehydratase/bile acid-inducible

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

Ligases: ligase synthase
BN6_RS24835: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS24890: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

BN6_RS43025: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001249.5 |  | 0.62 | NRPS | dimethylcoprogen | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001249.5 |  | 0.62 | NRPS | dimethylcoprogen | Alternaria alternata

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.07 out of 20.47
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.71 out of 26.33
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
Additional weak hits (7):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.58 out of 30.22
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.42 out of 26.85
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.44 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.97 out of 28.19
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.85 out of 36.53
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.90 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 40, location 5715153 - 5761384:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val - Ala)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BN6_RS24835: Val - Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (449..834): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDQAFDAYTLEGWLLVGGDVNGYGPTENTTFTSC
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (85% 8Å match)
    bOH-Val DALWLGGTFK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1469..1853): 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:
    LWATFDLSVFEVNTNLAGEYNLYGPTEDTTYSTA
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
VqsM | Regulator of quorum-sensing signalling systems

NC_019673.1 - Region 25 - amglyccycl
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: 5,878,506 - 5,899,633 nt. (total: 21,128 nt) Show pHMM detection rules used
amglyccycl: (DOIS or ValA or salQ or strH or strK1 or strK2 or NeoL or SpcFG or SpcDK_glyc)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
BN6_RS25435: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

BN6_RS25440: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

BN6_RS25480: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BN6_RS25495: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BN6_RS25500: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase
BN6_RS25430: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: hydrolase
BN6_RS25420: HAD-superfamily hydrolase, subfamily IA, variant

smcogs
  SMCOG1115: HAD-superfamily hydrolase, subfamily IA, variant

Ligases: synthase
BN6_RS25445: 3-dehydroquinate synthase

smcogs
  SMCOG1183: 3-dehydroquinate synthase

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

Reference | amglyccycl | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000701.5 |  | 0.51 | saccharide | jinggangmycin | Streptomyces hygroscopicus subsp. yingchengensis
BGC0001817.5 |  | 0.46 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0001774.5 |  | 0.42 | other (other) | spicamycin | Streptomyces fimbriatus
BGC0000903.3 |  | 0.42 | other (other) | fluorometabolite | Streptomyces cattleya
BGC0000898.5 |  | 0.42 | saccharide | desosamine, pikromycin, neomethymycin, narbomycin | Streptomyces venezuelae
BGC0002439.3 |  | 0.42 | other (other) | diastaphenazine, izumiphenazine C | Streptomyces diastaticus
BGC0000772.5 |  | 0.41 | saccharide | lipopolysaccharide | Brucella melitensis
BGC0000723.5 |  | 0.41 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. limoneus
BGC0002047.2 |  | 0.40 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0000791.3 |  | 0.40 | saccharide | O-antigen | Cronobacter sakazakii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000701.5 |  | 0.51 | saccharide | jinggangmycin | Streptomyces hygroscopicus subsp. yingchengensis
BGC0001817.5 |  | 0.46 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0001774.5 |  | 0.42 | other (other) | spicamycin | Streptomyces fimbriatus
BGC0000903.3 |  | 0.42 | other (other) | fluorometabolite | Streptomyces cattleya
BGC0000898.5 |  | 0.42 | saccharide | desosamine, pikromycin, neomethymycin, narbomycin | Streptomyces venezuelae
BGC0002439.3 |  | 0.42 | other (other) | diastaphenazine, izumiphenazine C | Streptomyces diastaticus
BGC0000772.5 |  | 0.41 | saccharide | lipopolysaccharide | Brucella melitensis
BGC0000723.5 |  | 0.41 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. limoneus
BGC0002047.2 |  | 0.40 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0000791.3 |  | 0.40 | saccharide | O-antigen | Cronobacter sakazakii

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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (1):
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.09 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production

NC_019673.1 - Region 26 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,909,193 - 5,952,159 nt. (total: 42,967 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
BN6_RS25570: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

BN6_RS25585: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

BN6_RS25650: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Hydrolases: deacetylase
BN6_RS25655: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

Ligases: ligase
BN6_RS25630: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS25680: carboxylate-amine ligase

smcogs
  SMCOG1165: carboxylate-amine ligase

BN6_RS25700: carboxylate-amine ligase

smcogs
  SMCOG1165: carboxylate-amine 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-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002164.2 |  | 0.61 | NRPS | peramine | Epichloe festucae
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  | 0.60 | NRPS | enniatin | Fusarium equiseti
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0000357.5 |  | 0.60 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001240.4 |  | 0.60 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  | 0.60 | NRPS | AM-toxin | Alternaria alternata
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002164.2 |  | 0.61 | NRPS | peramine | Epichloe festucae
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  | 0.60 | NRPS | enniatin | Fusarium equiseti
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0000357.5 |  | 0.60 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001240.4 |  | 0.60 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  | 0.60 | NRPS | AM-toxin | Alternaria alternata
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.50 out of 20.47
Confidence: medium
Additional weak hits (6):
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.14 out of 19.26
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.26 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.36 out of 35.63
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.12 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.97 out of 24.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.69 out of 35.63
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 42, location 5909192 - 5952159:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BN6_RS25630: X
AMP-binding (9..396): X
nrpys: (unknown)

