Select genomic region:
Overview
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### Identified secondary metabolite regions using strictness 'relaxed'

NZ_CP054019.1 (Streptomyces sp. A1-5)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | lanthipeptide-class-iv | 6,854 | 29,610 |  |
Region 2 | T1PKS,NRPS-like,terpene | 62,251 | 176,630 | High | tetramycin B | PKS
Region 3 | NRPS-like | 181,315 | 225,142 |  |
Region 4 | lanthipeptide-class-iii,NRPS,NRPS-like | 236,878 | 290,710 | Low | s56-p1 | NRPS:Type I
Region 5 | terpene,T3PKS,terpene-precursor,NRPS,T1PKS,NRPS-like | 360,239 | 443,511 | Low | canucin A/canucin B | ribosomal:RiPP
Region 6 | NRPS | 1,049,166 | 1,111,028 | Low | cadaside A/cadaside B | NRPS:Type I
Region 7 | NRPS-like | 1,122,534 | 1,165,557 |  |
Region 8 | NRPS-like,transAT-PKS | 1,168,468 | 1,238,147 | Low | cycloheximide | PKS:Trans-AT type I
Region 9 | terpene,hglE-KS | 1,287,743 | 1,338,806 |  |
Region 10 | T1PKS | 1,377,271 | 1,441,800 | Low | desulfoclethramycin/clethramycin | other:other
Region 11 | RiPP-like | 1,698,470 | 1,708,685 |  |
Region 12 | T2PKS,terpene | 1,739,591 | 1,821,280 | High | spore pigment | PKS
Region 13 | NI-siderophore | 2,522,634 | 2,552,439 | High | legonoxamine A/desferrioxamine B/legonoxamine B | other:other
Region 14 | ectoine | 2,621,044 | 2,631,448 | High | ectoine | other:ectoine
Region 15 | lanthipeptide-class-i | 3,562,241 | 3,586,706 |  |
Region 16 | terpene | 4,967,640 | 4,989,862 |  |
Region 17 | azole-containing-RiPP,PKS-like | 5,076,994 | 5,128,030 | High | radamycin/globimycin | ribosomal:RiPP
Region 18 | linaridin | 5,138,581 | 5,159,488 | Medium | legonaridin | ribosomal:RiPP
Region 19 | NAPAA | 5,597,555 | 5,631,721 |
Region 20 | T1PKS | 5,766,304 | 5,872,166 | Low | aldgamycin J/aldgamycin K/aldgamycin P/aldgamycin E | PKS
Region 21 | CDPS | 6,362,513 | 6,383,196 | High | albonoursin | other:other
Region 22 | NI-siderophore,NRPS,betalactone | 6,699,898 | 6,792,371 | High | ulleungmycin | NRPS:Type I
Region 23 | T3PKS | 6,851,519 | 6,892,574 | High | naringenin | PKS:Type III
Region 24 | RiPP-like | 7,000,104 | 7,011,400 |  |
Region 25 | hglE-KS | 7,354,414 | 7,400,647 |  |
Region 26 | linaridin | 7,430,968 | 7,451,579 |  |
Region 27 | lassopeptide | 7,488,607 | 7,511,141 | Low | citrulassin A | ribosomal:RiPP
Region 28 | terpene | 7,696,796 | 7,723,503 | Medium | hopene | terpene
Region 29 | hydrogen-cyanide | 7,909,379 | 7,922,411 | Low | aborycin | ribosomal:RiPP
Region 30 | NRPS-like | 7,929,858 | 7,973,394 | Low | WS-5995 D/WS-5995 B/WS-5995 C/SEK 43 | PKS
Region 31 | aminopolycarboxylic-acid | 7,998,835 | 8,012,334 | High | Ethylenediaminesuccinic acid hydroxyarginine | other:other
Region 32 | NAPAA,butyrolactone,RiPP-like | 8,050,301 | 8,091,968 | Low | landomycin A | PKS:Type II+saccharide:hybrid/tailoring
Region 33 | terpene-precursor | 8,094,047 | 8,115,123 |
Region 34 | butyrolactone | 8,302,898 | 8,313,833 |  |
Region 35 | atropopeptide | 8,530,388 | 8,551,437 |
Region 36 | RRE-containing,T1PKS | 8,653,361 | 8,799,274 | High | nystatin A1 | PKS:Type I+saccharide:hybrid/tailoring
Region 37 | RRE-containing,terpene | 8,841,110 | 8,881,436 |  |
Region 38 | terpene-precursor | 8,952,500 | 8,973,474 | Low | gougerotin | other:other
Region 39 | NRPS,lanthipeptide-class-ii,other | 9,068,958 | 9,143,501 |  |
Region 40 | terpene | 9,164,279 | 9,185,337 |  |
Region 41 | T1PKS,arylpolyene | 9,273,276 | 9,357,587 |  |
Region 42 | lanthipeptide-class-iv | 9,428,878 | 9,451,634 |

NZ_CP054019.1 - Region 1 - lanthipeptide-class-iv
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: 6,854 - 29,610 nt. (total: 22,757 nt) Show pHMM detection rules used
Region on contig edge.
lanthipeptide-class-iv: (cds(LANC_like and Pkinase) and not micKC)

#### 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
HRD51_RS00090: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

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

Reference | lanthipeptide-class-iv | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002337.2 |  | 0.57 | ribosomal | class IV lanthipeptide, SflA | Streptomyces sp. NRRL S-1022
BGC0000563.4 |  | 0.46 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  | 0.46 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0002318.2 |  | 0.42 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000519.4 |  | 0.40 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000874.5 |  | 0.39 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0000502.5 |  | 0.35 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001561.4 |  | 0.33 | NRPS | curacomycin | Streptomyces curacoi
BGC0001582.4 |  | 0.27 | NRPS | ecumicin | Nonomuraea sp. MJM5123
BGC0002015.4 |  | 0.27 | ribosomal | aborycin | Streptomyces sp. ZS0098

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002337.2 |  | 0.57 | ribosomal | class IV lanthipeptide, SflA | Streptomyces sp. NRRL S-1022
BGC0000563.4 |  | 0.46 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  | 0.46 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0002318.2 |  | 0.42 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000519.4 |  | 0.40 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000874.5 |  | 0.39 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0000502.5 |  | 0.35 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001561.4 |  | 0.33 | NRPS | curacomycin | Streptomyces curacoi
BGC0001582.4 |  | 0.27 | NRPS | ecumicin | Nonomuraea sp. MJM5123
BGC0002015.4 |  | 0.27 | ribosomal | aborycin | Streptomyces sp. ZS0098

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.
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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.35 out of 18.57
Confidence: medium
Additional weak hits (4):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.37 out of 32.74
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.87 out of 20.01
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.33 out of 27.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
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.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ToxT | Regulator of MSHA biosynthesis

NZ_CP054019.1 - Region 2 - NRPS-like,T1PKS,terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 62,251 - 176,630 nt. (total: 114,380 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-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
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
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
HRD51_RS00330: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

HRD51_RS00345: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

HRD51_RS00395: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

HRD51_RS00475: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: acetyltransferase aminotransferase glycosyltransferase methyltransferase
HRD51_RS00315: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

HRD51_RS00340: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

HRD51_RS00365: methyltransferase

smcogs
  SMCOG1089: methyltransferase

HRD51_RS00385: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

HRD51_RS00390: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Lyases: cyclase dehydratase
HRD51_RS00370: Terpene synthase/cyclase metal-binding domain protein

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

HRD51_RS00460: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
HRD51_RS00405: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HRD51_RS00415: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HRD51_RS00420: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HRD51_RS00430: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

HRD51_RS00435: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | T1PKS | NRPS-like | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000659.3 |  |  |  | 1.57 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000657.5 |  |  |  | 1.13 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000138.5 |  |  |  | 0.87 | PKS | rimocidin | Streptomyces diastaticus
BGC0000658.3 |  |  |  | 0.83 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002540.3 |  |  |  | 0.81 | PKS | tetramycin B | Streptomyces hygrospinosus subsp. beijingensis
BGC0002084.4 |  |  |  | 0.71 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  |  |  | 0.71 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0001273.3 |  |  |  | 0.70 | PKS | asperlactone | Aspergillus ochraceus
BGC0002106.3 |  |  |  | 0.65 | PKS | rimocidin | Streptomyces rimosus subsp. rimosus NRRL WC-3558
BGC0002631.2 |  |  |  | 0.61 | ribosomal | Myxarylin | Pyxidicoccus fallax

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000659.3 |  | 0.80 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0002540.3 |  | 0.80 | PKS | tetramycin B | Streptomyces hygrospinosus subsp. beijingensis
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.72 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000657.5 |  | 0.70 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002106.3 |  | 0.67 | PKS | rimocidin | Streptomyces rimosus subsp. rimosus NRRL WC-3558
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
BGC0000107.3 |  | 0.63 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
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
--- | --- | --- | --- | --- | ---
monoterpene |  | 2-methylisoborneol | C11 | C1-C6 | OH
monoterpene |  | 2-methylenebornane | C11 | C1-C6 | none

Genes with terpene domains:
HRD51_RS00370: T1TS
Domain 1 (45 - 397): Type 1 terpene synthase
Subtype: 2-Methylisoborneol synthase type

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.71 out of 20.47
Confidence: medium
Additional weak hits (7):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.87 out of 31.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.41 out of 26.85
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.98 out of 27.04
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.81 out of 31.73
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.82 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.13 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.31 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
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 2, location 62250 - 176630:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - ohmal - Me-ohmal - ohmal - ohmal - ohmal) + (redmal) + (redmal - ccmal) + (ohmal - ccmal - ccmal - ccmal) + (X - 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).
HRD51_RS00405: X - mal
AMP-binding (29..437): 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:
    NAVCHLFGLQAAFARTAGAVVVWGMSEIGTGSRT
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

PKS_AT (1185..1486): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 165.3
  Methoxymalonyl-CoA: 65.1
  inactive: 60.2
  Methylmalonyl-CoA: 56.0
  Propionyl-CoA: 32.3
  Isobutyryl-CoA: 28.3
  Ethylmalonyl-CoA: 24.8
  Acetyl-CoA: 22.2
  Benzoyl-CoA: 21.1
  2-Methylbutyryl-CoA: 17.3
  fatty_acid: 13.1
  CHC-CoA: 12.0
  trans-1,2-CPDA: 9.3
  3-Methylbutyryl-CoA: 0.0

HRD51_RS00415: mal - mal - mal - mal
PKS_AT (565..864): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 221.7
  inactive: 104.7
  Methoxymalonyl-CoA: 73.4
  Methylmalonyl-CoA: 66.1
  Isobutyryl-CoA: 52.2
  Propionyl-CoA: 39.2
  Ethylmalonyl-CoA: 29.5
  trans-1,2-CPDA: 22.7
  2-Methylbutyryl-CoA: 22.0
  Acetyl-CoA: 21.4
  Benzoyl-CoA: 21.1
  3-Methylbutyryl-CoA: 11.6
  CHC-CoA: 9.0
  fatty_acid: 0.0

PKS_AT (2104..2405): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 91.7%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 227.9
  inactive: 113.5
  Methoxymalonyl-CoA: 50.8
  Methylmalonyl-CoA: 44.9
  Propionyl-CoA: 23.8
  Acetyl-CoA: 17.4
  Ethylmalonyl-CoA: 16.8
  Benzoyl-CoA: 14.6
  fatty_acid: 12.1
  Isobutyryl-CoA: 11.5
  trans-1,2-CPDA: 7.0
  CHC-CoA: 3.7
  3-Methylbutyryl-CoA: 0.7
  2-Methylbutyryl-CoA: -2.6

PKS_AT (3844..4134): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 222.0
  inactive: 98.7
  Methoxymalonyl-CoA: 43.8
  Methylmalonyl-CoA: 34.6
  Propionyl-CoA: 27.7
  Acetyl-CoA: 23.1
  Benzoyl-CoA: 16.1
  fatty_acid: 11.1
  Isobutyryl-CoA: 8.6
  Ethylmalonyl-CoA: 8.4
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: -2.3

PKS_AT (5545..5835): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 221.6
  inactive: 119.8
  Methoxymalonyl-CoA: 54.1
  Methylmalonyl-CoA: 38.9
  Propionyl-CoA: 22.3
  Acetyl-CoA: 21.4
  Ethylmalonyl-CoA: 19.9
  2-Methylbutyryl-CoA: 18.8
  Benzoyl-CoA: 16.4
  fatty_acid: 15.7
  Isobutyryl-CoA: 10.3
  CHC-CoA: 7.5
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

HRD51_RS00420: mal - mal
PKS_AT (556..844): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 234.6
  inactive: 110.6
  Methoxymalonyl-CoA: 71.8
  Methylmalonyl-CoA: 63.9
  Propionyl-CoA: 40.5
  Isobutyryl-CoA: 35.9
  2-Methylbutyryl-CoA: 28.5
  Acetyl-CoA: 27.7
  Benzoyl-CoA: 24.5
  Ethylmalonyl-CoA: 23.8
  fatty_acid: 12.5
  trans-1,2-CPDA: 8.6
  CHC-CoA: 8.6
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2588..2874): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 70.8%
  Ethylmalonyl-CoA: 62.5%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 158.9
  Methylmalonyl-CoA: 82.3
  Methoxymalonyl-CoA: 73.0
  inactive: 60.5
  Isobutyryl-CoA: 50.3
  Ethylmalonyl-CoA: 44.9
  Propionyl-CoA: 37.8
  2-Methylbutyryl-CoA: 35.7
  Acetyl-CoA: 32.8
  Benzoyl-CoA: 26.9
  fatty_acid: 20.7
  CHC-CoA: 18.7
  3-Methylbutyryl-CoA: 13.6
  trans-1,2-CPDA: 13.5

HRD51_RS00430: mal
PKS_AT (551..836): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 223.5
  inactive: 107.0
  Methoxymalonyl-CoA: 66.1
  Methylmalonyl-CoA: 58.6
  Propionyl-CoA: 33.8
  Isobutyryl-CoA: 27.1
  2-Methylbutyryl-CoA: 20.5
  Acetyl-CoA: 20.1
  Benzoyl-CoA: 17.5
  Ethylmalonyl-CoA: 15.2
  fatty_acid: 14.9
  CHC-CoA: 12.1
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

HRD51_RS00435: mal - mal - mmal - mal - mal - mal
PKS_AT (563..866): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 79.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 219.2
  inactive: 90.2
  Methoxymalonyl-CoA: 55.1
  Methylmalonyl-CoA: 46.0
  Propionyl-CoA: 32.9
  Acetyl-CoA: 29.0
  Benzoyl-CoA: 19.0
  Ethylmalonyl-CoA: 18.5
  Isobutyryl-CoA: 16.8
  CHC-CoA: 13.5
  2-Methylbutyryl-CoA: 13.2
  trans-1,2-CPDA: 13.0
  fatty_acid: 8.6
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2327..2626): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 205.3
  inactive: 88.1
  Methoxymalonyl-CoA: 73.2
  Methylmalonyl-CoA: 66.1
  Propionyl-CoA: 36.2
  Isobutyryl-CoA: 35.6
  Acetyl-CoA: 32.1
  Benzoyl-CoA: 29.8
  Ethylmalonyl-CoA: 29.0
  2-Methylbutyryl-CoA: 27.1
  CHC-CoA: 25.6
  fatty_acid: 21.7
  trans-1,2-CPDA: 18.8
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3868..4165): 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: 212.3
  Ethylmalonyl-CoA: 201.1
  Methoxymalonyl-CoA: 174.1
  2-Methylbutyryl-CoA: 136.3
  trans-1,2-CPDA: 132.6
  Propionyl-CoA: 107.6
  CHC-CoA: 98.3
  Malonyl-CoA: 85.8
  Isobutyryl-CoA: 71.2
  Benzoyl-CoA: 57.5
  Acetyl-CoA: 39.5
  fatty_acid: 38.4
  3-Methylbutyryl-CoA: 35.4
  inactive: 15.4

PKS_AT (5401..5701): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 75.0%
  Propionyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 206.5
  inactive: 104.0
  Methoxymalonyl-CoA: 74.3
  Methylmalonyl-CoA: 64.9
  Isobutyryl-CoA: 54.0
  Ethylmalonyl-CoA: 26.6
  Propionyl-CoA: 26.3
  Acetyl-CoA: 25.5
  Benzoyl-CoA: 23.5
  fatty_acid: 21.8
  2-Methylbutyryl-CoA: 19.8
  3-Methylbutyryl-CoA: 15.8
  trans-1,2-CPDA: 14.0
  CHC-CoA: 13.1

PKS_AT (6921..7212): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 237.6
  inactive: 110.6
  Methoxymalonyl-CoA: 62.0
  Methylmalonyl-CoA: 59.8
  Propionyl-CoA: 33.8
  Acetyl-CoA: 24.5
  Benzoyl-CoA: 21.3
  Isobutyryl-CoA: 19.6
  2-Methylbutyryl-CoA: 17.2
  Ethylmalonyl-CoA: 9.1
  CHC-CoA: 8.5
  fatty_acid: 8.4
  trans-1,2-CPDA: 7.8
  3-Methylbutyryl-CoA: 0.0

