Select genomic region:
Overview
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1.32
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1.34
1.35

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

NZ_CP064192.1 (Saccharothrix sp. 6-C)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | redox-cofactor | 155,127 | 177,184 | Low | lankacidin C | NRPS:Type I+PKS
Region 2 | terpene | 584,044 | 606,251 | High | geosmin | terpene:Sesquiterpene
Region 3 | lanthipeptide-class-iii | 965,424 | 987,958 | Medium | Ery-9/Ery-6/Ery-8/Ery-7/Ery-5/Ery-4/Ery-3 | ribosomal:RiPP:Lanthipeptide
Region 4 | terpene | 1,070,707 | 1,094,271 | Low | isorenieratene | terpene
Region 5 | RiPP-like | 1,307,288 | 1,318,085 |
Region 6 | terpene | 1,512,140 | 1,539,761 | High | isorenieratene | terpene
Region 7 | T3PKS | 1,860,641 | 1,901,708 | High | naringenin | PKS:Type III
Region 8 | PKS-like | 2,083,255 | 2,124,289 |
Region 9 | betalactone | 2,147,109 | 2,174,737 |  |
Region 10 | NRP-metallophore,NRPS | 2,368,509 | 2,445,700 | Low | peucechelin | NRPS:Type I
Region 11 | thioamide-NRP,HR-T2PKS,NRPS | 2,598,445 | 2,725,746 | Low | colibrimycin | NRPS:Type I+other:other
Region 12 | NRPS,azole-containing-RiPP,T2PKS | 2,840,616 | 3,004,660 | Medium | saccharothrixin D/saccharothrixin E/saccharothrixin F/saccharothrixin G/saccharothrixin H/saccharothrixin I/saccharothrixin J/saccharothrixin K/saccharothrixin L/saccharothrixin M | PKS
Region 13 | T1PKS | 3,029,967 | 3,086,623 | Low | scopranone A/scopranone B/scopranone C | PKS
Region 14 | T1PKS,terpene-precursor | 3,093,450 | 3,188,116 |  |
Region 15 | T1PKS | 3,364,895 | 3,412,190 | Low | aborycin | ribosomal:RiPP
Region 16 | NAPAA | 3,647,506 | 3,681,294 |  |
Region 17 | NRPS | 3,919,779 | 3,979,788 |  |
Region 18 | terpene,NRPS,T1PKS,NRPS-like,oligosaccharide,PKS-like | 4,007,381 | 4,211,086 | Low | camporidine A/camporidine B | other:other+PKS
Region 19 | T1PKS | 4,221,599 | 4,328,268 | High | salinilactam | PKS
Region 20 | RRE-containing | 4,398,089 | 4,418,994 |
Region 21 | hydrogen-cyanide | 4,508,718 | 4,521,558 |  |
Region 22 | azole-containing-RiPP | 4,524,584 | 4,551,680 |  |
Region 23 | terpene-precursor,T1PKS | 4,566,665 | 4,611,915 | Low | JBIR-100 | PKS:Type I
Region 24 | oligosaccharide | 4,828,138 | 4,889,456 |  |
Region 25 | NRPS,terpene-precursor | 5,036,829 | 5,100,477 |  |
Region 26 | indole | 5,201,344 | 5,222,438 |  |
Region 27 | T1PKS,NRPS,transAT-PKS | 5,277,303 | 5,353,775 |  |
Region 28 | terpene-precursor | 5,474,384 | 5,496,045 |
Region 29 | betalactone,terpene | 5,551,916 | 5,603,434 | Low | brasilicardin A | terpene+saccharide
Region 30 | T1PKS | 5,828,842 | 5,874,628 |  |
Region 31 | terpene | 6,018,391 | 6,039,476 |  |
Region 32 | NI-siderophore | 6,136,128 | 6,169,409 | Low | speibonoxamine/desoxy-desferrioxamine D1/desferrioxamine D1/desferrioxamine B/didesoxy-desferrioxamine D1/desoxy-desferrioxamine B/didesoxy-desferrioxamine B | other:other
Region 33 | lanthipeptide-class-ii | 6,231,330 | 6,254,239 |  |
Region 34 | terpene-precursor | 6,258,191 | 6,279,330 |  |
Region 35 | lanthipeptide-class-i | 6,481,004 | 6,505,133 |

NZ_CP064192.1 - 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: 155,127 - 177,184 nt. (total: 22,058 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
IOD16_RS00750: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: acetyltransferase
IOD16_RS00835: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Ligases: synthase
IOD16_RS00845: cysteine synthase

smcogs
  SMCOG1081: cysteine 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 | 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
BGC0001483.4 |  | 0.40 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0002316.2 |  | 0.40 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0002213.3 |  | 0.40 | PKS | HEx-pks16 polyketide | Punctularia strigosozonata HHB-11173 SS5
BGC0000591.5 |  | 0.39 | ribosomal | marinostatin | Alteromonas sp. B-10-31
BGC0001587.5 |  | 0.38 | other (other) | ethylenediaminesuccinic acid hydroxyarginine (EDHA) | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000528.5 |  | 0.37 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000943.5 |  | 0.36 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325

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
BGC0001483.4 |  | 0.40 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0002316.2 |  | 0.40 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0002213.3 |  | 0.40 | PKS | HEx-pks16 polyketide | Punctularia strigosozonata HHB-11173 SS5
BGC0000591.5 |  | 0.39 | ribosomal | marinostatin | Alteromonas sp. B-10-31
BGC0001587.5 |  | 0.38 | other (other) | ethylenediaminesuccinic acid hydroxyarginine (EDHA) | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000528.5 |  | 0.37 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000943.5 |  | 0.36 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325

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 (5):
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.20 out of 30.11
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.35 out of 39.62
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.15 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.83 out of 35.63
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (155126...177184)
IOD16_RS00795
  RRE type: PqqD_RRE
  Location: 3 - 86
  Score: 75.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP064192.1 - 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: 584,044 - 606,251 nt. (total: 22,208 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
IOD16_RS02745: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Lyases: cyclase
IOD16_RS02725: 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)
BGC0000658.3 |  | 0.56 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002531.3 |  | 0.41 | NRPS | cepaciachelin | Burkholderia ambifaria AMMD
BGC0002683.2 |  | 0.39 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002682.2 |  | 0.38 | other (other) | aerobactin | Vibrio mimicus
BGC0001498.5 |  | 0.36 | other (other) | aerobactin | Xenorhabdus szentirmaii DSM 16338
BGC0002073.3 |  | 0.36 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0000041.3 |  | 0.35 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000708.5 |  | 0.34 | saccharide | lividomycin | Streptomyces lividus
BGC0000277.5 |  | 0.33 | PKS | urdamycin | Streptomyces fradiae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.81 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000658.3 |  | 0.56 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002531.3 |  | 0.41 | NRPS | cepaciachelin | Burkholderia ambifaria AMMD
BGC0002683.2 |  | 0.39 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002682.2 |  | 0.38 | other (other) | aerobactin | Vibrio mimicus
BGC0001498.5 |  | 0.36 | other (other) | aerobactin | Xenorhabdus szentirmaii DSM 16338
BGC0002073.3 |  | 0.36 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0000041.3 |  | 0.35 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000708.5 |  | 0.34 | saccharide | lividomycin | Streptomyces lividus
BGC0000277.5 |  | 0.33 | PKS | urdamycin | Streptomyces fradiae

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:
IOD16_RS02725: T1TS + T1TS
Domain 1 (2 - 329): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (331 - 697): 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:
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 32.79 out of 36.53
Confidence: strong
Additional weak hits (1):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.37 out of 32.74
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
--- | ---
DmdR1 | Iron(II)-dependent repressor

NZ_CP064192.1 - 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: 965,424 - 987,958 nt. (total: 22,535 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
IOD16_RS04565: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: acylase transferase
IOD16_RS04610: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

IOD16_RS04630: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: synthase
IOD16_RS04615: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS04625: 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
BGC0001160.5 |  | 0.59 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000496.5 |  | 0.58 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000518.3 |  | 0.52 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002700.2 |  | 0.52 | ribosomal | bacinapeptin | Bacillus nakamurai
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
BGC0001160.5 |  | 0.59 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000496.5 |  | 0.58 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000518.3 |  | 0.52 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002700.2 |  | 0.52 | ribosomal | bacinapeptin | Bacillus nakamurai
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 IOD16_RS04600

IOD16_RS04595
Leader:
MDFILDLQDMETPEAASNAMAS
Core:
G G S S S G G G G S T S A S G L S L L G C G A H S T V S L V I C
Core with dehydrations:
G G Dha Dha Dha G G G G Dha Dhb Dha A Dha G L Dha L L G Cys G A H Dha Dhb V Dha L V I Cys

#### antiSMASH-DB 4.0 matches for IOD16_RS04595

100.0%
NZ_CP064192.1:
Lanthipeptides: IOD16_RS04595_lanthipeptide
1
G G S S S G G G G S T S A S G L S L L G C G A H S T V S L V I C
32
G G S S S G G G G S T S A S G L S L L G C G A H S T V S L V I C
1
G G S S S G G G G S T S A S G L S L L G C G A H S T V S L V I C
32
56.2%
NZ_PVTF01000018.1:
Lanthipeptides: CLV43_RS41575_lanthipeptide
2
G S S S G G G G S T S A S G L S L L G C G A H S T V S L V I C
32
S G G G G S T+A S S L L +H S+ S L V+C
1
A S G H G G G G S T T A S S A S L L L P C S H S S A S L V L C
31
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
7
G G G S T S A S G L S L L G C G A H S T V S L V I C
32
G G G S T+A S S L L +H S T V S L+ C
7
G 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
32
with 82 more sequence matches
Only the first 10 are displayed here.
53.1%
NZ_JACHJN010000006.1:
Lanthipeptides: FHS29_RS22065_lanthipeptide
7
G G G S T S A S G L S L L G C G A H S T V S L V I C
32
G G G S T+A S +S L L +H S T S L V+C
7
G G G S T T A S N V S L L L P C S H S T A S L V L C
32
52.9%
NZ_JAJHUO010000006.1:
Lanthipeptides: LNK82_RS10890_lanthipeptide
7
G G G S T S A S G L S L L G C G A H S T V S L V I C
32
G G G S T+A S S L L +H S T V S L V+C
9
G G G S T T A S N A S L L L P C S H S T V S L V L C
34
50.0%
NZ_CP097289.1:
Lanthipeptides: M4V62_RS29260_lanthipeptide
6
G G G G S T S A S G L S L L G C G A H S T V S L V I C
32
G G G S T+ S L L C S V S L V I C
1
G G G Q S T A----S L L L C--W S E V S L V I C
21
50.0%
NZ_LWLC01000002.1:
Lanthipeptides: A6A25_RS42770_lanthipeptide
7
G G G S T S A S G L S L L G C G A H S T V S L V I C
32
G G G S T+A S S L L +H S T V S L++C
9
G G G S T T A S N A S L L L P C S H S T V S L I L C
34
46.9%
NC_013729.1:
Lanthipeptides: KFLA_RS37060_lanthipeptide
6
G G G G S T S A S G L S L L G C G A--H S T V S L V I C
32
G G G G S T L++L G C G+ S +S L++C
1
G G G G S T----L T V L G C G S A K P S N L S L L L C
25
46.9%
NZ_CP090063.1:
Lanthipeptides: LWP59_RS37170_lanthipeptide
6
G G G G S T S A S G L S L L G C G A H S T V S L V I C
32
G G G G S L S L L A+S T+S L+ C
1
G G G G G H P I S N L S L L A G C A N S T L S L L G C
27
46.9%
NZ_CP114065.1:
Lanthipeptides: OX958_RS15815_lanthipeptide
6
G G G G S T S A S G L S L L G C G A H--S T V S L V I C
32
G G G G S T L++L G C + S +S L V+C
1
G G G G S T----L T V L G C E S K T P S N I S L V L C
25
45.5%
NZ_BMRG01000002.1:
Lanthipeptides: IEZ00_RS05680_lanthipeptide
10
S T S A S G L S L L G C G A H S T V S L V I C
32
S T+A S S L L +H S T V S L+I C
11
S T T A S N A S L L L P C S H S T V S L L I C
33
43.8%
NC_013131.1:
Lanthipeptides: CACI_RS49205_lanthipeptide
6
G G G G S T S A S G L S L L G C G A H S T V S L V
30
G G G G S G L S+ G C H S +S L+
1
G G G G D---S G L S V T G C N G H S G I S L L
22
43.8%
NC_013595.1:
Lanthipeptides: SROS_RS48825_lanthipeptide
6
G G G G S T S A S G L S L L G C G A H--S T V S L V I C
32
G G G G S T L++L G C ++ S +S L++C
1
G G G G S T----L T V L G C E S Y K P S N L S L L L C
25

#### MIBiG 4.0 matches for IOD16_RS04595

15.6%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
25
S T V S L V I C
32
S V S L++C
3
S Q V S L L V C
10

#### 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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
Additional weak hits (8):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.12 out of 27.55
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.32 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.06 out of 36.54
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.36 out of 27.55
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 20.50 out of 31.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.24 out of 26.85
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.98 out of 24.78
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.

IOD16_RS04595 - Class III
  Cleavage pHMM score: 17.80
  RODEO score: 0
  Monoisotopic mass: 2567.3 Da
  Molecular weight: 2568.8 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2586.8 Da N = 1
    2604.8 Da N = 2
    2622.9 Da N = 3
    2640.9 Da N = 4
    2658.9 Da N = 5
    2676.9 Da N = 6
    2694.9 Da N = 7
    2713.0 Da N = 8
    2731.0 Da N = 9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein

NZ_CP064192.1 - 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: 1,070,707 - 1,094,271 nt. (total: 23,565 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
IOD16_RS05095: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Ligases: synthetase
IOD16_RS05100: 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 |  | 0.55 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.54 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.51 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.51 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000649.3 |  | 0.49 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000648.3 |  | 0.49 | terpene | carotenoid | Myxococcus xanthus
BGC0000650.3 |  | 0.48 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0002309.2 |  | 0.47 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000644.3 |  | 0.46 | terpene | carotenoid | Dietzia sp. CQ4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.55 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.54 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.51 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.51 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000649.3 |  | 0.49 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000648.3 |  | 0.49 | terpene | carotenoid | Myxococcus xanthus
BGC0000650.3 |  | 0.48 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0002309.2 |  | 0.47 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000644.3 |  | 0.46 | terpene | carotenoid | Dietzia sp. CQ4

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:
IOD16_RS05090: PT_phytoene_like
Domain 1 (4 - 291): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

IOD16_RS05100: 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.00 out of 20.47
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 23.59 out of 24.78
Confidence: strong
Additional weak hits (4):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
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 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.75 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.56 out of 29.65
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
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 2 | Repressor of DNA damage response
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP064192.1 - 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: 1,307,288 - 1,318,085 nt. (total: 10,798 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
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 | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000595.3 |  | 0.32 | 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 |  | 0.32 | 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:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.86 out of 25.31
Confidence: medium
Additional weak hits (5):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.88 out of 25.88
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.17 out of 26.06
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.38 out of 20.97
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.52 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.81 out of 36.54
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP064192.1 - Region 6 - 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: 1,512,140 - 1,539,761 nt. (total: 27,622 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
IOD16_RS07020: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

IOD16_RS07050: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: acetyltransferase methyltransferase
IOD16_RS06995: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

IOD16_RS07055: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: ligase synthetase
IOD16_RS06975: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS07025: 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 |  | 0.69 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.65 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.60 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.59 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.59 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0002193.2 |  | 0.56 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0002135.2 |  | 0.56 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000648.3 |  | 0.56 | terpene | carotenoid | Myxococcus xanthus
BGC0001250.4 |  | 0.56 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.56 | NRPS | epichloenin A | Epichloe festucae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.69 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.65 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.60 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.59 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.59 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0002193.2 |  | 0.56 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0002135.2 |  | 0.56 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000648.3 |  | 0.56 | terpene | carotenoid | Myxococcus xanthus
BGC0001250.4 |  | 0.56 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.56 | 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.