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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHVFDVSQWESYAFCAGEVDYYGPTEATIYATY
  Nearest Stachelhaus code(s):
    Aol DVWYVAAIYK (56% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

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

NC_019673.1 - Region 27 - RRE-containing,azole-containing-RiPP,lassopeptide,other
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: 6,028,417 - 6,089,588 nt. (total: 61,172 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)
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)
other: (Neocarzinostat or bcpB or frbD or mitE or prnB or CaiA or bacilysin or orf2_PTase)
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lasso peptides
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: oxygenase
BN6_RS26160: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BN6_RS26225: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: glycosyltransferase
BN6_RS26100: glycosyltransferase

smcogs
  SMCOG1102: glycosyltransferase

Hydrolases: hydrolase protease
BN6_RS26065: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

BN6_RS26075: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

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 | lassopeptide | azole-containing-RiPP | other | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001640.3 |  |  |  |  | 0.64 | ribosomal | kocurin | Kocuria rosea
BGC0001146.5 |  |  |  |  | 0.63 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0000605.5 |  |  |  |  | 0.59 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365
BGC0000603.5 |  |  |  |  | 0.57 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0001145.5 |  |  |  |  | 0.55 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0002311.3 |  |  |  |  | 0.54 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0000606.5 |  |  |  |  | 0.50 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0001174.4 |  |  |  |  | 0.49 | ribosomal | corynazolicin | Corynebacterium urealyticum DSM 7111
BGC0001860.4 |  |  |  |  | 0.47 | ribosomal | thiomuracin | Thermobispora bispora DSM 43833
BGC0001655.3 |  |  |  |  | 0.47 | ribosomal | LP2006 | Nocardiopsis alba DSM 43377

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002053.3 |  | 0.73 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001507.3 |  | 0.69 | ribosomal | anantin C | Streptomyces olindensis
BGC0001551.4 |  | 0.68 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001889.2 |  | 0.67 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0001549.3 |  | 0.62 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001493.5 |  | 0.60 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001506.5 |  | 0.60 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146
BGC0001176.4 |  | 0.60 | ribosomal | streptomonomicin | Streptomonospora alba
BGC0001548.4 |  | 0.59 | ribosomal | citrulassin A | Streptomyces albulus
BGC0002289.2 |  | 0.59 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii

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.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
Additional weak hits (15):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.94 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.14 out of 28.19
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.13 out of 27.04
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.48 out of 27.18
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.74 out of 23.43
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.11 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.79 out of 28.14
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.49 out of 30.22
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.66 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.35 out of 28.14
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.17 out of 31.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.09 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.81 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.17 out of 24.78
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.
Lasso peptides
RREFinder
TFBS Finder
Azole RiPPs
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (6028416...6050981)
BN6_RS26080
  RRE type: Stand_Alone_Lasso_RRE
  Location: 2 - 75
  Score: 77.8
azole-containing-RiPP protocluster (6047141...6076059)
BN6_RS46960
  RRE type: Thiopeptide_F_RRE
  Location: 14 - 95
  Score: 59.7
  RRE type: Heterocycloanthracin_C_RRE
  Location: 15 - 106
  Score: 44.1
RRE-containing protocluster (6056055...6078014)
BN6_RS46960
  RRE type: Thiopeptide_F_RRE
  Location: 14 - 95
  Score: 59.7
  RRE type: Heterocycloanthracin_C_RRE
  Location: 15 - 106
  Score: 44.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

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_019673.1 - Region 28 - NRPS,T1PKS,T2PKS,lassopeptide,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: 6,102,782 - 6,189,332 nt. (total: 86,551 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)
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)
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase reductase
BN6_RS26450: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BN6_RS26480: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

BN6_RS26495: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

BN6_RS26530: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BN6_RS26540: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

BN6_RS26545: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

BN6_RS26610: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

BN6_RS26615: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

BN6_RS26640: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BN6_RS26645: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BN6_RS26660: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Transferases: aminotransferase carboxylase methyltransferase transferase
BN6_RS26460: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

BN6_RS26465: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

BN6_RS26505: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

BN6_RS26550: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

BN6_RS26650: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Hydrolases: esterase hydrolase
BN6_RS26425: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

BN6_RS26620: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: cyclase
BN6_RS26410: Terpene synthase/cyclase metal-binding domain protein