PKS_AT (8435..8732): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 233.0
  inactive: 106.3
  Methoxymalonyl-CoA: 67.1
  Methylmalonyl-CoA: 58.8
  Isobutyryl-CoA: 31.2
  Propionyl-CoA: 27.3
  Benzoyl-CoA: 27.1
  Acetyl-CoA: 21.7
  Ethylmalonyl-CoA: 21.3
  trans-1,2-CPDA: 17.2
  fatty_acid: 15.9
  CHC-CoA: 14.9
  2-Methylbutyryl-CoA: 11.2
  3-Methylbutyryl-CoA: 0.0

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

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
MexT | Global virulence regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP054019.1 - Region 3 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 181,315 - 225,142 nt. (total: 43,828 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase
HRD51_RS00610: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Lyases: dehydratase
HRD51_RS00615: 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 | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.62 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.62 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.62 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.62 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002075.3 |  | 0.62 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.62 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.62 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.62 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.62 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002075.3 |  | 0.62 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 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
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 23.28 out of 27.55
Confidence: medium
Additional weak hits (8):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.75 out of 29.65
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.98 out of 36.53
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.20 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.74 out of 29.65
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.17 out of 39.62
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.58 out of 29.25
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
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 4, location 181314 - 225142:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gln)

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).
HRD51_RS00605: Gln
Search NORINE for peptide: strict or relaxed
AMP-binding (22..421): Gln
nrpys: Gln

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:
    glu,gln (Glu, Gln)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    QSMTFDAAQWEAQCFSGGEVNLYGPTEATINATA
  Nearest Stachelhaus code(s):
    Gln DAWQFGLINK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
GnfM | Regulator of nitrogen-fixation genes
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP054019.1 - Region 4 - NRPS,NRPS-like,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: 236,878 - 290,710 nt. (total: 53,833 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
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
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
HRD51_RS00780: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

HRD51_RS00820: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

HRD51_RS00855: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

HRD51_RS00860: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

HRD51_RS00865: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

HRD51_RS00870: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

HRD51_RS00910: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

HRD51_RS00970: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: acetyltransferase kinase
HRD51_RS00785: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

HRD51_RS00900: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: esterase hydrolase
HRD51_RS00815: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

HRD51_RS00835: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: cyclase
HRD51_RS00800: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Ligases: ligase synthase
HRD51_RS00845: 3-oxoacyl-(acyl carrier protein) synthase III

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

HRD51_RS00880: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

HRD51_RS00885: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

HRD51_RS00890: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | lanthipeptide-class-iii | NRPS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001833.4 |  |  |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  |  |  | 0.62 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  |  |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  |  |  | 0.59 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  |  |  | 0.59 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001250.4 |  |  |  | 0.58 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  |  |  | 0.58 | NRPS | epichloenin A | Epichloe festucae
BGC0001240.4 |  |  |  | 0.57 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001268.4 |  |  |  | 0.47 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002765.2 |  |  |  | 0.43 | NRPS | Keanumycin A, Keanumycin B, Keanumycin C | Pseudomonas sp. QS1027

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001250.4 |  | 0.62 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.62 | NRPS | epichloenin A | Epichloe festucae
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001268.4 |  | 0.57 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002765.2 |  | 0.54 | NRPS | Keanumycin A, Keanumycin B, Keanumycin C | Pseudomonas sp. QS1027

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

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 HRD51_RS00800

allorf_0246767_0246871
Leader:
MAMILELQELETPHGPSLAP
Core:
S N V L S T L L H G R A C V
Core with dehydrations:
Dha N V L Dha Dhb L L H G R A Cys V

#### antiSMASH-DB 4.0 matches for allorf_0246767_0246871

100.0%
NZ_CP003987.1 and 4 others:
NZ_CP054019.1 Lanthipeptides: allorf_0246767_0246871_lanthipeptide NZ_CP070326.1 Lanthipeptides: allorf_0263289_0263393_lanthipeptide NZ_CP095749.1 Lanthipeptides: allorf_9554269_9554373_lanthipeptide NZ_LJSN01000002.1 Lanthipeptides: allorf_0522547_0522651_lanthipeptide
Lanthipeptides: allorf_09643772_09643876_lanthipeptide
1
S N V L S T L L H G R A C V
14
S N V L S T L L H G R A C V
1
S N V L S T L L H G R A C V
14
56.2%
NZ_CP081497.1:
Lanthipeptides: allorf_2111783_2111890_lanthipeptide
1
S N V L S T L L H G
10
S N V L S T L L H
2
S N V L S T L L H A
11
50.0%
NZ_CP034550.1:
Lanthipeptides: EKG83_RS47045_lanthipeptide
3
V L S T L L H G R A C V
14
V L S T L H C+
1
V L S T A L H S T L C L
12
with 2 more sequence matches
50.0%
NZ_JAPTYM010000001.1:
Lanthipeptides: allorf_09789968_09790069_lanthipeptide
1
S N V L S T L L H
9
S N V L S T L H
4
S N V L S T F L H
12
27.8%
NZ_CP101417.1:
Lanthipeptides: allorf_0369305_0369400_lanthipeptide
8
L H G R A C
13
L H G R C
7
L H G R T C
12

#### 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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.75 out of 23.05
Confidence: medium
Additional weak hits (18):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.54 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 20.37 out of 31.73
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.68 out of 32.74
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
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.58 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.93 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.60 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.80 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.90 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.85 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.43 out of 29.38
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.82 out of 18.57
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.79 out of 30.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.33 out of 30.97
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.37 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.44 out of 35.63
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.17 out of 20.01
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
Lanthipeptides
NRPS/PKS products
NRPS/PKS substrates
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_0246767_0246871 - Class III
  Cleavage pHMM score: 8.90
  RODEO score: 0
  Monoisotopic mass: 1414.8 Da
  Molecular weight: 1415.6 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1433.7 Da N = 1
    1451.7 Da N = 2

Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 5, location 236877 - 290710:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Cys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 247408 - 290710:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Cys)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
HRD51_RS00885: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (29..304): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VDCSFDLSVYDGNSMMSGDVALGGPTETTIWNVV
  Nearest Stachelhaus code(s):
    Cys DLYNMSLIWK (65% 8Å match)
  Stachelhaus code match:
    100% (strong)

HRD51_RS00890: X
AMP-binding (26..388): 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:
    SAVL--LSLLQSMGWTGSAFEGYGLNETCIVTKN
  Nearest Stachelhaus code(s):
    Gly DLLMWCAITK (32% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

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

NZ_CP054019.1 - Region 5 - NRPS,NRPS-like,T1PKS,T3PKS,terpene,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: 360,239 - 443,511 nt. (total: 83,273 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)
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
terpene-precursor: (PT_FPPS_like and not PT_HPP)
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)

#### 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
HRD51_RS01520: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

HRD51_RS01630: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

HRD51_RS01720: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: aminotransferase methyltransferase
HRD51_RS01430: methyltransferase

smcogs
  SMCOG1089: methyltransferase

HRD51_RS01640: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: amidase hydrolase
HRD51_RS01380: hydrolase

smcogs
  SMCOG1179: hydrolase

HRD51_RS01470: amidase

smcogs
  SMCOG1105: amidase

HRD51_RS01675: HAD-superfamily hydrolase, subfamily IA, variant

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

Lyases: cyclase
HRD51_RS01385: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: ligase synthase synthetase
HRD51_RS01495: 1-deoxy-D-xylulose-5-phosphate synthase

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

HRD51_RS01510: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

HRD51_RS01540: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

HRD51_RS01585: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

HRD51_RS01600: 3-oxoacyl-(acyl carrier protein) synthase III

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

HRD51_RS01610: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

HRD51_RS01625: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transport
HRD51_RS01545: 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 | terpene | T3PKS | terpene-precursor | NRPS | T1PKS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001825.4 |  |  |  |  |  |  | 1.20 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000342.4 |  |  |  |  |  |  | 1.19 | NRPS | enniatin | Fusarium equiseti
BGC0000307.4 |  |  |  |  |  |  | 1.16 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001250.4 |  |  |  |  |  |  | 1.16 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  |  |  |  |  |  | 1.16 | NRPS | epichloenin A | Epichloe festucae
BGC0002135.2 |  |  |  |  |  |  | 1.16 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  |  |  |  |  | 1.16 | NRPS | AM-toxin | Alternaria alternata
BGC0001240.4 |  |  |  |  |  |  | 1.15 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001641.4 |  |  |  |  |  |  | 1.14 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  |  |  |  |  |  | 1.13 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000683.3 |  | 0.77 | terpene | avermitilol | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001825.4 |  | 0.63 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000342.4 |  | 0.63 | NRPS | enniatin | Fusarium equiseti
BGC0001273.3 |  | 0.63 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000357.5 |  | 0.63 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001244.3 |  | 0.63 | PKS | (-)-Mellein | Parastagonospora nodorum

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.
Terpene cluster 1 (360,238 - 381,228):
Product predictions:
No product predictions
Genes with terpene domains:
HRD51_RS01385: T1TS
Domain 1 (4 - 310): Type 1 terpene synthase
Subtype: unknown
Terpene cluster 2 (381,743 - 402,841):
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:
HRD51_RS01510: PT_FPPS_like
Domain 1 (50 - 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:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.73 out of 18.46
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (14):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.01 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.39 out of 36.54
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.30 out of 27.55
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.41 out of 27.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.62 out of 29.38
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.03 out of 24.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.60 out of 30.98
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.65 out of 32.93
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.44 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.46 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.29 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.39 out of 35.63
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.78 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 9, location 376566 - 443511:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 10, location 376566 - 417589:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal) + (Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 12, location 387682 - 430790:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 13, location 396706 - 443511:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (ccmal) + (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).
HRD51_RS01585: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (17..415): 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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LPDAWDAASLESWLLAGGEVNGYGPAESTVFATT
  Nearest Stachelhaus code(s):
    Val DALWLGGVFK (59% 8Å match)
  Stachelhaus code match:
    100% (strong)

HRD51_RS01620: mal
PKS_AT (575..870): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 160.2
  inactive: 86.7
  Methoxymalonyl-CoA: 84.2
  Methylmalonyl-CoA: 68.3
  Propionyl-CoA: 58.2
  Ethylmalonyl-CoA: 45.3
  2-Methylbutyryl-CoA: 42.5
  Isobutyryl-CoA: 29.1
  CHC-CoA: 24.6
  trans-1,2-CPDA: 22.6
  Benzoyl-CoA: 14.3
  Acetyl-CoA: 13.2
  fatty_acid: 12.7
  3-Methylbutyryl-CoA: 7.4

HRD51_RS01625: X
AMP-binding (29..425): X
nrpys: Asp, Asn, Glu, Gln, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HVWSWDSAVQDAHSALGGDAGAYGSTECSCALLR
  Nearest Stachelhaus code(s):
    Phe DAGALGACAK (38% 8Å match)
    Leu DALHSGAVAK (35% 8Å match)
  Stachelhaus code match:
    60% (weak)

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
CRP | Cyclic AMP receptor protein
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP054019.1 - Region 6 - 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: 1,049,166 - 1,111,028 nt. (total: 61,863 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 oxidoreductase
HRD51_RS05045: nucleotide sugar dehydrogenase

smcogs
  SMCOG1152: nucleotide sugar dehydrogenase

HRD51_RS05070: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Transferases: glycosyltransferase
HRD51_RS05040: sugar transferase

smcogs
  SMCOG1146: sugar transferase

HRD51_RS05050: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

HRD51_RS05090: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: dehalogenase hydrolase
HRD51_RS04975: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

HRD51_RS05065: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Ligases: ligase
HRD51_RS05020: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

HRD51_RS05025: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001133.4 |  | 0.71 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002071.2 |  | 0.69 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001133.4 |  | 0.71 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002071.2 |  | 0.69 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.19 out of 20.47
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.75 out of 23.05
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 20.47
Confidence: medium
Additional weak hits (12):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.23 out of 30.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.80 out of 29.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.42 out of 29.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.76 out of 21.55
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.46 out of 27.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.77 out of 27.78
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.79 out of 20.01
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.74 out of 23.43
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.51 out of 26.06
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 14, location 1049165 - 1111028:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ile - Gln - Ile - D-Gln) + (Val - Phe)

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).
HRD51_RS05020: Val - Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (470..873): 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:
    LDASFDASTCEVFLATGGEVNAYGPTEATTFATR
  Nearest Stachelhaus code(s):
    Leu or Ile DALFMGATFK (71% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1534..1930): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MTQAFDAAFWDMTLVLAGEVNAYGPTETTVCAAM
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

HRD51_RS05025: Ile - Gln - Ile - Gln
Search NORINE for peptide: strict or relaxed
AMP-binding (488..888): 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDSSFDASTFEVFLCTGGEHHVYGPTETTTFATR
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTFK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1558..1954): Gln
nrpys: Gln

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:
    glu,gln (Glu, Gln)
  Single AA prediction:
    gln (Gln)

Stachelhaus prediction details:
  Stachelhaus sequence:
    HWLTFDASVWELQFLCGGEHNLYGPTEATIDATV
  Nearest Stachelhaus code(s):
    Gln DAWQFGLIDK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2614..3015): 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDSSFDASTFEVFLCAGGEHHVYGPTETTTFATR
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTFK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (3675..4071): Gln
nrpys: Gln

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:
    glu,gln (Glu, Gln)
  Single AA prediction:
    gln (Gln)

Stachelhaus prediction details:
  Stachelhaus sequence:
    HWLTFDASVWELQFLCGGEHNLYGPTEATIDATV
  Nearest Stachelhaus code(s):
    Gln DAWQFGLIDK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

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

NZ_CP054019.1 - Region 7 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,122,534 - 1,165,557 nt. (total: 43,024 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
HRD51_RS05205: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

HRD51_RS05325: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: dehydratase
HRD51_RS05285: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
HRD51_RS05250: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

HRD51_RS05280: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

HRD51_RS05295: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

HRD51_RS05305: 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 | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.62 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  | 0.60 | NRPS | enniatin | Fusarium equiseti
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
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001833.4 |  | 0.60 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001240.4 |  | 0.59 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001261.3 |  | 0.59 | NRPS | AM-toxin | Alternaria alternata
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.62 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  | 0.60 | NRPS | enniatin | Fusarium equiseti
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
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001833.4 |  | 0.60 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001240.4 |  | 0.59 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001261.3 |  | 0.59 | NRPS | AM-toxin | Alternaria alternata
BGC0001641.4 |  | 0.59 | 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.

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: 24.47 out of 29.72
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.29 out of 23.79
Confidence: medium
Additional weak hits (15):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.71 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.27 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.33 out of 29.38
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.59 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.27 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.06 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.38 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.01 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.22 out of 26.06
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.02 out of 30.22
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.68 out of 30.97
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.66 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.76 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.23 out of 32.93
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.93 out of 24.78
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 15, location 1122533 - 1165557:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Phe)

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).
HRD51_RS05250: Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (424..816): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWACFDVAQISLALMVIGEINLYGPAEATIGVSH
  Nearest Stachelhaus code(s):
    Ser DVWHMSLIDK (50% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C

NZ_CP054019.1 - Region 8 - NRPS-like,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: 1,168,468 - 1,238,147 nt. (total: 69,680 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
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
HRD51_RS05425: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

HRD51_RS05430: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

HRD51_RS05435: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

Transferases: acylase transketolase
HRD51_RS05375: transketolase

smcogs
  SMCOG1204: transketolase

HRD51_RS05455: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase
HRD51_RS05445: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Ligases: ligase synthase
HRD51_RS05420: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

HRD51_RS05440: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | NRPS-like | transAT-PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002084.4 |  |  | 0.48 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  |  | 0.48 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0000175.5 |  |  | 0.41 | PKS | cycloheximide | Streptomyces sp. YIM 56141
BGC0001201.3 |  |  | 0.39 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0000384.6 |  |  | 0.36 | NRPS | lyngbyatoxin | Lyngbya majuscula
BGC0002127.3 |  |  | 0.35 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001928.2 |  |  | 0.33 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0002494.3 |  |  | 0.30 | NRPS | vibriobactin | Vibrio cholerae
BGC0001986.3 |  |  | 0.30 | other (other) | purincyclamide | Streptomyces chrestomyceticus
BGC0001075.5 |  |  | 0.30 | PKS, terpene | aurachin RE | Rhodococcus erythropolis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000175.5 |  | 0.61 | PKS | cycloheximide | Streptomyces sp. YIM 56141
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0000384.6 |  | 0.52 | NRPS | lyngbyatoxin | Lyngbya majuscula
BGC0001201.3 |  | 0.52 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0002083.3 |  | 0.51 | PKS | gladiofungin A, gladiofungin B | Burkholderia gladioli
BGC0001928.2 |  | 0.50 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0001991.2 |  | 0.49 | PKS | toblerol A, toblerol B, toblerol C, toblerol D, toblerol E, toblerol F, toblerol G, toblerol H | Methylorubrum extorquens AM1
BGC0002127.3 |  | 0.49 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0002494.3 |  | 0.48 | NRPS | vibriobactin | Vibrio cholerae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.30 out of 20.97
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 23.31 out of 27.18
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.90 out of 36.53
Confidence: medium
Additional weak hits (12):
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.23 out of 36.53
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.22 out of 29.51
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.19 out of 23.43
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.76 out of 27.55
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.56 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.92 out of 30.25
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.43 out of 27.04
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.54 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.83 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.52 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.91 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.09 out of 26.06
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 16, location 1168467 - 1238147:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - mal - ccmal - mal - Me-ccmal) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 17, location 1168467 - 1211869:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - mal - ccmal - mal - Me-ccmal) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 18, location 1175757 - 1238147:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - mal - ccmal - mal - Me-ccmal) + (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).
HRD51_RS05420: X
AMP-binding (49..479): 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:
    AGFMHLAGRYAGTMFLGGAFTGYGSTEAGGVLLD
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