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:
IOD16_RS07025: PT_FPPS_like
Domain 1 (44 - 366): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

IOD16_RS07030: PT_phytoene_like
Domain 1 (17 - 306): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

IOD16_RS07060: Lycopene_cycl
Domain 1 (5 - 95): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

IOD16_RS07065: Lycopene_cycl
Domain 1 (5 - 94): 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: 17.80 out of 20.47
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 21.45 out of 25.31
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.40 out of 23.79
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (7):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.14 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.10 out of 36.54
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.85 out of 29.65
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.54 out of 35.63
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.81 out of 29.65
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.92 out of 23.43
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
--- | ---
AbrC3 | Antibiotic production activator
CatR | H2O2-responsive repressor
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP064192.1 - Region 7 - T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,860,641 - 1,901,708 nt. (total: 41,068 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
IOD16_RS08625: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

IOD16_RS08685: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IOD16_RS08760: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Hydrolases: dehalogenase
IOD16_RS08705: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: dehydratase hydratase
IOD16_RS08630: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

IOD16_RS08785: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: synthase
IOD16_RS08690: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase 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 | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001310.5 |  | 0.82 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0002127.3 |  | 0.71 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.67 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.58 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000282.3 |  | 0.54 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000844.5 |  | 0.51 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0000280.5 |  | 0.48 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0000281.3 |  | 0.45 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0002034.3 |  | 0.45 | other (other) | perquinoline A, perquinoline B, perquinoline C | Streptomyces sp. IB2014 016-6
BGC0001336.5 |  | 0.44 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001310.5 |  | 0.82 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0002127.3 |  | 0.71 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.67 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.58 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000282.3 |  | 0.54 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000844.5 |  | 0.51 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0000280.5 |  | 0.48 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0000281.3 |  | 0.45 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0002034.3 |  | 0.45 | other (other) | perquinoline A, perquinoline B, perquinoline C | Streptomyces sp. IB2014 016-6
BGC0001336.5 |  | 0.44 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium

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 (7):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.35 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.20 out of 21.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.90 out of 29.65
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.86 out of 26.85
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.88 out of 33.14
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: 17.14 out of 28.19
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP064192.1 - Region 8 - PKS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,083,255 - 2,124,289 nt. (total: 41,035 nt) Show pHMM detection rules used
PKS-like: (t2pks2 or ksIII)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
IOD16_RS09635: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

IOD16_RS09645: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

IOD16_RS09705: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

IOD16_RS09730: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

IOD16_RS09760: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Hydrolases: phosphatase
IOD16_RS09715: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Lyases: lyase
IOD16_RS09665: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

IOD16_RS09690: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: synthase
IOD16_RS09720: 3-oxoacyl-(acyl carrier protein) synthase III

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

Translocases: permease
IOD16_RS09755: 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 | PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002313.3 |  | 0.51 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000387.5 |  | 0.48 | NRPS | mangotoxin | Pseudomonas syringae pv. syringae
BGC0001985.4 |  | 0.45 | other (other) | Pyrazofurin | Streptomyces candidus
BGC0000941.3 |  | 0.45 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.44 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0002282.2 |  | 0.44 | other (other) | formycin A | Streptomyces kaniharaensis
BGC0002536.3 |  | 0.43 | NRPS | alazopeptin | Kitasatospora azatica KCTC 9699
BGC0002040.3 |  | 0.43 | other (other) | coformycin, formycin A | Streptomyces kaniharaensis
BGC0001964.2 |  | 0.43 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0001387.5 |  | 0.42 | other (other) | nucleocidin | Streptomyces calvus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002313.3 |  | 0.51 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000387.5 |  | 0.48 | NRPS | mangotoxin | Pseudomonas syringae pv. syringae
BGC0001985.4 |  | 0.45 | other (other) | Pyrazofurin | Streptomyces candidus
BGC0000941.3 |  | 0.45 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.44 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0002282.2 |  | 0.44 | other (other) | formycin A | Streptomyces kaniharaensis
BGC0002536.3 |  | 0.43 | NRPS | alazopeptin | Kitasatospora azatica KCTC 9699
BGC0002040.3 |  | 0.43 | other (other) | coformycin, formycin A | Streptomyces kaniharaensis
BGC0001964.2 |  | 0.43 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0001387.5 |  | 0.42 | other (other) | nucleocidin | Streptomyces calvus

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:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.52 out of 29.72
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.09 out of 26.33
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.77 out of 36.53
Confidence: medium
Additional weak hits (9):
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.74 out of 25.31
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.55 out of 30.22
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.48 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.05 out of 27.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.42 out of 35.63
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.76 out of 18.57
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.53 out of 39.62
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.85 out of 35.63
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
DmdR1 | Iron(II)-dependent repressor
NtrC | Nitrogen regulatory protein C

NZ_CP064192.1 - Region 9 - betalactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,147,109 - 2,174,737 nt. (total: 27,629 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase phosphate reductase
IOD16_RS09925: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

IOD16_RS09980: N-acetyl-gamma-glutamyl-phosphate reductase

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

IOD16_RS10020: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acyltransferase aminotransferase kinase
IOD16_RS09955: aminotransferase

smcogs
  SMCOG1019: aminotransferase

IOD16_RS09975: acetylglutamate kinase

smcogs
  SMCOG1174: acetylglutamate kinase

IOD16_RS10010: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

Lyases: dehydratase hydratase
IOD16_RS09920: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

IOD16_RS09935: L-carnitine dehydratase/bile acid-inducible

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

Ligases: ligase synthase
IOD16_RS09930: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS09960: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS09995: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

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

Reference | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001224.5 |  | 0.46 | other (other) | reductasporine | uncultured bacterium
BGC0000286.3 |  | 0.46 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0001485.4 |  | 0.45 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002405.2 |  | 0.45 | saccharide | mid-chain acyl sugars | Solanum lycopersicum
BGC0000895.5 |  | 0.44 | other (other) | citrulline | Lactobacillus plantarum subsp. plantarum
BGC0002347.3 |  | 0.44 | other (other) | cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D | Actinoalloteichus caeruleus WH1-2216-6
BGC0000131.5 |  | 0.43 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0001137.5 |  | 0.43 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0001302.5 |  | 0.42 | other (other) | lomofungin | Streptomyces lomondensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001224.5 |  | 0.46 | other (other) | reductasporine | uncultured bacterium
BGC0000286.3 |  | 0.46 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0001485.4 |  | 0.45 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002405.2 |  | 0.45 | saccharide | mid-chain acyl sugars | Solanum lycopersicum
BGC0000895.5 |  | 0.44 | other (other) | citrulline | Lactobacillus plantarum subsp. plantarum
BGC0002347.3 |  | 0.44 | other (other) | cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D | Actinoalloteichus caeruleus WH1-2216-6
BGC0000131.5 |  | 0.43 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0001137.5 |  | 0.43 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0001302.5 |  | 0.42 | other (other) | lomofungin | Streptomyces lomondensis

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
Additional weak hits (12):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.81 out of 27.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.03 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.78 out of 30.25
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.08 out of 21.55
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.61 out of 30.97
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.26 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.65 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.27 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.47 out of 28.14
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.56 out of 21.55
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.33 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP064192.1 - 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: 2,368,509 - 2,445,700 nt. (total: 77,192 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 oxygenase
IOD16_RS10890: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IOD16_RS10930: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IOD16_RS10935: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IOD16_RS10955: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

IOD16_RS10990: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Hydrolases: hydrolase
IOD16_RS10855: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: lyase
IOD16_RS10850: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase
IOD16_RS10915: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS10925: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

IOD16_RS10945: 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 | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002424.3 |  |  | 1.41 | NRPS | saccharochelin A, saccharochelin B, saccharochelin C, saccharochelin D, saccharochelin E, saccharochelin F, saccharochelin G, saccharochelin H | Saccharothrix sp.
BGC0001833.4 |  |  | 0.87 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  |  | 0.86 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  |  | 0.85 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001758.4 |  |  | 0.85 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  |  | 0.83 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  | 0.82 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  | 0.82 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  | 0.81 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  |  | 0.81 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002424.3 |  | 0.89 | NRPS | saccharochelin A, saccharochelin B, saccharochelin C, saccharochelin D, saccharochelin E, saccharochelin F, saccharochelin G, saccharochelin H | Saccharothrix sp.
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001758.4 |  | 0.73 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.01 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.44 out of 36.53
Confidence: medium
Additional weak hits (15):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.76 out of 29.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.44 out of 30.22
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.25 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.80 out of 21.55
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.71 out of 23.43
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.23 out of 20.97
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.09 out of 30.22
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.97 out of 26.06
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.93 out of 25.88
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 26.85
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.85 out of 30.22
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.88 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.49 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 10, location 2368508 - 2445700:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Fo-OH-Orn - Ser - OH-Orn - OH-Orn) + (Ser - 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).
IOD16_RS10915: Ser - X
Search NORINE for peptide: strict or relaxed
AMP-binding (479..879): 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:
    RWMTFDVSVWEWHFFCSGEVNLYGPTEATVDVSA
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1511..1911): X
nrpys: Aze

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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWQAFDMSFQESLLVSSGEENQYGPTETHQVTYH
  Nearest Stachelhaus code(s):
    Aze DMQLVSQQVK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

IOD16_RS11000: Fo-OH-Orn - Ser - OH-Orn - OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (423..797): Fo-OH-Orn
nrpys: Fo-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:
    LTAAFDVAVWDMILVVGTEVAAYGLTEATVNSTL
  Nearest Stachelhaus code(s):
    Fo-OH-Orn DVWIIGAVNK (94% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1423..1802): 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:
    RWMTFDVSVWEWHFFSSGEHNLYGPTEAAVDVTY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2438..2829): OH-Orn
nrpys: OH-Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MNHVFDMSWEEWNVLLGGEYNLYGPTEYTINTLG
  Nearest Stachelhaus code(s):
    OH-Orn DMENLGLINK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3471..3864): OH-Orn
nrpys: 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:
    LTAAFDVAVFEMILLVGTELAAYGLTEATVNSTL
  Nearest Stachelhaus code(s):
    OH-Orn DVFILGAVNK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
DmdR1 | Iron(II)-dependent repressor

NZ_CP064192.1 - Region 11 - 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: 2,598,445 - 2,725,746 nt. (total: 127,302 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
IOD16_RS11925: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IOD16_RS11935: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

IOD16_RS11985: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

IOD16_RS12015: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IOD16_RS12040: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

IOD16_RS12060: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

IOD16_RS12185: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Transferases: glycosyltransferase halogenase methyltransferase
IOD16_RS11990: flavin-dependent trp 6 7 halogenase

halogenases
  flavin-dependent trp 6 7 halogenase
MITE
  MITE0000130Halogenation (identity: 65.30%)
smcogs
  SMCOG1119: halogenase

IOD16_RS12110: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

IOD16_RS12130: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: deaminase hydrolase
IOD16_RS11900: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

IOD16_RS11995: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

IOD16_RS12160: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: cyclase decarboxylase
IOD16_RS11830: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

IOD16_RS11850: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

IOD16_RS11965: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase
IOD16_RS11895: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS11910: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS11955: 3-oxoacyl-(acyl carrier protein) synthase III

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

IOD16_RS12000: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

IOD16_RS12150: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS12155: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS40945: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Translocases: transport
IOD16_RS12020: 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 | thioamide-NRP | HR-T2PKS | NRPS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001132.4 |  |  |  |  | 1.15 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002135.2 |  |  |  |  | 1.13 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  |  |  | 1.13 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  |  | 1.12 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  |  |  | 1.12 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  |  |  |  | 1.10 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  |  |  | 1.09 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  |  |  |  | 1.06 | NRPS | enniatin | Fusarium equiseti
BGC0001758.4 |  |  |  |  | 1.04 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  |  |  |  | 0.98 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.74 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001758.4 |  | 0.73 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001249.5 |  | 0.72 | 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.
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:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.57 out of 26.33
Confidence: medium
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: 18.37 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (28):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.60 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.28 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.06 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.53 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.75 out of 29.38
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.88 out of 25.75
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.06 out of 31.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.44 out of 29.38
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.20 out of 26.85
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.46 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.27 out of 19.26
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.61 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.05 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.62 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.09 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.89 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.98 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.39 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.44 out of 28.14
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.36 out of 30.22
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.40 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.17 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.10 out of 28.19
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.23 out of 27.18
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.24 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.13 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 11, location 2598444 - 2725746:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 12, location 2598444 - 2673463:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-X - Trp - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 13, location 2659181 - 2725746:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
IOD16_RS40945: X - Trp - X
Search NORINE for peptide: strict or relaxed
AMP-binding (453..846): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  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:
    HAKAFDVSVWQAEVVVTGEVNAYGPTECSDDVTH
  Nearest Stachelhaus code(s):
    Ser DVWEMTADDK (94% 8Å match)
    Dpr DIWEVTADDK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1931..2324): 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:
    MSLAFDATVWELALVVAGEFNGYGPTEAVLASTV
  Nearest Stachelhaus code(s):
    Trp DAWAFAGVAK (56% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2990..3388): 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)

IOD16_RS12150: Orn - Orn - Orn - Thr - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (473..863): 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:
    LNHAFDTSWEGLDLVLGGEHNFYGPTETTVDAVS
  Nearest Stachelhaus code(s):
    Orn DTEDMGFVDK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1896..2282): 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:
    LANAFDTSWEGFDLMLGGEFNYYGPTEVTVDSVA
  Nearest Stachelhaus code(s):
    Orn DTEDMGYVDK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2899..3280): 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:
    LNHAFDTSWEGFDLMLGGEHNYYGPTEVAVDSVS
  Nearest Stachelhaus code(s):
    Orn DTEDMGYVDK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4320..4686): 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:
    LGTHFDFSVWEGNQIFGGEINMYGITETTVHVTW
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5302..5676): 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)

