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Overview
2.1
2.2
3.1

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

NZ_CCYM01000002 (original name was: NZ_CCYM01000002.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 2.1 | terpene | 289,950 | 313,386 | carotenoid | Terpene | 21%
Region 2.2 | NAPAA,betalactone | 695,494 | 731,999 |

NZ_CCYM01000003 (original name was: NZ_CCYM01000003.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 3.1 | lanthipeptide-class-iii | 1,155,058 | 1,177,724 |

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 2.1 | terpene | 289,950 | 313,386 | carotenoid | Terpene | 21%
Region 2.2 | NAPAA,betalactone | 695,494 | 731,999 |
Region 3.1 | lanthipeptide-class-iii | 1,155,058 | 1,177,724 |

No secondary metabolite regions were found in these records:
  NZ_CCYM01000001 (original name was: NZ_CCYM01000001.1)

Compact view
c00002_NZ_CCYM.. - Region 1 - terpene
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: 289,950 - 313,386 nt. (total: 23,437 nt) Show pHMM detection rules used
terpene: (Terpene_synth or Terpene_synth_C or phytoene_synt or Lycopene_cycl or terpene_cyclase or NapT7 or fung_ggpps or fung_ggpps2 or trichodiene_synth or TRI5)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000647.1 |  | 0.33 | Terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.1 |  | 0.33 | Terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000664.1 |  | 0.28 | Terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000642.1 |  | 0.27 | Terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000638.1 |  | 0.26 | Terpene | carotenoid | Pantoea ananatis
BGC0001911.1 |  | 0.26 | Terpene | raimonol | Streptomyces anulatus
BGC0000640.1 |  | 0.26 | Terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0001910.1 |  | 0.25 | Terpene | cyslabdan | Streptomyces cyslabdanicus
BGC0000648.1 |  | 0.25 | Terpene | carotenoid | Myxococcus xanthus
BGC0001227.1 |  | 0.24 | Terpene | isorenieratene | Streptomyces collinus Tu 365

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000647.1 |  | 0.66 | Terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.1 |  | 0.66 | Terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000664.1 |  | 0.62 | Terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000642.1 |  | 0.60 | Terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000638.1 |  | 0.60 | Terpene | carotenoid | Pantoea ananatis
BGC0001911.1 |  | 0.59 | Terpene | raimonol | Streptomyces anulatus
BGC0000640.1 |  | 0.59 | Terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0001910.1 |  | 0.59 | Terpene | cyslabdan | Streptomyces cyslabdanicus
BGC0000648.1 |  | 0.59 | Terpene | carotenoid | Myxococcus xanthus
BGC0001227.1 |  | 0.57 | Terpene | isorenieratene | Streptomyces collinus Tu 365

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.
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
c00002_NZ_CCYM.. - Region 2 - NAPAA,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: 695,494 - 731,999 nt. (total: 36,506 nt) Show pHMM detection rules used
NAPAA: (AMP-binding and PP-binding and TIGR02353)
betalactone: (HMGL-like and AMP-binding)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
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 | NAPAA | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000234.1 |  |  | 0.48 | Polyketide | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000427.1 |  |  | 0.43 | NRP | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413
BGC0000375.1 |  |  | 0.43 | NRP | indigoidine | Streptomyces chromofuscus
BGC0001399.1 |  |  | 0.41 | NRP | fellutamide B | Aspergillus nidulans FGSC A4
BGC0001135.1 |  |  | 0.37 | NRP | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.1 |  |  | 0.37 | NRP | icosalide A, icosalide B | Burkholderia gladioli
BGC0001131.1 |  |  | 0.36 | NRP | ambactin | Xenorhabdus miraniensis
BGC0001479.1 |  |  | 0.36 | NRP | anabaenopeptin NZ857, nostamide A | Nostoc punctiforme PCC 73102
BGC0001128.1 |  |  | 0.36 | NRP | luminmide | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.1 |  |  | 0.36 | NRP | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000234.1 |  | 0.58 | Polyketide | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001483.1 |  | 0.55 | Other | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000427.1 |  | 0.55 | NRP | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413
BGC0000375.1 |  | 0.54 | NRP | indigoidine | Streptomyces chromofuscus
BGC0001940.1 |  | 0.53 | Polyketide | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0001399.1 |  | 0.53 | NRP | fellutamide B | Aspergillus nidulans FGSC A4
BGC0000843.1 |  | 0.51 | Other (Non-NRP beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0001796.1 |  | 0.51 | NRP | tauramamide | Brevibacillus laterosporus DSM 25
BGC0001135.1 |  | 0.50 | NRP | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.1 |  | 0.50 | NRP | icosalide A, icosalide B | Burkholderia gladioli

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 2, location 695493 - 731999:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

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).

ctg2_633: X
  Search NORINE for peptide: strict or relaxed
  AMP-binding (42..428): X
  NRPSPredictor2: hydrophilic
  SVM prediction details:
    Predicted physicochemical class:
      hydrophilic
    Large clusters prediction:
      N/A
    Small clusters prediction:
      N/A
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DfEHNgTaSK
    Nearest Stachelhaus code:
      dab
    Stachelhaus code match:
      70% (weak)

c00003_NZ_CCYM.. - Region 1 - lanthipeptide-class-iii
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: 1,155,058 - 1,177,724 nt. (total: 22,667 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
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
Lanthipeptides
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 | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000553.1 |  | 0.34 | RiPP | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000563.1 |  | 0.32 | RiPP | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0000528.1 |  | 0.24 | RiPP | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000518.1 |  | 0.22 | RiPP | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000554.1 |  | 0.22 | RiPP | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000501.1 |  | 0.21 | RiPP | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000513.1 |  | 0.21 | RiPP | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000551.1 |  | 0.21 | RiPP | SapB | Streptomyces coelicolor A3(2)
BGC0000496.1 |  | 0.21 | RiPP | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000516.1 |  | 0.20 | RiPP | geobacillin II | Geobacillus thermodenitrificans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000553.1 |  | 0.67 | RiPP | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000563.1 |  | 0.66 | RiPP | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0000528.1 |  | 0.57 | RiPP | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000518.1 |  | 0.56 | RiPP | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000554.1 |  | 0.55 | RiPP | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000501.1 |  | 0.54 | RiPP | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000513.1 |  | 0.54 | RiPP | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000551.1 |  | 0.54 | RiPP | SapB | Streptomyces coelicolor A3(2)
BGC0000496.1 |  | 0.53 | RiPP | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000516.1 |  | 0.52 | RiPP | geobacillin II | Geobacillus thermodenitrificans

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.

Lanthipeptide 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.
Lanthipeptides - 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
Lanthipeptides
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.