HRD51_RS05455: mal
PKS_AT (0..255): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 66.7%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 89.4
  inactive: 44.6
  Methylmalonyl-CoA: 26.0
  Methoxymalonyl-CoA: 24.7
  Propionyl-CoA: 22.4
  Acetyl-CoA: 18.1
  2-Methylbutyryl-CoA: 14.1
  Isobutyryl-CoA: 11.4
  CHC-CoA: 9.1
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: -3.0

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

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
DmdR1 | Iron(II)-dependent repressor
NrdR | Represses ribonucleotide reductase encoding genes

NZ_CP054019.1 - Region 9 - hglE-KS,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: 1,287,743 - 1,338,806 nt. (total: 51,064 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)
hglE-KS: (hglE or hglD)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
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
HRD51_RS05970: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

HRD51_RS05980: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: acylase
HRD51_RS05875: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

HRD51_RS05880: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Lyases: cyclase dehydratase hydratase
HRD51_RS05805: Terpene synthase/cyclase metal-binding domain protein

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

HRD51_RS05865: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

HRD51_RS05965: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

HRD51_RS05975: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Isomerases: mutase
HRD51_RS05945: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

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 | hglE-KS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001276.3 |  |  | 0.26 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  |  | 0.26 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  | 0.26 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002192.3 |  |  | 0.25 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  |  | 0.25 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001164.3 |  |  | 0.24 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001268.4 |  |  | 0.24 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001160.5 |  |  | 0.24 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002648.2 |  |  | 0.20 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL
BGC0000861.5 |  |  | 0.20 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.60 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.60 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.59 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002192.3 |  | 0.58 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.58 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001164.3 |  | 0.58 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001268.4 |  | 0.58 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001160.5 |  | 0.57 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002648.2 |  | 0.53 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL
BGC0000861.5 |  | 0.53 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2

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:
HRD51_RS05805: T1TS
Domain 1 (14 - 325): Type 1 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.77 out of 23.79
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.25 out of 20.01
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.36 out of 20.97
Confidence: medium
Additional weak hits (10):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.27 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.46 out of 39.62
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.47 out of 30.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.39 out of 29.25
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.93 out of 19.26
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.95 out of 33.14
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.63 out of 27.18
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
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 1287742 - 1338806:
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 21, location 1294165 - 1338806:
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).
HRD51_RS05875: mal
PKS_AT (565..848): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 70.8%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 83.8
  Methoxymalonyl-CoA: 30.7
  inactive: 25.0
  Methylmalonyl-CoA: 21.9
  Propionyl-CoA: 19.2
  fatty_acid: 12.2
  2-Methylbutyryl-CoA: 5.4
  CHC-CoA: 3.8
  trans-1,2-CPDA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 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
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
ArgR | Regulator of arginine biosynthesis genes
CcpA | Catabolite control protein A
IolR | Regulator of the inositol catabolism

NZ_CP054019.1 - Region 10 - 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: 1,377,271 - 1,441,800 nt. (total: 64,530 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 oxidoreductase oxygenase
HRD51_RS06215: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

HRD51_RS06230: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

HRD51_RS06250: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

HRD51_RS06310: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

Transferases: acylase methyltransferase
HRD51_RS06155: isoprenylcysteine carboxyl methyltransferase

smcogs
  SMCOG1150: isoprenylcysteine carboxyl methyltransferase

HRD51_RS06255: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

HRD51_RS06260: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: synthase
HRD51_RS06235: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HRD51_RS06240: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HRD51_RS06245: 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
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.78 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.78 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.78 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.78 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002191.2 |  | 0.65 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001164.3 |  | 0.65 | 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
BGC0001258.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.78 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.78 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.78 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.78 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002191.2 |  | 0.65 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001164.3 |  | 0.65 | 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
BGC0001258.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245

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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
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 (30):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.70 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.31 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.84 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.39 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.41 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.61 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.85 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.42 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.44 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.52 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.81 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.26 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.36 out of 31.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.17 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.85 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.04 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.55 out of 18.57
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.78 out of 32.74
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.84 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.24 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.47 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.61 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.51 out of 20.97
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.88 out of 24.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.75 out of 35.63
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 24.68 out of 30.98
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.68 out of 35.63
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.84 out of 28.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 22, location 1377270 - 1441800:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (ccmal) + (Me-ccmal - Me-mal) + (mal)
Non-colinear ordering:
  HRD51_RS06235 + HRD51_RS06240 + HRD51_RS06250 + HRD51_RS06255 + HRD51_RS06260

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).
HRD51_RS06240: mal - mal
PKS_AT (95..389): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 199.7
  inactive: 90.8
  Methoxymalonyl-CoA: 58.7
  Methylmalonyl-CoA: 54.0
  Isobutyryl-CoA: 41.6
  Propionyl-CoA: 38.0
  2-Methylbutyryl-CoA: 27.4
  Ethylmalonyl-CoA: 26.0
  Acetyl-CoA: 13.1
  Benzoyl-CoA: 12.4
  fatty_acid: 11.4
  CHC-CoA: 1.0
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (1119..1418): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 200.8
  inactive: 108.4
  Methoxymalonyl-CoA: 65.7
  Methylmalonyl-CoA: 47.4
  Isobutyryl-CoA: 35.3
  Propionyl-CoA: 30.4
  Acetyl-CoA: 27.0
  fatty_acid: 21.1
  Benzoyl-CoA: 17.6
  CHC-CoA: 16.5
  Ethylmalonyl-CoA: 13.3
  2-Methylbutyryl-CoA: 13.0
  trans-1,2-CPDA: 9.9
  3-Methylbutyryl-CoA: 8.9

HRD51_RS06250: mmal
PKS_AT (563..860): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 196.9
  Ethylmalonyl-CoA: 188.8
  Methoxymalonyl-CoA: 161.8
  2-Methylbutyryl-CoA: 137.2
  trans-1,2-CPDA: 121.7
  CHC-CoA: 108.2
  Propionyl-CoA: 105.4
  Malonyl-CoA: 104.7
  Isobutyryl-CoA: 81.8
  Benzoyl-CoA: 55.2
  3-Methylbutyryl-CoA: 43.6
  inactive: 37.3
  Acetyl-CoA: 36.7
  fatty_acid: 27.7

HRD51_RS06255: mmal
PKS_AT (39..337): 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: 211.0
  Ethylmalonyl-CoA: 205.2
  Methoxymalonyl-CoA: 167.5
  2-Methylbutyryl-CoA: 156.8
  trans-1,2-CPDA: 138.2
  Propionyl-CoA: 106.9
  Malonyl-CoA: 101.2
  CHC-CoA: 86.2
  Isobutyryl-CoA: 71.9
  Benzoyl-CoA: 59.1
  Acetyl-CoA: 47.1
  3-Methylbutyryl-CoA: 31.1
  inactive: 30.7
  fatty_acid: 27.7

HRD51_RS06260: mal
PKS_AT (568..864): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 204.1
  inactive: 104.8
  Methoxymalonyl-CoA: 56.9
  Methylmalonyl-CoA: 52.6
  Propionyl-CoA: 34.2
  Ethylmalonyl-CoA: 21.5
  Acetyl-CoA: 20.3
  CHC-CoA: 16.6
  Isobutyryl-CoA: 14.8
  Benzoyl-CoA: 10.9
  2-Methylbutyryl-CoA: 6.7
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP054019.1 - Region 11 - 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: 1,698,470 - 1,708,685 nt. (total: 10,216 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
Ligases: synthase
HRD51_RS07610: 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 | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000948.5 |  | 0.53 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0001555.4 |  | 0.51 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  | 0.51 | ribosomal | microcin N | Escherichia coli
BGC0000588.5 |  | 0.50 | ribosomal | microcin L | Escherichia coli
BGC0002698.2 |  | 0.45 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000589.5 |  | 0.45 | ribosomal | microcin M | Escherichia coli Nissle 1917
BGC0000484.5 |  | 0.43 | ribosomal | glycocin F | Lactobacillus plantarum
BGC0001210.5 |  | 0.43 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000587.5 |  | 0.42 | ribosomal | microcin H47 | Escherichia coli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000948.5 |  | 0.53 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0001555.4 |  | 0.51 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  | 0.51 | ribosomal | microcin N | Escherichia coli
BGC0000588.5 |  | 0.50 | ribosomal | microcin L | Escherichia coli
BGC0002698.2 |  | 0.45 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000589.5 |  | 0.45 | ribosomal | microcin M | Escherichia coli Nissle 1917
BGC0000484.5 |  | 0.43 | ribosomal | glycocin F | Lactobacillus plantarum
BGC0001210.5 |  | 0.43 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000587.5 |  | 0.42 | ribosomal | microcin H47 | Escherichia coli

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (11):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.37 out of 26.12
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.56 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.62 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.98 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.16 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.26 out of 36.54
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.91 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.68 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.67 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator

NZ_CP054019.1 - Region 12 - T2PKS,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: 1,739,591 - 1,821,280 nt. (total: 81,690 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### 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 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 synthase
HRD51_RS07770: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

HRD51_RS07855: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

HRD51_RS07880: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

HRD51_RS07965: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

HRD51_RS08055: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

HRD51_RS08080: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

HRD51_RS08085: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

HRD51_RS08090: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

HRD51_RS08150: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: glycosyltransferase methyltransferase
HRD51_RS07835: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

HRD51_RS07870: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

HRD51_RS07925: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: amidase hydrolase synthase
HRD51_RS07820: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

HRD51_RS07855: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

HRD51_RS08000: amidase

smcogs
  SMCOG1105: amidase

HRD51_RS08155: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: cyclase hydratase
HRD51_RS07930: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

HRD51_RS07935: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

HRD51_RS08050: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

Ligases: synthase synthetase
HRD51_RS07945: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

HRD51_RS07950: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HRD51_RS08110: 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 | T2PKS | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000271.5 |  |  | 0.50 | PKS | spore pigment | Streptomyces avermitilis
BGC0002276.2 |  |  | 0.47 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000272.3 |  |  | 0.44 | PKS | spore pigment | Streptomyces collinus
BGC0000231.5 |  |  | 0.42 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000215.5 |  |  | 0.41 | PKS | curamycin | Streptomyces cyaneus
BGC0000234.5 |  |  | 0.37 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001723.5 |  |  | 0.34 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000867.3 |  |  | 0.34 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0001928.2 |  |  | 0.33 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000204.5 |  |  | 0.32 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000271.5 |  | 0.79 | PKS | spore pigment | Streptomyces avermitilis
BGC0000272.3 |  | 0.74 | PKS | spore pigment | Streptomyces collinus
BGC0000215.5 |  | 0.73 | PKS | curamycin | Streptomyces cyaneus
BGC0000231.5 |  | 0.63 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001197.5 |  | 0.61 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001513.3 |  | 0.60 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0002000.4 |  | 0.59 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0000234.5 |  | 0.58 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0002276.2 |  | 0.58 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291

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
--- | --- | --- | --- | --- | ---
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:
HRD51_RS08105: PT_phytoene_like
Domain 1 (15 - 229): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.71 out of 20.47
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.01 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.87 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 (31):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.53 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.59 out of 29.38
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.04 out of 25.88
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 21.84
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.52 out of 30.22
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.36 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.93 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.65 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.07 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.75 out of 26.06
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.82 out of 26.85
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.28 out of 32.74
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.51 out of 30.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.51 out of 30.97
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.02 out of 31.73
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.38 out of 32.74
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.57 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.72 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.85 out of 27.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.19 out of 32.93
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.71 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.32 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.86 out of 24.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.22 out of 29.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.96 out of 28.19
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.72 out of 32.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.02 out of 26.06
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
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.77 out of 28.19
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.56 out of 36.53
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.33 out of 27.18
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
Type II PKS
Terpene
TFBS Finder
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:
  1739590 to 1812106
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Product class(es):
  pentangular polyphenol
  tetracenomycin

HRD51_RS07835
  MET (Score: 293.9; E-value: 3.4e-90)
HRD51_RS07925
  MET C6|C8 (Score: 524.9; E-value: 1.6e-160)
HRD51_RS07930
  CYC C4-C21/C2-C23|C2-C19 (Score: 161.6; E-value: 1.2e-50)
HRD51_RS07935
  CYC C9-C14 (Score: 248.9; E-value: 3.2e-77)
HRD51_RS07940
  ACP (Score: 69.6; E-value: 4e-22)
HRD51_RS07945
  CLF (Score: 536.5; E-value: 8.8e-164)
HRD51_RS07950
  KS (Score: 728.7; E-value: 4.3e-222)
HRD51_RS07955
  CYC C5-C18 (Score: 211.1; E-value: 1e-65)
HRD51_RS07965
  OXY (Score: 288.0; E-value: 3.4e-88)
HRD51_RS08085
  KR (Score: 151.8; E-value: 6.2e-47)
HRD51_RS08090
  KR (Score: 181.3; E-value: 6.3e-56)

Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism
MexT | Global virulence regulator
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NZ_CP054019.1 - Region 13 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,522,634 - 2,552,439 nt. (total: 29,806 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
HRD51_RS11400: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Lyases: decarboxylase
HRD51_RS11395: 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
--- | --- | --- | --- | --- | ---
BGC0001478.5 |  | 0.86 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.80 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000941.3 |  | 0.79 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000940.5 |  | 0.66 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.66 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0002073.3 |  | 0.60 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0002464.3 |  | 0.56 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002620.2 |  | 0.55 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002690.2 |  | 0.55 | other (other) | FW0622 | Verrucosispora sp. FIM060022

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001478.5 |  | 0.86 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.80 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000941.3 |  | 0.79 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000940.5 |  | 0.66 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.66 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0002073.3 |  | 0.60 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0002464.3 |  | 0.56 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002620.2 |  | 0.55 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002690.2 |  | 0.55 | other (other) | FW0622 | Verrucosispora sp. FIM060022

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: 33.62 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.03 out of 36.53
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.27 out of 25.31
Confidence: medium
Additional weak hits (22):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.93 out of 21.55
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.46 out of 39.62
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.96 out of 28.14
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.03 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.10 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.67 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
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.25 out of 30.25
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.22 out of 39.62
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.92 out of 27.55
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.97 out of 31.73
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.77 out of 32.74
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.40 out of 32.74
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.03 out of 30.12
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.29 out of 32.93
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.08 out of 32.93
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.82 out of 18.57
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.19 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.16 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
DmdR1 | Iron(II)-dependent repressor

NZ_CP054019.1 - Region 14 - ectoine
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: 2,621,044 - 2,631,448 nt. (total: 10,405 nt) Show pHMM detection rules used
ectoine: ectoine_synt

#### 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
HRD51_RS11840: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

Transferases: aminotransferase
HRD51_RS11825: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

HRD51_RS42115: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

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

Reference | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.88 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.85 | other (other) | ectoine | Streptomyces anulatus
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000860.3 |  | 0.60 | other (other) | ectoine | Methylarcula marina
BGC0000857.3 |  | 0.60 | other (other) | ectoine | Methylophaga alcalica
BGC0000854.3 |  | 0.59 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.88 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.85 | other (other) | ectoine | Streptomyces anulatus
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000860.3 |  | 0.60 | other (other) | ectoine | Methylarcula marina
BGC0000857.3 |  | 0.60 | other (other) | ectoine | Methylophaga alcalica
BGC0000854.3 |  | 0.59 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.52 out of 19.26
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.15 out of 23.79
Confidence: medium
Additional weak hits (6):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.25 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.37 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.87 out of 27.78
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.37 out of 26.12
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.04 out of 26.12
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.04 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism

NZ_CP054019.1 - Region 15 - 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: 3,562,241 - 3,586,706 nt. (total: 24,466 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
HRD51_RS15940: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Transferases: methyltransferase
HRD51_RS15925: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Hydrolases: esterase
HRD51_RS15990: putative esterase

smcogs
  SMCOG1104: putative esterase

Lyases: cyclase dehydratase
HRD51_RS15950: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

HRD51_RS15955: 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 |  | 0.76 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.57 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0002316.2 |  | 0.55 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000542.3 |  | 0.54 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.54 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000515.4 |  | 0.51 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0000506.4 |  | 0.51 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000538.3 |  | 0.47 | ribosomal | nisin Z | Lactococcus lactis
BGC0000528.5 |  | 0.46 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.76 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.57 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0002316.2 |  | 0.55 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000542.3 |  | 0.54 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.54 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000515.4 |  | 0.51 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0000506.4 |  | 0.51 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000538.3 |  | 0.47 | ribosomal | nisin Z | Lactococcus lactis
BGC0000528.5 |  | 0.46 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

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.
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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.40 out of 20.97
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.31 out of 28.19
Confidence: medium
Additional weak hits (8):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.47 out of 31.73
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.54 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.50 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.47 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.25 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.09 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.04 out of 35.63
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
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 (3562240...3586706)
HRD51_RS15950
  RRE type: Lanthipeptide_LanB_RRE
  Location: 166 - 258
  Score: 52.0