IOD16_RS12155: Leu - X
Search NORINE for peptide: strict or relaxed
AMP-binding (12..377): 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)

AMP-binding (2030..2397): 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:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LATHFDVSVFEASQIFAGEINMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Ser DVWSIAMVHK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AfsR | Pleiotropic regulatory for antibiotic production
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP064192.1 - Region 12 - NRPS,T2PKS,azole-containing-RiPP
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,840,616 - 3,004,660 nt. (total: 164,045 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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)
T2PKS: (t2ks and t2clf)

#### 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
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase oxidoreductase oxygenase
IOD16_RS12785: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

IOD16_RS12825: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IOD16_RS12865: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IOD16_RS13040: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

IOD16_RS13065: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IOD16_RS13070: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

IOD16_RS13110: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

IOD16_RS13135: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IOD16_RS13160: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

IOD16_RS13175: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

IOD16_RS13180: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IOD16_RS13185: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IOD16_RS41220: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: carboxylase methyltransferase transferase
IOD16_RS13105: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

IOD16_RS13150: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

IOD16_RS13190: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: amidase esterase hydrolase
IOD16_RS12750: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

IOD16_RS12815: thioesterase

smcogs
  SMCOG1004: thioesterase

IOD16_RS12925: amidase

smcogs
  SMCOG1105: amidase

IOD16_RS13245: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: cyclase
IOD16_RS13115: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

IOD16_RS13140: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

Ligases: ligase synthase
IOD16_RS12780: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS12790: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS12795: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS12805: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

IOD16_RS12910: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

IOD16_RS12915: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

IOD16_RS13120: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS13125: Beta-ketoacyl synthase

smcogs
  SMCOG1093: 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 | azole-containing-RiPP | T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000606.5 |  |  |  | 0.69 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0001146.5 |  |  |  | 0.62 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0000231.5 |  |  |  | 0.58 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001145.5 |  |  |  | 0.56 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000234.5 |  |  |  | 0.56 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0002311.3 |  |  |  | 0.56 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0000605.5 |  |  |  | 0.54 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365
BGC0001640.3 |  |  |  | 0.53 | ribosomal | kocurin | Kocuria rosea
BGC0002276.2 |  |  |  | 0.52 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001174.4 |  |  |  | 0.50 | ribosomal | corynazolicin | Corynebacterium urealyticum DSM 7111

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000231.5 |  | 0.83 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.82 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001723.5 |  | 0.77 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.75 | 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

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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.41 out of 20.97
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.39 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.56 out of 30.11
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.17 out of 27.04
Confidence: medium
Additional weak hits (41):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.29 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.85 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.23 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.15 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.82 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.68 out of 30.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.37 out of 25.88
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.84 out of 39.62
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.35 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.21 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.70 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.76 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.33 out of 30.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.09 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.66 out of 29.38
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.17 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.37 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.41 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.85 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.40 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 12.89 out of 18.57
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.12 out of 26.85
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.84 out of 39.62
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.70 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.68 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.66 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.57 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 30.98
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.85 out of 35.63
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.00 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.26 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.29 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.93 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.19 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.78 out of 29.65
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.47 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.01 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.34 out of 28.19
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
(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.
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
RREFinder
Type II PKS
TFBS Finder
Azole RiPPs
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 2840615 - 3004660:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - Val - D-Orn) + (Asn - Ala - D-Val) + (Ser) + (X - Leu - Ser) + (Val - Val - X - Ile - Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 15, location 2840615 - 2944395:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - Val - D-Orn) + (Asn - Ala - D-Val) + (Ser) + (X - Leu - Ser) + (Val - Val - X - Ile - Val)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
IOD16_RS12780: X
AMP-binding (12..373): 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:
    NRTLHQYGLSMLDACVGGELDGYGSSEAGNIALS
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

IOD16_RS12795: X - Val - Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (461..901): 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:
    HAKAFDISIWQAEVVATGEMNAYGPTECADDVTH
  Nearest Stachelhaus code(s):
    Dpr DIWEVTADDK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1556..1948): 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:
    LDRSFDAATYEAWLWTGGDVDGYGPTETTTFATR
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2610..3001): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LHHAFDASWDPWETLLGGELNLYGPTESTVDSMI
  Nearest Stachelhaus code(s):
    Arg DADDVGLVDK (71% 8Å match)
    OH-Orn DAQEGGLVDK (71% 8Å match)
  Stachelhaus code match:
    80% (moderate)

IOD16_RS12800: Asn - Ala - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (462..860): 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:
    YWSSFDLTVTGAKGVLGGEVNEYGPTETTVGCTS
  Nearest Stachelhaus code(s):
    Asn DLTKVGEVGK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1521..1912): 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:
    LWATFDVSVFETSGVLAGEDNIYGPTEATVYTLQ
  Nearest Stachelhaus code(s):
    Ala DVFSVAIVYK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2572..2965): 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:
    LDSSFDASTYEVWIWTGGDVNGYGPTETTTFASR
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

IOD16_RS12805: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (470..854): 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:
    RWMTFDVSVWEWHFVCSGEHNLYGPTEASVDVTS
  Nearest Stachelhaus code(s):
    Ser DVWHVSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

IOD16_RS12910: X - Leu - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (458..839): X
nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

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:
    TGQAWDAFATEGKAMTGGETNGYGPAESMGYSTA
  Nearest Stachelhaus code(s):
    CysA DATKMGHVGK (50% 8Å match)
    bMe-Asp or Asp DLTKMGGVNK (44% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1482..1870): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSHAFDAAVWEPFLLTGGDRNLYGPTEFSVVATG
  Nearest Stachelhaus code(s):
    Leu or Tyr DAWFLGNVVK (82% 8Å match)
    Leu DAWFLGNVVK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2524..2905): 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:
    RWMTFDVSVWEWHFVCSGEHNLYGPTEAAVDVTS
  Nearest Stachelhaus code(s):
    Ser DVWHVSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

IOD16_RS12915: Val - Val - X - Ile - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (17..405): 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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    TGQSWDAFALEGHFMTGGEVNGYSPVENMIFTLC
  Nearest Stachelhaus code(s):
    Val DALWMGGTFK (41% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1036..1430): 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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    TGQSWDAFALEGHFMTGGEVNGYSPVENMIFTLC
  Nearest Stachelhaus code(s):
    Val DALWMGGTFK (41% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2081..2472): 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:
    TGQAWDAFATQGDAMTGGEVNGYGPAESMGFTTT
  Nearest Stachelhaus code(s):
    Val DALWMGGTFK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (3119..3508): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TGQAWDGFVLEGFLMTGGEVNGYGPAEHMVYTSF
  Nearest Stachelhaus code(s):
    Ile DALFMGGVYK (47% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (4171..4577): 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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    TSQSWDAFALEGHLMTGGEVNGYSPVENMIFTVC
  Nearest Stachelhaus code(s):
    Val DALWMGGTFK (44% 8Å match)
  Stachelhaus code match:
    80% (moderate)

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (2927261...2956586)
IOD16_RS12990
  RRE type: Thiopeptide_F_RRE
  Location: 3 - 87
  Score: 38.2

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:
  2932177 to 3004660
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Malonyl elongations:
  8|9 (Score: 690.4; E-value: 1.5e-210)
Product class(es):
  angucycline
Product molecular weight(s):
  acetyl-CoA_8: 384 Da
  acetyl-CoA_9: 426 Da

IOD16_RS13065
  KR (Score: 42.0; E-value: 1.9e-13)
IOD16_RS13110
  OXY (Score: 594.9; E-value: 2.7e-181)
IOD16_RS13115
  CYC C4-C17/C2-C19 (Score: 193.8; E-value: 6.6e-60)
IOD16_RS13120
  KS (Score: 791.4; E-value: 4.2e-241)
IOD16_RS13125
  CLF 8|9 (Score: 690.4; E-value: 1.5e-210)
IOD16_RS13130
  ACP (Score: 134.0; E-value: 3.2e-42)
IOD16_RS13135
  KR C9 (Score: 477.6; E-value: 2.2e-146)
IOD16_RS13140
  CYC C7-C12 (Score: 491.6; E-value: 1.7e-150)
IOD16_RS13185
  KR (Score: 173.1; E-value: 2e-53)
IOD16_RS13190
  MET (Score: 263.4; E-value: 6.6e-81)
IOD16_RS41220
  OXY (Score: 532.4; E-value: 2.6e-162)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
CelR | Cellobiose uptake repressor
DasR | N-acetylglucosamine dependent repressor
ToxT | Regulator of MSHA biosynthesis

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.
NZ_CP064192.1 - Region 13 - 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: 3,029,967 - 3,086,623 nt. (total: 56,657 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
IOD16_RS13435: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

IOD16_RS13455: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

IOD16_RS13475: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

IOD16_RS13480: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

IOD16_RS13485: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IOD16_RS13490: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IOD16_RS13520: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IOD16_RS13525: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Transferases: acylase transferase
IOD16_RS13440: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

IOD16_RS13470: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: synthase
IOD16_RS13450: 3-oxoacyl-(acyl carrier protein) synthase III

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

IOD16_RS13460: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS41225: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transporter
IOD16_RS13395: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  | 0.68 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001276.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002154.2 |  | 0.64 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0000107.3 |  | 0.63 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  | 0.68 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001276.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002154.2 |  | 0.64 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0000107.3 |  | 0.63 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15

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
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.24 out of 19.26
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.79 out of 23.79
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.22 out of 28.19
Confidence: medium
Additional weak hits (2):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.55 out of 31.73
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 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 18, location 3029966 - 3086623:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal - ccmal) + (mal) + (pk)
Non-colinear ordering:
  IOD16_RS13460 + IOD16_RS41225 + IOD16_RS13470

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).
IOD16_RS13460: mal - mal
PKS_AT (637..918): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 213.2
  inactive: 117.6
  Methoxymalonyl-CoA: 67.1
  Methylmalonyl-CoA: 61.6
  Propionyl-CoA: 36.2
  Isobutyryl-CoA: 28.9
  Ethylmalonyl-CoA: 23.1
  Acetyl-CoA: 17.8
  CHC-CoA: 17.1
  Benzoyl-CoA: 15.4
  2-Methylbutyryl-CoA: 9.0
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (1573..1859): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 87.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 211.2
  inactive: 116.7
  Methoxymalonyl-CoA: 68.9
  Methylmalonyl-CoA: 54.7
  Propionyl-CoA: 40.4
  Isobutyryl-CoA: 30.7
  Acetyl-CoA: 19.6
  Ethylmalonyl-CoA: 16.4
  2-Methylbutyryl-CoA: 14.6
  Benzoyl-CoA: 14.2
  CHC-CoA: 7.7
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

IOD16_RS41225: mal
PKS_AT (559..850): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 87.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 225.1
  inactive: 107.8
  Methoxymalonyl-CoA: 56.7
  Methylmalonyl-CoA: 42.3
  Isobutyryl-CoA: 30.8
  Propionyl-CoA: 25.9
  Ethylmalonyl-CoA: 19.7
  Benzoyl-CoA: 18.1
  Acetyl-CoA: 15.5
  2-Methylbutyryl-CoA: 10.3
  fatty_acid: 8.5
  CHC-CoA: 5.7
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

IOD16_RS13470: pk
PKS_AT (560..855): pk
ATSignature: Ethylmalonyl-CoA

Top 3 matches:
  Ethylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 91.7%
  Methylmalonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 195.8
  Ethylmalonyl-CoA: 186.0
  Methoxymalonyl-CoA: 164.2
  2-Methylbutyryl-CoA: 142.6
  trans-1,2-CPDA: 120.9
  Propionyl-CoA: 111.0
  CHC-CoA: 109.7
  Malonyl-CoA: 100.9
  Isobutyryl-CoA: 86.5
  Acetyl-CoA: 53.6
  Benzoyl-CoA: 49.7
  fatty_acid: 44.5
  inactive: 34.6
  3-Methylbutyryl-CoA: 32.2

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

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

NZ_CP064192.1 - Region 14 - T1PKS,terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,093,450 - 3,188,116 nt. (total: 94,667 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))
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
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
IOD16_RS13630: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

IOD16_RS13735: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

IOD16_RS13770: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IOD16_RS13820: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Transferases: kinase
IOD16_RS13765: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

Ligases: synthase synthetase
IOD16_RS13680: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS13810: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

IOD16_RS40195: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS40200: 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 | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000041.3 |  |  | 0.34 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001273.3 |  |  | 0.33 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.32 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001160.5 |  |  | 0.29 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  | 0.29 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000037.4 |  |  | 0.26 | PKS | cichorine | Aspergillus nidulans FGSC A4
BGC0000067.5 |  |  | 0.25 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0002698.2 |  |  | 0.24 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001051.5 |  |  | 0.24 | NRPS, PKS | thuggacin A | Sorangium cellulosum
BGC0002144.3 |  |  | 0.23 | ribosomal | phazolicin | Rhizobium sp. Pop5

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000041.3 |  | 0.67 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001273.3 |  | 0.66 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000037.4 |  | 0.59 | PKS | cichorine | Aspergillus nidulans FGSC A4
BGC0000067.5 |  | 0.59 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0001051.5 |  | 0.58 | NRPS, PKS | thuggacin A | Sorangium cellulosum
BGC0000113.5 |  | 0.56 | PKS | niddamycin | Streptomyces caelestis
BGC0001012.3 |  | 0.55 | NRPS, PKS | meridamycin | Streptomyces violaceusniger

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

No significant matches found.

