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Overview
1.1
1.2

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

NZ_CM001773.1

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1.1 | thiopeptide | 1,655,700 | 1,681,972 |
Region 1.2 | betalactone,NRPS-like,NRPS | 3,104,557 | 3,171,910 | turnerbactin | NRP | 15%

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1.1 | thiopeptide | 1,655,700 | 1,681,972 |
Region 1.2 | betalactone,NRPS-like,NRPS | 3,104,557 | 3,171,910 | turnerbactin | NRP | 15%

No secondary metabolite regions were found in these records:
  NZ_CM001853.1
  NZ_CM001854.1
  NZ_CM001855.1

Compact view
NZ_CM001773.1 - Region 1 - 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: 1,655,700 - 1,681,972 nt. (total: 26,273 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
--- | --- | --- | --- | --- | ---
BGC0000619.1 |  | 0.12 | RiPP | gassericin T | Lactobacillus gasseri
BGC0001388.1 |  | 0.12 | RiPP | gassericin E | Lactobacillus gasseri
BGC0001602.1 |  | 0.12 | RiPP | gassericin-T | Lactobacillus gasseri
BGC0000504.1 |  | 0.12 | RiPP | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0001311.1 |  | 0.12 | RiPP | flavecins | Ruminococcus flavefaciens FD-1
BGC0001391.1 |  | 0.11 | RiPP | thusin | Bacillus thuringiensis serovar rongseni
BGC0000555.1 |  | 0.10 | RiPP | staphylococcin C55 α, staphylococcin C55 β | Staphylococcus aureus
BGC0001889.1 |  | 0.10 | RiPP | fusilassin | Thermobifida fusca YX
BGC0001285.1 |  | 0.10 | Other (Fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0001407.1 |  | 0.08 | RiPP | bicereucin | Bacillus cereus SJ1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000619.1 |  | 0.41 | RiPP | gassericin T | Lactobacillus gasseri
BGC0001388.1 |  | 0.41 | RiPP | gassericin E | Lactobacillus gasseri
BGC0001602.1 |  | 0.41 | RiPP | gassericin-T | Lactobacillus gasseri
BGC0000504.1 |  | 0.39 | RiPP | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0001311.1 |  | 0.39 | RiPP | flavecins | Ruminococcus flavefaciens FD-1
BGC0001391.1 |  | 0.39 | RiPP | thusin | Bacillus thuringiensis serovar rongseni
BGC0000555.1 |  | 0.35 | RiPP | staphylococcin C55 α, staphylococcin C55 β | Staphylococcus aureus
BGC0001889.1 |  | 0.35 | RiPP | fusilassin | Thermobifida fusca YX
BGC0001285.1 |  | 0.35 | Other (Fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0001407.1 |  | 0.32 | RiPP | bicereucin | Bacillus cereus SJ1

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.

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.
NZ_CM001773.1 - Region 2 - NRPS,NRPS-like,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: 3,104,557 - 3,171,910 nt. (total: 67,354 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX))
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 | betalactone | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002002.1 |  |  |  | 0.63 | NRP | 1,6-phenazinedimethanol, fontizine A | Serratia fonticola
BGC0001527.1 |  |  |  | 0.62 | Other | basidioferrin | Gelatoporia subvermispora
BGC0001444.1 |  |  |  | 0.57 | Other | caboxamycin | Streptomyces sp. NTK 937
BGC0001538.1 |  |  |  | 0.57 | NRP, Polyketide | caboxamycin | Streptomyces sp. NTK 937
BGC0000375.1 |  |  |  | 0.57 | NRP | indigoidine | Streptomyces chromofuscus
BGC0001758.1 |  |  |  | 0.55 | NRP | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001343.1 |  |  |  | 0.52 | Polyketide | aurachin A, aurachin D | Stigmatella aurantiaca Sg a15
BGC0002000.1 |  |  |  | 0.51 | Polyketide | setomimycin | Streptomyces aurantiacus JA 4570
BGC0000449.1 |  |  |  | 0.50 | NRP | tridecaptin | Paenibacillus terrae
BGC0001723.1 |  |  |  | 0.49 | Polyketide | oviedomycin | Streptomyces antibioticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002002.1 |  | 0.65 | NRP | 1,6-phenazinedimethanol, fontizine A | Serratia fonticola
BGC0001527.1 |  | 0.64 | Other | basidioferrin | Gelatoporia subvermispora
BGC0001444.1 |  | 0.62 | Other | caboxamycin | Streptomyces sp. NTK 937
BGC0001538.1 |  | 0.62 | NRP, Polyketide | caboxamycin | Streptomyces sp. NTK 937
BGC0001343.1 |  | 0.59 | Polyketide | aurachin A, aurachin D | Stigmatella aurantiaca Sg a15
BGC0002000.1 |  | 0.59 | Polyketide | setomimycin | Streptomyces aurantiacus JA 4570
BGC0000236.1 |  | 0.58 | Polyketide | kinamycin | Streptomyces murayamaensis
BGC0001596.1 |  | 0.58 | Polyketide | fluostatins M-Q | Streptomyces albus
BGC0001723.1 |  | 0.58 | Polyketide | oviedomycin | Streptomyces antibioticus
BGC0000231.1 |  | 0.58 | Polyketide | griseusin | Streptomyces griseus

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 3104556 - 3171910:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (leu)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 3128029 - 3170039:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (leu)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 3130050 - 3171910:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (leu)

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_2620: X
  Search NORINE for peptide: strict or relaxed
  AMP-binding (25..474): X
  NRPSPredictor2: (unknown)
  SVM prediction details:
    NOTE: outside applicability domain
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      N/A
    Small clusters prediction:
      N/A
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      erWcLGgatK
    Nearest Stachelhaus code:
      leu
    Stachelhaus code match:
      40% (weak)
ctg1_2645: leu
  Search NORINE for peptide: strict or relaxed
  AMP-binding (89..469): leu
  NRPSPredictor2: leu
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      gly, ala, val, leu, ile, abu, iva
    Small clusters prediction:
      val, leu, ile, abu, iva
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DALFlGLVmK
    Nearest Stachelhaus code:
      leu
    Stachelhaus code match:
      80% (moderate)