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

BN6_RS26510: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

BN6_RS26535: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

Ligases: ligase synthase
BN6_RS26515: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BN6_RS26520: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

BN6_RS26605: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS26625: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN6_RS26630: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl 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 | T2PKS | terpene | lassopeptide | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002070.3 |  |  |  |  |  | 1.93 | PKS | SEK90, pentangumycin | Saccharothrix espanaensis DSM 44229
BGC0001825.4 |  |  |  |  |  | 1.02 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  |  |  |  |  | 1.00 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001160.5 |  |  |  |  |  | 0.99 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001135.5 |  |  |  |  |  | 0.99 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  |  |  |  |  | 0.99 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  |  |  |  |  | 0.98 | NRPS | AM-toxin | Alternaria alternata
BGC0001166.5 |  |  |  |  |  | 0.98 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001128.4 |  |  |  |  |  | 0.98 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  |  |  |  |  | 0.98 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002070.3 |  | 1.00 | PKS | SEK90, pentangumycin | Saccharothrix espanaensis DSM 44229
BGC0000234.5 |  | 0.84 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000231.5 |  | 0.83 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001723.5 |  | 0.76 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.66 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001160.5 |  | 0.66 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - No core peptides 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:
No product predictions
Genes with terpene domains:
BN6_RS26410: T1TS
Domain 1 (4 - 320): Type 1 terpene synthase
Subtype: unknown
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: 17.11 out of 19.52
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.29 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 24.07 out of 30.11
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.05 out of 27.55
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.86 out of 21.84
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.02 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.03 out of 29.72
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.38 out of 23.79
Confidence: medium
Additional weak hits (22):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.37 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.92 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.82 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.18 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.33 out of 27.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.62 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.26 out of 18.57
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.47 out of 31.73
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.50 out of 39.62
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.83 out of 26.85
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.58 out of 31.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.90 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.12 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.83 out of 29.65
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.28 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.46 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.44 out of 29.65
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.96 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.67 out of 32.93
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Lasso peptides
NRPS/PKS products
NRPS/PKS substrates
RREFinder
Type II PKS
Terpene
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
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 47, location 6102781 - 6189332:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-ccmal) + (Cys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 48, location 6102781 - 6175261:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-ccmal) + (Cys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 51, location 6139208 - 6183888:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-ccmal) + (Cys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 52, location 6143908 - 6189332:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-ccmal) + (Cys)

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).
BN6_RS26605: NH2
CAL_domain (154..498): NH2
minowa: NH2

Prediction, score:
  NH2: 102.3
  Acetyl-CoA: 50.9
  fatty_acid: 19.1
  AHBA: 10.9
  shikimic_acid: 0.0

BN6_RS26625: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (534..935): Cys
nrpys: Cys

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:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Small clusters prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Single AA prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDISFDLSVYDGNSMLSGDISLGGATEASIWSIT
  Nearest Stachelhaus code(s):
    Cys DLYNMSLIWK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

BN6_RS26630: mmal
PKS_AT (534..831): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 79.2%
  Malonyl-CoA: 70.8%
  Methoxymalonyl-CoA: 70.8%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 143.9
  Methoxymalonyl-CoA: 129.2
  Malonyl-CoA: 111.2
  Ethylmalonyl-CoA: 102.2
  Isobutyryl-CoA: 90.9
  Propionyl-CoA: 80.8
  Benzoyl-CoA: 71.1
  2-Methylbutyryl-CoA: 71.0
  trans-1,2-CPDA: 62.6
  Acetyl-CoA: 60.9
  CHC-CoA: 57.3
  fatty_acid: 54.0
  3-Methylbutyryl-CoA: 44.6
  inactive: 34.6

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (6107319...6129892)
BN6_RS44145
  RRE type: Stand_Alone_Lasso_RRE
  Location: 13 - 90
  Score: 30.0

Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  6102781 to 6175261
Starter unit(s):
  hexadienyl-CoA (Score: 125.0; E-value: 6.29e-34)
Malonyl elongations:
  8|9 (Score: 683.6; E-value: 1.7e-208)
Product class(es):
  angucycline
Product molecular weight(s):
  hexadienyl-CoA_8: 434 Da
  hexadienyl-CoA_9: 476 Da

