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Overview
1.1
1.2

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

NZ_HE578907.1

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1.1 | ranthipeptide | 145,988 | 167,573 |
Region 1.2 | NRPS | 565,179 | 608,619 | equibactin | NRP | 35%

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1.1 | ranthipeptide | 145,988 | 167,573 |
Region 1.2 | NRPS | 565,179 | 608,619 | equibactin | NRP | 35%

No secondary metabolite regions were found in these records:
  NZ_HE578908.1
  NZ_HE578909.1
  NZ_HE578910.1
  NZ_CAEK01000024 (original name was: NZ_CAEK01000024.1)
  NZ_CAEK01000023 (original name was: NZ_CAEK01000023.1)

Compact view
NZ_HE578907.1 - Region 1 - ranthipeptide
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: 145,988 - 167,573 nt. (total: 21,586 nt) Show pHMM detection rules used
ranthipeptide: (TIGR03973 or SCIFF or (cds(PF04055 and (TIGR04085 or SPASM)) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]) and not (TIGR01716 or subtilosin or TIGR02111 or TIGR03966 or TIGR04103 or YcaO or TIGR03882)))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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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
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 | ranthipeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001387.1 |  | 0.17 | Other | nucleocidin | Streptomyces calvus
BGC0001410.1 |  | 0.15 | Saccharide | polysaccharide A | Bacteroides fragilis
BGC0000786.1 |  | 0.15 | Saccharide | O-antigen | Edwardsiella ictaluri 93-146
BGC0001314.1 |  | 0.15 | Terpene | tirucalla | Arabidopsis thaliana
BGC0000734.1 |  | 0.15 | Saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000739.1 |  | 0.15 | Saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000744.1 |  | 0.15 | Saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000745.1 |  | 0.15 | Saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000741.1 |  | 0.15 | Saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000748.1 |  | 0.14 | Saccharide | capsular polysaccharide | Streptococcus agalactiae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001387.1 |  | 0.49 | Other | nucleocidin | Streptomyces calvus
BGC0001410.1 |  | 0.45 | Saccharide | polysaccharide A | Bacteroides fragilis
BGC0000786.1 |  | 0.45 | Saccharide | O-antigen | Edwardsiella ictaluri 93-146
BGC0001314.1 |  | 0.45 | Terpene | tirucalla | Arabidopsis thaliana
BGC0000734.1 |  | 0.44 | Saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000739.1 |  | 0.44 | Saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000744.1 |  | 0.44 | Saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000745.1 |  | 0.44 | Saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000741.1 |  | 0.44 | Saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000748.1 |  | 0.44 | Saccharide | capsular polysaccharide | Streptococcus agalactiae

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
NZ_HE578907.1 - Region 2 - 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: 565,179 - 608,619 nt. (total: 43,441 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
--- | --- | --- | --- | --- | ---
BGC0000347.1 |  | 0.29 | NRP | equibactin | Streptococcus equi subsp. equi
BGC0000460.1 |  | 0.29 | NRP | vulnibactin | Vibrio vulnificus CMCP6
BGC0000373.1 |  | 0.25 | NRP | holomycin | Streptomyces clavuligerus ATCC 27064
BGC0000343.1 |  | 0.23 | NRP | enterobactin | Pseudomonas sp. J465
BGC0000412.1 |  | 0.22 | NRP | pyochelin | Pseudomonas aeruginosa PAO1
BGC0000889.1 |  | 0.21 | Other | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001479.1 |  | 0.21 | NRP | anabaenopeptin NZ857, nostamide A | Nostoc punctiforme PCC 73102
BGC0001185.1 |  | 0.21 | NRP | bacillibactin | Bacillus velezensis FZB42
BGC0001699.1 |  | 0.21 | Polyketide | nidulanin A | Aspergillus nidulans FGSC A4
BGC0000427.1 |  | 0.21 | NRP | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000347.1 |  | 0.63 | NRP | equibactin | Streptococcus equi subsp. equi
BGC0000460.1 |  | 0.62 | NRP | vulnibactin | Vibrio vulnificus CMCP6
BGC0000373.1 |  | 0.58 | NRP | holomycin | Streptomyces clavuligerus ATCC 27064
BGC0000343.1 |  | 0.57 | NRP | enterobactin | Pseudomonas sp. J465
BGC0000412.1 |  | 0.55 | NRP | pyochelin | Pseudomonas aeruginosa PAO1
BGC0000889.1 |  | 0.54 | Other | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001479.1 |  | 0.54 | NRP | anabaenopeptin NZ857, nostamide A | Nostoc punctiforme PCC 73102
BGC0001185.1 |  | 0.54 | NRP | bacillibactin | Bacillus velezensis FZB42
BGC0001699.1 |  | 0.53 | Polyketide | nidulanin A | Aspergillus nidulans FGSC A4
BGC0000427.1 |  | 0.53 | NRP | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413

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 2, location 565178 - 608619:
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 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_589: cys
  Search NORINE for peptide: strict or relaxed
  AMP-binding (561..959): 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:
      DLFdMSmIWK
    Nearest Stachelhaus code:
      cys
    Stachelhaus code match:
      80% (moderate)
ctg1_590: X
  Search NORINE for peptide: strict or relaxed
  AMP-binding (29..433): X
  NRPSPredictor2: dhb, sal
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aromatic
    Large clusters prediction:
      N/A
    Small clusters prediction:
      dhb, sal
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      PLPgQGiisK
    Nearest Stachelhaus code:
      dhb
    Stachelhaus code match:
      60% (weak)