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

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

Genes with terpene domains:
IOD16_RS13810: PT_FPPS_like
Domain 1 (59 - 343): 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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.99 out of 20.97
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.56 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.76 out of 30.11
Confidence: medium
Additional weak hits (25):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.68 out of 30.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.16 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.08 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.26 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.50 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.12 out of 27.78
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.14 out of 19.26
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.42 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.22 out of 21.55
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.53 out of 31.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.67 out of 29.38
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.19 out of 25.75
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.28 out of 31.73
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.16 out of 30.22
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.39 out of 20.97
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.05 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.83 out of 23.43
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.00 out of 32.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.19 out of 28.19
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.18 out of 30.11
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.33 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.85 out of 28.19
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
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 19, location 3093449 - 3188116:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal - pk - ccmal) + (pk - ccmal) + (ccmal - ccmal)
Non-colinear ordering:
  IOD16_RS40195 + IOD16_RS13680 + IOD16_RS40200

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 20, location 3093449 - 3168981:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal - pk - ccmal) + (pk - ccmal) + (ccmal - ccmal)
Non-colinear ordering:
  IOD16_RS40195 + IOD16_RS13680 + IOD16_RS40200

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).
IOD16_RS40195: mal - pk - mal
PKS_AT (506..795): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 66.7%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 194.2
  Methoxymalonyl-CoA: 80.9
  inactive: 80.2
  Methylmalonyl-CoA: 76.5
  Isobutyryl-CoA: 54.8
  Propionyl-CoA: 45.1
  Ethylmalonyl-CoA: 39.7
  Acetyl-CoA: 31.1
  Benzoyl-CoA: 23.6
  2-Methylbutyryl-CoA: 21.0
  trans-1,2-CPDA: 20.8
  CHC-CoA: 17.1
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: -3.1

PKS_AT (1489..1781): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 214.0
  Methylmalonyl-CoA: 211.8
  2-Methylbutyryl-CoA: 173.0
  Methoxymalonyl-CoA: 167.4
  Propionyl-CoA: 129.5
  trans-1,2-CPDA: 128.0
  CHC-CoA: 110.1
  Malonyl-CoA: 109.9
  Isobutyryl-CoA: 91.3
  Benzoyl-CoA: 69.7
  Acetyl-CoA: 58.8
  3-Methylbutyryl-CoA: 50.4
  fatty_acid: 37.8
  inactive: 35.2

PKS_AT (4114..4382): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 187.9
  inactive: 80.1
  Methoxymalonyl-CoA: 73.8
  Methylmalonyl-CoA: 64.2
  Isobutyryl-CoA: 31.6
  Propionyl-CoA: 31.4
  Ethylmalonyl-CoA: 21.2
  Acetyl-CoA: 16.4
  Benzoyl-CoA: 14.6
  CHC-CoA: 11.6
  fatty_acid: 9.3
  3-Methylbutyryl-CoA: 8.3
  2-Methylbutyryl-CoA: 5.2
  trans-1,2-CPDA: 3.3

IOD16_RS13680: pk - mal
PKS_AT (534..802): pk
ATSignature: Methoxymalonyl-CoA, Methylmalonyl-CoA

Top 3 matches:
  Methoxymalonyl-CoA: 87.5%
  Methylmalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 83.3%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 195.5
  Methylmalonyl-CoA: 191.8
  Methoxymalonyl-CoA: 156.4
  2-Methylbutyryl-CoA: 130.0
  trans-1,2-CPDA: 109.4
  Propionyl-CoA: 109.1
  CHC-CoA: 104.0
  Malonyl-CoA: 81.2
  Isobutyryl-CoA: 74.2
  Benzoyl-CoA: 67.9
  Acetyl-CoA: 46.5
  3-Methylbutyryl-CoA: 38.1
  fatty_acid: 30.2
  inactive: 21.0

PKS_AT (2411..2667): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 75.0%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 198.2
  inactive: 80.6
  Methoxymalonyl-CoA: 69.0
  Methylmalonyl-CoA: 58.7
  Propionyl-CoA: 35.2
  Benzoyl-CoA: 28.4
  Isobutyryl-CoA: 26.1
  Ethylmalonyl-CoA: 23.7
  Acetyl-CoA: 18.9
  2-Methylbutyryl-CoA: 13.2
  trans-1,2-CPDA: 12.0
  fatty_acid: 9.3
  CHC-CoA: 8.0
  3-Methylbutyryl-CoA: 0.0

IOD16_RS40200: mal - mal
PKS_AT (535..793): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 70.8%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 185.5
  inactive: 77.7
  Methylmalonyl-CoA: 69.9
  Methoxymalonyl-CoA: 65.6
  Propionyl-CoA: 29.0
  Ethylmalonyl-CoA: 27.9
  Benzoyl-CoA: 18.5
  Isobutyryl-CoA: 18.3
  fatty_acid: 12.3
  CHC-CoA: 9.4
  Acetyl-CoA: 8.2
  trans-1,2-CPDA: 6.3
  2-Methylbutyryl-CoA: 4.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2029..2293): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 155.6
  Methoxymalonyl-CoA: 64.9
  inactive: 61.8
  Methylmalonyl-CoA: 59.7
  Propionyl-CoA: 50.4
  Isobutyryl-CoA: 28.7
  CHC-CoA: 24.5
  Benzoyl-CoA: 23.8
  2-Methylbutyryl-CoA: 23.1
  fatty_acid: 18.4
  trans-1,2-CPDA: 12.1
  3-Methylbutyryl-CoA: 0.0
  Ethylmalonyl-CoA: -0.6
  Acetyl-CoA: -1.2

Link to PARAS substrate predictor
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
--- | ---
CcpA | Catabolite control protein A
CelR | Cellobiose uptake repressor

NZ_CP064192.1 - Region 15 - 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: 3,364,895 - 3,412,190 nt. (total: 47,296 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
Transferases: aminotransferase glycosyltransferase
IOD16_RS14535: aminotransferase

smcogs
  SMCOG1019: aminotransferase

IOD16_RS14575: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

Hydrolases: esterase glucosidase hydrolase
IOD16_RS14520: thioesterase

smcogs
  SMCOG1004: thioesterase

IOD16_RS14570: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

IOD16_RS14650: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

IOD16_RS14675: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

Lyases: dehydratase
IOD16_RS14610: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
IOD16_RS14525: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS14530: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

IOD16_RS14540: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS14565: 1-deoxy-D-xylulose-5-phosphate synthase

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

IOD16_RS14600: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transporter
IOD16_RS14655: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001244.3 |  | 0.66 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.66 | PKS | asperlactone | Aspergillus ochraceus
BGC0001268.4 |  | 0.64 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002192.3 |  | 0.64 | PKS | FR901512 | fungal sp. No.14919
BGC0002164.2 |  | 0.63 | NRPS | peramine | Epichloe festucae
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001258.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001244.3 |  | 0.66 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.66 | PKS | asperlactone | Aspergillus ochraceus
BGC0001268.4 |  | 0.64 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002192.3 |  | 0.64 | PKS | FR901512 | fungal sp. No.14919
BGC0002164.2 |  | 0.63 | NRPS | peramine | Epichloe festucae
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001258.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis

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
Additional weak hits (4):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.60 out of 27.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.25 out of 35.63
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
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 22, location 3364894 - 3412190:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-pk)

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).
IOD16_RS14525: X
AMP-binding (38..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:
    AAVLHAAGIIVQFGSSTGDIDTLGSTEMGHSAFA
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

IOD16_RS14540: X
AMP-binding (40..377): 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:
    ERYAH---VLGGVLTTGGEGNMWGMTEVGVIATD
  Nearest Stachelhaus code(s):
    Phe DALVMGAVIK (38% 8Å match)
  Stachelhaus code match:
    60% (weak)

IOD16_RS14600: pk
PKS_AT (531..821): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  Methylmalonyl-CoA: 66.7%
  Propionyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 108.8
  Malonyl-CoA: 104.9
  Methoxymalonyl-CoA: 89.5
  Isobutyryl-CoA: 80.6
  Ethylmalonyl-CoA: 69.4
  2-Methylbutyryl-CoA: 59.0
  Propionyl-CoA: 57.1
  inactive: 49.6
  Acetyl-CoA: 32.5
  fatty_acid: 25.7
  Benzoyl-CoA: 24.9
  3-Methylbutyryl-CoA: 22.0
  trans-1,2-CPDA: 19.8
  CHC-CoA: 18.3

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein

NZ_CP064192.1 - 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: 3,647,506 - 3,681,294 nt. (total: 33,789 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: oxidoreductase
IOD16_RS15615: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Transferases: aminotransferase
IOD16_RS15710: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: hydrolase
IOD16_RS15690: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Lyases: dehydratase hydratase
IOD16_RS15600: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

IOD16_RS15705: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
IOD16_RS15650: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS15655: 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 | 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
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
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
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

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
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
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
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
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: 17.99 out of 20.47
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 30.11
Confidence: strong
Additional weak hits (4):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.73 out of 25.88
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.45 out of 26.85
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.50 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 23, location 3647505 - 3681294:
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).
IOD16_RS15650: X
AMP-binding (35..404): X
nrpys: Gln, Tyr

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:
    FAELFDASCEELSTVFGGEWNTYGPTEATVVACA
  Nearest Stachelhaus code(s):
    Gln or Tyr DAESVGTVVK (68% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP064192.1 - Region 17 - 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: 3,919,779 - 3,979,788 nt. (total: 60,010 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
IOD16_RS16895: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase
IOD16_RS16955: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: deacetylase
IOD16_RS17030: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

Lyases: decarboxylase dehydratase
IOD16_RS16885: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

IOD16_RS16950: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
IOD16_RS16920: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS16925: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

IOD16_RS16940: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Translocases: transporter
IOD16_RS16855: 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 | 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 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.70 | 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
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
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 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.70 | 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
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 24.54 out of 30.11
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.61 out of 26.85
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.90 out of 23.79
Confidence: medium
Additional weak hits (11):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.43 out of 21.55
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.64 out of 30.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.46 out of 20.97
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.89 out of 33.73
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.49 out of 19.26
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.61 out of 21.55
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.46 out of 32.93
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.38 out of 24.78
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
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 24, location 3919778 - 3979788:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (Gly) + (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).
IOD16_RS16920: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (457..848): 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:
    LRPSFDLTTLEGWLLAGGDVNGYGPTENTTFTTC
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (82% 8Å match)
    bOH-Val DALWLGGTFK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

IOD16_RS16925: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (446..834): 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:
    N/A
  Single AA prediction:
    gly (Gly)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAMTFDVSAVEAQGISGGEIDGYGPTETTVYSAA
  Nearest Stachelhaus code(s):
    Val DGGQIAGVYK (59% 8Å match)
  Stachelhaus code match:
    70% (weak)

IOD16_RS16940: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (499..869): 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:
    LSFTFDISVLELQAICGGEWNAYGPTETTVWSSA
  Nearest Stachelhaus code(s):
    Gly DILQIGMVWK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

IOD16_RS16950: X
AMP-binding (494..899): X
nrpys: Gly, Ala, 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAFPFDASVGDPDAMIGGEVNHYGPTETTVCATA
  Nearest Stachelhaus code(s):
    CysA DATKMGHVGK (59% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

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

NZ_CP064192.1 - Region 18 - NRPS,NRPS-like,PKS-like,T1PKS,oligosaccharide,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: 4,007,381 - 4,211,086 nt. (total: 203,706 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))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
oligosaccharide: (repeatable(3, [DUF1205, Glyco_transf_28, Glycos_transf_1, Glycos_transf_2, MGT]) and minscore(MGT, 150))
PKS-like: (t2pks2 or ksIII)

#### 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 oxidoreductase oxygenase
IOD16_RS17205: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

IOD16_RS17305: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

IOD16_RS17315: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

IOD16_RS17325: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IOD16_RS17330: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

IOD16_RS17340: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IOD16_RS17360: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IOD16_RS17365: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IOD16_RS17375: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IOD16_RS17450: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

IOD16_RS17490: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

IOD16_RS17650: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

IOD16_RS17795: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

IOD16_RS17810: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

IOD16_RS17815: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

IOD16_RS17820: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IOD16_RS17830: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

IOD16_RS17840: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

IOD16_RS41275: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: aminotransferase glycosyltransferase methyltransferase transferase
IOD16_RS17300: aminotransferase

smcogs
  SMCOG1019: aminotransferase

IOD16_RS17310: methyltransferase

smcogs
  SMCOG1248: methyltransferase

IOD16_RS17460: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

IOD16_RS17470: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

IOD16_RS17505: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

IOD16_RS17785: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

IOD16_RS17790: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

IOD16_RS17825: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: deacetylase dehalogenase esterase glucosidase hydrolase
IOD16_RS17240: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

IOD16_RS17290: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

IOD16_RS17335: thioesterase

smcogs
  SMCOG1004: thioesterase

IOD16_RS17370: thioesterase

smcogs
  SMCOG1004: thioesterase

IOD16_RS17435: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

IOD16_RS17480: amidohydrolase

smcogs
  SMCOG1244: amidohydrolase

Ligases: ligase synthase
IOD16_RS17320: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

IOD16_RS17345: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

IOD16_RS17350: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS17380: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS17750: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS17775: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS40370: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS40385: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS41015: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: permease transporter
IOD16_RS17410: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

IOD16_RS17645: 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 | NRPS | T1PKS | NRPS-like | oligosaccharide | PKS-like | T1PKS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  |  |  |  |  |  |  | 1.43 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  |  |  |  |  |  |  | 1.41 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0002434.2 |  |  |  |  |  |  |  |  | 1.26 | NRPS, PKS | clifednamide D, clifednamide E, clifednamide F, clifednamide G, clifednamide H, clifednamide I, clifednamide J | Kitasatospora sp.
BGC0001249.5 |  |  |  |  |  |  |  |  | 1.24 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0000041.3 |  |  |  |  |  |  |  |  | 1.20 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001012.3 |  |  |  |  |  |  |  |  | 1.19 | NRPS, PKS | meridamycin | Streptomyces violaceusniger
BGC0002191.2 |  |  |  |  |  |  |  |  | 1.18 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  |  |  |  |  |  |  |  | 1.15 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001224.5 |  |  |  |  |  |  |  |  | 1.15 | other (other) | reductasporine | uncultured bacterium
BGC0001164.3 |  |  |  |  |  |  |  |  | 1.14 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002164.2 |  | 0.70 | NRPS | peramine | Epichloe festucae
BGC0001757.3 |  | 0.69 | other (other) | rhabduscin | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

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:
No domains 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
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.34 out of 20.97
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.28 out of 26.33
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.36 out of 25.31
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.11 out of 23.79
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.35 out of 26.85
Confidence: medium
Additional weak hits (32):
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: 17.82 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.07 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.25 out of 21.55
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.13 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.16 out of 27.78
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
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.32 out of 26.85
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.81 out of 21.55
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.52 out of 32.93
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.98 out of 35.63
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.20 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.30 out of 30.11
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.64 out of 30.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.32 out of 29.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.48 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.32 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.14 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.97 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.45 out of 30.25
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.65 out of 27.04
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.07 out of 29.38
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.62 out of 25.75
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.12 out of 35.63
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.62 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.79 out of 29.65
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.41 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.28 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.96 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
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 25, location 4007380 - 4069493:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 27, location 4016008 - 4059359:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 28, location 4025821 - 4069493:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 29, location 4034420 - 4211086:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal - ccmal - ccmal) + (ccmal - ohmal) + (ccmal) + (pk - pk - pk - pk - ccmal) + (Me-redmal - pk - ccmal) + (Thr) + (mal) + (Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 30, location 4034420 - 4077030:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 32, location 4071760 - 4153416:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk - pk - pk - pk - ccmal) + (Me-redmal - pk - ccmal)
Non-colinear ordering:
  IOD16_RS41015 + IOD16_RS40370

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 33, location 4143721 - 4211086:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal - ccmal - ccmal) + (ccmal - ohmal) + (ccmal)
Non-colinear ordering:
  IOD16_RS17775 + IOD16_RS40385 + IOD16_RS17750

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).
IOD16_RS17320: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (547..937): 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:
    LEPSFDASTLEGWLITGGDTNGYGPTENTTFTAT
  Nearest Stachelhaus code(s):
    Val DALWIGGTFK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