BN6_RS26465
  MET (Score: 307.2; E-value: 3.2e-94)
BN6_RS26495
  KR (Score: 36.4; E-value: 1.1e-11)
BN6_RS26510
  CYC C4-C17/C2-C19 (Score: 190.0; E-value: 9.6e-59)
BN6_RS26515
  KS (Score: 770.8; E-value: 7.3e-235)
BN6_RS26520
  CLF 8|9 (Score: 683.6; E-value: 1.7e-208)
BN6_RS26525
  ACP (Score: 120.8; E-value: 4.1e-38)
BN6_RS26530
  KR C9 (Score: 472.7; E-value: 6.7e-145)
BN6_RS26535
  CYC C7-C12 (Score: 478.8; E-value: 1.3e-146)
BN6_RS26540
  OXY (Score: 558.7; E-value: 2.7e-170)
BN6_RS26545
  OXY (Score: 586.0; E-value: 1.4e-178)
BN6_RS26630
  AT (Score: 172.2; E-value: 3.5e-53)
  AT ADG86309.1_A-74528_hexadienyl-CoA (Score: 125.0; E-value: 6.29e-34)

Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CelR | Cellobiose uptake repressor
GnfM | Regulator of nitrogen-fixation genes
IolR | Regulator of the inositol catabolism
MexT | Global virulence regulator
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NC_019673.1 - Region 29 - NRPS,T1PKS,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: 6,285,999 - 6,385,448 nt. (total: 99,450 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)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
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 oxygenase phosphate reductase
BN6_RS27325: N-acetyl-gamma-glutamyl-phosphate reductase

smcogs
  SMCOG1219: N-acetyl-gamma-glutamyl-phosphate reductase

BN6_RS27355: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BN6_RS27360: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

BN6_RS27365: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: acylase aminotransferase kinase transketolase
BN6_RS27270: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

BN6_RS27315: acetylglutamate kinase

smcogs
  SMCOG1174: acetylglutamate kinase

BN6_RS27345: transketolase

smcogs
  SMCOG1204: transketolase

BN6_RS27350: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: back translocase deacetylase
BN6_RS27295: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

BN6_RS27320: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

Lyases: cyclase
BN6_RS27250: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Ligases: ligase synthase
BN6_RS27280: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS27340: 1-deoxy-D-xylulose-5-phosphate synthase

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

BN6_RS27370: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BN6_RS27390: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BN6_RS27400: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | terpene | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  |  | 0.83 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  |  | 0.78 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  |  | 0.78 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  |  |  | 0.77 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  |  |  | 0.77 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  | 0.76 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  | 0.74 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  |  |  | 0.72 | NRPS | enniatin | Fusarium equiseti
BGC0001825.4 |  |  |  | 0.71 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  |  |  | 0.71 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae

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
--- | --- | --- | --- | --- | ---
tetraterpene | C40 carotenoid |  | C40 | unknown | unknown

Genes with terpene domains:
BN6_RS27180: Lycopene_cycl
Domain 1 (2 - 357): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.04 out of 26.85
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.64 out of 26.33
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.86 out of 21.84
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.36 out of 19.26
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.51 out of 25.31
Confidence: medium
Additional weak hits (15):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.96 out of 26.85
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.83 out of 26.85
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.91 out of 23.43
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.14 out of 29.51
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.82 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.71 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.36 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.40 out of 20.01
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.70 out of 23.43
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.44 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.98 out of 29.25
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Terpene
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 53, location 6285998 - 6385448:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (X) + (X) + (Ala - X) + (ohmal) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 55, location 6297787 - 6385448:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (X) + (X) + (Ala - X) + (ohmal) + (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BN6_RS27265: X
A-OX (524..1272): X
No predictions made
BN6_RS27270: mal
PKS_AT (538..813): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 75.0%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 147.9
  inactive: 70.8
  Methoxymalonyl-CoA: 68.3
  Methylmalonyl-CoA: 58.2
  Isobutyryl-CoA: 34.4
  Propionyl-CoA: 28.2
  CHC-CoA: 25.6
  Ethylmalonyl-CoA: 21.5
  2-Methylbutyryl-CoA: 17.2
  fatty_acid: 15.3
  Benzoyl-CoA: 13.9
  Acetyl-CoA: 10.2
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

BN6_RS27280: Ala - X
Search NORINE for peptide: strict or relaxed
AMP-binding (466..837): 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LALTFDMSMVEAQAFAGGEWNLYGPTEVTVYATG
  Nearest Stachelhaus code(s):
    Ala DIVQLGLVYK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1477..1874): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FWQAYDAAYTELETQLSGEHNQYGPTECVLATHH
  Nearest Stachelhaus code(s):
    aza-bTyr DACELALLAK (59% 8Å match)
  Stachelhaus code match:
    60% (weak)

BN6_RS27370: X
AMP-binding (504..897): X
nrpys: dn-dohHep

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FSAAFDVSVFEADLFVGGEFNGYGPTECTVTMIV
  Nearest Stachelhaus code(s):
    dn-dohHep DVFDFGGVTK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

BN6_RS27390: X
AMP-binding (11..333): X
nrpys: Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LHLALGCAVVELHGLSSGEWQLYGQAETSVFAAL
  Nearest Stachelhaus code(s):
    Ser DVWHLSLVDK (38% 8Å match)
  Stachelhaus code match:
    60% (weak)

