Select genomic region:
Overview
1.1
1.2
1.3

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

NC_022567.1

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1 | NRPS | 65,579 | 118,816 |
Region 2 | RRE-containing | 359,838 | 380,095 |
Region 3 | betalactone | 1,197,201 | 1,221,159 |

NC_022567.1 - 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: 65,579 - 118,816 nt. (total: 53,238 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
--- | --- | --- | --- | --- | ---
BGC0001806.1 |  | 0.23 | NRP | tolaasin A | Pseudomonas tolaasii
BGC0000412.1 |  | 0.23 | NRP | pyochelin | Pseudomonas aeruginosa PAO1
BGC0000410.1 |  | 0.22 | NRP | pseudomonine | Pseudomonas fluorescens
BGC0000396.1 |  | 0.22 | NRP | nodularin | Nostoc sp. 73.1
BGC0001699.1 |  | 0.21 | Polyketide | nidulanin A | Aspergillus nidulans FGSC A4
BGC0001758.1 |  | 0.21 | NRP | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.1 |  | 0.21 | NRP | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001185.1 |  | 0.21 | NRP | bacillibactin | Bacillus velezensis FZB42
BGC0001833.1 |  | 0.21 | NRP | icosalide A, icosalide B | Burkholderia gladioli
BGC0000460.1 |  | 0.21 | NRP | vulnibactin | Vibrio vulnificus CMCP6

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001806.1 |  | 0.56 | NRP | tolaasin A | Pseudomonas tolaasii
BGC0000412.1 |  | 0.56 | NRP | pyochelin | Pseudomonas aeruginosa PAO1
BGC0000410.1 |  | 0.55 | NRP | pseudomonine | Pseudomonas fluorescens
BGC0000396.1 |  | 0.54 | NRP | nodularin | Nostoc sp. 73.1
BGC0001699.1 |  | 0.54 | Polyketide | nidulanin A | Aspergillus nidulans FGSC A4
BGC0001758.1 |  | 0.54 | NRP | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.1 |  | 0.54 | NRP | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001185.1 |  | 0.53 | NRP | bacillibactin | Bacillus velezensis FZB42
BGC0001833.1 |  | 0.53 | NRP | icosalide A, icosalide B | Burkholderia gladioli
BGC0000460.1 |  | 0.53 | NRP | vulnibactin | Vibrio vulnificus CMCP6

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.

No matches found.

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 65578 - 118816:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (cys - cys) + (Me-cys)

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_70: cys
  Search NORINE for peptide: strict or relaxed
  AMP-binding (533..923): cys
  NRPSPredictor2: cys
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      cys
    Small clusters prediction:
      cys
    Single AA prediction:
      cys
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DLYNLSLIWK
    Nearest Stachelhaus code:
      cys
    Stachelhaus code match:
      100% (strong)
ctg1_71: cys - cys
  Search NORINE for peptide: strict or relaxed
  AMP-binding (724..1095): cys
  NRPSPredictor2: cys
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      cys
    Small clusters prediction:
      cys
    Single AA prediction:
      cys
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DLFNLSmIWK
    Nearest Stachelhaus code:
      cys
    Stachelhaus code match:
      90% (moderate)
  AMP-binding (2050..2421): cys
  NRPSPredictor2: cys
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      cys
    Small clusters prediction:
      cys
    Single AA prediction:
      cys
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DLFNLSmIWK
    Nearest Stachelhaus code:
      cys
    Stachelhaus code match:
      90% (moderate)
ctg1_74: X
  Search NORINE for peptide: strict or relaxed
  AMP-binding (17..418): X
  NRPSPredictor2: dhb, sal
  SVM prediction details:
    Predicted physicochemical class:
      N/A
    Large clusters prediction:
      N/A
    Small clusters prediction:
      dhb, sal
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      PLPthGsLtK
    Nearest Stachelhaus code:
      sal
    Stachelhaus code match:
      60% (weak)

NC_022567.1 - Region 2 - RRE-containing
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 359,838 - 380,095 nt. (total: 20,258 nt) Show pHMM detection rules used
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
Pfam 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 | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000774.1 |  | 0.13 | Saccharide | lipopolysaccharide | Xanthomonas campestris pv. campestris

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000774.1 |  | 0.42 | Saccharide | lipopolysaccharide | Xanthomonas campestris pv. campestris

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.

No matches 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
NC_022567.1 - Region 3 - 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: 1,197,201 - 1,221,159 nt. (total: 23,959 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
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 | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000904.1 |  | 0.21 | Other | FR-900098 | Streptomyces rubellomurinus
BGC0001859.1 |  | 0.20 | Other (Phosphonate) | fosfomycin | Pseudomonas syringae
BGC0000779.1 |  | 0.19 | Saccharide | lipopolysaccharide | Aeromonas piscicola
BGC0000780.1 |  | 0.17 | Saccharide | O&K-antigen | Vibrio parahaemolyticus
BGC0000259.1 |  | 0.17 | Polyketide | prodigiosin | Serratia marcescens
BGC0001897.1 |  | 0.16 | Polyketide | cepacin A | Burkholderia ambifaria IOP40-10
BGC0001137.1 |  | 0.15 | Alkaloid | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0000805.1 |  | 0.14 | Saccharide | moenomycin | Streptomyces viridosporus ATCC 14672
BGC0000774.1 |  | 0.14 | Saccharide | lipopolysaccharide | Xanthomonas campestris pv. campestris
BGC0001925.1 |  | 0.14 | Alkaloid | altemicidin, SB-203207, SB-203208 | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000904.1 |  | 0.54 | Other | FR-900098 | Streptomyces rubellomurinus
BGC0001859.1 |  | 0.52 | Other (Phosphonate) | fosfomycin | Pseudomonas syringae
BGC0000779.1 |  | 0.50 | Saccharide | lipopolysaccharide | Aeromonas piscicola
BGC0000780.1 |  | 0.49 | Saccharide | O&K-antigen | Vibrio parahaemolyticus
BGC0000259.1 |  | 0.49 | Polyketide | prodigiosin | Serratia marcescens
BGC0001897.1 |  | 0.46 | Polyketide | cepacin A | Burkholderia ambifaria IOP40-10
BGC0001137.1 |  | 0.44 | Alkaloid | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0000805.1 |  | 0.44 | Saccharide | moenomycin | Streptomyces viridosporus ATCC 14672
BGC0000774.1 |  | 0.44 | Saccharide | lipopolysaccharide | Xanthomonas campestris pv. campestris
BGC0001925.1 |  | 0.43 | Alkaloid | altemicidin, SB-203207, SB-203208 | Streptomyces sp.

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.

No matches 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