Select genomic region:
Overview
1.1
1.2

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

NZ_CP081105.1

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1 | NRPS | 1,444,722 | 1,488,579 | colicin V | RiPP | 3%
Region 2 | thiopeptide | 1,842,837 | 1,869,139 | O-antigen | Saccharide | 14%

NZ_CP081105.1 - Region 1 - 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: 1,444,722 - 1,488,579 nt. (total: 43,858 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
NRPS/PKS domains
MIBiG comparison
KnownClusterBlast
NRPS/PKS modules
Pfam domains
TIGRFAM domains
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 glossary is available here.
Selected features only
Show module domains
Similar gene clusters
Shows careas 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
--- | --- | --- | --- | --- | ---
BGC0001185.1 |  | 0.36 | NRP | bacillibactin | Bacillus velezensis FZB42
BGC0001615.1 |  | 0.32 | NRP | hexose-palythine-serine, hexose-shinorine | Heteroscytonema crispum UCFS10
BGC0000401.1 |  | 0.30 | NRP | paenibactin | Paenibacillus elgii B69
BGC0001184.1 |  | 0.27 | Other | bacilysin | Bacillus velezensis FZB42
BGC0000888.1 |  | 0.26 | Other | bacilysin | Bacillus sp. CS93
BGC0001132.1 |  | 0.25 | NRP | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.1 |  | 0.25 | NRP | icosalide A, icosalide B | Burkholderia gladioli
BGC0001197.1 |  | 0.24 | Polyketide | frankiamicin | Frankia sp. EAN1pec
BGC0001844.1 |  | 0.23 | NRP | holrhizin | Paraburkholderia rhizoxinica HKI 454
BGC0000836.1 |  | 0.23 | Other | APE Ec | Escherichia coli CFT073

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001185.1 |  | 0.68 | NRP | bacillibactin | Bacillus velezensis FZB42
BGC0001615.1 |  | 0.65 | NRP | hexose-palythine-serine, hexose-shinorine | Heteroscytonema crispum UCFS10
BGC0000401.1 |  | 0.64 | NRP | paenibactin | Paenibacillus elgii B69
BGC0001184.1 |  | 0.60 | Other | bacilysin | Bacillus velezensis FZB42
BGC0000888.1 |  | 0.60 | Other | bacilysin | Bacillus sp. CS93
BGC0001132.1 |  | 0.58 | NRP | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.1 |  | 0.58 | NRP | icosalide A, icosalide B | Burkholderia gladioli
BGC0001197.1 |  | 0.57 | Polyketide | frankiamicin | Frankia sp. EAN1pec
BGC0001844.1 |  | 0.57 | NRP | holrhizin | Paraburkholderia rhizoxinica HKI 454
BGC0000836.1 |  | 0.56 | Other | APE Ec | Escherichia coli CFT073

Similar known gene clusters
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.
Click on reference genes to show details of similarities to genes within the current region.
Click on an accession to open that entry in the MiBIG database.
Module view
Shows module structures for each candidate 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.
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
NRPS/PKS products
NRPS/PKS monomers
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 1444721 - 1488579:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ser)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS monomer predictions
Shows the predicted monomers for each adynelation 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).

ctg1_1336: ser
  Search NORINE for peptide: strict or relaxed
  AMP-binding (456..856): ser
  NRPSPredictor2: ser
  SVM prediction details:
    NOTE: outside applicability domain
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      ser, thr, dhpg, hpg
    Small clusters prediction:
      ser
    Single AA prediction:
      ser
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DVWHFSLVDK
    Nearest Stachelhaus code:
      ser
    Stachelhaus code match:
      100% (strong)
ctg1_1343: dhb
  Search NORINE for peptide: strict or relaxed
  AMP-binding (34..437): dhb
  NRPSPredictor2: dhb
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aromatic
    Large clusters prediction:
      dhb, sal
    Small clusters prediction:
      dhb, sal
    Single AA prediction:
      dhb
  Stachelhaus prediction details:
    Stachelhaus sequence:
      aMPSQGVVNK
    Nearest Stachelhaus code:
      dhb
    Stachelhaus code match:
      90% (moderate)

NZ_CP081105.1 - Region 2 - thiopeptide
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: 1,842,837 - 1,869,139 nt. (total: 26,303 nt) Show pHMM detection rules used
thiopeptide: ((YcaO or TIGR03882) and ((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or PF07366 or PF06968 or PF04055) or thiostrepton)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
MIBiG comparison
KnownClusterBlast
Thiopeptides
Pfam domains
TIGRFAM domains
Similar gene clusters
Shows careas 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 | thiopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000784.1 |  | 0.25 | Saccharide | O-antigen | Pseudomonas aeruginosa
BGC0000781.1 |  | 0.16 | Saccharide | O-antigen | Pseudomonas aeruginosa
BGC0001285.1 |  | 0.09 | Other (Fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0001441.1 |  | 0.07 | Other | belactosin A, belactosin C | Streptomyces sp.
BGC0000981.1 |  | 0.07 | NRP, Polyketide | cylindrospermopsin | Aphanizomenon sp. 10E6
BGC0001302.1 |  | 0.06 | Other | lomofungin | Streptomyces lomondensis
BGC0002012.1 |  | 0.05 | Polyketide | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772
BGC0001283.1 |  | 0.05 | Polyketide | arsono-polyketide | Streptomyces lividans 1326
BGC0000957.1 |  | 0.04 | NRP, Polyketide | mycotrienin I | Streptomyces sp. XZQH13
BGC0000123.1 |  | 0.03 | Polyketide | phoslactomycin B | Streptomyces sp. HK803

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000784.1 |  | 0.58 | Saccharide | O-antigen | Pseudomonas aeruginosa
BGC0000781.1 |  | 0.47 | Saccharide | O-antigen | Pseudomonas aeruginosa
BGC0001285.1 |  | 0.34 | Other (Fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0001441.1 |  | 0.29 | Other | belactosin A, belactosin C | Streptomyces sp.
BGC0000981.1 |  | 0.28 | NRP, Polyketide | cylindrospermopsin | Aphanizomenon sp. 10E6
BGC0001302.1 |  | 0.24 | Other | lomofungin | Streptomyces lomondensis
BGC0002012.1 |  | 0.23 | Polyketide | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772
BGC0001283.1 |  | 0.22 | Polyketide | arsono-polyketide | Streptomyces lividans 1326
BGC0000957.1 |  | 0.19 | NRP, Polyketide | mycotrienin I | Streptomyces sp. XZQH13
BGC0000123.1 |  | 0.15 | Polyketide | phoslactomycin B | Streptomyces sp. HK803

Similar known gene clusters
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.
Click on reference genes to show details of similarities to genes within the current region.
Click on an accession to open that entry in the MiBIG database.
Thiopeptide predictions
Lists the possible core peptides for each biosynthetic enzyme, including the predicted class. Each core peptide shows the leader and core peptide sequences, separated by a dash. Predicted tail sequences are also shown.
No core peptides found.
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
Thiopeptides
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.