BN6_RS27400: X
AMP-binding (420..819): X
nrpys: (unknown)

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:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Small clusters prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Single AA prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDISFDLSVYDGNSILAGDIGSGGPAESCVWSVI
  Nearest Stachelhaus code(s):
    Gly DLYNVASVWK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

Link to PARAS substrate predictor
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor
MexT | Global virulence regulator
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems

NC_019673.1 - Region 30 - oligosaccharide
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: 6,552,566 - 6,585,668 nt. (total: 33,103 nt) Show pHMM detection rules used
oligosaccharide: (repeatable(3, [DUF1205, Glyco_transf_28, Glycos_transf_1, Glycos_transf_2, MGT]) and minscore(MGT, 150))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
BN6_RS28295: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: glycosyltransferase methyltransferase transferase
BN6_RS28215: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

BN6_RS28230: methyltransferase

smcogs
  SMCOG1089: methyltransferase

BN6_RS28240: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

BN6_RS28245: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

BN6_RS28250: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

BN6_RS28255: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

BN6_RS28260: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

BN6_RS28265: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

BN6_RS28270: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

BN6_RS28275: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

BN6_RS28280: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

BN6_RS28285: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

Lyases: dehydratase
BN6_RS28290: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

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 | oligosaccharide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001817.5 |  | 0.47 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0000277.5 |  | 0.46 | PKS | urdamycin | Streptomyces fradiae
BGC0000898.5 |  | 0.45 | saccharide | desosamine, pikromycin, neomethymycin, narbomycin | Streptomyces venezuelae
BGC0000249.5 |  | 0.44 | PKS | nogalamycin | Streptomyces nogalater
BGC0001198.3 |  | 0.43 | terpene | (+)-O-methylkolavelool | Herpetosiphon aurantiacus DSM 785
BGC0000019.5 |  | 0.42 | PKS | angolamycin | Streptomyces eurythermus
BGC0000899.4 |  | 0.40 | saccharide | desosamine | Streptomyces narbonensis
BGC0000791.3 |  | 0.40 | saccharide | O-antigen | Cronobacter sakazakii
BGC0000214.5 |  | 0.40 | PKS | cosmomycin B | Streptomyces olindensis
BGC0000193.3 |  | 0.40 | PKS | aclacinomycin | Streptomyces galilaeus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001817.5 |  | 0.47 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0000277.5 |  | 0.46 | PKS | urdamycin | Streptomyces fradiae
BGC0000898.5 |  | 0.45 | saccharide | desosamine, pikromycin, neomethymycin, narbomycin | Streptomyces venezuelae
BGC0000249.5 |  | 0.44 | PKS | nogalamycin | Streptomyces nogalater
BGC0001198.3 |  | 0.43 | terpene | (+)-O-methylkolavelool | Herpetosiphon aurantiacus DSM 785
BGC0000019.5 |  | 0.42 | PKS | angolamycin | Streptomyces eurythermus
BGC0000899.4 |  | 0.40 | saccharide | desosamine | Streptomyces narbonensis
BGC0000791.3 |  | 0.40 | saccharide | O-antigen | Cronobacter sakazakii
BGC0000214.5 |  | 0.40 | PKS | cosmomycin B | Streptomyces olindensis
BGC0000193.3 |  | 0.40 | PKS | aclacinomycin | Streptomyces galilaeus

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.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.49 out of 25.31
Confidence: medium
Additional weak hits (12):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.14 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.54 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.51 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.07 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.29 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.40 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.04 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.24 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.89 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.00 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.75 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor

NC_019673.1 - Region 31 - 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: 6,620,360 - 6,641,823 nt. (total: 21,464 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
BN6_RS28525: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: cyclase
BN6_RS28555: Terpene synthase/cyclase metal-binding domain protein

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000657.5 |  | 0.57 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002276.2 |  | 0.52 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000888.5 |  | 0.40 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001579.4 |  | 0.40 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0001210.5 |  | 0.39 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0001928.2 |  | 0.39 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000498.5 |  | 0.38 | ribosomal | bovicin HJ50 | Streptococcus equinus
BGC0000561.5 |  | 0.38 | ribosomal | thermophilin 1277 | Streptococcus thermophilus
BGC0001184.4 |  | 0.37 | other (other) | bacilysin | Bacillus velezensis FZB42

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000657.5 |  | 0.57 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002276.2 |  | 0.52 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000888.5 |  | 0.40 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001579.4 |  | 0.40 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0001210.5 |  | 0.39 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0001928.2 |  | 0.39 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000498.5 |  | 0.38 | ribosomal | bovicin HJ50 | Streptococcus equinus
BGC0000561.5 |  | 0.38 | ribosomal | thermophilin 1277 | Streptococcus thermophilus
BGC0001184.4 |  | 0.37 | other (other) | bacilysin | Bacillus velezensis FZB42

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

No significant matches found.