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NZ_CP054019.1 - Region 16 - 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: 4,967,640 - 4,989,862 nt. (total: 22,223 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
HRD51_RS22235: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Lyases: cyclase
HRD51_RS22275: 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 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002382.3 |  | 0.43 | ribosomal | grimoviridin | Grimontia marina
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0002683.2 |  | 0.40 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000501.3 |  | 0.40 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000802.5 |  | 0.40 | saccharide | succinoglycan | Sinorhizobium meliloti
BGC0001928.2 |  | 0.40 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002382.3 |  | 0.43 | ribosomal | grimoviridin | Grimontia marina
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0002683.2 |  | 0.40 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000501.3 |  | 0.40 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000802.5 |  | 0.40 | saccharide | succinoglycan | Sinorhizobium meliloti
BGC0001928.2 |  | 0.40 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae

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:
HRD51_RS22275: T1TS + T1TS
Domain 1 (1 - 315): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (339 - 704): 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:
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 25.09 out of 27.55
Confidence: strong
Additional weak hits (14):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.70 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.38 out of 27.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.58 out of 29.65
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
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.69 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.04 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.38 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.78 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.36 out of 35.63
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.48 out of 29.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.80 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.18 out of 28.19
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
--- | ---
GnfM | Regulator of nitrogen-fixation genes

NZ_CP054019.1 - Region 17 - PKS-like,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: 5,076,994 - 5,128,030 nt. (total: 51,037 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)
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
Azole RiPPs
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
HRD51_RS22820: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

HRD51_RS22835: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase methyltransferase
HRD51_RS22815: methyltransferase

smcogs
  SMCOG1089: methyltransferase

HRD51_RS22855: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

Hydrolases: hydrolase
HRD51_RS22885: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: dehydratase hydratase
HRD51_RS22780: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

HRD51_RS22930: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

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 | PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001753.3 |  |  | 0.84 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus
BGC0002311.3 |  |  | 0.67 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0001472.5 |  |  | 0.51 | ribosomal | berninamycin A | Streptomyces bernensis
BGC0002276.2 |  |  | 0.44 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002363.3 |  |  | 0.43 | ribosomal | berninamycin K, berninamycin J, berninamycin A, berninamycin B | Streptomyces sp.
BGC0000615.4 |  |  | 0.41 | ribosomal | TP-1161 | Nocardiopsis sp. TFS65-07
BGC0001146.5 |  |  | 0.40 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0001201.3 |  |  | 0.39 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0001145.5 |  |  | 0.38 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001640.3 |  |  | 0.36 | ribosomal | kocurin | Kocuria rosea

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001753.3 |  | 0.70 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus
BGC0002311.3 |  | 0.67 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0001472.5 |  | 0.58 | ribosomal | berninamycin A | Streptomyces bernensis
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002363.3 |  | 0.53 | ribosomal | berninamycin K, berninamycin J, berninamycin A, berninamycin B | Streptomyces sp.
BGC0001146.5 |  | 0.52 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0000615.4 |  | 0.52 | ribosomal | TP-1161 | Nocardiopsis sp. TFS65-07
BGC0001201.3 |  | 0.52 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0001145.5 |  | 0.51 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001640.3 |  | 0.50 | ribosomal | kocurin | Kocuria rosea

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: 17.92 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
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.65 out of 28.19
Confidence: medium
Additional weak hits (30):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.47 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.06 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.34 out of 21.55
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.96 out of 23.43
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.92 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.69 out of 32.74
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.94 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.64 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.73 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.34 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.22 out of 39.62
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.50 out of 20.97
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.17 out of 27.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.12 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.27 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.98 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.41 out of 20.97
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.80 out of 24.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.63 out of 27.04
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.91 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.25 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.18 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.91 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.34 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.65 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.13 out of 28.19
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.

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

HRD51_RS22765
Leader:
MDSTQELDLNALEISDLIEDSNYSDETLSQAMAA
HRD51_RS22770
Leader:
MDSTQELDLNALEISDLIEDSNYSDETLSQAMAA
Shared core:
S T T T T G C T T S S C S S S S S
Core with dehydrations:
Dha Dhb Dhb Dhb Dhb G Cys Dhb Dhb Dha Dha Cys Dha Dha Dha Dha Dha

#### antiSMASH-DB 4.0 matches for HRD51_RS22765

100.0%
NZ_CP051486.1 and 9 others:
NZ_CP054019.1 Thiopeptides: HRD51_RS22770_thiopeptide NZ_CP054019.1 Thiopeptides: HRD51_RS22765_thiopeptide NZ_CP070326.1 Thiopeptides: JNO44_RS24110_thiopeptide NZ_CP070326.1 Thiopeptides: JNO44_RS24105_thiopeptide NZ_CP072931.1 Thiopeptides: SU9_RS14055_thiopeptide NZ_JAPTYM010000001.1 Thiopeptides: O1M07_RS24000_thiopeptide NZ_JAPTYM010000001.1 Thiopeptides: O1M07_RS23995_thiopeptide NZ_LJSN01000005.1 Thiopeptides: AOB60_RS40645_thiopeptide NZ_LJSN01000005.1 Thiopeptides: AOB60_RS40640_thiopeptide
Thiopeptides: HED23_RS03525_thiopeptide
1
S T T T T G C T T S S C S S S S S
17
S T T T T G C T T S S C S S S S S
1
S T T T T G C T T S S C S S S S S
17

#### MIBiG 4.0 matches for HRD51_RS22765

15.4%
BGC0002110.3 (QKV49894.1):
Lanthipeptide: birimositide
7
C T T S S C S S S
15
C T+ C+S
17
C P T T K C T S K
25
10.8%
BGC0001229.4 (SBI_06989):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
7
C T T S S C S S
14
C T+ C+S
28
C P T T K C T S
35

#### 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)
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
RREFinder
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (5076993...5113320)
HRD51_RS22790
  RRE type: Thiopeptide_F_RRE
  Location: 12 - 89
  Score: 43.3
HRD51_RS22800
  RRE type: Thiopeptide_F_RRE
  Location: 23 - 103
  Score: 25.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.

HRD51_RS22765
  Putative Type III
  Cleavage pHMM score: 11.70
  RODEO score: 34
  Monoisotopic mass: 1583.6 Da
  Molecular weight: 1584.6 Da
  Predicted peptide features:
  Central ring: pyridine trisubstituted
  Macrocycle: 29-member
  Tail reaction: dealkylation of C-Terminal residue; amidation
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1602.6 Da N = 1
    1620.6 Da N = 2
    1638.7 Da N = 3
    1656.7 Da N = 4
    1674.7 Da N = 5
    1692.7 Da N = 6
    1710.7 Da N = 7
    1728.8 Da N = 8
    1746.8 Da N = 9
    1764.8 Da N = 10
    1782.8 Da N = 11
    1800.8 Da N = 12
    1818.9 Da N = 13
    1836.9 Da N = 14
HRD51_RS22770
  Putative Type III
  Cleavage pHMM score: 11.70
  RODEO score: 34
  Monoisotopic mass: 1583.6 Da
  Molecular weight: 1584.6 Da
  Predicted peptide features:
  Central ring: pyridine trisubstituted
  Macrocycle: 29-member
  Tail reaction: dealkylation of C-Terminal residue; amidation
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1602.6 Da N = 1
    1620.6 Da N = 2
    1638.7 Da N = 3
    1656.7 Da N = 4
    1674.7 Da N = 5
    1692.7 Da N = 6
    1710.7 Da N = 7
    1728.8 Da N = 8
    1746.8 Da N = 9
    1764.8 Da N = 10
    1782.8 Da N = 11
    1800.8 Da N = 12
    1818.9 Da N = 13
    1836.9 Da N = 14

NZ_CP054019.1 - Region 18 - linaridin
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: 5,138,581 - 5,159,488 nt. (total: 20,908 nt) Show pHMM detection rules used
linaridin: (cypemycin or cypI)

#### 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
HRD51_RS23045: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: methyltransferase
HRD51_RS23050: methyltransferase

smcogs
  SMCOG1248: methyltransferase

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 | linaridin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001188.3 |  | 0.64 | ribosomal | legonaridin | Streptomyces sp. CT34
BGC0001735.5 |  | 0.49 | other (other) | pentostatine, vidarabine | Streptomyces antibioticus
BGC0002319.3 |  | 0.48 | ribosomal | salinipeptin A, salinipeptin B, salinipeptin C, salinipeptin D | Streptomyces sp.
BGC0000582.4 |  | 0.47 | ribosomal | cypemycin | Streptomyces sp. OH-4156
BGC0000583.5 |  | 0.44 | ribosomal | grisemycin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002150.2 |  | 0.43 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0002151.2 |  | 0.43 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0001229.4 |  | 0.42 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0000571.3 |  | 0.42 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0001937.4 |  | 0.41 | other (other) | tubercidin | Streptomyces tubercidicus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001188.3 |  | 0.64 | ribosomal | legonaridin | Streptomyces sp. CT34
BGC0001735.5 |  | 0.49 | other (other) | pentostatine, vidarabine | Streptomyces antibioticus
BGC0002319.3 |  | 0.48 | ribosomal | salinipeptin A, salinipeptin B, salinipeptin C, salinipeptin D | Streptomyces sp.
BGC0000582.4 |  | 0.47 | ribosomal | cypemycin | Streptomyces sp. OH-4156
BGC0000583.5 |  | 0.44 | ribosomal | grisemycin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002150.2 |  | 0.43 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0002151.2 |  | 0.43 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0001229.4 |  | 0.42 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0000571.3 |  | 0.42 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0001937.4 |  | 0.41 | other (other) | tubercidin | Streptomyces tubercidicus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (6):
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.04 out of 19.26
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.27 out of 30.97
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.26 out of 35.63
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.63 out of 18.57
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.37 out of 30.98
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 20.07 out of 22.40
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP054019.1 - Region 19 - 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: 5,597,555 - 5,631,721 nt. (total: 34,167 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: dehydrogenase
HRD51_RS25045: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: aminotransferase
HRD51_RS25145: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

HRD51_RS25155: aminotransferase

smcogs
  SMCOG1019: aminotransferase

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 |  | 0.63 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001641.4 |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
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

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.63 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001641.4 |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
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

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 27.52 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.56 out of 30.11
Confidence: medium
Additional weak hits (10):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.37 out of 26.12
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.41 out of 18.57
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.32 out of 26.12
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.72 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.88 out of 31.73
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.69 out of 30.97
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.78 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.47 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.82 out of 20.01
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 35, location 5597554 - 5631721:
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).
HRD51_RS25095: X
AMP-binding (14..428): 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:
    FVVMFDFSIEEPYCVVGGELNTYGPTEITVTATV
  Nearest Stachelhaus code(s):
    Gln or Tyr DAESVGTVVK (62% 8Å match)
    Arg DVENVGAVTK (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
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP054019.1 - Region 20 - 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: 5,766,304 - 5,872,166 nt. (total: 105,863 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 oxidoreductase oxygenase
HRD51_RS25935: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

HRD51_RS25965: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

HRD51_RS25975: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

HRD51_RS25990: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

HRD51_RS25995: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

HRD51_RS26005: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

HRD51_RS26035: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: acylase aminotransferase glycosyltransferase sulfhydrylase transferase
HRD51_RS25850: O-succinylhomoserine sulfhydrylase

smcogs
  SMCOG1168: O-succinylhomoserine sulfhydrylase

HRD51_RS25900: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

HRD51_RS25915: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

HRD51_RS25940: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

HRD51_RS25960: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

HRD51_RS25980: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

Hydrolases: amidase esterase
HRD51_RS25970: thioesterase

smcogs
  SMCOG1004: thioesterase

HRD51_RS26040: amidase

smcogs
  SMCOG1105: amidase

Lyases: dehydratase
HRD51_RS25905: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
HRD51_RS25860: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

HRD51_RS25920: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

HRD51_RS25925: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HRD51_RS25930: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HRD51_RS25945: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HRD51_RS26010: 1-deoxy-D-xylulose-5-phosphate synthase

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

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

Reference | 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
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000018.5 |  | 0.72 | PKS | angolamycin | Streptomyces eurythermus
BGC0000067.5 |  | 0.65 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
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
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
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
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1

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
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000018.5 |  | 0.72 | PKS | angolamycin | Streptomyces eurythermus
BGC0000067.5 |  | 0.65 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
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
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
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
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-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.
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:
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 22.27 out of 23.43
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.09 out of 20.47
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.03 out of 20.97
Confidence: medium
Additional weak hits (16):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.62 out of 27.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.95 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.39 out of 28.19
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.00 out of 32.38
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.37 out of 23.43
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.76 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.44 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.37 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.99 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.15 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.42 out of 26.06
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.78 out of 26.85
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.57 out of 20.97
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.42 out of 31.73
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.23 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 36, location 5766303 - 5872166:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal - pk) + (pk - ohmal) + (ccmal) + (pk - pk) + (pk) + (ccmal) + (pk - pk) + (pk - ohmal)
Non-colinear ordering:
  HRD51_RS25920 + HRD51_RS25925 + HRD51_RS25930 + HRD51_RS25935 + HRD51_RS25940 + HRD51_RS25945 + HRD51_RS25960 + HRD51_RS25965

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).
HRD51_RS25920: mal - pk
PKS_AT (534..822): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 236.4
  inactive: 125.3
  Methoxymalonyl-CoA: 69.4
  Methylmalonyl-CoA: 60.7
  Propionyl-CoA: 43.6
  Isobutyryl-CoA: 33.9
  2-Methylbutyryl-CoA: 29.9
  Acetyl-CoA: 26.1
  Ethylmalonyl-CoA: 24.0
  Benzoyl-CoA: 22.2
  CHC-CoA: 12.2
  trans-1,2-CPDA: 11.1
  fatty_acid: 7.5
  3-Methylbutyryl-CoA: 0.0

PKS_AT (1535..1824): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 224.4
  Methylmalonyl-CoA: 222.2
  Methoxymalonyl-CoA: 186.7
  2-Methylbutyryl-CoA: 151.6
  trans-1,2-CPDA: 140.0
  Propionyl-CoA: 114.9
  CHC-CoA: 103.6
  Malonyl-CoA: 93.9
  Isobutyryl-CoA: 80.9
  Benzoyl-CoA: 72.6
  Acetyl-CoA: 61.3
  3-Methylbutyryl-CoA: 45.2
  inactive: 32.5
  fatty_acid: 32.3

HRD51_RS25925: pk - mal
PKS_AT (560..850): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 233.2
  Methylmalonyl-CoA: 227.2
  Methoxymalonyl-CoA: 195.4
  2-Methylbutyryl-CoA: 156.6
  trans-1,2-CPDA: 153.7
  Propionyl-CoA: 122.1
  CHC-CoA: 110.7
  Malonyl-CoA: 109.5
  Isobutyryl-CoA: 89.2
  Benzoyl-CoA: 75.0
  Acetyl-CoA: 61.2
  3-Methylbutyryl-CoA: 50.8
  inactive: 38.6
  fatty_acid: 33.9

PKS_AT (2063..2360): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 233.3
  inactive: 114.0
  Methoxymalonyl-CoA: 65.1
  Methylmalonyl-CoA: 56.8
  Isobutyryl-CoA: 30.9
  Propionyl-CoA: 28.5
  Acetyl-CoA: 20.6
  Ethylmalonyl-CoA: 19.2
  Benzoyl-CoA: 19.2
  2-Methylbutyryl-CoA: 11.1
  CHC-CoA: 9.8
  fatty_acid: 9.1
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

HRD51_RS25930: mal
PKS_AT (571..864): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 243.9
  inactive: 118.2
  Methoxymalonyl-CoA: 71.4
  Methylmalonyl-CoA: 61.8
  Propionyl-CoA: 34.6
  Isobutyryl-CoA: 31.3
  Acetyl-CoA: 20.8
  Ethylmalonyl-CoA: 20.3
  Benzoyl-CoA: 19.2
  2-Methylbutyryl-CoA: 12.2
  CHC-CoA: 10.2
  fatty_acid: 9.9
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

HRD51_RS25935: pk - pk
PKS_AT (563..853): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 227.8
  Methylmalonyl-CoA: 225.3
  Methoxymalonyl-CoA: 189.8
  2-Methylbutyryl-CoA: 154.9
  trans-1,2-CPDA: 142.6
  Propionyl-CoA: 118.1
  CHC-CoA: 110.2
  Malonyl-CoA: 99.4
  Isobutyryl-CoA: 82.7
  Benzoyl-CoA: 72.5
  Acetyl-CoA: 57.8
  3-Methylbutyryl-CoA: 45.4
  fatty_acid: 34.7
  inactive: 31.6

PKS_AT (2083..2372): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 223.7
  Methylmalonyl-CoA: 221.6
  Methoxymalonyl-CoA: 186.2
  2-Methylbutyryl-CoA: 153.3
  trans-1,2-CPDA: 136.8
  Propionyl-CoA: 114.7
  CHC-CoA: 99.4
  Malonyl-CoA: 94.4
  Isobutyryl-CoA: 82.6
  Benzoyl-CoA: 71.8
  Acetyl-CoA: 60.7
  3-Methylbutyryl-CoA: 46.8
  inactive: 32.4
  fatty_acid: 28.6

HRD51_RS25940: pk
PKS_AT (565..854): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 227.1
  Methylmalonyl-CoA: 222.5
  Methoxymalonyl-CoA: 185.1
  2-Methylbutyryl-CoA: 150.6
  trans-1,2-CPDA: 139.5
  Propionyl-CoA: 114.9
  CHC-CoA: 105.6
  Malonyl-CoA: 94.5
  Isobutyryl-CoA: 80.3
  Benzoyl-CoA: 71.5
  Acetyl-CoA: 63.2
  3-Methylbutyryl-CoA: 44.3
  fatty_acid: 34.6
  inactive: 32.4