IOD16_RS17350: mal
PKS_AT (526..806): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 52.8
  Methoxymalonyl-CoA: 19.3
  Methylmalonyl-CoA: 16.7
  Propionyl-CoA: 11.1
  Acetyl-CoA: 4.7
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

IOD16_RS17380: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (294..688): 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:
    LATHFDFSVWEGSQVLGGEVNMFGITETTVHVTH
  Nearest Stachelhaus code(s):
    Thr DFWSVGMVHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

IOD16_RS40370: mmal - pk - mal
PKS_AT (541..830): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 203.3
  Ethylmalonyl-CoA: 196.0
  Methoxymalonyl-CoA: 173.3
  2-Methylbutyryl-CoA: 139.6
  trans-1,2-CPDA: 119.9
  Malonyl-CoA: 116.0
  Propionyl-CoA: 106.8
  CHC-CoA: 105.1
  Isobutyryl-CoA: 82.8
  Benzoyl-CoA: 68.0
  Acetyl-CoA: 62.1
  fatty_acid: 39.2
  inactive: 35.8
  3-Methylbutyryl-CoA: 32.5

PKS_AT (2436..2712): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 212.7
  Methylmalonyl-CoA: 199.5
  Methoxymalonyl-CoA: 161.3
  2-Methylbutyryl-CoA: 137.9
  trans-1,2-CPDA: 116.1
  Propionyl-CoA: 110.3
  Malonyl-CoA: 108.7
  CHC-CoA: 96.2
  Benzoyl-CoA: 74.9
  Isobutyryl-CoA: 60.9
  Acetyl-CoA: 41.2
  inactive: 37.6
  3-Methylbutyryl-CoA: 30.0
  fatty_acid: 23.8

PKS_AT (4330..4604): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 79.2%
  Propionyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 210.8
  inactive: 98.5
  Methoxymalonyl-CoA: 86.6
  Methylmalonyl-CoA: 80.5
  Ethylmalonyl-CoA: 48.8
  Propionyl-CoA: 46.0
  Isobutyryl-CoA: 38.8
  Benzoyl-CoA: 30.1
  Acetyl-CoA: 29.3
  trans-1,2-CPDA: 24.6
  CHC-CoA: 17.2
  2-Methylbutyryl-CoA: 13.7
  fatty_acid: 12.8
  3-Methylbutyryl-CoA: 0.0

IOD16_RS41015: pk - pk - pk - pk - mal
PKS_AT (514..793): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 209.8
  Methylmalonyl-CoA: 204.9
  Methoxymalonyl-CoA: 170.0
  2-Methylbutyryl-CoA: 135.1
  trans-1,2-CPDA: 125.5
  Propionyl-CoA: 123.6
  CHC-CoA: 102.9
  Malonyl-CoA: 97.4
  Isobutyryl-CoA: 83.7
  Benzoyl-CoA: 63.5
  Acetyl-CoA: 52.0
  3-Methylbutyryl-CoA: 44.6
  fatty_acid: 32.0
  inactive: 31.6

PKS_AT (1467..1737): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 223.6
  Methylmalonyl-CoA: 209.6
  Methoxymalonyl-CoA: 175.2
  2-Methylbutyryl-CoA: 147.5
  trans-1,2-CPDA: 127.2
  Propionyl-CoA: 117.5
  CHC-CoA: 110.8
  Malonyl-CoA: 97.8
  Isobutyryl-CoA: 81.0
  Benzoyl-CoA: 72.4
  Acetyl-CoA: 59.3
  3-Methylbutyryl-CoA: 45.2
  inactive: 34.5
  fatty_acid: 29.1

PKS_AT (2844..3114): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 231.7
  Methylmalonyl-CoA: 215.9
  Methoxymalonyl-CoA: 179.9
  2-Methylbutyryl-CoA: 150.7
  trans-1,2-CPDA: 136.2
  Propionyl-CoA: 126.8
  CHC-CoA: 119.0
  Malonyl-CoA: 106.0
  Isobutyryl-CoA: 85.7
  Benzoyl-CoA: 75.1
  Acetyl-CoA: 59.8
  3-Methylbutyryl-CoA: 47.4
  fatty_acid: 38.3
  inactive: 34.3

PKS_AT (4716..4986): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 210.4
  Methylmalonyl-CoA: 202.2
  Methoxymalonyl-CoA: 169.0
  2-Methylbutyryl-CoA: 148.6
  Propionyl-CoA: 124.6
  trans-1,2-CPDA: 122.5
  CHC-CoA: 117.9
  Malonyl-CoA: 102.9
  Isobutyryl-CoA: 79.7
  Benzoyl-CoA: 56.8
  Acetyl-CoA: 51.4
  3-Methylbutyryl-CoA: 45.4
  fatty_acid: 39.5
  inactive: 32.2

PKS_AT (6298..6574): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 79.2%
  Propionyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 209.8
  inactive: 96.6
  Methoxymalonyl-CoA: 79.9
  Methylmalonyl-CoA: 73.5
  Isobutyryl-CoA: 38.3
  Ethylmalonyl-CoA: 37.9
  Propionyl-CoA: 36.6
  Acetyl-CoA: 27.1
  Benzoyl-CoA: 25.1
  fatty_acid: 8.7
  2-Methylbutyryl-CoA: 7.8
  trans-1,2-CPDA: 6.2
  CHC-CoA: 5.1
  3-Methylbutyryl-CoA: 0.0

IOD16_RS17750: mal
PKS_AT (548..828): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 87.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 217.6
  inactive: 111.4
  Methoxymalonyl-CoA: 68.1
  Methylmalonyl-CoA: 45.3
  Propionyl-CoA: 27.9
  Isobutyryl-CoA: 27.9
  Ethylmalonyl-CoA: 17.5
  Acetyl-CoA: 14.3
  CHC-CoA: 14.1
  Benzoyl-CoA: 12.2
  fatty_acid: 9.4
  2-Methylbutyryl-CoA: 4.2
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

IOD16_RS40385: mal - mal
PKS_AT (551..818): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 66.7%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 185.7
  inactive: 79.0
  Methoxymalonyl-CoA: 75.0
  Methylmalonyl-CoA: 62.4
  Propionyl-CoA: 46.3
  Isobutyryl-CoA: 33.2
  Ethylmalonyl-CoA: 31.8
  Benzoyl-CoA: 27.8
  Acetyl-CoA: 25.6
  2-Methylbutyryl-CoA: 22.3
  trans-1,2-CPDA: 21.0
  CHC-CoA: 19.4
  fatty_acid: 17.2
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2085..2357): 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: 191.7
  inactive: 86.8
  Methoxymalonyl-CoA: 72.5
  Methylmalonyl-CoA: 68.9
  Propionyl-CoA: 38.3
  Ethylmalonyl-CoA: 31.0
  Isobutyryl-CoA: 30.8
  Acetyl-CoA: 27.7
  Benzoyl-CoA: 25.5
  2-Methylbutyryl-CoA: 18.3
  trans-1,2-CPDA: 15.2
  fatty_acid: 14.0
  CHC-CoA: 12.0
  3-Methylbutyryl-CoA: 5.8

IOD16_RS17775: mal - mal - mal
PKS_AT (519..777): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Propionyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 203.8
  inactive: 96.9
  Methoxymalonyl-CoA: 68.7
  Methylmalonyl-CoA: 56.7
  Isobutyryl-CoA: 31.2
  Propionyl-CoA: 30.9
  Ethylmalonyl-CoA: 29.9
  Acetyl-CoA: 20.0
  Benzoyl-CoA: 18.4
  fatty_acid: 15.5
  2-Methylbutyryl-CoA: 13.7
  CHC-CoA: 12.8
  3-Methylbutyryl-CoA: 9.3
  trans-1,2-CPDA: 7.4

PKS_AT (1441..1707): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 170.0
  inactive: 90.1
  Methoxymalonyl-CoA: 49.9
  Methylmalonyl-CoA: 38.3
  Propionyl-CoA: 35.0
  Isobutyryl-CoA: 18.9
  2-Methylbutyryl-CoA: 16.5
  fatty_acid: 15.4
  Acetyl-CoA: 14.3
  Benzoyl-CoA: 7.9
  3-Methylbutyryl-CoA: 7.8
  CHC-CoA: 3.8
  Ethylmalonyl-CoA: 2.1
  trans-1,2-CPDA: 0.0

PKS_AT (3017..3311): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 87.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 195.6
  inactive: 109.6
  Methoxymalonyl-CoA: 59.3
  Methylmalonyl-CoA: 55.9
  Isobutyryl-CoA: 32.5
  Propionyl-CoA: 32.4
  2-Methylbutyryl-CoA: 19.1
  Ethylmalonyl-CoA: 15.8
  Acetyl-CoA: 15.2
  Benzoyl-CoA: 14.0
  fatty_acid: 9.9
  CHC-CoA: 5.3
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

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
CcpA | Catabolite control protein A
IolR | Regulator of the inositol catabolism
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP064192.1 - Region 19 - 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
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Location: 4,221,599 - 4,328,268 nt. (total: 106,670 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
IOD16_RS17915: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

IOD16_RS17960: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IOD16_RS18015: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IOD16_RS18055: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase aminotransferase
IOD16_RS17970: aminotransferase

smcogs
  SMCOG1019: aminotransferase

IOD16_RS17975: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: dehalogenase esterase protease
IOD16_RS17910: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

IOD16_RS17995: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

IOD16_RS18030: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase synthase
IOD16_RS17955: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS17980: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS17985: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS18000: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS18005: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

IOD16_RS18010: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.75 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  | 0.67 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002154.2 |  | 0.64 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0000142.3 |  | 0.64 | PKS | salinilactam | Salinispora tropica CNB-440

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.75 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  | 0.67 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002154.2 |  | 0.64 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0000142.3 |  | 0.64 | PKS | salinilactam | Salinispora tropica CNB-440

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:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.30 out of 25.31
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.07 out of 20.47
Confidence: medium
Additional weak hits (12):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.62 out of 30.22
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.58 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.46 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.07 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.61 out of 28.14
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.10 out of 20.97
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.92 out of 30.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.55 out of 30.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.52 out of 20.97
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.01 out of 28.19
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.08 out of 36.53
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 34, location 4221598 - 4328268:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - ccmal - Me-ccmal - ccmal) + (ccmal) + (ohmal - ohmal) + (Me-ohmal) + (ccmal - ccmal - ccmal)
Non-colinear ordering:
  IOD16_RS17955 + IOD16_RS18015 + IOD16_RS18010 + IOD16_RS18005 + IOD16_RS18000

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).
IOD16_RS17955: mal - mal - mmal - mal
PKS_AT (659..957): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 62.5%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 203.2
  inactive: 112.0
  Methoxymalonyl-CoA: 88.3
  Methylmalonyl-CoA: 74.6
  Isobutyryl-CoA: 49.0
  Propionyl-CoA: 45.3
  Ethylmalonyl-CoA: 41.1
  2-Methylbutyryl-CoA: 38.5
  Acetyl-CoA: 32.6
  Benzoyl-CoA: 29.7
  trans-1,2-CPDA: 15.7
  CHC-CoA: 8.1
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2388..2681): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 79.2%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 189.4
  inactive: 91.3
  Methylmalonyl-CoA: 58.8
  Methoxymalonyl-CoA: 56.0
  Propionyl-CoA: 34.8
  Ethylmalonyl-CoA: 26.1
  Isobutyryl-CoA: 25.8
  fatty_acid: 20.8
  Benzoyl-CoA: 11.5
  CHC-CoA: 9.1
  Acetyl-CoA: 9.1
  2-Methylbutyryl-CoA: 4.3
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4088..4383): 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: 205.0
  Ethylmalonyl-CoA: 195.0
  Methoxymalonyl-CoA: 166.1
  trans-1,2-CPDA: 129.4
  2-Methylbutyryl-CoA: 128.2
  Propionyl-CoA: 91.7
  Malonyl-CoA: 90.6
  CHC-CoA: 88.7
  Isobutyryl-CoA: 67.8
  Benzoyl-CoA: 53.1
  Acetyl-CoA: 39.1
  3-Methylbutyryl-CoA: 38.8
  inactive: 27.1
  fatty_acid: 24.5

PKS_AT (5790..6075): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 79.2%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 197.1
  inactive: 94.4
  Methylmalonyl-CoA: 61.4
  Methoxymalonyl-CoA: 57.7
  Propionyl-CoA: 33.8
  Isobutyryl-CoA: 25.4
  Ethylmalonyl-CoA: 25.3
  fatty_acid: 23.5
  Benzoyl-CoA: 16.9
  CHC-CoA: 5.9
  2-Methylbutyryl-CoA: 5.9
  Acetyl-CoA: 5.6
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

IOD16_RS17975: pk
PKS_AT (31..277): pk
ATSignature: (unknown)
No matches above 50%
minowa: trans-1,2-CPDA

Prediction, score:
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Malonyl-CoA: 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

IOD16_RS17980: X
AMP-binding (21..418): 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:
    YVIFFDCAMFDCFSLFAGEENIYGPTELTVTITG
  Nearest Stachelhaus code(s):
    Ala DCFFFALITK (79% 8Å match)
    bMe-Asp DCFFFALITK (74% 8Å match)
  Stachelhaus code match:
    70% (weak)

IOD16_RS17985: X
AMP-binding (23..431): 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:
    FGMSFDFSLLDLNGLYSGEVNCFGSSE-SVAASF
  Nearest Stachelhaus code(s):
    Abu DALFLSAVVK (47% 8Å match)
    Gly DILQLGCVWK (44% 8Å match)
    Ile or Val DFLCLGVVIK (38% 8Å match)
    Cys DLFNLSLVWK (35% 8Å match)
  Stachelhaus code match:
    60% (weak)

IOD16_RS18000: mal - mal - mal
PKS_AT (557..838): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 194.6
  inactive: 87.1
  Methylmalonyl-CoA: 74.0
  Methoxymalonyl-CoA: 64.9
  Propionyl-CoA: 50.6
  Isobutyryl-CoA: 44.2
  Ethylmalonyl-CoA: 36.0
  Acetyl-CoA: 22.5
  CHC-CoA: 20.4
  Benzoyl-CoA: 20.1
  2-Methylbutyryl-CoA: 18.4
  trans-1,2-CPDA: 17.1
  fatty_acid: 12.5
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2204..2480): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 198.3
  inactive: 86.8
  Methylmalonyl-CoA: 61.5
  Methoxymalonyl-CoA: 60.2
  Propionyl-CoA: 31.9
  Isobutyryl-CoA: 28.2
  Acetyl-CoA: 18.6
  Ethylmalonyl-CoA: 14.3
  Benzoyl-CoA: 11.8
  fatty_acid: 11.4
  CHC-CoA: 6.1
  2-Methylbutyryl-CoA: 6.0
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3865..4136): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 185.4
  inactive: 88.4
  Methoxymalonyl-CoA: 50.7
  Methylmalonyl-CoA: 50.1
  Propionyl-CoA: 30.8
  Isobutyryl-CoA: 18.3
  Acetyl-CoA: 14.8
  fatty_acid: 12.8
  CHC-CoA: 6.7
  Benzoyl-CoA: 6.4
  Ethylmalonyl-CoA: 5.5
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

IOD16_RS18005: mmal
PKS_AT (547..845): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 196.6
  Ethylmalonyl-CoA: 179.6
  Methoxymalonyl-CoA: 160.7
  trans-1,2-CPDA: 128.2
  2-Methylbutyryl-CoA: 121.6
  Malonyl-CoA: 98.5
  Propionyl-CoA: 96.9
  Isobutyryl-CoA: 76.9
  CHC-CoA: 71.4
  Benzoyl-CoA: 66.5
  3-Methylbutyryl-CoA: 48.7
  Acetyl-CoA: 45.7
  inactive: 40.0
  fatty_acid: 24.1

IOD16_RS18010: mal - mal
PKS_AT (548..825): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 189.3
  inactive: 88.7
  Methoxymalonyl-CoA: 57.2
  Methylmalonyl-CoA: 53.4
  Propionyl-CoA: 34.8
  Acetyl-CoA: 18.6
  fatty_acid: 16.1
  Isobutyryl-CoA: 13.9
  Ethylmalonyl-CoA: 10.9
  CHC-CoA: 3.4
  trans-1,2-CPDA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

PKS_AT (2047..2320): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 209.6
  inactive: 95.5
  Methylmalonyl-CoA: 67.1
  Methoxymalonyl-CoA: 62.5
  Propionyl-CoA: 38.2
  Isobutyryl-CoA: 30.0
  Ethylmalonyl-CoA: 26.7
  Benzoyl-CoA: 21.0
  Acetyl-CoA: 20.2
  2-Methylbutyryl-CoA: 15.0
  CHC-CoA: 14.8
  trans-1,2-CPDA: 14.4
  fatty_acid: 10.8
  3-Methylbutyryl-CoA: 0.0

IOD16_RS18015: mal
PKS_AT (555..826): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 169.8
  inactive: 81.0
  Methoxymalonyl-CoA: 42.1
  Methylmalonyl-CoA: 41.4
  Propionyl-CoA: 30.9
  fatty_acid: 15.0
  Acetyl-CoA: 14.7
  Isobutyryl-CoA: 10.4
  Benzoyl-CoA: 7.2
  CHC-CoA: 6.7
  Ethylmalonyl-CoA: 3.1
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP064192.1 - Region 20 - 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: 4,398,089 - 4,418,994 nt. (total: 20,906 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
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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
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 |  | 0.40 | ribosomal | microcin C7 | Escherichia coli
BGC0000812.3 |  | 0.31 | other (other) | huperzine A | Shiraia sp. slf14
BGC0002294.3 |  | 0.30 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0001513.3 |  | 0.29 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000821.5 |  | 0.27 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0000877.5 |  | 0.27 | other (other) | polyoxin A, polyoxin H | Streptomyces cacaoi subsp. asoensis
BGC0002064.2 |  | 0.26 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0000197.5 |  | 0.26 | PKS, saccharide | aranciamycin | Streptomyces echinatus
BGC0002443.3 |  | 0.26 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002317.2 |  | 0.45 | ribosomal | herbicolin O, mcceh252, pantocin A | Pantoea agglomerans
BGC0000585.5 |  | 0.40 | ribosomal | microcin C7 | Escherichia coli
BGC0000812.3 |  | 0.31 | other (other) | huperzine A | Shiraia sp. slf14
BGC0002294.3 |  | 0.30 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0001513.3 |  | 0.29 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000821.5 |  | 0.27 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0000877.5 |  | 0.27 | other (other) | polyoxin A, polyoxin H | Streptomyces cacaoi subsp. asoensis
BGC0002064.2 |  | 0.26 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0000197.5 |  | 0.26 | PKS, saccharide | aranciamycin | Streptomyces echinatus
BGC0002443.3 |  | 0.26 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus

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:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33
Confidence: medium
Additional weak hits (11):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 20.86 out of 31.73
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.95 out of 30.97
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.07 out of 29.38
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.03 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.90 out of 21.55
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.75 out of 32.93
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.60 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.26 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.67 out of 28.19
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (4398088...4418994)
IOD16_RS18370
  RRE type: Pantocin_Microcin_RRE
  Location: 1 - 87
  Score: 70.3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator

NZ_CP064192.1 - Region 21 - hydrogen-cyanide
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: 4,508,718 - 4,521,558 nt. (total: 12,841 nt) Show pHMM detection rules used
hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)

#### 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 reductase
IOD16_RS18925: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

IOD16_RS18935: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent 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 | hydrogen-cyanide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0002436.2 |  | 0.40 | other (other) | coformycin | Streptomyces citricolor
BGC0002285.2 |  | 0.31 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000260.3 |  | 0.30 | PKS | prodigiosin | Hahella chejuensis KCTC 2396
BGC0001007.5 |  | 0.29 | NRPS, PKS | lymphostin, neolymphostinol B, lymphostinol, neolymphostin b | Salinispora arenicola CNS-205
BGC0001985.4 |  | 0.28 | other (other) | Pyrazofurin | Streptomyces candidus
BGC0001006.5 |  | 0.28 | NRPS, PKS | lymphostin, neolymphostinol B, lymphostinol, neolymphostin B | Salinispora tropica CNB-440
BGC0002039.3 |  | 0.25 | other (other) | coformycin, formycin A | Nocardia interforma ATCC 21072
BGC0001783.5 |  | 0.21 | other (other) | streptonigrin | Streptomyces flocculus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0002436.2 |  | 0.40 | other (other) | coformycin | Streptomyces citricolor
BGC0002285.2 |  | 0.31 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000260.3 |  | 0.30 | PKS | prodigiosin | Hahella chejuensis KCTC 2396
BGC0001007.5 |  | 0.29 | NRPS, PKS | lymphostin, neolymphostinol B, lymphostinol, neolymphostin b | Salinispora arenicola CNS-205
BGC0001985.4 |  | 0.28 | other (other) | Pyrazofurin | Streptomyces candidus
BGC0001006.5 |  | 0.28 | NRPS, PKS | lymphostin, neolymphostinol B, lymphostinol, neolymphostin B | Salinispora tropica CNB-440
BGC0002039.3 |  | 0.25 | other (other) | coformycin, formycin A | Nocardia interforma ATCC 21072
BGC0001783.5 |  | 0.21 | other (other) | streptonigrin | Streptomyces flocculus

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:
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.40 out of 22.40
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.09 out of 20.47
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.49 out of 25.31
Confidence: medium
Additional weak hits (8):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
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
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.76 out of 27.55
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.28 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 20.07 out of 22.40
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.14 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.55 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
HypR | L-hydroxyproline utilization repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP064192.1 - Region 22 - 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: 4,524,584 - 4,551,680 nt. (total: 27,097 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
Oxidoreductases: oxygenase
IOD16_RS19045: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Translocases: transporter
IOD16_RS18975: 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 | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002099.3 |  | 0.59 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0002084.4 |  | 0.59 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002631.2 |  | 0.55 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000606.5 |  | 0.51 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0000569.5 |  | 0.50 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0000605.5 |  | 0.49 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365
BGC0002013.4 |  | 0.48 | ribosomal | curacozole | Streptomyces curacoi
BGC0001174.4 |  | 0.48 | ribosomal | corynazolicin | Corynebacterium urealyticum DSM 7111
BGC0001640.3 |  | 0.46 | ribosomal | kocurin | Kocuria rosea
BGC0002115.3 |  | 0.46 | ribosomal | streptamidine | Streptomyces albidoflavus J1074

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002099.3 |  | 0.59 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0002084.4 |  | 0.59 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002631.2 |  | 0.55 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000606.5 |  | 0.51 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0000569.5 |  | 0.50 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0000605.5 |  | 0.49 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365
BGC0002013.4 |  | 0.48 | ribosomal | curacozole | Streptomyces curacoi
BGC0001174.4 |  | 0.48 | ribosomal | corynazolicin | Corynebacterium urealyticum DSM 7111
BGC0001640.3 |  | 0.46 | ribosomal | kocurin | Kocuria rosea
BGC0002115.3 |  | 0.46 | ribosomal | streptamidine | Streptomyces albidoflavus J1074

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: 19.75 out of 23.05
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.05 out of 20.97
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.06 out of 20.01
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.36 out of 25.31
Confidence: medium
Additional weak hits (5):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.75 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.67 out of 21.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.83 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.37 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.76 out of 23.43
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.

#### (Thi)azol(in)e containing peptide(s)

IOD16_RS19015
Leader:
MNEFDLTFDAEDLVLDDLAVTTMRDTVALPESGASIGA
Core:
S C G S S C C C Q P Q L P Q P T F
Core with dehydrations:
Dha Cys G Dha Dha Cys Cys Cys Q P Q L P Q P Dhb F

#### antiSMASH-DB 4.0 matches for IOD16_RS19015

100.0%
NZ_CP064192.1:
Thiopeptides: IOD16_RS19015_thiopeptide
1
S C G S S C C C Q P Q L P Q P T F
17
S C G S S C C C Q P Q L P Q P T F
1
S C G S S C C C Q P Q L P Q P T F
17

#### MIBiG 4.0 matches for IOD16_RS19015

29.4%
BGC0001155.5 (AGY49587.1):
Thiopeptide: GE2270
2
C G S S C C C Q P
10
C G C C P
6
C G F C C S C S P
14

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

#### Types:

Type I: Featuring genes encoding indolic acid side ring (series e)
Type II: Featuring the gene coding for quinaldic acid moiety formation (series a, b, and c)
Type III: No genes for synthesizing L-Trp derivatives (series d)
RREFinder
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (4524583...4551680)
IOD16_RS19005
  RRE type: Thiopeptide_F_RRE
  Location: 11 - 95
  Score: 32.0

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
ArgR | Regulator of arginine biosynthesis genes
CatR | H2O2-responsive repressor
CcpA | Catabolite control protein A

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.

IOD16_RS19015
  Putative Type III
  Cleavage pHMM score: 3.20
  RODEO score: 29
  Monoisotopic mass: 1784.7 Da
  Molecular weight: 1786.0 Da
  Predicted peptide features:
  Central ring: pyridine trisubstituted
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1804.1 Da N = 1
    1822.1 Da N = 2
    1840.1 Da N = 3
    1858.1 Da N = 4

NZ_CP064192.1 - Region 23 - T1PKS,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: 4,566,665 - 4,611,915 nt. (total: 45,251 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)
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
Transferases: halogenase
IOD16_RS19160: flavin-dependent cycline orsellinic halogenase

halogenases
  flavin-dependent cycline orsellinic halogenase
smcogs
  SMCOG1119: halogenase

Ligases: synthase synthetase
IOD16_RS19130: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

IOD16_RS19165: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS19170: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS19175: 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 | terpene-precursor | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002608.2 |  |  | 0.96 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0002341.2 |  |  | 0.93 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0001164.3 |  |  | 0.34 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.33 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001273.3 |  |  | 0.31 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  | 0.31 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002191.2 |  |  | 0.31 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0000041.3 |  |  | 0.30 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001276.3 |  |  | 0.30 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  |  | 0.30 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002608.2 |  | 0.77 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0002341.2 |  | 0.76 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0001164.3 |  | 0.67 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.67 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001273.3 |  | 0.65 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.65 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002191.2 |  | 0.64 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0000041.3 |  | 0.64 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis

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

No significant matches found.

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

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

Genes with terpene domains:
IOD16_RS19130: PT_FPPS_like
Domain 1 (59 - 304): 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:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 26.55 out of 29.72
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.11 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.00 out of 20.47
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.42 out of 19.52
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
Additional weak hits (7):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.21 out of 20.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.48 out of 21.55
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.20 out of 30.98
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.61 out of 24.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.13 out of 26.85
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.88 out of 29.65
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 38, location 4566664 - 4611915:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 40, location 4567193 - 4611915:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal)

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).
IOD16_RS19165: mal
PKS_AT (555..842): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 87.5%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 180.1
  inactive: 114.9
  Methoxymalonyl-CoA: 57.4
  Methylmalonyl-CoA: 47.8
  Propionyl-CoA: 27.2
  Ethylmalonyl-CoA: 26.0
  2-Methylbutyryl-CoA: 24.1
  Isobutyryl-CoA: 23.3
  CHC-CoA: 19.5
  fatty_acid: 16.9
  Benzoyl-CoA: 15.4
  trans-1,2-CPDA: 11.5
  Acetyl-CoA: 10.2
  3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP064192.1 - Region 24 - 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: 4,828,138 - 4,889,456 nt. (total: 61,319 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 electron transfer
IOD16_RS20190: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

IOD16_RS20330: flavodoxin

smcogs
  SMCOG1134: flavodoxin

IOD16_RS20340: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acyltransferase glycosyltransferase
IOD16_RS20200: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

IOD16_RS20285: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

IOD16_RS20290: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

IOD16_RS20350: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Hydrolases: hydrolase
IOD16_RS20210: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: cyclase
IOD16_RS20395: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Translocases: transport
IOD16_RS20275: 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 | oligosaccharide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000410.5 |  | 0.50 | NRPS | pseudomonine | Pseudomonas fluorescens
BGC0001525.3 |  | 0.49 | other (other) | bartoloside B, bartoloside C, bartoloside D | Synechocystis salina LEGE 06155
BGC0001526.4 |  | 0.48 | other (other) | bartoloside E, bartoloside F, bartoloside G, bartoloside H, bartoloside I, bartoloside J, bartoloside K | Synechocystis salina LEGE 06099
BGC0001843.2 |  | 0.47 | NRPS | tridecaptin M | Paenibacillus sp. M-152
BGC0001928.2 |  | 0.47 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000231.5 |  | 0.47 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002496.3 |  | 0.47 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0000713.5 |  | 0.47 | saccharide | ribostamycin | Streptomyces ribosidificus
BGC0000277.5 |  | 0.47 | PKS | urdamycin | Streptomyces fradiae
BGC0000708.5 |  | 0.46 | saccharide | lividomycin | Streptomyces lividus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000410.5 |  | 0.50 | NRPS | pseudomonine | Pseudomonas fluorescens
BGC0001525.3 |  | 0.49 | other (other) | bartoloside B, bartoloside C, bartoloside D | Synechocystis salina LEGE 06155
BGC0001526.4 |  | 0.48 | other (other) | bartoloside E, bartoloside F, bartoloside G, bartoloside H, bartoloside I, bartoloside J, bartoloside K | Synechocystis salina LEGE 06099
BGC0001843.2 |  | 0.47 | NRPS | tridecaptin M | Paenibacillus sp. M-152
BGC0001928.2 |  | 0.47 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000231.5 |  | 0.47 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002496.3 |  | 0.47 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0000713.5 |  | 0.47 | saccharide | ribostamycin | Streptomyces ribosidificus
BGC0000277.5 |  | 0.47 | PKS | urdamycin | Streptomyces fradiae
BGC0000708.5 |  | 0.46 | saccharide | lividomycin | Streptomyces lividus

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:
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 30.11
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.69 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 24.57 out of 30.11
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
Additional weak hits (18):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.23 out of 23.43
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.04 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.33 out of 29.38
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.36 out of 27.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.48 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.24 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.76 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.21 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.80 out of 29.38
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 19.26
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.08 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.64 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.14 out of 28.19
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.30 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.20 out of 30.11
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.10 out of 28.19
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.08 out of 27.18
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP064192.1 - Region 25 - NRPS,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: 5,036,829 - 5,100,477 nt. (total: 63,649 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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
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
IOD16_RS21115: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

IOD16_RS21125: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

IOD16_RS21180: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

IOD16_RS21235: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: acyltransferase methyltransferase
IOD16_RS21105: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

IOD16_RS21140: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

IOD16_RS21220: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Hydrolases: phosphatase
IOD16_RS21120: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Lyases: cyclase
IOD16_RS21085: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Ligases: synthase synthetase
IOD16_RS21095: 3-oxoacyl-(acyl carrier protein) synthase III

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

IOD16_RS21100: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS21210: 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 | NRPS | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001135.5 |  |  | 0.34 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002164.2 |  |  | 0.33 | NRPS | peramine | Epichloe festucae
BGC0001261.3 |  |  | 0.33 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  |  | 0.32 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  | 0.32 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  |  | 0.32 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002135.2 |  |  | 0.31 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  |  | 0.31 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  |  | 0.31 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001641.4 |  |  | 0.30 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002164.2 |  | 0.66 | NRPS | peramine | Epichloe festucae
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.64 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001641.4 |  | 0.64 | NRPS | kolossin | 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
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:
IOD16_RS21210: PT_FPPS_like
Domain 1 (60 - 344): 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.20 out of 26.33
Confidence: medium
Additional weak hits (24):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.68 out of 39.62
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.79 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.17 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.01 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.11 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.68 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.78 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.95 out of 30.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.59 out of 20.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.83 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.21 out of 29.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.78 out of 25.88
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.34 out of 28.19
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
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.08 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 30.25
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.82 out of 27.55
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.20 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.52 out of 27.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.18 out of 29.65
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.43 out of 35.63
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.24 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
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 42, location 5036828 - 5100477:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - D-Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 43, location 5036828 - 5084385:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - D-Val)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
IOD16_RS21105: X - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (14..395): 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LHHAFDAMWLPWDEVTGGEHNAYGTTEVAVESLL
  Nearest Stachelhaus code(s):
    Leu DALLVGAVAK (41% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1017..1407): 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:
    LGDSFDASTFEAWLGSGGDVDGYGPTEGTTFASA
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

Link to PARAS substrate predictor
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
--- | ---
ANR | Anaerobic transcriptional regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP064192.1 - Region 26 - 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: 5,201,344 - 5,222,438 nt. (total: 21,095 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
IOD16_RS21730: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

IOD16_RS21770: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Hydrolases: hydrolase
IOD16_RS21765: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Translocases: permease
IOD16_RS21745: 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
--- | --- | --- | --- | --- | ---
BGC0001294.5 |  | 0.54 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0001197.5 |  | 0.45 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001483.4 |  | 0.43 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0002128.3 |  | 0.42 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0002643.2 |  | 0.42 | other (other) | aetokthonotoxin | Aetokthonos hydrillicola Thurmond2011
BGC0000706.3 |  | 0.40 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001910.4 |  | 0.38 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001840.2 |  | 0.37 | NRPS, PKS | detoxin S1 | Streptomyces sp. NRRL S-325
BGC0001865.4 |  | 0.35 | PKS | elsinochrome C | Parastagonospora nodorum SN15
BGC0001911.3 |  | 0.35 | terpene | raimonol | Streptomyces anulatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001294.5 |  | 0.54 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0001197.5 |  | 0.45 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001483.4 |  | 0.43 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0002128.3 |  | 0.42 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0002643.2 |  | 0.42 | other (other) | aetokthonotoxin | Aetokthonos hydrillicola Thurmond2011
BGC0000706.3 |  | 0.40 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001910.4 |  | 0.38 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001840.2 |  | 0.37 | NRPS, PKS | detoxin S1 | Streptomyces sp. NRRL S-325
BGC0001865.4 |  | 0.35 | PKS | elsinochrome C | Parastagonospora nodorum SN15
BGC0001911.3 |  | 0.35 | terpene | raimonol | Streptomyces anulatus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
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: 18.96 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.60 out of 19.26
Confidence: medium
Additional weak hits (4):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.37 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.28 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.30 out of 28.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism

NZ_CP064192.1 - Region 27 - NRPS,T1PKS,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: 5,277,303 - 5,353,775 nt. (total: 76,473 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)
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: dehydrogenase oxidoreductase oxygenase
IOD16_RS22090: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

IOD16_RS22100: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

IOD16_RS22135: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

IOD16_RS22205: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

IOD16_RS22220: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Transferases: acylase aminotransferase halogenase
IOD16_RS22195: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

IOD16_RS22200: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

IOD16_RS22245: halogenase

smcogs
  SMCOG1119: halogenase

Hydrolases: esterase phosphatase
IOD16_RS22155: thioesterase

smcogs
  SMCOG1004: thioesterase

IOD16_RS22215: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Ligases: ligase synthase
IOD16_RS22170: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

IOD16_RS22175: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS22180: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS22185: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

IOD16_RS22190: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IOD16_RS22250: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

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

Reference | T1PKS | NRPS | transAT-PKS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000357.5 |  |  |  |  | 1.40 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001250.4 |  |  |  |  | 1.39 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  |  |  |  | 1.39 | NRPS | epichloenin A | Epichloe festucae
BGC0001273.3 |  |  |  |  | 1.35 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  |  |  | 1.34 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  |  |  |  | 1.34 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001825.4 |  |  |  |  | 1.30 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001023.5 |  |  |  |  | 1.21 | NRPS, PKS | myxochromide S1 | Stigmatella aurantiaca
BGC0001758.4 |  |  |  |  | 1.20 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  |  |  |  | 1.19 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000357.5 |  | 0.68 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001250.4 |  | 0.68 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.68 | NRPS | epichloenin A | Epichloe festucae
BGC0001273.3 |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001825.4 |  | 0.66 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001133.4 |  | 0.65 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001023.5 |  | 0.65 | NRPS, PKS | myxochromide S1 | Stigmatella aurantiaca
BGC0001758.4 |  | 0.64 | 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47
Confidence: medium
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.66 out of 30.22
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.11 out of 23.79
Confidence: medium
Additional weak hits (15):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.71 out of 21.55
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.12 out of 27.78
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.44 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.25 out of 27.78
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
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.76 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.82 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.83 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.76 out of 31.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.95 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.93 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.67 out of 33.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 30.98
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 46, location 5277302 - 5353775:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - mal - Gly) + (ccmal) + (ccmal) + (mal - D-Ile) + (Val) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 47, location 5277302 - 5323218:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal) + (ccmal) + (mal - D-Ile) + (Val) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 48, location 5283220 - 5353775:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - mal - Gly) + (ccmal) + (ccmal) + (mal - D-Ile) + (Val) + (mal)

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).
IOD16_RS22170: mal
PKS_AT (544..836): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 62.5%
  inactive: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 118.8
  Methoxymalonyl-CoA: 64.4
  inactive: 58.8
  Methylmalonyl-CoA: 56.1
  Propionyl-CoA: 37.9
  Ethylmalonyl-CoA: 33.8
  Isobutyryl-CoA: 23.5
  fatty_acid: 17.8
  2-Methylbutyryl-CoA: 17.5
  Benzoyl-CoA: 15.6
  CHC-CoA: 12.1
  Acetyl-CoA: 9.7
  trans-1,2-CPDA: 7.1
  3-Methylbutyryl-CoA: 0.0

IOD16_RS22175: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (465..858): 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:
    LDQGFDASTFEGWLLVGGSTNGYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

IOD16_RS22180: Ile
Search NORINE for peptide: strict or relaxed
AMP-binding (1211..1609): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VRSSFDGSVYDGFIIFGGEGHAYGPTETTVFATV
  Nearest Stachelhaus code(s):
    Leu DGYIIGGVFK (47% 8Å match)
  Stachelhaus code match:
    80% (moderate)

IOD16_RS22195: mal
PKS_AT (6..292): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 101.4
  Methoxymalonyl-CoA: 56.2
  Methylmalonyl-CoA: 49.4
  inactive: 41.7
  CHC-CoA: 23.9
  2-Methylbutyryl-CoA: 22.9
  Propionyl-CoA: 20.8
  trans-1,2-CPDA: 19.8
  fatty_acid: 19.7
  Isobutyryl-CoA: 15.5
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  Ethylmalonyl-CoA: -1.1

IOD16_RS22200: mmal - mal - Gly
Search NORINE for peptide: strict or relaxed
PKS_AT (89..385): mmal
ATSignature: Isobutyryl-CoA

Top 3 matches:
  Isobutyryl-CoA: 75.0%
  Methylmalonyl-CoA: 66.7%
  Ethylmalonyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 146.9
  Ethylmalonyl-CoA: 137.9
  2-Methylbutyryl-CoA: 129.7
  Methoxymalonyl-CoA: 126.7
  Propionyl-CoA: 107.5
  trans-1,2-CPDA: 95.8
  CHC-CoA: 71.6
  Malonyl-CoA: 60.4
  Benzoyl-CoA: 40.1
  Isobutyryl-CoA: 33.6
  inactive: 29.4
  fatty_acid: 23.6
  3-Methylbutyryl-CoA: 15.4
  Acetyl-CoA: 14.3

PKS_AT (1056..1348): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 70.8%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 103.0
  inactive: 58.0
  Methylmalonyl-CoA: 55.8
  Methoxymalonyl-CoA: 54.3
  Propionyl-CoA: 33.9
  Ethylmalonyl-CoA: 30.8
  Benzoyl-CoA: 24.4
  fatty_acid: 18.8
  2-Methylbutyryl-CoA: 17.2
  3-Methylbutyryl-CoA: 16.0
  trans-1,2-CPDA: 15.1
  Isobutyryl-CoA: 14.8
  CHC-CoA: 12.9
  Acetyl-CoA: 6.1

AMP-binding (2530..2921): 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:
    FGMTFDIFLLELQMIVGGEHNVYGPTETCIWSSV
  Nearest Stachelhaus code(s):
    Gly DILQFGVIWK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
ClgR | Caseinolytic protease gene regulator
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP064192.1 - Region 28 - 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: 5,474,384 - 5,496,045 nt. (total: 21,662 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 oxygenase
IOD16_RS22760: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IOD16_RS22765: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Ligases: synthetase
IOD16_RS22740: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.52 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002127.3 |  | 0.46 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000636.3 |  | 0.36 | terpene | carotenoid | Brevibacterium linens
BGC0001364.3 |  | 0.36 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0002404.2 |  | 0.35 | other (other) | falcarindiol | Solanum lycopersicum
BGC0000231.5 |  | 0.35 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000644.3 |  | 0.35 | terpene | carotenoid | Dietzia sp. CQ4
BGC0002434.2 |  | 0.31 | NRPS, PKS | clifednamide D, clifednamide E, clifednamide F, clifednamide G, clifednamide H, clifednamide I, clifednamide J | Kitasatospora sp.
BGC0002220.2 |  | 0.31 | terpene | Ent-kauren-16alpha-ol | Punctularia strigosozonata HHB-11173 SS5
BGC0000234.5 |  | 0.31 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.52 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002127.3 |  | 0.46 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000636.3 |  | 0.36 | terpene | carotenoid | Brevibacterium linens
BGC0001364.3 |  | 0.36 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0002404.2 |  | 0.35 | other (other) | falcarindiol | Solanum lycopersicum
BGC0000231.5 |  | 0.35 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000644.3 |  | 0.35 | terpene | carotenoid | Dietzia sp. CQ4
BGC0002434.2 |  | 0.31 | NRPS, PKS | clifednamide D, clifednamide E, clifednamide F, clifednamide G, clifednamide H, clifednamide I, clifednamide J | Kitasatospora sp.
BGC0002220.2 |  | 0.31 | terpene | Ent-kauren-16alpha-ol | Punctularia strigosozonata HHB-11173 SS5
BGC0000234.5 |  | 0.31 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
IOD16_RS22740: PT_FPPS_like
Domain 1 (248 - 549): 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.
No hits above weak threshold.
Weak hits (3):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.25 out of 32.74
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 25.75
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.21 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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP064192.1 - Region 29 - betalactone,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: 5,551,916 - 5,603,434 nt. (total: 51,519 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)
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: oxygenase
IOD16_RS23130: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

IOD16_RS23135: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

IOD16_RS23195: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

IOD16_RS23220: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

IOD16_RS23225: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IOD16_RS23235: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: aminotransferase glycosyltransferase methyltransferase
IOD16_RS23185: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

IOD16_RS23190: aminotransferase

smcogs
  SMCOG1019: aminotransferase

IOD16_RS23215: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

IOD16_RS23230: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

Hydrolases: hydrolase
IOD16_RS23095: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: dehydratase
IOD16_RS23080: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase synthetase
IOD16_RS23085: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IOD16_RS23125: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

IOD16_RS23210: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

IOD16_RS23240: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

IOD16_RS23255: 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 | betalactone | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001160.5 |  |  | 0.28 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  | 0.28 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001841.2 |  |  | 0.26 | NRPS, PKS | detoxin P1, detoxin P2, detoxin P3 | Amycolatopsis jejuensis
BGC0000197.5 |  |  | 0.23 | PKS, saccharide | aranciamycin | Streptomyces echinatus
BGC0000444.5 |  |  | 0.23 | NRPS | thaxtomin A | Streptomyces turgidiscabies Car8
BGC0002089.2 |  |  | 0.22 | NRPS | thaxtomin D, thaxtomin A, thaxtomin C, thaxtomin B | Streptomyces scabiei 87.22
BGC0000336.5 |  |  | 0.21 | NRPS | daptomycin | Streptomyces filamentosus NRRL 11379
BGC0002007.2 |  |  | 0.20 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0000677.5 |  |  | 0.20 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001203.4 |  |  | 0.20 | NRPS, PKS | Clarexpoxcin A, Clarexpoxcin B, Clarexpoxcin C, Clarexpoxcin D, Clarexpoxcin E | uncultured bacterium AR_456

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.61 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002007.2 |  | 0.57 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0002347.3 |  | 0.55 | other (other) | cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D | Actinoalloteichus caeruleus WH1-2216-6
BGC0000677.5 |  | 0.52 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001529.5 |  | 0.52 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0001969.3 |  | 0.51 | terpene | asperterpenoid A | Talaromyces wortmannii
BGC0002019.3 |  | 0.51 | terpene | tiancilactone A, tiancilactone B, tiancilactone C, tiancilactone D, tiancilactone E, tiancilactone F, tiancilactone G, tiancilactone H | Streptomyces sp. CB03234
BGC0000844.5 |  | 0.51 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001310.5 |  | 0.51 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064