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
monoterpene |  | 2-methylisoborneol | C11 | C1-C6 | OH
monoterpene |  | 2-methylenebornane | C11 | C1-C6 | none

Genes with terpene domains:
BN6_RS28555: T1TS
Domain 1 (128 - 485): Type 1 terpene synthase
Subtype: 2-Methylisoborneol synthase type

Reactions:
  2-MeGPP → 2-methylisoborneol
  2-MeGPP → 2-methylenebornane

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:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.44 out of 27.04
Confidence: medium
Additional weak hits (7):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.21 out of 20.97
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.04 out of 29.65
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.16 out of 30.98
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.41 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.75 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
2-MeGPP | 2-methylgeranyl diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor

NC_019673.1 - Region 32 - 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: 6,786,167 - 6,807,207 nt. (total: 21,041 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
BN6_RS29235: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Lyases: cyclase
BN6_RS29225: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Ligases: synthase synthetase
BN6_RS29255: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

BN6_RS29265: 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
--- | --- | --- | --- | --- | ---
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0000665.5 |  | 0.46 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000666.5 |  | 0.46 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0000657.5 |  | 0.46 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0001594.3 |  | 0.45 | other (other) | fischerindole L | Fischerella muscicola UTEX 1829
BGC0000663.5 |  | 0.44 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0002591.2 |  | 0.44 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0000665.5 |  | 0.46 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000666.5 |  | 0.46 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0000657.5 |  | 0.46 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0001594.3 |  | 0.45 | other (other) | fischerindole L | Fischerella muscicola UTEX 1829
BGC0000663.5 |  | 0.44 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0002591.2 |  | 0.44 | PKS, terpene | aurachin C, aurachin D, aurachin SS | 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.
Location:
Identifier
Identity
Coverage
Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP
diterpene precursor |  | GGPP | C20 | acyclic | PP
sesterterpene precursor |  | GFPP | C25 | acyclic | PP
triterpene precursor |  | HPP | C30 | acyclic | PP

Genes with terpene domains:
BN6_RS29255: PT_FPPS_like
Domain 1 (60 - 345): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

Reactions:
  IPP, DMAPP → FPP
  IPP, DMAPP → GGPP
  IPP, DMAPP → GFPP
  IPP, DMAPP → HPP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.91 out of 19.26
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.79 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.16 out of 30.11
Confidence: medium
Additional weak hits (5):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.98 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.92 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.21 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.98 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.11 out of 29.38
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CelR | Cellobiose uptake repressor

NC_019673.1 - Region 33 - 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: 6,944,768 - 6,965,850 nt. (total: 21,083 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase
BN6_RS29990: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Ligases: ligase
BN6_RS29965: carboxylate-amine ligase

smcogs
  SMCOG1165: carboxylate-amine 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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0002172.3 |  | 0.31 | NRPS | fusatrixin, fusapentaxin, fusaoctaxin A | Fusarium graminearum PH-1
BGC0001343.3 |  | 0.29 | PKS | aurachin A, aurachin D | Stigmatella aurantiaca Sg a15
BGC0001565.4 |  | 0.29 | NRPS | cyclosporin C | Beauveria felina
BGC0000713.5 |  | 0.29 | saccharide | ribostamycin | Streptomyces ribosidificus
BGC0000269.5 |  | 0.28 | PKS, saccharide | SF2575 | Streptomyces sp. SF2575
BGC0000334.4 |  | 0.28 | NRPS | cyclosporin A | Tolypocladium inflatum NRRL 8044
BGC0002261.2 |  | 0.28 | PKS | lucilactaene | Fusarium sp.
BGC0000579.4 |  | 0.27 | ribosomal | SSV-2083 | Streptomyces sviceus ATCC 29083
BGC0001312.5 |  | 0.26 | NRPS | viscosin | Pseudomonas fluorescens SBW25

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0002172.3 |  | 0.31 | NRPS | fusatrixin, fusapentaxin, fusaoctaxin A | Fusarium graminearum PH-1
BGC0001343.3 |  | 0.29 | PKS | aurachin A, aurachin D | Stigmatella aurantiaca Sg a15
BGC0001565.4 |  | 0.29 | NRPS | cyclosporin C | Beauveria felina
BGC0000713.5 |  | 0.29 | saccharide | ribostamycin | Streptomyces ribosidificus
BGC0000269.5 |  | 0.28 | PKS, saccharide | SF2575 | Streptomyces sp. SF2575
BGC0000334.4 |  | 0.28 | NRPS | cyclosporin A | Tolypocladium inflatum NRRL 8044
BGC0002261.2 |  | 0.28 | PKS | lucilactaene | Fusarium sp.
BGC0000579.4 |  | 0.27 | ribosomal | SSV-2083 | Streptomyces sviceus ATCC 29083
BGC0001312.5 |  | 0.26 | NRPS | viscosin | Pseudomonas fluorescens SBW25