HRD51_RS25945: mal
PKS_AT (572..865): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 243.7
  inactive: 115.4
  Methoxymalonyl-CoA: 68.9
  Methylmalonyl-CoA: 60.4
  Propionyl-CoA: 35.3
  Isobutyryl-CoA: 28.0
  Ethylmalonyl-CoA: 22.1
  Acetyl-CoA: 20.8
  Benzoyl-CoA: 19.2
  2-Methylbutyryl-CoA: 12.0
  CHC-CoA: 10.6
  fatty_acid: 10.3
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

HRD51_RS25960: pk - pk
PKS_AT (567..856): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 223.7
  Methylmalonyl-CoA: 221.6
  Methoxymalonyl-CoA: 186.2
  2-Methylbutyryl-CoA: 153.3
  trans-1,2-CPDA: 136.8
  Propionyl-CoA: 114.7
  CHC-CoA: 99.4
  Malonyl-CoA: 94.4
  Isobutyryl-CoA: 82.6
  Benzoyl-CoA: 71.8
  Acetyl-CoA: 60.7
  3-Methylbutyryl-CoA: 46.8
  inactive: 32.4
  fatty_acid: 28.6

PKS_AT (2088..2377): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 228.2
  Methylmalonyl-CoA: 222.8
  Methoxymalonyl-CoA: 185.6
  2-Methylbutyryl-CoA: 154.4
  trans-1,2-CPDA: 138.9
  Propionyl-CoA: 116.9
  CHC-CoA: 104.6
  Malonyl-CoA: 98.3
  Isobutyryl-CoA: 84.3
  Benzoyl-CoA: 70.4
  Acetyl-CoA: 60.3
  3-Methylbutyryl-CoA: 45.1
  fatty_acid: 33.2
  inactive: 31.2

HRD51_RS25965: pk - mal
PKS_AT (568..858): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 226.6
  Methylmalonyl-CoA: 221.4
  Methoxymalonyl-CoA: 185.0
  2-Methylbutyryl-CoA: 151.3
  trans-1,2-CPDA: 146.7
  Propionyl-CoA: 118.1
  CHC-CoA: 105.7
  Malonyl-CoA: 92.8
  Isobutyryl-CoA: 77.1
  Benzoyl-CoA: 68.2
  Acetyl-CoA: 65.4
  3-Methylbutyryl-CoA: 49.4
  fatty_acid: 39.2
  inactive: 26.6

PKS_AT (2086..2378): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 87.5%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 227.0
  inactive: 118.0
  Methoxymalonyl-CoA: 67.7
  Methylmalonyl-CoA: 62.4
  Propionyl-CoA: 34.6
  Benzoyl-CoA: 29.8
  Isobutyryl-CoA: 28.6
  Ethylmalonyl-CoA: 22.8
  Acetyl-CoA: 17.0
  2-Methylbutyryl-CoA: 16.9
  trans-1,2-CPDA: 15.7
  CHC-CoA: 11.6
  fatty_acid: 10.1
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
CcpA | Catabolite control protein A
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP054019.1 - Region 21 - CDPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,362,513 - 6,383,196 nt. (total: 20,684 nt) Show pHMM detection rules used
CDPS: CDPS

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
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
HRD51_RS28195: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

HRD51_RS28225: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase
HRD51_RS28180: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

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

Reference | CDPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000851.5 |  | 0.88 | other (other) | albonoursin | Streptomyces noursei ATCC 11455
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001986.3 |  | 0.55 | other (other) | purincyclamide | Streptomyces chrestomyceticus
BGC0001948.3 |  | 0.49 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000558.5 |  | 0.42 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0001336.5 |  | 0.40 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0000678.5 |  | 0.39 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000207.5 |  | 0.37 | PKS | chartreusin | Streptomyces chartreusis
BGC0002425.3 |  | 0.37 | ribosomal | stlassin | Streptomyces sp.
BGC0000218.5 |  | 0.36 | PKS | doxorubicin | Streptomyces peucetius

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000851.5 |  | 0.88 | other (other) | albonoursin | Streptomyces noursei ATCC 11455
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001986.3 |  | 0.55 | other (other) | purincyclamide | Streptomyces chrestomyceticus
BGC0001948.3 |  | 0.49 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000558.5 |  | 0.42 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0001336.5 |  | 0.40 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0000678.5 |  | 0.39 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000207.5 |  | 0.37 | PKS | chartreusin | Streptomyces chartreusis
BGC0002425.3 |  | 0.37 | ribosomal | stlassin | Streptomyces sp.
BGC0000218.5 |  | 0.36 | PKS | doxorubicin | Streptomyces peucetius

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: 18.44 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.48 out of 23.79
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
Additional weak hits (6):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.91 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.92 out of 30.97
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.34 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.07 out of 39.62
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.37 out of 35.63
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.31 out of 32.93
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP054019.1 - Region 22 - NI-siderophore,NRPS,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: 6,699,898 - 6,792,371 nt. (total: 92,474 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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
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 oxygenase
HRD51_RS29700: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

HRD51_RS29815: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

HRD51_RS29845: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

Transferases: acyltransferase aminotransferase halogenase
HRD51_RS29650: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

HRD51_RS29800: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

HRD51_RS29835: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
MITE
  MITE0000030Halogenation (identity: 64.60%)
smcogs
  SMCOG1119: halogenase

HRD51_RS29870: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: esterase hydrolase
HRD51_RS29690: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

HRD51_RS29750: thioesterase

smcogs
  SMCOG1004: thioesterase

HRD51_RS29795: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Isomerases: isomerase mutase
HRD51_RS29715: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

HRD51_RS29880: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
HRD51_RS29805: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

HRD51_RS29855: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

HRD51_RS29875: carbamoyl phosphate synthase small subunit

smcogs
  SMCOG1249: carbamoyl phosphate synthase small subunit

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

Reference | NI-siderophore | NRPS | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001569.4 |  |  |  | 1.13 | NRPS | dechlorocuracomycin | Streptomyces noursei ATCC 11455
BGC0001562.5 |  |  |  | 0.87 | NRPS | curacomycin | Streptomyces curacoi
BGC0001814.5 |  |  |  | 0.84 | NRPS | ulleungmycin | Streptomyces sp. KCB13F003
BGC0002135.2 |  |  |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  |  |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  |  |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  |  |  | 0.72 | NRPS | enniatin | Fusarium equiseti
BGC0001128.4 |  |  |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  |  | 0.69 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001569.4 |  | 0.92 | NRPS | dechlorocuracomycin | Streptomyces noursei ATCC 11455
BGC0001814.5 |  | 0.78 | NRPS | ulleungmycin | Streptomyces sp. KCB13F003
BGC0001561.4 |  | 0.78 | NRPS | curacomycin | Streptomyces curacoi
BGC0001562.5 |  | 0.78 | NRPS | curacomycin | Streptomyces curacoi
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  | 0.72 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.70 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 26.51 out of 29.51
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.70 out of 23.79
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.93 out of 24.78
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.83 out of 27.18
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.20 out of 27.18
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.51 out of 25.31
Confidence: medium
Additional weak hits (17):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.18 out of 23.43
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.28 out of 20.97
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.77 out of 25.88
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.92 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.65 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.69 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.88 out of 29.65
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.11 out of 23.43
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.20 out of 36.54
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.20 out of 26.12
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.09 out of 29.65
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.60 out of 35.63
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.62 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.66 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.26 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 38, location 6699897 - 6792371:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - D-Val - D-X - Val) + (Orn - D-X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 40, location 6730235 - 6792371:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - D-Val - D-X - Val) + (Orn - D-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).
HRD51_RS29800: X - Val - X - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (23..430): X
nrpys: 5-clTrp

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:
    LAHAFDVSIADQMIATGGEFNAYGPTEATVTVTL
  Nearest Stachelhaus code(s):
    5-clTrp DVAMAGAVTK (100% 8Å match)
    6-clTrp DVAMAGAVTK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1096..1495): 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:
    VHTAFDAATFEGWLLAGGDINGYGPTETTTFAAA
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2609..3002): X
nrpys: Leu, Phe

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:
    LTVAFDASVIEMMILVGAEVNGYGPTEATIATSF
  Nearest Stachelhaus code(s):
    Leu or Phe DAIMLGGIAK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4129..4534): 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:
    VDPAFDAGTLESWIMSGGDINGYGPTEGTVFTSL
  Nearest Stachelhaus code(s):
    Val DALWMGGVFK (100% 8Å match)
    Ile or Val DALWMGGVFK (62% 8Å match)
  Stachelhaus code match:
    100% (strong)

HRD51_RS29805: Orn - X
Search NORINE for peptide: strict or relaxed
AMP-binding (518..929): Orn
nrpys: Orn

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

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

AMP-binding (1599..2005): X
nrpys: OH-Asn, 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:
    YWCSFDLTVTTGKAVVGGEVNEYGPTEATVGCVV
  Nearest Stachelhaus code(s):
    OH-Asn or Asn DLTKVGEVGK (100% 8Å match)
    Trp DLTKVGEVGK (94% 8Å match)
    Asn DLTKVGEVGK (71% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism
LexA variant 2 | Repressor of DNA damage response
NrdR | Represses ribonucleotide reductase encoding genes
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP054019.1 - Region 23 - 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: 6,851,519 - 6,892,574 nt. (total: 41,056 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
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 oxygenase
HRD51_RS30230: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

HRD51_RS30295: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Ligases: synthase
HRD51_RS30225: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

Translocases: permease
HRD51_RS30195: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001310.5 |  | 0.85 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0002127.3 |  | 0.72 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.67 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.61 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000844.5 |  | 0.50 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0000280.5 |  | 0.48 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0000281.3 |  | 0.47 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0002332.2 |  | 0.44 | PKS | 4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A | Candidatus Entotheonella sp.
BGC0001579.4 |  | 0.41 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000528.5 |  | 0.41 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001310.5 |  | 0.85 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0002127.3 |  | 0.72 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.67 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.61 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000844.5 |  | 0.50 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0000280.5 |  | 0.48 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0000281.3 |  | 0.47 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0002332.2 |  | 0.44 | PKS | 4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A | Candidatus Entotheonella sp.
BGC0001579.4 |  | 0.41 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000528.5 |  | 0.41 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

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:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.27 out of 25.31
Confidence: medium
Additional weak hits (23):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.15 out of 30.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.77 out of 32.74
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.82 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.97 out of 31.73
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.92 out of 27.55
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.22 out of 39.62
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.25 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.92 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.67 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: 15.03 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.46 out of 39.62
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.93 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.91 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.64 out of 31.73
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.36 out of 27.18
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.19 out of 30.98
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.08 out of 32.93
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.96 out of 28.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.29 out of 32.93
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
OsdR | Development and stress management regulator

NZ_CP054019.1 - Region 24 - 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: 7,000,104 - 7,011,400 nt. (total: 11,297 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
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
--- | --- | --- | --- | --- | ---
BGC0000541.5 |  | 0.33 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000351.5 |  | 0.33 | NRPS | exochelin | Mycolicibacterium smegmatis MC2 155
BGC0001889.2 |  | 0.32 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0002490.2 |  | 0.30 | other (other) | yersinopine | Yersinia pestis CO92
BGC0000502.5 |  | 0.29 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001427.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus
BGC0001423.4 |  | 0.29 | NRPS, PKS | myxochromide C | Myxococcus hansupus
BGC0001426.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus
BGC0001425.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus DK 1622
BGC0001421.4 |  | 0.29 | NRPS, PKS | myxochromide B | Myxococcus sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000541.5 |  | 0.33 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000351.5 |  | 0.33 | NRPS | exochelin | Mycolicibacterium smegmatis MC2 155
BGC0001889.2 |  | 0.32 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0002490.2 |  | 0.30 | other (other) | yersinopine | Yersinia pestis CO92
BGC0000502.5 |  | 0.29 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001427.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus
BGC0001423.4 |  | 0.29 | NRPS, PKS | myxochromide C | Myxococcus hansupus
BGC0001426.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus
BGC0001425.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus DK 1622
BGC0001421.4 |  | 0.29 | NRPS, PKS | myxochromide B | Myxococcus sp.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (2):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.28 out of 29.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 15.87 out of 30.97
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP054019.1 - Region 25 - hglE-KS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,354,414 - 7,400,647 nt. (total: 46,234 nt) Show pHMM detection rules used
hglE-KS: (hglE or hglD)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidase
HRD51_RS32355: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

Transferases: acylase methyltransferase
HRD51_RS32410: methyltransferase

smcogs
  SMCOG1089: methyltransferase

HRD51_RS32435: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Lyases: dehydratase
HRD51_RS32350: L-carnitine dehydratase/bile acid-inducible

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

Ligases: synthase
HRD51_RS32445: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transport
HRD51_RS32450: 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 | hglE-KS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002175.3 |  | 0.59 | PKS | YWA1 | Aspergillus oryzae RIB40
BGC0001273.3 |  | 0.59 | PKS | asperlactone | Aspergillus ochraceus
BGC0000107.3 |  | 0.59 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0002192.3 |  | 0.58 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.58 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001164.3 |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.57 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002648.2 |  | 0.56 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL
BGC0000861.5 |  | 0.56 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002175.3 |  | 0.59 | PKS | YWA1 | Aspergillus oryzae RIB40
BGC0001273.3 |  | 0.59 | PKS | asperlactone | Aspergillus ochraceus
BGC0000107.3 |  | 0.59 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0002192.3 |  | 0.58 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.58 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001164.3 |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.57 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002648.2 |  | 0.56 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL
BGC0000861.5 |  | 0.56 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.39 out of 25.31
Confidence: medium
Additional weak hits (11):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.98 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.24 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.45 out of 36.54
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.42 out of 30.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.96 out of 26.85
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.64 out of 27.55
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 20.13 out of 33.14
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
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.48 out of 27.55
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 43, location 7354413 - 7400647:
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).
HRD51_RS32445: mal
PKS_AT (575..871): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 95.7
  inactive: 42.2
  Methoxymalonyl-CoA: 36.4
  Methylmalonyl-CoA: 26.7
  Isobutyryl-CoA: 24.2
  fatty_acid: 15.2
  CHC-CoA: 14.0
  Acetyl-CoA: 11.3
  Propionyl-CoA: 9.3
  Ethylmalonyl-CoA: 5.2
  trans-1,2-CPDA: 0.0
  Benzoyl-CoA: 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
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CatR | H2O2-responsive repressor

NZ_CP054019.1 - Region 26 - linaridin
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,430,968 - 7,451,579 nt. (total: 20,612 nt) Show pHMM detection rules used
linaridin: (cypemycin or cypI)

#### 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
HRD51_RS32670: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: methyltransferase
HRD51_RS32680: methyltransferase

smcogs
  SMCOG1248: methyltransferase

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 | linaridin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001188.3 |  | 0.51 | ribosomal | legonaridin | Streptomyces sp. CT34
BGC0001735.5 |  | 0.50 | other (other) | pentostatine, vidarabine | Streptomyces antibioticus
BGC0000528.5 |  | 0.45 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000513.3 |  | 0.45 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0002150.2 |  | 0.43 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0002151.2 |  | 0.43 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0000563.4 |  | 0.43 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  | 0.42 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000558.5 |  | 0.42 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0002669.2 |  | 0.41 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001188.3 |  | 0.51 | ribosomal | legonaridin | Streptomyces sp. CT34
BGC0001735.5 |  | 0.50 | other (other) | pentostatine, vidarabine | Streptomyces antibioticus
BGC0000528.5 |  | 0.45 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000513.3 |  | 0.45 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0002150.2 |  | 0.43 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0002151.2 |  | 0.43 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0000563.4 |  | 0.43 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  | 0.42 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000558.5 |  | 0.42 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0002669.2 |  | 0.41 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (6):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.54 out of 27.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.37 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.31 out of 27.78
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.34 out of 32.74
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.51 out of 30.98
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP054019.1 - Region 27 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,488,607 - 7,511,141 nt. (total: 22,535 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lasso peptides
TFBS Finder
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
HRD51_RS33005: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Hydrolases: hydrolase
HRD51_RS32960: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: dehydratase hydratase
HRD51_RS32995: L-carnitine dehydratase/bile acid-inducible

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

HRD51_RS33000: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

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

Reference | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001548.4 |  | 0.72 | ribosomal | citrulassin A | Streptomyces albulus
BGC0001552.3 |  | 0.69 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001507.3 |  | 0.67 | ribosomal | anantin C | Streptomyces olindensis
BGC0001550.3 |  | 0.65 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001549.3 |  | 0.65 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001889.2 |  | 0.63 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0001645.3 |  | 0.62 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0001493.5 |  | 0.61 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0002053.3 |  | 0.59 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001781.4 |  | 0.59 | ribosomal | sphaericin | Planomonospora sphaerica

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001548.4 |  | 0.72 | ribosomal | citrulassin A | Streptomyces albulus
BGC0001552.3 |  | 0.69 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001507.3 |  | 0.67 | ribosomal | anantin C | Streptomyces olindensis
BGC0001550.3 |  | 0.65 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001549.3 |  | 0.65 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001889.2 |  | 0.63 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0001645.3 |  | 0.62 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0001493.5 |  | 0.61 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0002053.3 |  | 0.59 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001781.4 |  | 0.59 | ribosomal | sphaericin | Planomonospora sphaerica

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

No significant matches found.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.

#### Lassopeptide(s) for HRD51_RS32955

HRD51_RS32955
Leader:
MQGNELQETDKLQTYEAPKMIECGSFQEDTG
Full core:
Y F G L T G Y E N L F H F Y D K L H
Putative macrolactam:
Y F G L T G Y E

#### antiSMASH-DB 4.0 matches for HRD51_RS32955

100.0%
NZ_CP003987.1 and 5 others:
NZ_CP054019.1 Lassopeptides: HRD51_RS32955_lassopeptide NZ_CP070326.1 Lassopeptides: JNO44_RS41200_lassopeptide NZ_CP095749.1 Lassopeptides: MOV08_RS09695_lassopeptide NZ_JAPTYM010000001.1 Lassopeptides: O1M07_RS33870_lassopeptide NZ_LJSN01000003.1 Lassopeptides: AOB60_RS44775_lassopeptide
Lassopeptides: GZL_RS47650_lassopeptide
1
Y F G L T G Y E N L F H F Y D K L H
18
Y F G L T G Y E N L F H F Y D K L H
1
Y F G L T G Y E N L F H F Y D K L H
18
94.4%
NZ_CP047146.1:
Lassopeptides: GR130_RS08740_lassopeptide
1
Y F G L T G Y E N L F H F Y D K L H
18
Y F G L T G Y E N L F H F Y D+L H
1
Y F G L T G Y E N L F H F Y D R L H
18

#### 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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.74 out of 23.79
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
Additional weak hits (5):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.93 out of 28.14
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.71 out of 33.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.29 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.30 out of 35.63
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

HRD51_RS32955 - Class II
  Cleavage pHMM score: 2.20
  RODEO score: 17
  Monoisotopic mass: 2245.1 Da
  Molecular weight: 2246.5 Da
  Number of bridges: 0

RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (7488606...7511141)
HRD51_RS32965
  RRE type: Stand_Alone_Lasso_RRE
  Location: 0 - 84
  Score: 86.4

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

NZ_CP054019.1 - Region 28 - 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: 7,696,796 - 7,723,503 nt. (total: 26,708 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
HRD51_RS33890: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

Transferases: aminotransferase kinase transferase
HRD51_RS33885: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

HRD51_RS33950: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

HRD51_RS33985: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Ligases: synthetase
HRD51_RS33930: 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
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.67 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0001839.3 |  | 0.51 | terpene | squalestatin S1 | Aspergillus sp. Z5
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000664.5 |  | 0.47 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.67 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0001839.3 |  | 0.51 | terpene | squalestatin S1 | Aspergillus sp. Z5
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000664.5 |  | 0.47 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350

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 | hopanoid |  | C30 | hopanoid skeleton | unknown
triterpene | polypodane |  | C30 | polypodane skeleton | unknown

Genes with terpene domains:
HRD51_RS33915: PT_phytoene_like
Domain 1 (6 - 268): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  PSPP → hydroxysqualene

HRD51_RS33920: PT_phytoene_like
Domain 1 (17 - 300): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

HRD51_RS33930: PT_FPPS_like
Domain 1 (74 - 369): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

HRD51_RS33935: T2TS
Domain 1 (40 - 684): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47
Confidence: strong
Additional weak hits (12):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.15 out of 30.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.82 out of 36.54
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.66 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.83 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.68 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.98 out of 29.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.98 out of 29.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.41 out of 32.74
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.04 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.99 out of 27.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
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
--- | ---
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP054019.1 - Region 29 - 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: 7,909,379 - 7,922,411 nt. (total: 13,033 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: dehydrogenase oxidoreductase reductase
HRD51_RS34785: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

HRD51_RS34800: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

HRD51_RS34810: 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
BGC0002285.2 |  | 0.30 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001057.4 |  | 0.30 | NRPS, PKS | zearalenone | Fusarium graminearum
BGC0001739.3 |  | 0.30 | other (other) | phosphonoacetic Acid | Streptomyces sp. NRRL F-525
BGC0000877.5 |  | 0.30 | other (other) | polyoxin A, polyoxin H | Streptomyces cacaoi subsp. asoensis
BGC0002556.2 |  | 0.29 | other (other) | cervinomycin B3, cervinomycin C1, cervinomycin C2, cervinomycin C3, cervinomycin C4 | Streptomyces sp.
BGC0000274.5 |  | 0.27 | PKS | tetarimycin A, tetarimycin B | uncultured bacterium
BGC0001819.3 |  | 0.26 | PKS | Venemycin | Streptomyces venezuelae
BGC0000844.5 |  | 0.26 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0000845.5 |  | 0.25 | other (non-nrp beta-lactam) | clavulanic acid | Streptomyces clavuligerus ATCC 27064

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0002285.2 |  | 0.30 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001057.4 |  | 0.30 | NRPS, PKS | zearalenone | Fusarium graminearum
BGC0001739.3 |  | 0.30 | other (other) | phosphonoacetic Acid | Streptomyces sp. NRRL F-525
BGC0000877.5 |  | 0.30 | other (other) | polyoxin A, polyoxin H | Streptomyces cacaoi subsp. asoensis
BGC0002556.2 |  | 0.29 | other (other) | cervinomycin B3, cervinomycin C1, cervinomycin C2, cervinomycin C3, cervinomycin C4 | Streptomyces sp.
BGC0000274.5 |  | 0.27 | PKS | tetarimycin A, tetarimycin B | uncultured bacterium
BGC0001819.3 |  | 0.26 | PKS | Venemycin | Streptomyces venezuelae
BGC0000844.5 |  | 0.26 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0000845.5 |  | 0.25 | other (non-nrp beta-lactam) | clavulanic acid | 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.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47
Confidence: strong
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.40 out of 22.40
Confidence: strong
Additional weak hits (9):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.84 out of 30.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.48 out of 33.14
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.71 out of 27.04
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.30 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 20.42 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP054019.1 - Region 30 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,929,858 - 7,973,394 nt. (total: 43,537 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase oxygenase
HRD51_RS34930: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

HRD51_RS34945: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

HRD51_RS34950: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

Transferases: aminotransferase carboxylase
HRD51_RS34890: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

HRD51_RS34955: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: amidase dehalogenase hydrolase
HRD51_RS34985: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

HRD51_RS34990: amidase

smcogs
  SMCOG1105: amidase

HRD51_RS35000: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Ligases: ligase synthase
HRD51_RS34895: carbamoyl phosphate synthase small subunit

smcogs
  SMCOG1249: carbamoyl phosphate synthase small subunit

HRD51_RS34935: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002631.2 |  | 0.53 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000895.5 |  | 0.52 | other (other) | citrulline | Lactobacillus plantarum subsp. plantarum
BGC0000662.5 |  | 0.51 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001295.5 |  | 0.50 | other (other) | cremeomycin | Streptomyces cremeus
BGC0002826.2 |  | 0.50 | other (other) | closoxazole A, closoxazole B | Clostridium cavendishii DSM 21758
BGC0000820.5 |  | 0.49 | other (other) | physostigmine | Streptomyces griseofuscus
BGC0000889.5 |  | 0.48 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001336.5 |  | 0.47 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001592.5 |  | 0.47 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002631.2 |  | 0.53 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000895.5 |  | 0.52 | other (other) | citrulline | Lactobacillus plantarum subsp. plantarum
BGC0000662.5 |  | 0.51 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001295.5 |  | 0.50 | other (other) | cremeomycin | Streptomyces cremeus
BGC0002826.2 |  | 0.50 | other (other) | closoxazole A, closoxazole B | Clostridium cavendishii DSM 21758
BGC0000820.5 |  | 0.49 | other (other) | physostigmine | Streptomyces griseofuscus
BGC0000889.5 |  | 0.48 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001336.5 |  | 0.47 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001592.5 |  | 0.47 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis

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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (5):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.72 out of 31.73
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.45 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 48, location 7929857 - 7973394:
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).
HRD51_RS34935: X
AMP-binding (89..522): 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:
    MPNLHLVARRITTVLCGSAHNGYGTTETGFLMLD
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

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

NZ_CP054019.1 - Region 31 - aminopolycarboxylic-acid
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,998,835 - 8,012,334 nt. (total: 13,500 nt) Show pHMM detection rules used
aminopolycarboxylic-acid: (AesA and AesB and AesC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: deaminase
HRD51_RS35150: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Lyases: decarboxylase
HRD51_RS35155: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: synthase
HRD51_RS35160: 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 | aminopolycarboxylic-acid | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001587.5 |  | 0.84 | other (other) | ethylenediaminesuccinic acid hydroxyarginine (EDHA) | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002568.2 |  | 0.80 | other (other) | Ethylenediaminesuccinic acid hydroxyarginine | Streptomyces scabiei 87.22
BGC0002567.2 |  | 0.68 | other (other) | EDHA | Streptomyces sp. MA5143a
BGC0000918.3 |  | 0.40 | other (other) | ochronotic pigment | Streptomyces avermitilis
BGC0000943.5 |  | 0.40 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002487.3 |  | 0.37 | other (other) | staphylopine | Staphylococcus aureus subsp. aureus Mu50
BGC0000188.5 |  | 0.34 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0001790.4 |  | 0.33 | NRPS | sulfazecin | Pseudomonas acidophila
BGC0002213.3 |  | 0.33 | PKS | HEx-pks16 polyketide | Punctularia strigosozonata HHB-11173 SS5
BGC0001200.4 |  | 0.32 | PKS | lorneic acid A | Streptomyces sp. NBRC 109706

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001587.5 |  | 0.84 | other (other) | ethylenediaminesuccinic acid hydroxyarginine (EDHA) | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002568.2 |  | 0.80 | other (other) | Ethylenediaminesuccinic acid hydroxyarginine | Streptomyces scabiei 87.22
BGC0002567.2 |  | 0.68 | other (other) | EDHA | Streptomyces sp. MA5143a
BGC0000918.3 |  | 0.40 | other (other) | ochronotic pigment | Streptomyces avermitilis
BGC0000943.5 |  | 0.40 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002487.3 |  | 0.37 | other (other) | staphylopine | Staphylococcus aureus subsp. aureus Mu50
BGC0000188.5 |  | 0.34 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0001790.4 |  | 0.33 | NRPS | sulfazecin | Pseudomonas acidophila
BGC0002213.3 |  | 0.33 | PKS | HEx-pks16 polyketide | Punctularia strigosozonata HHB-11173 SS5
BGC0001200.4 |  | 0.32 | PKS | lorneic acid A | Streptomyces sp. NBRC 109706

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: 28.57 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.57 out of 36.53
Confidence: medium
Additional weak hits (4):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.61 out of 25.88
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.68 out of 39.62
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.50 out of 21.55
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP054019.1 - Region 32 - NAPAA,RiPP-like,butyrolactone
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: 8,050,301 - 8,091,968 nt. (total: 41,668 nt) Show pHMM detection rules used
NAPAA: (AMP-binding and TIGR02353)
butyrolactone: AfsA
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
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: electron transfer oxidoreductase
HRD51_RS35410: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

HRD51_RS35545: flavodoxin

smcogs
  SMCOG1134: flavodoxin

Transferases: glycosyltransferase methyltransferase transferase
HRD51_RS35390: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

HRD51_RS35400: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

HRD51_RS35470: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
HRD51_RS35520: HAD-superfamily hydrolase, subfamily IA, variant

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

HRD51_RS35555: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: dehydratase
HRD51_RS35385: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
HRD51_RS35460: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NAPAA | butyrolactone | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000849.4 |  |  |  | 1.06 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  |  |  | 0.89 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002174.2 |  |  |  | 0.48 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0002578.2 |  |  |  | 0.45 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000850.5 |  |  |  | 0.40 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000914.5 |  |  |  | 0.28 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0001135.5 |  |  |  | 0.27 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001250.4 |  |  |  | 0.27 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  |  |  | 0.26 | NRPS | epichloenin A | Epichloe festucae
BGC0001261.3 |  |  |  | 0.26 | NRPS | AM-toxin | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.77 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0000849.4 |  | 0.76 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.75 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001261.3 |  | 0.60 | NRPS | AM-toxin | Alternaria alternata
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 20.47
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.13 out of 20.97
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.18 out of 20.97
Confidence: medium
Additional weak hits (14):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.79 out of 25.88
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.75 out of 30.25
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.25 out of 26.85
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.51 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.21 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.78 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.25 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.99 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.99 out of 36.54
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.80 out of 31.73
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.27 out of 24.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.85 out of 27.04
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.87 out of 25.88
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 50, location 8050300 - 8091968:
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

For candidate cluster 51, location 8050300 - 8084260:
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).
HRD51_RS35460: X
AMP-binding (37..409): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAELFDASCEELSTIVGGEWNTYGPTETTVVACA
  Nearest Stachelhaus code(s):
    Lys DAEDIGTVVK (68% 8Å match)
    Gln or Tyr DAESVGTVVK (59% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP054019.1 - Region 33 - 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: 8,094,047 - 8,115,123 nt. (total: 21,077 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
HRD51_RS35620: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

HRD51_RS35635: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

Transferases: methyltransferase
HRD51_RS35650: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: synthetase
HRD51_RS35640: 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
--- | --- | --- | --- | --- | ---
BGC0002631.2 |  | 0.43 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000528.5 |  | 0.40 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001077.4 |  | 0.40 | PKS | 6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone | Actinoplanes missouriensis 431
BGC0001364.3 |  | 0.39 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0001887.3 |  | 0.39 | ribosomal | huazacin | Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0000545.5 |  | 0.38 | ribosomal | ruminococcin A | [Ruminococcus] gnavus E1
BGC0000643.3 |  | 0.37 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000634.3 |  | 0.37 | terpene | carotenoid | Brevundimonas sp. SD212
BGC0001618.3 |  | 0.37 | ribosomal | hyicin 3682 | Staphylococcus hyicus
BGC0001911.3 |  | 0.37 | terpene | raimonol | Streptomyces anulatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002631.2 |  | 0.43 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000528.5 |  | 0.40 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001077.4 |  | 0.40 | PKS | 6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone | Actinoplanes missouriensis 431
BGC0001364.3 |  | 0.39 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0001887.3 |  | 0.39 | ribosomal | huazacin | Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0000545.5 |  | 0.38 | ribosomal | ruminococcin A | [Ruminococcus] gnavus E1
BGC0000643.3 |  | 0.37 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000634.3 |  | 0.37 | terpene | carotenoid | Brevundimonas sp. SD212
BGC0001618.3 |  | 0.37 | ribosomal | hyicin 3682 | Staphylococcus hyicus
BGC0001911.3 |  | 0.37 | 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.

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:
HRD51_RS35640: PT_FPPS_like
Domain 1 (51 - 336): 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:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
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
--- | ---
AbrC3 | Antibiotic production activator
MexT | Global virulence regulator

NZ_CP054019.1 - Region 34 - butyrolactone
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: 8,302,898 - 8,313,833 nt. (total: 10,936 nt) Show pHMM detection rules used
butyrolactone: AfsA

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
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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
HRD51_RS36655: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

HRD51_RS36675: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

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 | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.78 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.69 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000849.4 |  | 0.60 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000844.5 |  | 0.49 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001224.5 |  | 0.44 | other (other) | reductasporine | uncultured bacterium
BGC0001485.4 |  | 0.43 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000908.3 |  | 0.41 | other (other) | melanin | Streptomyces avermitilis
BGC0002013.4 |  | 0.41 | ribosomal | curacozole | Streptomyces curacoi
BGC0000888.5 |  | 0.41 | other (other) | bacilysin | Bacillus sp. CS93
BGC0002313.3 |  | 0.38 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.78 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.69 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000849.4 |  | 0.60 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000844.5 |  | 0.49 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001224.5 |  | 0.44 | other (other) | reductasporine | uncultured bacterium
BGC0001485.4 |  | 0.43 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000908.3 |  | 0.41 | other (other) | melanin | Streptomyces avermitilis
BGC0002013.4 |  | 0.41 | ribosomal | curacozole | Streptomyces curacoi
BGC0000888.5 |  | 0.41 | other (other) | bacilysin | Bacillus sp. CS93
BGC0002313.3 |  | 0.38 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus

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:
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 (3):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.86 out of 26.06
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.78 out of 23.43
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.10 out of 25.88
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP054019.1 - Region 35 - atropopeptide
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: 8,530,388 - 8,551,437 nt. (total: 21,050 nt) Show pHMM detection rules used
atropopeptide: atropopeptide_p450

#### 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
HRD51_RS37760: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Hydrolases: deaminase
HRD51_RS37720: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

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 | atropopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002751.2 |  | 0.51 | ribosomal | Amyxirubin B | Amycolatopsis xylanica
BGC0000842.5 |  | 0.26 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0000943.5 |  | 0.22 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0001041.4 |  | 0.22 | NRPS, PKS | salinosporamide A | Salinispora tropica CNB-440
BGC0001558.5 |  | 0.21 | PKS | cosmomycin C | Streptomyces sp. CNT302
BGC0000001.5 |  | 0.20 | PKS | abyssomicin C, atrop-abyssomicin C | Verrucosispora maris AB-18-032

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002751.2 |  | 0.51 | ribosomal | Amyxirubin B | Amycolatopsis xylanica
BGC0000842.5 |  | 0.26 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0000943.5 |  | 0.22 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0001041.4 |  | 0.22 | NRPS, PKS | salinosporamide A | Salinispora tropica CNB-440
BGC0001558.5 |  | 0.21 | PKS | cosmomycin C | Streptomyces sp. CNT302
BGC0000001.5 |  | 0.20 | PKS | abyssomicin C, atrop-abyssomicin C | Verrucosispora maris AB-18-032

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:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.40 out of 27.04
Confidence: strong
Additional weak hits (2):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.85 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.63 out of 18.57
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP054019.1 - Region 36 - RRE-containing,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: 8,653,361 - 8,799,274 nt. (total: 145,914 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])
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
HRD51_RS38430: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

HRD51_RS38435: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

HRD51_RS38445: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: PPTase acylase aminotransferase glycosyltransferase
HRD51_RS38450: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

HRD51_RS38455: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

HRD51_RS38475: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

HRD51_RS41975: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

HRD51_RS41980: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: deformylase esterase hydrolase
HRD51_RS38485: thioesterase

smcogs
  SMCOG1004: thioesterase

HRD51_RS38525: amidohydrolase

smcogs
  SMCOG1244: amidohydrolase

HRD51_RS38540: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Lyases: dehydratase
HRD51_RS38355: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

HRD51_RS38395: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
HRD51_RS38425: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HRD51_RS38460: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HRD51_RS38480: 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 | RRE-containing | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002576.2 |  |  | 0.90 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0000115.5 |  |  | 0.73 | PKS, saccharide | nystatin A1 | Streptomyces noursei ATCC 11455
BGC0001709.5 |  |  | 0.62 | PKS | nystatin | Streptomyces albulus
BGC0001273.3 |  |  | 0.43 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.43 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  | 0.42 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  |  | 0.42 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000116.5 |  |  | 0.41 | PKS | nystatin-like Pseudonocardia polyene A1 | Pseudonocardia autotrophica
BGC0000016.4 |  |  | 0.40 | other (other) | amphotericin B | Streptomyces nodosus
BGC0001289.5 |  |  | 0.38 | ribosomal | penisin | Paenibacillus ehimensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000115.5 |  | 0.85 | PKS, saccharide | nystatin A1 | Streptomyces noursei ATCC 11455
BGC0001709.5 |  | 0.80 | PKS | nystatin | Streptomyces albulus
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000016.4 |  | 0.72 | other (other) | amphotericin B | Streptomyces nodosus
BGC0000041.3 |  | 0.69 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000116.5 |  | 0.66 | PKS | nystatin-like Pseudonocardia polyene A1 | Pseudonocardia autotrophica

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: 19.02 out of 25.31
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.01 out of 26.85
Confidence: medium
Additional weak hits (28):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.54 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.04 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.30 out of 29.38
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.63 out of 26.85
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.67 out of 29.72
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.55 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.22 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.07 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.28 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.44 out of 27.78
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.83 out of 32.74
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.81 out of 39.62
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.95 out of 36.54
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.70 out of 20.97
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.86 out of 24.78
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.88 out of 27.18
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.41 out of 24.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.14 out of 35.63
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 32.93
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.52 out of 29.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.30 out of 29.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.62 out of 25.88
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.87 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.08 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
RREFinder
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 57, location 8653360 - 8799274:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (redmal - ohmal - ccmal) + (Me-ohmal - Me-ohmal) + (ccmal - ccmal - redmal - ccmal - ccmal - ccmal) + (ccmal)
Non-colinear ordering:
  HRD51_RS38460 + HRD51_RS38465 + HRD51_RS38425 + HRD51_RS38475 + HRD51_RS38480 + HRD51_RS38430

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 59, location 8655133 - 8799274:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (redmal - ohmal - ccmal) + (Me-ohmal - Me-ohmal) + (ccmal - ccmal - redmal - ccmal - ccmal - ccmal) + (ccmal)
Non-colinear ordering:
  HRD51_RS38460 + HRD51_RS38465 + HRD51_RS38425 + HRD51_RS38475 + HRD51_RS38480 + HRD51_RS38430

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).
HRD51_RS41980: mal
PKS_AT (571..866): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 215.4
  inactive: 112.7
  Methoxymalonyl-CoA: 52.7
  Methylmalonyl-CoA: 40.9
  Acetyl-CoA: 20.4
  Benzoyl-CoA: 15.2
  Ethylmalonyl-CoA: 14.7
  Isobutyryl-CoA: 11.2
  CHC-CoA: 9.7
  trans-1,2-CPDA: 6.6
  Propionyl-CoA: 1.3
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: -1.3

HRD51_RS38425: mal - mal - mal
PKS_AT (574..866): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 233.0
  inactive: 107.6
  Methoxymalonyl-CoA: 59.1
  Methylmalonyl-CoA: 50.1
  Isobutyryl-CoA: 25.3
  Ethylmalonyl-CoA: 22.0
  Propionyl-CoA: 21.0
  Benzoyl-CoA: 17.3
  Acetyl-CoA: 13.7
  CHC-CoA: 9.1
  2-Methylbutyryl-CoA: 5.0
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2634..2929): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 203.6
  inactive: 91.0
  Methylmalonyl-CoA: 45.3
  Methoxymalonyl-CoA: 42.4
  Propionyl-CoA: 23.9
  Benzoyl-CoA: 20.5
  Isobutyryl-CoA: 16.7
  Ethylmalonyl-CoA: 16.3
  Acetyl-CoA: 12.3
  CHC-CoA: 12.0
  fatty_acid: 9.3
  2-Methylbutyryl-CoA: 7.0
  trans-1,2-CPDA: 5.7
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4150..4447): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 209.4
  inactive: 100.8
  Methylmalonyl-CoA: 50.2
  Methoxymalonyl-CoA: 48.3
  Propionyl-CoA: 30.6
  Isobutyryl-CoA: 23.7
  fatty_acid: 10.3
  Acetyl-CoA: 9.2
  CHC-CoA: 8.0
  Benzoyl-CoA: 7.8
  2-Methylbutyryl-CoA: 7.4
  trans-1,2-CPDA: 5.6
  Ethylmalonyl-CoA: 5.5
  3-Methylbutyryl-CoA: 0.0

HRD51_RS38430: mal
PKS_AT (566..857): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 79.2%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 208.3
  inactive: 85.5
  Methoxymalonyl-CoA: 58.0
  Methylmalonyl-CoA: 49.9
  Propionyl-CoA: 22.0
  Isobutyryl-CoA: 21.7
  CHC-CoA: 18.3
  Ethylmalonyl-CoA: 14.0
  2-Methylbutyryl-CoA: 13.5
  Benzoyl-CoA: 11.3
  Acetyl-CoA: 8.3
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

HRD51_RS38460: mal
PKS_AT (512..803): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 209.4
  inactive: 89.8
  Methoxymalonyl-CoA: 68.1
  Methylmalonyl-CoA: 66.4
  Isobutyryl-CoA: 36.4
  Ethylmalonyl-CoA: 36.2
  CHC-CoA: 31.2
  Propionyl-CoA: 27.2
  2-Methylbutyryl-CoA: 26.7
  Benzoyl-CoA: 17.0
  Acetyl-CoA: 12.3
  trans-1,2-CPDA: 10.8
  fatty_acid: 10.7
  3-Methylbutyryl-CoA: 0.0

HRD51_RS38475: mmal - mmal
PKS_AT (576..874): 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: 217.2
  Ethylmalonyl-CoA: 210.4
  Methoxymalonyl-CoA: 172.0
  2-Methylbutyryl-CoA: 141.1
  trans-1,2-CPDA: 124.2
  Propionyl-CoA: 107.6
  CHC-CoA: 98.2
  Malonyl-CoA: 92.0
  Isobutyryl-CoA: 83.6
  Benzoyl-CoA: 68.6
  3-Methylbutyryl-CoA: 45.0
  Acetyl-CoA: 40.3
  fatty_acid: 33.6
  inactive: 17.9

PKS_AT (2115..2416): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 214.7
  Ethylmalonyl-CoA: 207.7
  Methoxymalonyl-CoA: 178.3
  2-Methylbutyryl-CoA: 141.1
  trans-1,2-CPDA: 139.2
  Propionyl-CoA: 115.7
  CHC-CoA: 113.2
  Malonyl-CoA: 109.6
  Isobutyryl-CoA: 81.9
  Benzoyl-CoA: 73.0
  fatty_acid: 48.3
  Acetyl-CoA: 46.1
  3-Methylbutyryl-CoA: 34.4
  inactive: 26.7

HRD51_RS38480: mal - mal - mal - mal - mal - mal
PKS_AT (544..834): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 231.7
  inactive: 104.6
  Methoxymalonyl-CoA: 63.3
  Methylmalonyl-CoA: 49.9
  Propionyl-CoA: 35.5
  Benzoyl-CoA: 20.2
  Acetyl-CoA: 19.3
  Isobutyryl-CoA: 18.6
  Ethylmalonyl-CoA: 18.2
  CHC-CoA: 18.1
  2-Methylbutyryl-CoA: 14.7
  trans-1,2-CPDA: 10.8
  fatty_acid: 10.8
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2290..2581): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 240.6
  inactive: 120.2
  Methoxymalonyl-CoA: 64.3
  Methylmalonyl-CoA: 59.5
  Isobutyryl-CoA: 35.0
  Propionyl-CoA: 32.4
  Benzoyl-CoA: 24.5
  Acetyl-CoA: 22.4
  Ethylmalonyl-CoA: 21.5
  2-Methylbutyryl-CoA: 19.9
  CHC-CoA: 14.3
  trans-1,2-CPDA: 12.8
  fatty_acid: 10.3
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4030..4322): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 79.2%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 239.4
  inactive: 109.9
  Methoxymalonyl-CoA: 61.6
  Methylmalonyl-CoA: 57.2
  Ethylmalonyl-CoA: 31.8
  Propionyl-CoA: 31.3
  Isobutyryl-CoA: 28.6
  Benzoyl-CoA: 22.1
  Acetyl-CoA: 18.6
  CHC-CoA: 16.2
  2-Methylbutyryl-CoA: 15.2
  fatty_acid: 12.3
  trans-1,2-CPDA: 11.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (6172..6465): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 79.2%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 226.4
  inactive: 99.5
  Methylmalonyl-CoA: 55.8
  Methoxymalonyl-CoA: 52.0
  Propionyl-CoA: 32.3
  Ethylmalonyl-CoA: 25.4
  Acetyl-CoA: 22.6
  trans-1,2-CPDA: 21.7
  Benzoyl-CoA: 21.6
  Isobutyryl-CoA: 20.3
  CHC-CoA: 18.4
  2-Methylbutyryl-CoA: 14.7
  fatty_acid: 9.4
  3-Methylbutyryl-CoA: 0.0

PKS_AT (7946..8238): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 75.0%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 234.6
  inactive: 106.3
  Methoxymalonyl-CoA: 59.3
  Methylmalonyl-CoA: 48.9
  Propionyl-CoA: 30.1
  Isobutyryl-CoA: 23.3
  Ethylmalonyl-CoA: 19.0
  Acetyl-CoA: 17.4
  Benzoyl-CoA: 16.2
  2-Methylbutyryl-CoA: 12.2
  CHC-CoA: 9.8
  fatty_acid: 8.6
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (9768..10060): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 75.0%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 237.6
  inactive: 109.0
  Methoxymalonyl-CoA: 55.2
  Methylmalonyl-CoA: 52.7
  Propionyl-CoA: 30.2
  Ethylmalonyl-CoA: 24.0
  Isobutyryl-CoA: 19.3
  Acetyl-CoA: 18.9
  Benzoyl-CoA: 18.7
  CHC-CoA: 15.3
  trans-1,2-CPDA: 14.8
  2-Methylbutyryl-CoA: 12.1
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (8653360...8676621)
HRD51_RS38355
  RRE type: Lanthipeptide_LanB_RRE
  Location: 176 - 281
  Score: 52.5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CatR | H2O2-responsive repressor
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CP054019.1 - Region 37 - RRE-containing,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: 8,841,110 - 8,881,436 nt. (total: 40,327 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])
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
HRD51_RS38880: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Lyases: cyclase
HRD51_RS38885: 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 | RRE-containing | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000683.3 |  |  | 0.45 | terpene | avermitilol | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001910.4 |  |  | 0.13 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001911.3 |  |  | 0.12 | terpene | raimonol | Streptomyces anulatus
BGC0001483.4 |  |  | 0.10 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001840.2 |  |  | 0.09 | NRPS, PKS | detoxin S1 | Streptomyces sp. NRRL S-325
BGC0001197.5 |  |  | 0.09 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000603.5 |  |  | 0.09 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0002582.3 |  |  | 0.08 | NRPS | guanipiperazine A, guanipiperazine B | Streptomyces chrestomyceticus
BGC0002805.2 |  |  | 0.07 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0001334.5 |  |  | 0.07 | other (other) | caldoniamide A, cladoniamide B, cladoniamide C7, cladoniamide D, cladoniamide E, cladoniamide F, cladoniamide G | Streptomyces uncialis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000683.3 |  | 0.76 | terpene | avermitilol | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001910.4 |  | 0.44 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001911.3 |  | 0.42 | terpene | raimonol | Streptomyces anulatus
BGC0000603.5 |  | 0.37 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0001364.3 |  | 0.36 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0001840.2 |  | 0.36 | NRPS, PKS | detoxin S1 | Streptomyces sp. NRRL S-325
BGC0001197.5 |  | 0.36 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001483.4 |  | 0.35 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000143.5 |  | 0.34 | PKS | salinomycin | Streptomyces albus
BGC0001441.5 |  | 0.32 | other (other) | belactosin A, belactosin C | Streptomyces sp.

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

No significant matches found.

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:
HRD51_RS38885: T1TS
Domain 1 (4 - 318): Type 1 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 26.54 out of 32.74
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.79 out of 20.97
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.83 out of 28.19
Confidence: medium
Additional weak hits (21):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.85 out of 26.12
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 30.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.38 out of 29.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.27 out of 36.54
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.93 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.48 out of 27.78
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.48 out of 31.73
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.76 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.76 out of 30.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.81 out of 20.97
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 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.52 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.05 out of 35.63
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: 23.20 out of 30.11
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.94 out of 29.65
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.57 out of 28.19
Confidence: weak
RREFinder
Terpene
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (8841109...8863107)
HRD51_RS38805
  RRE type: Thiopeptide_F_RRE
  Location: 6 - 89
  Score: 74.3
  RRE type: Heterocycloanthracin_C_RRE
  Location: 8 - 99
  Score: 44.1

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CcpA | Catabolite control protein A
FuR variant 2 | Ferric Uptake Regulator
ZuR variant 1 | Zinc-responsive repressor

NZ_CP054019.1 - Region 38 - 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: 8,952,500 - 8,973,474 nt. (total: 20,975 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 electron transfer
HRD51_RS39280: flavodoxin

smcogs
  SMCOG1134: flavodoxin

HRD51_RS39350: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: aminotransferase methyltransferase
HRD51_RS39340: methyltransferase

smcogs
  SMCOG1248: methyltransferase

HRD51_RS39365: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: dehalogenase
HRD51_RS39275: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Ligases: synthetase
HRD51_RS39315: 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
--- | --- | --- | --- | --- | ---
BGC0001610.5 |  | 0.50 | other (other) | gougerotin | Streptomyces ahygroscopicus subsp. wuzhouensis
BGC0002007.2 |  | 0.41 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0001862.4 |  | 0.40 | ribosomal | pallidocin | Aeribacillus pallidus
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0000906.3 |  | 0.40 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000905.5 |  | 0.40 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000678.5 |  | 0.40 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001774.5 |  | 0.39 | other (other) | spicamycin | Streptomyces fimbriatus
BGC0001529.5 |  | 0.39 | 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
BGC0002047.2 |  | 0.39 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001610.5 |  | 0.50 | other (other) | gougerotin | Streptomyces ahygroscopicus subsp. wuzhouensis
BGC0002007.2 |  | 0.41 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0001862.4 |  | 0.40 | ribosomal | pallidocin | Aeribacillus pallidus
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0000906.3 |  | 0.40 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000905.5 |  | 0.40 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000678.5 |  | 0.40 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001774.5 |  | 0.39 | other (other) | spicamycin | Streptomyces fimbriatus
BGC0001529.5 |  | 0.39 | 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
BGC0002047.2 |  | 0.39 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis

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:
HRD51_RS39315: PT_FPPS_like
Domain 1 (39 - 310): 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:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.36 out of 25.31
Confidence: medium
Additional weak hits (2):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.98 out of 33.14
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
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
--- | ---
CatR | H2O2-responsive repressor
MexT | Global virulence regulator

NZ_CP054019.1 - Region 39 - NRPS,lanthipeptide-class-ii,other
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 9,068,958 - 9,143,501 nt. (total: 74,544 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
lanthipeptide-class-ii: cds(LANC_like and DUF4135)
other: (Neocarzinostat or bcpB or frbD or mitE or prnB or CaiA or bacilysin or orf2_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
Lanthipeptides
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
HRD51_RS39905: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

HRD51_RS39915: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

HRD51_RS39960: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

HRD51_RS40015: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

Hydrolases: hydrolase phosphatase
HRD51_RS39975: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

HRD51_RS39985: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

HRD51_RS40110: inositol monophosphatase

smcogs
  SMCOG1207: inositol monophosphatase

Lyases: cyclase
HRD51_RS39925: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Ligases: ligase synthase
HRD51_RS39950: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