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:
IOD16_RS23210: PT_FPPS_like
Domain 1 (50 - 318): 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.22 out of 18.46
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.21 out of 23.79
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: 18.21 out of 20.47
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.64 out of 26.85
Confidence: medium
Additional weak hits (6):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.12 out of 39.62
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.73 out of 26.85
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.12 out of 29.65
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.62 out of 23.43
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.67 out of 20.01
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.00 out of 23.43
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
--- | ---
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator
RpoN | Regulator of nitrogen assimilation and virulence
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP064192.1 - Region 30 - 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: 5,828,842 - 5,874,628 nt. (total: 45,787 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
IOD16_RS24325: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

IOD16_RS24360: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IOD16_RS24375: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Transferases: acylase transferase
IOD16_RS24315: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

IOD16_RS24335: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Lyases: dehydratase hydratase
IOD16_RS24285: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

IOD16_RS24320: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002154.2 |  | 0.55 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0000056.3 |  | 0.55 | PKS | esperamicin | Actinomadura verrucosospora
BGC0001254.3 |  | 0.55 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002192.3 |  | 0.55 | PKS | FR901512 | fungal sp. No.14919
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0000660.5 |  | 0.52 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0000674.5 |  | 0.47 | terpene | (-)-δ-cadinene | Streptomyces clavuligerus ATCC 27064
BGC0002216.3 |  | 0.46 | terpene | HEx-tc1 terpene | Trichoderma virens Gv29-8
BGC0001528.4 |  | 0.44 | terpene | betaestacin I, betaestacin II | Phoma betae
BGC0002275.2 |  | 0.42 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger CBS 101883

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002154.2 |  | 0.55 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0000056.3 |  | 0.55 | PKS | esperamicin | Actinomadura verrucosospora
BGC0001254.3 |  | 0.55 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002192.3 |  | 0.55 | PKS | FR901512 | fungal sp. No.14919
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0000660.5 |  | 0.52 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0000674.5 |  | 0.47 | terpene | (-)-δ-cadinene | Streptomyces clavuligerus ATCC 27064
BGC0002216.3 |  | 0.46 | terpene | HEx-tc1 terpene | Trichoderma virens Gv29-8
BGC0001528.4 |  | 0.44 | terpene | betaestacin I, betaestacin II | Phoma betae
BGC0002275.2 |  | 0.42 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger CBS 101883

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:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.79 out of 23.79
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.66 out of 30.12
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
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 26.67 out of 32.93
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.22 out of 29.51
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 21.53 out of 23.43
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
Additional weak hits (18):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.54 out of 29.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.01 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.01 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.54 out of 24.78
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.88 out of 23.43
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.37 out of 28.14
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.19 out of 30.22
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.58 out of 30.25
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.36 out of 23.43
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.98 out of 23.43
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.20 out of 26.12
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.98 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.06 out of 28.19
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
TFBS Finder
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).
IOD16_RS24335: mal
PKS_AT (615..849): 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: 66.4
  Methoxymalonyl-CoA: 48.3
  Methylmalonyl-CoA: 45.9
  fatty_acid: 32.7
  Propionyl-CoA: 32.2
  Ethylmalonyl-CoA: 26.5
  Isobutyryl-CoA: 26.3
  inactive: 22.1
  2-Methylbutyryl-CoA: 14.5
  trans-1,2-CPDA: 13.9
  CHC-CoA: 10.2
  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
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
BldD | Development and antibiotic global regulator
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator
RicR | Copper-responsive regulator
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP064192.1 - 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: 6,018,391 - 6,039,476 nt. (total: 21,086 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
IOD16_RS25125: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Ligases: ligase
IOD16_RS25105: 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
--- | --- | --- | --- | --- | ---
BGC0000616.4 |  | 0.39 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0000646.5 |  | 0.38 | terpene | β-carotein | uncultured bacterium
BGC0002716.2 |  | 0.37 | NRPS | gamexpeptide A, gamexpeptide B, gamexpeptide E, luminmide B, luminmide D, luminmide E, luminmide F, luminmide G | Photorhabdus laumondii subsp. laumondii
BGC0000555.3 |  | 0.34 | ribosomal | staphylococcin C55 α, staphylococcin C55 β | Staphylococcus aureus
BGC0000627.4 |  | 0.31 | ribosomal | ustiloxin B | Aspergillus flavus NRRL3357
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

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000616.4 |  | 0.39 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0000646.5 |  | 0.38 | terpene | β-carotein | uncultured bacterium
BGC0002716.2 |  | 0.37 | NRPS | gamexpeptide A, gamexpeptide B, gamexpeptide E, luminmide B, luminmide D, luminmide E, luminmide F, luminmide G | Photorhabdus laumondii subsp. laumondii
BGC0000555.3 |  | 0.34 | ribosomal | staphylococcin C55 α, staphylococcin C55 β | Staphylococcus aureus
BGC0000627.4 |  | 0.31 | ribosomal | ustiloxin B | Aspergillus flavus NRRL3357
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

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:
IOD16_RS25095: Lycopene_cycl
Domain 1 (2 - 326): 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:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.84 out of 30.12
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.58 out of 27.04
Confidence: medium
Additional weak hits (15):
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
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 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.40 out of 32.93
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.19 out of 30.98
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.64 out of 24.78
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
OsdR | Development and stress management regulator

NZ_CP064192.1 - Region 32 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,136,128 - 6,169,409 nt. (total: 33,282 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
IOD16_RS25670: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Transferases: methyltransferase phosphotransferase
IOD16_RS25615: Glucose-specific phosphotransferase enzyme IIA

smcogs
  SMCOG1145: Glucose-specific phosphotransferase enzyme IIA

IOD16_RS25680: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: decarboxylase
IOD16_RS25655: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.68 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0001478.5 |  | 0.62 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0001572.3 |  | 0.61 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000941.3 |  | 0.60 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001453.5 |  | 0.59 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0000940.5 |  | 0.59 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0002305.2 |  | 0.59 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001531.5 |  | 0.58 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002683.2 |  | 0.55 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000244.4 |  | 0.54 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.68 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0001478.5 |  | 0.62 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0001572.3 |  | 0.61 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000941.3 |  | 0.60 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001453.5 |  | 0.59 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0000940.5 |  | 0.59 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0002305.2 |  | 0.59 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001531.5 |  | 0.58 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002683.2 |  | 0.55 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000244.4 |  | 0.54 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus

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: 21.15 out of 23.79
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.47 out of 27.04
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.30 out of 36.53
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 30.11
Confidence: strong
Additional weak hits (2):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
DasR | N-acetylglucosamine dependent repressor
DmdR1 | Iron(II)-dependent repressor
IolR | Regulator of the inositol catabolism

NZ_CP064192.1 - Region 33 - 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: 6,231,330 - 6,254,239 nt. (total: 22,910 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
IOD16_RS26030: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

IOD16_RS26105: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

IOD16_RS26110: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Hydrolases: glucosidase
IOD16_RS26040: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

Lyases: cyclase
IOD16_RS26075: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Translocases: transporter
IOD16_RS26055: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002285.2 |  | 0.61 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000528.5 |  | 0.50 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000554.4 |  | 0.49 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002704.2 |  | 0.47 | ribosomal | archalan β | Halorussus salinus
BGC0000527.5 |  | 0.44 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001364.3 |  | 0.44 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
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
--- | --- | --- | --- | --- | ---
BGC0002285.2 |  | 0.61 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000528.5 |  | 0.50 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000554.4 |  | 0.49 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002704.2 |  | 0.47 | ribosomal | archalan β | Halorussus salinus
BGC0000527.5 |  | 0.44 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001364.3 |  | 0.44 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
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 IOD16_RS26075

allorf_6233503_6233592
Leader:
MSGRGHGSSLAA
Core:
R D R E R C H S E T S E C T P C C
Core with dehydrations:
R D R E R Cys H Dha E Dhb Dha E Cys Dhb P Cys Cys

#### antiSMASH-DB 4.0 matches for allorf_6233503_6233592

100.0%
NZ_CP064192.1:
Lanthipeptides: allorf_6233503_6233592_lanthipeptide
1
R D R E R C H S E T S E C T P C C
17
R D R E R C H S E T S E C T P C C
1
R D R E R C H S E T S E C T P C C
17
33.3%
NZ_JAASAG010000001.1:
Lanthipeptides: allorf_346005_346232_lanthipeptide
2
D R E R C H S E T S E
12
D R R H T S E
1
D R A R A H H G T S E
11
21.2%
NZ_KL997439.1 and 1 other:
NZ_KL997439.1 Lanthipeptides: IQ62_RS47105_lanthipeptide
Lanthipeptides: IQ62_RS47105_lanthipeptide
2
D R E R C H S E T S E C T P C C
17
D+ C + T E C P C
17
D K G D C C T A T K E C Q P S C
32
with 1 more sequence matches
11.5%
NZ_MQUS01000030.1:
Lanthipeptides: allorf_019028_019261_lanthipeptide
1
R D R E R C H S
8
R R+R C H S
40
R P R Q R C H S
47

#### MIBiG 4.0 matches for allorf_6233503_6233592

17.9%
BGC0000517.4 (BAB04173.1):
Lanthipeptide: haloduracin β or haloduracin α
10
T S E C T P C C
17
T E C P C
20
T V E C M P S C
27
16.7%
BGC0002110.3 (QKV49893.1):
Lanthipeptide: birimositide
10
T S E C T P C C
17
T E C P C
22
T K E C Q P N C
29
14.7%
BGC0000535.4 (ADJ56352.1):
Lanthipeptide: nisin A
8
S E T S E C T P C C
17
+ S C T P C
2
T S I S L C T P G C
11
with 1 more sequence matches
10.3%
BGC0001229.4 (SBI_06990):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
10
T S E C T P C C
17
+ E C P C
31
S K E C Q P N C
38
allorf_6238745_6238822
Leader:
MEVGLSRVGVRGA
Core:
A Y E L M S G S C E F S
Core with dehydrations:
A Y E L M Dha G Dha Cys E F Dha

#### antiSMASH-DB 4.0 matches for allorf_6238745_6238822

100.0%
NZ_CP064192.1:
Lanthipeptides: allorf_6238745_6238822_lanthipeptide
1
A Y E L M S G S C E F S
12
A Y E L M S G S C E F S
1
A Y E L M S G S C E F S
12
58.3%
NZ_JAJHUO010000017.1:
Lanthipeptides: allorf_222512_222592_lanthipeptide
4
L M S G S C E F S
12
+M S S C E F S
1
V M S R S C E F S
9

#### 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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
Additional weak hits (7):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.52 out of 26.85
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.76 out of 20.97
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.47 out of 26.85
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.08 out of 26.85
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.05 out of 31.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.49 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.28 out of 33.14
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_6233503_6233592 - Class II
  Cleavage pHMM score: -5.80
  RODEO score: 0
  Monoisotopic mass: 1938.8 Da
  Molecular weight: 1940.1 Da
  Number of bridges: 4
allorf_6238745_6238822 - Class II
  Cleavage pHMM score: -5.00
  RODEO score: 0
  Monoisotopic mass: 1268.5 Da
  Molecular weight: 1269.4 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1287.4 Da N = 1
    1305.4 Da N = 2

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein

NZ_CP064192.1 - Region 34 - 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: 6,258,191 - 6,279,330 nt. (total: 21,140 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 oxidoreductase
IOD16_RS26175: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

IOD16_RS26235: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Ligases: synthase synthetase
IOD16_RS26195: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

IOD16_RS26200: 1-deoxy-D-xylulose-5-phosphate synthase

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

IOD16_RS26220: 3-oxoacyl-(acyl carrier protein) synthase III

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

IOD16_RS26225: 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 | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002711.2 |  | 0.54 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002554.2 |  | 0.46 | other (other) | carquinostatin A, carquinostatin B | Streptomyces exfoliatus
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
BGC0001903.3 |  | 0.45 | other (other) | neocarazostatin A | Streptomyces sp. MA37
BGC0001987.2 |  | 0.45 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0000196.4 |  | 0.44 | PKS | AQ-256, AQ-270a, AQ-284a | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000272.3 |  | 0.43 | PKS | spore pigment | Streptomyces collinus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002711.2 |  | 0.54 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002554.2 |  | 0.46 | other (other) | carquinostatin A, carquinostatin B | Streptomyces exfoliatus
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
BGC0001903.3 |  | 0.45 | other (other) | neocarazostatin A | Streptomyces sp. MA37
BGC0001987.2 |  | 0.45 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0000196.4 |  | 0.44 | PKS | AQ-256, AQ-270a, AQ-284a | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000272.3 |  | 0.43 | PKS | spore pigment | Streptomyces collinus

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:
IOD16_RS26195: PT_FPPS_like
Domain 1 (72 - 364): 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:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 27.15 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.19 out of 30.11
Confidence: medium
Additional weak hits (10):
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.41 out of 29.65
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.01 out of 26.85
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.88 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.01 out of 26.06
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.20 out of 30.98
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.46 out of 25.88
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 20.83 out of 36.53
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
--- | ---
ANR | Anaerobic transcriptional regulator
CelR | Cellobiose uptake repressor

NZ_CP064192.1 - Region 35 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,481,004 - 6,505,133 nt. (total: 24,130 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase dehydratase
IOD16_RS27245: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

IOD16_RS27250: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: 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-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002635.2 |  | 0.52 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000541.5 |  | 0.49 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000542.3 |  | 0.48 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000544.4 |  | 0.46 | ribosomal | planosporicin | Planomonospora alba
BGC0000506.4 |  | 0.40 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000529.5 |  | 0.39 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0001727.3 |  | 0.39 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000559.4 |  | 0.39 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000511.5 |  | 0.36 | ribosomal | ericin S | Bacillus subtilis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002635.2 |  | 0.52 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000541.5 |  | 0.49 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000542.3 |  | 0.48 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000544.4 |  | 0.46 | ribosomal | planosporicin | Planomonospora alba
BGC0000506.4 |  | 0.40 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000529.5 |  | 0.39 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0001727.3 |  | 0.39 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000559.4 |  | 0.39 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000511.5 |  | 0.36 | ribosomal | ericin S | Bacillus subtilis

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

No significant matches found.

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

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - 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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.89 out of 23.79
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.17 out of 30.25
Confidence: medium
Additional weak hits (9):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.76 out of 26.33
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.60 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.66 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.26 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.75 out of 35.63
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.65 out of 22.40
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.29 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.52 out of 26.06
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (6481003...6505133)
IOD16_RS27245
  RRE type: Lanthipeptide_LanB_RRE
  Location: 154 - 234
  Score: 43.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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