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
--- | --- | --- | --- | --- | ---
tetraterpene | C40 carotenoid |  | C40 | unknown | unknown

Genes with terpene domains:
BN6_RS29955: Lycopene_cycl
Domain 1 (2 - 339): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

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:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.58 out of 27.04
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.48 out of 23.79
Confidence: medium
Additional weak hits (19):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.67 out of 26.33
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.83 out of 30.22
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.34 out of 30.25
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.46 out of 39.62
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.96 out of 28.14
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.03 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.10 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.92 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.27 out of 18.57
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.76 out of 21.55
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.62 out of 39.62
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.97 out of 31.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.38 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.24 out of 27.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.87 out of 24.78
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.19 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
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism

NC_019673.1 - Region 34 - lanthipeptide-class-ii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,144,344 - 7,167,229 nt. (total: 22,886 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
BN6_RS30875: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

BN6_RS30925: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

BN6_RS30930: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: acetyltransferase
BN6_RS30910: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Lyases: cyclase
BN6_RS30890: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

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

Reference | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000532.3 |  | 0.51 | ribosomal | mutacin II | Streptococcus mutans
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002704.2 |  | 0.47 | ribosomal | archalan β | Halorussus salinus
BGC0001210.5 |  | 0.46 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000527.5 |  | 0.43 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001407.5 |  | 0.43 | ribosomal | bicereucin | Bacillus cereus SJ1
BGC0002699.2 |  | 0.43 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0000516.4 |  | 0.43 | ribosomal | geobacillin II | Geobacillus thermodenitrificans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000532.3 |  | 0.51 | ribosomal | mutacin II | Streptococcus mutans
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002704.2 |  | 0.47 | ribosomal | archalan β | Halorussus salinus
BGC0001210.5 |  | 0.46 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000527.5 |  | 0.43 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001407.5 |  | 0.43 | ribosomal | bicereucin | Bacillus cereus SJ1
BGC0002699.2 |  | 0.43 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0000516.4 |  | 0.43 | ribosomal | geobacillin II | Geobacillus thermodenitrificans

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 BN6_RS30890

allorf_7149539_7149760
Leader:
MWGQRVWGGERRSAAA
Core:
T D R A G D P A V V D V P A G A E D G H S R S P S R L V L T I R C T E P V S H D W T R S C H F A R S R T R V P T C
Core with dehydrations:
Dhb D R A G D P A V V D V P A G A E D G H Dha R Dha P Dha R L V L Dhb I R Cys Dhb E P V Dha H D W Dhb R Dha Cys H F A R Dha R Dhb R V P Dhb Cys

#### antiSMASH-DB 4.0 matches for allorf_7149539_7149760

100.0%
NC_019673.1:
Lanthipeptides: allorf_7149539_7149760_lanthipeptide
1
T D R A G D P A V V D V P A G A E D G H S R S P S R L V L T I R C T E P V S H D W T R S C H F A R S R T R V P T C
57
T D R A G D P A V V D V P A G A E D G H S R S P S R L V L T I R C T E P V S H D W T R S C H F A R S R T R V P T C
1
T D R A G D P A V V D V P A G A E D G H S R S P S R L V L T I R C T E P V S H D W T R S C H F A R S R T R V P T C
57
19.3%
NZ_BMRY01000003.1 and 5 others:
NZ_BMRY01000003.1 Lanthipeptides: allorf_458543_458737_lanthipeptide NZ_CP084357.1 Lanthipeptides: allorf_8050125_8050319_lanthipeptide NZ_CP084357.1 Lanthipeptides: allorf_8050125_8050319_lanthipeptide NZ_KZ819178.1 Lanthipeptides: allorf_4075416_4075610_lanthipeptide NZ_KZ819178.1 Lanthipeptides: allorf_4075416_4075610_lanthipeptide
Lanthipeptides: allorf_458543_458737_lanthipeptide
22
R S P S R L V L T I R C T E-P V S H D W T R S C
45
R P S L+L R C P W S C
19
R P P S P L L L R P R C P W T P S P R P W N W S C
43
allorf_7149575_7149646
Leader:
MAVLCSRRHVDYG
Core:
R V S S A I C R R G
Core with dehydrations:
R V Dha Dha A I Cys R R G