HRD51_RS40045: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

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 | lanthipeptide-class-ii | other | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001873.3 |  |  |  | 0.47 | NRPS | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0000342.4 |  |  |  | 0.35 | NRPS | enniatin | Fusarium equiseti
BGC0001833.4 |  |  |  | 0.34 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  |  |  | 0.34 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  |  |  | 0.34 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  |  |  | 0.33 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  | 0.33 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  | 0.33 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  |  | 0.33 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  |  |  | 0.32 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001873.3 |  | 0.77 | NRPS | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.66 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

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 HRD51_RS39925

HRD51_RS42010
Leader:
MSDDLLGTYDETQLIEMSQEPEQESAPNA
Core:
S Q I G C S F S F C F R D
Core with dehydrations:
Dha Q I G Cys Dha F Dha F Cys F R D

#### antiSMASH-DB 4.0 matches for HRD51_RS42010

100.0%
NZ_CP003987.1 and 5 others:
NZ_CP047146.1 Lanthipeptides: GR130_RS41340_lanthipeptide NZ_CP054019.1 Lanthipeptides: HRD51_RS42010_lanthipeptide NZ_CP070326.1 Lanthipeptides: allorf_7791541_7791669_lanthipeptide NZ_CP095749.1 Lanthipeptides: MOV08_RS01935_lanthipeptide NZ_JAPTYM010000001.1 Lanthipeptides: O1M07_RS01425_lanthipeptide
Lanthipeptides: allorf_00521316_00521444_lanthipeptide
1
S Q I G C S F S F C F R D
13
S Q I G C S F S F C F R D
1
S Q I G C S F S F C F R D
13
17.9%
NZ_JAQFWW010000005.1:
Lanthipeptides: allorf_186247_186390_lanthipeptide
1
S Q I G C S F S F
9
S Q+G C S+
13
S Q L G C Y L S Y
21
allorf_9072958_9073107
Leader:
MGLQEFLRTRAGAHREIRTMCGA
Core:
R H S E R P H C C H A P P H A Q R E S L S T G F A S
Core with dehydrations:
R H Dha E R P H Cys Cys H A P P H A Q R E Dha L Dha Dhb G F A Dha

#### antiSMASH-DB 4.0 matches for allorf_9072958_9073107

100.0%
NZ_CP054019.1:
Lanthipeptides: allorf_9072958_9073107_lanthipeptide
1
R H S E R P H C C H A P P H A Q R E S L S T G F A S
26
R H S E R P H C C H A P P H A Q R E S L S T G F A S
1
R H S E R P H C C H A P P H A Q R E S L S T G F A S
26
96.2%
NZ_CP070326.1:
Lanthipeptides: allorf_7802999_7803148_lanthipeptide
1
R H S E R P H C C H A P P H A Q R E S L S T G F A S
26
R H S E R P H C C H A P P H A Q R E S L S T F A S
1
R H S E R P H C C H A P P H A Q R E S L S T D F A S
26
34.6%
NZ_CP059997.1:
Lanthipeptides: allorf_02572182_02572382_lanthipeptide
2
H S E R P H C C H A P P H A Q R E S L S T G
23
+S R P C ++ P A+R T G
1
N S T R P P C A Y S-P C A R R P G F L T G
21
with 3 more sequence matches
28.6%
NZ_CP071090.1:
Lanthipeptides: allorf_11048315_11048452_lanthipeptide
4
E R P H C C---H A P P H A Q R E S L S T
22
E R P C A P H A R ++ T
2
E R P R V C K S I Q A P T H A M R C T V V T
23
26.9%
NZ_CP014168.1:
Lassopeptides: allorf_2423975_2424094_lassopeptide
12
P P H A Q R E S L S T G F
24
P A++E S L G F
3
P I G A K Q E S L M V G F
15
26.9%
NZ_FMWX01000015.1:
Lassopeptides: allorf_13438_13626_lassopeptide
12
P P H A Q R E S L S T G F
24
P A++E S L G F
3
P I G A R Q E S L M V G F
15
allorf_9072976_9073158
Leader:
MAQSGGSERGGDSRRACSGG
Core:
E A C R K A F P L G M W W R V T A M R S L R M A R P A H R P N F A V C P G T G P
Core with dehydrations:
E A Cys R K A F P L G M W W R V Dhb A M R Dha L R M A R P A H R P N F A V Cys P G Dhb G P

#### antiSMASH-DB 4.0 matches for allorf_9072976_9073158

100.0%
NZ_CP054019.1:
Lanthipeptides: allorf_9072976_9073158_lanthipeptide
1
E A C R K A F P L G M W W R V T A M R S L R M A R P A H R P N F A V C P G T G P
40
E A C R K A F P L G M W W R V T A M R S L R M A R P A H R P N F A V C P G T G P
1
E A C R K A F P L G M W W R V T A M R S L R M A R P A H R P N F A V C P G T G P
40
97.5%
NZ_CP070326.1:
Lanthipeptides: allorf_7802948_7803130_lanthipeptide
1
E A C R K A F P L G M W W R V T A M R S L R M A R P A H R P N F A V C P G T G P
40
E C R K A F P L G M W W R V T A M R S L R M A R P A H R P N F A V C P G T G P
1
E V C R K A F P L G M W W R V T A M R S L R M A R P A H R P N F A V C P G T G P
40
allorf_9073053_9073163
Leader:
MSWRRAAAARGA
Core:
E I L D V P A Q E A K P V E R L S R W A C G G A
Core with dehydrations:
E I L D V P A Q E A K P V E R L Dha R W A Cys G G A

#### antiSMASH-DB 4.0 matches for allorf_9073053_9073163

100.0%
NZ_CP054019.1:
Lanthipeptides: allorf_9073053_9073163_lanthipeptide
1
E I L D V P A Q E A K P V E R L S R W A C G G A
24
E I L D V P A Q E A K P V E R L S R W A C G G A
1
E I L D V P A Q E A K P V E R L S R W A C G G A
24
95.8%
NZ_CP070326.1:
Lanthipeptides: allorf_7802943_7803053_lanthipeptide
1
E I L D V P A Q E A K P V E R L S R W A C G G A
24
E I L D V P A Q E A K V E R L S R W A C G G A
1
E I L D V P A Q E A K S V E R L S R W A C G G A
24
36.0%
NZ_CP022753.1 and 1 other:
NZ_CP022753.1 Lanthipeptides: CDO52_RS14300_lanthipeptide
Lanthipeptides: CDO52_RS14300_lanthipeptide
6
P A Q E A K P V E R L S R W A C G G
23
P Q E+ R L S C G G
2
P M Q E S----R L S V I T C G G
15
with 1 more sequence matches
16.2%
NZ_CP012752.1:
Lanthipeptides: allorf_02330276_02330440_lanthipeptide
13
V E R L S R W A C G
22
V+ L W A C G
27
V D H L R E W A C G
36
allorf_9075074_9075199
Leader:
MHEVAGG
Core:
A A R M P G S A F A M A R P P H D R C A A G R P S R R G R D R R E G
Core with dehydrations:
A A R M P G Dha A F A M A R P P H D R Cys A A G R P Dha R R G R D R R E G

#### antiSMASH-DB 4.0 matches for allorf_9075074_9075199

100.0%
NZ_CP054019.1 and 1 other:
NZ_CP070326.1 Lanthipeptides: allorf_7800907_7801032_lanthipeptide
Lanthipeptides: allorf_9075074_9075199_lanthipeptide
1
A A R M P G S A F A M A R P P H D R C A A G R P S R R G R D R R E G
34
A A R M P G S A F A M A R P P H D R C A A G R P S R R G R D R R E G
1
A A R M P G S A F A M A R P P H D R C A A G R P S R R G R D R R E G
34

#### 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:
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.33 out of 29.51
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26
Confidence: strong
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 (16):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.18 out of 32.74
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.59 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.29 out of 36.54
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.30 out of 24.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.20 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.69 out of 29.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.57 out of 20.01
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.44 out of 29.65
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.65 out of 22.40
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75
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
Lanthipeptides
NRPS/PKS products
NRPS/PKS substrates
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.

HRD51_RS42010 - Class II
  Cleavage pHMM score: -6.40
  RODEO score: 0
  Monoisotopic mass: 1441.6 Da
  Molecular weight: 1442.6 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1460.6 Da N = 1
allorf_9072958_9073107 - Class II
  Cleavage pHMM score: -1.70
  RODEO score: 0
  Monoisotopic mass: 2807.3 Da
  Molecular weight: 2809.0 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2827.1 Da N = 1
    2845.1 Da N = 2
    2863.1 Da N = 3
allorf_9072976_9073158 - Class II
  Cleavage pHMM score: -7.00
  RODEO score: 0
  Monoisotopic mass: 4470.3 Da
  Molecular weight: 4473.3 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4491.3 Da N = 1
allorf_9073053_9073163 - Class II
  Cleavage pHMM score: -4.90
  RODEO score: 0
  Monoisotopic mass: 2576.3 Da
  Molecular weight: 2577.9 Da
  Number of bridges: 1
allorf_9075074_9075199 - Class II
  Cleavage pHMM score: -2.90
  RODEO score: 0
  Monoisotopic mass: 3682.9 Da
  Molecular weight: 3685.1 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3703.2 Da N = 1

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 64, location 9068957 - 9143501:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 65, location 9068957 - 9116205:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser - X)

Direct lookup in NORINE database: strict or relaxed
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).
HRD51_RS39950: Ser - X
Search NORINE for peptide: strict or relaxed
AMP-binding (480..889): 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:
    RWMTFDVSVWEWHFFCSGEVNLYGPTEATVDVSY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1536..1938): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    pro (Pro)
  Single AA prediction:
    pro (Pro)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQAFDVSFQESFLISSGEENQYGPTETHVATAF
  Nearest Stachelhaus code(s):
    Aze DVQFISQIAK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
DosR | Hypoxia stress response regulator

NZ_CP054019.1 - Region 40 - 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: 9,164,279 - 9,185,337 nt. (total: 21,059 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: methyltransferase
HRD51_RS40285: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: cyclase
HRD51_RS40290: 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
--- | --- | --- | --- | --- | ---
BGC0000658.3 |  | 0.80 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3 |  | 0.80 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000657.5 |  | 0.64 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0001992.3 |  | 0.35 | other (other) | thioguanine | Erwinia amylovora CFBP1430
BGC0002621.2 |  | 0.35 | other (other) | angustmycin A, angustmycin B, angustmycin C, aristeromycin, arabinofuranosyladenine | Streptomyces angustmyceticus
BGC0000885.3 |  | 0.34 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000678.5 |  | 0.34 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000821.5 |  | 0.32 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0002194.3 |  | 0.32 | PKS | epipyrone A | Epicoccum nigrum
BGC0001778.5 |  | 0.32 | other (other) | showdomycin | Streptomyces showdoensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000658.3 |  | 0.80 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3 |  | 0.80 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000657.5 |  | 0.64 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0001992.3 |  | 0.35 | other (other) | thioguanine | Erwinia amylovora CFBP1430
BGC0002621.2 |  | 0.35 | other (other) | angustmycin A, angustmycin B, angustmycin C, aristeromycin, arabinofuranosyladenine | Streptomyces angustmyceticus
BGC0000885.3 |  | 0.34 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000678.5 |  | 0.34 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000821.5 |  | 0.32 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0002194.3 |  | 0.32 | PKS | epipyrone A | Epicoccum nigrum
BGC0001778.5 |  | 0.32 | other (other) | showdomycin | Streptomyces showdoensis

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
--- | --- | --- | --- | --- | ---
monoterpene |  | 2-methylisoborneol | C11 | C1-C6 | OH
monoterpene |  | 2-methylenebornane | C11 | C1-C6 | none

Genes with terpene domains:
HRD51_RS40290: T1TS
Domain 1 (24 - 346): Type 1 terpene synthase
Subtype: 2-Methylisoborneol synthase type

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.22 out of 18.46
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
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 (9):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.65 out of 27.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.75 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.98 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.91 out of 20.01
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.85 out of 29.25
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.10 out of 39.62
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.14 out of 28.19
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.34 out of 27.04
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP054019.1 - Region 41 - T1PKS,arylpolyene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 9,273,276 - 9,357,587 nt. (total: 84,312 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))
arylpolyene: (APE_KS1 or APE_KS2)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase oxidoreductase oxygenase
HRD51_RS40800: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

HRD51_RS40805: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

HRD51_RS40820: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

HRD51_RS40865: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

HRD51_RS40870: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

HRD51_RS40890: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

HRD51_RS40900: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

HRD51_RS40940: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

HRD51_RS40975: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

HRD51_RS40980: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

HRD51_RS41005: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

HRD51_RS41095: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase acylase
HRD51_RS40815: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

HRD51_RS40950: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

HRD51_RS40970: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase
HRD51_RS40775: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Ligases: ligase synthase
HRD51_RS40930: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

HRD51_RS40955: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HRD51_RS41015: 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 | arylpolyene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001254.3 |  |  | 0.54 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001276.3 |  |  | 0.33 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  |  | 0.33 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001273.3 |  |  | 0.33 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.33 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001917.4 |  |  | 0.32 | PKS | 5aTHQ-9i, 5aTHQ-9n, 5aTHQ-10a, STAMs-9i, STAMs-9n | Streptomyces nigrescens
BGC0001160.5 |  |  | 0.30 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  | 0.29 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002191.2 |  |  | 0.29 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  |  | 0.29 | PKS | alternariol | Parastagonospora nodorum SN15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.66 | PKS | (-)-Mellein | Parastagonospora nodorum
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
BGC0002191.2 |  | 0.62 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002192.3 |  | 0.60 | PKS | FR901512 | fungal sp. No.14919

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:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.81 out of 27.04
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.27 out of 23.79
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.46 out of 27.55
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.99 out of 26.85
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.73 out of 20.97
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: 28.62 out of 30.11
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.38 out of 23.79
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.76 out of 25.31
Confidence: medium
Additional weak hits (29):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.87 out of 21.55
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.50 out of 25.75
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.92 out of 21.55
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.71 out of 28.14
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.17 out of 21.55
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.69 out of 23.43
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.24 out of 30.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.64 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.15 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.96 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.37 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.62 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.99 out of 28.14
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 20.27 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.09 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.89 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.56 out of 26.06
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.02 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.53 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.08 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.99 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.84 out of 30.98
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.71 out of 27.04
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.25 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.52 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.84 out of 33.14
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.67 out of 20.01
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 69, location 9273275 - 9357587:
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

For candidate cluster 70, location 9273275 - 9320769:
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).
HRD51_RS40865: pk
PKS_AT (551..846): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  Methylmalonyl-CoA: 70.8%
  CE-Malonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 112.3
  Methoxymalonyl-CoA: 99.0
  Malonyl-CoA: 88.8
  Ethylmalonyl-CoA: 69.5
  Isobutyryl-CoA: 68.5
  Propionyl-CoA: 61.7
  trans-1,2-CPDA: 51.6
  2-Methylbutyryl-CoA: 51.3
  fatty_acid: 51.0
  CHC-CoA: 43.4
  Benzoyl-CoA: 39.3
  Acetyl-CoA: 36.7
  3-Methylbutyryl-CoA: 27.8
  inactive: 16.3

HRD51_RS40930: X
AMP-binding (21..400): 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:
    NRTLHQYGLSVLDAGVGGALDGYGLSELGNVALA
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

HRD51_RS40970: mxmal
PKS_AT (54..288): mxmal
ATSignature: (unknown)
No matches above 50%
minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 22.9
  Methylmalonyl-CoA: 10.5
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-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

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
CatR | H2O2-responsive repressor
CcpA | Catabolite control protein A
CelR | Cellobiose uptake repressor
DasR | N-acetylglucosamine dependent repressor
GnfM | Regulator of nitrogen-fixation genes
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CP054019.1 - Region 42 - lanthipeptide-class-iv
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: 9,428,878 - 9,451,634 nt. (total: 22,757 nt) Show pHMM detection rules used
Region on contig edge.
lanthipeptide-class-iv: (cds(LANC_like and Pkinase) and not micKC)

#### 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
HRD51_RS41575: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

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

Reference | lanthipeptide-class-iv | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002337.2 |  | 0.57 | ribosomal | class IV lanthipeptide, SflA | Streptomyces sp. NRRL S-1022
BGC0000563.4 |  | 0.46 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  | 0.46 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000519.4 |  | 0.40 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002318.2 |  | 0.38 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000502.5 |  | 0.32 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001561.4 |  | 0.30 | NRPS | curacomycin | Streptomyces curacoi
BGC0000874.5 |  | 0.29 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0002015.4 |  | 0.27 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001582.4 |  | 0.24 | NRPS | ecumicin | Nonomuraea sp. MJM5123

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002337.2 |  | 0.57 | ribosomal | class IV lanthipeptide, SflA | Streptomyces sp. NRRL S-1022
BGC0000563.4 |  | 0.46 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  | 0.46 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000519.4 |  | 0.40 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002318.2 |  | 0.38 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000502.5 |  | 0.32 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001561.4 |  | 0.30 | NRPS | curacomycin | Streptomyces curacoi
BGC0000874.5 |  | 0.29 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0002015.4 |  | 0.27 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001582.4 |  | 0.24 | NRPS | ecumicin | Nonomuraea sp. MJM5123

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:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.39 out of 25.31
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.35 out of 18.57
Confidence: medium
Additional weak hits (2):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.33 out of 27.78
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.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
ToxT | Regulator of MSHA biosynthesis