BGC0001042 - Region 1 - NRPS,PKS-like,T1PKS,hglE-KS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key. More detailed help is available here.
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)) hglE-KS: (hglE or hglD) PKS-like: (t2pks2 or ksIII)
Legend:
core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
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Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
ClusterBlast
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
Pfam domains
TIGRFAM domains
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.
sfaN: 3-oxoacyl-(acyl carrier protein) synthase III
smcogs
SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III
Similar gene clusters
Shows areas that are similar to the current region to a reference database. Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Shows regions from the antiSMASH 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 a reference name to open that entry in the antiSMASH database (if applicable).
Location:
Identifier
Identity
Coverage
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: 18.54 out of 23.79
Confidence: medium
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: 18.92 out of 20.47
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes Species: Geobacter sulfurreducens PCA Score: 21.64 out of 27.55
Confidence: medium
Additional weak hits (15):
ToxT
Description: Regulator of MSHA biosynthesis Species: Vibrio cholerae O395 Score: 13.04 out of 18.57
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator Species: Corynebacterium glutamicum ATCC 13032 Score: 23.54 out of 30.22
Confidence: weak
MexT
Description: Global virulence regulator Species: Pseudomonas aeruginosa PAO1 Score: 15.53 out of 21.84
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator Species: Pseudomonas putida KT2440 Score: 17.82 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator Species: Pseudomonas putida KT2440 Score: 17.84 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator Species: Bacillus, Pseudomonas, Yersinia sp. Score: 15.31 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator Species: Bacillus & Staphylococcus sp. Score: 12.33 out of 28.14
Confidence: weak
CcpA
Description: Catabolite control protein A Species: Streptococcus & Clostridium sp. Score: 15.82 out of 20.97
Confidence: weak
MexT
Description: Global virulence regulator Species: Pseudomonas aeruginosa PAO1 Score: 16.64 out of 21.84
Confidence: weak
MexT
Description: Global virulence regulator Species: Pseudomonas aeruginosa PAO1 Score: 17.30 out of 21.84
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator Species: Pseudomonas putida KT2440 Score: 18.18 out of 26.33
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator Species: Geobacter sulfurreducens PCA Score: 17.25 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator Species: Geobacter sulfurreducens PCA Score: 17.10 out of 36.54
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor Species: Streptomyces coelicolor Score: 18.59 out of 22.40
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes Species: Streptomyces coelicolor Score: 20.46 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 Pfam domain annotation
Shows Pfam domains found in each gene within the region. Click on each domain for more information about the domain's accession, location, and description. Domains with a bold border have Gene Ontology information.
Selected features only
Expand to show all names
Detailed TIGRFAM domain annotation
Shows TIGRFAM domains found in each gene within the region. Click on each domain for more information about the domain's accession, location, and description.
Selected features only
Expand to show all names
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details. A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 0 - 118372:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account
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).
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