#### antiSMASH-DB 4.0 matches for allorf_7149575_7149646

100.0%
NC_019673.1:
Lanthipeptides: allorf_7149575_7149646_lanthipeptide
1
R V S S A I C R R G
10
R V S S A I C R R G
1
R V S S A I C R R G
10
allorf_7149698_7149895
Leader:
MPPRAEVRVRWRAQPAYGPVSPPVHARHWSIRVMRGLVNRRHIVVSAGG
Core:
H S C S R A G E V A T S R P V V
Core with dehydrations:
H Dha Cys Dha R A G E V A Dhb Dha R P V V

#### antiSMASH-DB 4.0 matches for allorf_7149698_7149895

100.0%
NC_019673.1:
Lanthipeptides: allorf_7149698_7149895_lanthipeptide
1
H S C S R A G E V A T S R P V V
16
H S C S R A G E V A T S R P V V
1
H S C S R A G E V A T S R P V V
16
29.4%
NZ_CP054839.1:
Lanthipeptides: allorf_3732024_3732125_lanthipeptide
2
S C S R A G E V A T S R P V
15
+C R + + S R P+
1
T C R R Q A D Q S R S R P L
14
25.9%
NZ_CP076103.1:
Lanthipeptides: allorf_4159188_4159313_lanthipeptide
5
R A G E V A T S R P V
15
+A G V A T S P+
3
Q A G R V A T S P P M
13
with 2 more sequence matches
24.0%
NZ_CP061072.1:
Lanthipeptides: allorf_5575476_5575628_lanthipeptide
1
H S C S R A G E V A T S R P
14
C R G A +R P
6
R R C G R V G G A A P T R P
19
16.2%
NZ_CP016795.1 and 3 others:
NZ_CP016795.1 Lanthipeptides: allorf_4181859_4182014_lanthipeptide NZ_CP036534.1 Lanthipeptides: allorf_4249417_4249572_lanthipeptide NZ_CP036534.1 Lanthipeptides: allorf_4249417_4249572_lanthipeptide
Lanthipeptides: allorf_4181859_4182014_lanthipeptide
2
S C S R A G E V A T S
12
+C R A G+V T+
20
T C R R A G K V R T A
30
allorf_7166508_7166597
Leader:
MVDLLVGAGG
Core:
C P G L P D S K A P L L S S W L D S S
Core with dehydrations:
Cys P G L P D Dha K A P L L Dha Dha W L D Dha Dha

#### antiSMASH-DB 4.0 matches for allorf_7166508_7166597

100.0%
NC_019673.1:
Lanthipeptides: allorf_7166508_7166597_lanthipeptide
1
C P G L P D S K A P L L S S W L D S S
19
C P G L P D S K A P L L S S W L D S S
1
C P G L P D S K A P L L S S W L D S S
19
17.6%
NZ_CP022163.1:
Lanthipeptides: allorf_7478650_7478796_lanthipeptide
1
C P G L P D S K A P L L S
13
C P + + A P L S
9
C P S V T F T G A P L F S
21
15.8%
NZ_WWJS01000019.1:
Lanthipeptides: allorf_025167_025319_lanthipeptide
1
C P G L P D S
7
C P G P D S
4
C P G P P D S
10
with 1 more sequence matches
9.4%
NZ_NNBP01000002.1:
Lanthipeptides: allorf_467447_467647_lanthipeptide
1
C P G L P D S
7
C P G P D+
5
C P G A P D A
11

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.31 out of 26.85
Confidence: medium
Additional weak hits (10):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.13 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.95 out of 30.25
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.69 out of 19.26
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.89 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.52 out of 29.65
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.56 out of 26.06
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.19 out of 24.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.31 out of 28.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.41 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.62 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_7149539_7149760 - Class II
  Cleavage pHMM score: -5.90
  RODEO score: 0
  Monoisotopic mass: 6011.0 Da
  Molecular weight: 6014.6 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    6032.6 Da N = 1
    6050.7 Da N = 2
    6068.7 Da N = 3
    6086.7 Da N = 4
    6104.7 Da N = 5
    6122.7 Da N = 6
    6140.8 Da N = 7
    6158.8 Da N = 8
    6176.8 Da N = 9
allorf_7149575_7149646 - Class II
  Cleavage pHMM score: -7.20
  RODEO score: 0
  Monoisotopic mass: 1067.6 Da
  Molecular weight: 1068.2 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1086.3 Da N = 1
allorf_7149698_7149895 - Class II
  Cleavage pHMM score: -5.20
  RODEO score: 0
  Monoisotopic mass: 1582.8 Da
  Molecular weight: 1583.8 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1601.8 Da N = 1
    1619.8 Da N = 2
    1637.8 Da N = 3
allorf_7166508_7166597 - Class II
  Cleavage pHMM score: -6.90
  RODEO score: 0
  Monoisotopic mass: 1882.0 Da
  Molecular weight: 1883.1 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1901.1 Da N = 1
    1919.1 Da N = 2
    1937.2 Da N = 3
    1955.2 Da N = 4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems