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Overview
5.1
5.2

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

c00005_NZ_CABK.. (original name was: NZ_CABKWO010000005.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 5.1 | ranthipeptide | 1,100,911 | 1,129,386 |
Region 5.2 | NRPS,NRPS-like | 2,209,603 | 2,287,433 |

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 5.1 | ranthipeptide | 1,100,911 | 1,129,386 |
Region 5.2 | NRPS,NRPS-like | 2,209,603 | 2,287,433 |

No secondary metabolite regions were found in these records:
  c00001_NZ_CABK.. (original name was: NZ_CABKWO010000001.1)
  c00002_NZ_CABK.. (original name was: NZ_CABKWO010000002.1)
  c00003_NZ_CABK.. (original name was: NZ_CABKWO010000003.1)
  c00004_NZ_CABK.. (original name was: NZ_CABKWO010000004.1)

Compact view
c00005_NZ_CABK.. - 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: 1,100,911 - 1,129,386 nt. (total: 28,476 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
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 | ranthipeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001387.1 |  | 0.18 | Other | nucleocidin | Streptomyces calvus
BGC0001298.1 |  | 0.10 | Polyketide | 4-Z-annimycin | Streptomyces calvus
BGC0001155.1 |  | 0.09 | RiPP | GE2270 | Planobispora rosea
BGC0001591.1 |  | 0.09 | Other | fatty acid enol ester | uncultured bacterium CSLC2
BGC0001688.1 |  | 0.09 | Other | N-tetradecanoyl tyrosine | uncultured bacterium CSLC2
BGC0000604.1 |  | 0.09 | RiPP | GE2270A | Nonomuraea sp. WU8817
BGC0000610.1 |  | 0.08 | RiPP | nosiheptide | Streptomyces actuosus
BGC0000027.1 |  | 0.08 | Polyketide | ankaflavin, monascin, rubropunctatine, monascorubrin | Monascus pilosus
BGC0002026.1 |  | 0.07 | NRP | thaxteramide A1, thaxteramide A2, thaxteramide B1, thaxteramide B2 | Jahnella sp. MSr9139
BGC0000172.1 |  | 0.07 | Polyketide | basiliskamide A, basiliskamide B | Brevibacillus laterosporus PE36

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001387.1 |  | 0.49 | Other | nucleocidin | Streptomyces calvus
BGC0001298.1 |  | 0.35 | Polyketide | 4-Z-annimycin | Streptomyces calvus
BGC0001155.1 |  | 0.33 | RiPP | GE2270 | Planobispora rosea
BGC0001591.1 |  | 0.32 | Other | fatty acid enol ester | uncultured bacterium CSLC2
BGC0001688.1 |  | 0.32 | Other | N-tetradecanoyl tyrosine | uncultured bacterium CSLC2
BGC0000604.1 |  | 0.32 | RiPP | GE2270A | Nonomuraea sp. WU8817
BGC0000610.1 |  | 0.31 | RiPP | nosiheptide | Streptomyces actuosus
BGC0000027.1 |  | 0.31 | Polyketide | ankaflavin, monascin, rubropunctatine, monascorubrin | Monascus pilosus
BGC0002026.1 |  | 0.28 | NRP | thaxteramide A1, thaxteramide A2, thaxteramide B1, thaxteramide B2 | Jahnella sp. MSr9139
BGC0000172.1 |  | 0.28 | Polyketide | basiliskamide A, basiliskamide B | Brevibacillus laterosporus PE36

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
c00005_NZ_CABK.. - Region 2 - NRPS,NRPS-like
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: 2,209,603 - 2,287,433 nt. (total: 77,831 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX))
NRPS-like: cds((PP-binding or NAD_binding_4) 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 | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000427.1 |  |  | 0.71 | NRP | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413
BGC0000457.1 |  |  | 0.65 | NRP | vicibactin | Rhizobium etli CFN 42
BGC0001479.1 |  |  | 0.65 | NRP | anabaenopeptin NZ857, nostamide A | Nostoc punctiforme PCC 73102
BGC0000375.1 |  |  | 0.65 | NRP | indigoidine | Streptomyces chromofuscus
BGC0000348.1 |  |  | 0.63 | NRP | ergovaline | Epichloe festucae var. lolii
BGC0000900.1 |  |  | 0.63 | Other | ferrichrome | Aspergillus oryzae
BGC0001249.1 |  |  | 0.62 | NRP | dimethylcoprogen | Alternaria alternata
BGC0001135.1 |  |  | 0.61 | NRP | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.1 |  |  | 0.60 | NRP | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.1 |  |  | 0.59 | NRP | AM-toxin | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001479.1 |  | 0.69 | NRP | anabaenopeptin NZ857, nostamide A | Nostoc punctiforme PCC 73102
BGC0000427.1 |  | 0.68 | NRP | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413
BGC0001135.1 |  | 0.67 | NRP | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000457.1 |  | 0.67 | NRP | vicibactin | Rhizobium etli CFN 42
BGC0001131.1 |  | 0.67 | NRP | ambactin | Xenorhabdus miraniensis
BGC0001844.1 |  | 0.66 | NRP | holrhizin | Paraburkholderia rhizoxinica HKI 454
BGC0000389.1 |  | 0.66 | NRP | massetolide A | Pseudomonas fluorescens SS101
BGC0000375.1 |  | 0.66 | NRP | indigoidine | Streptomyces chromofuscus
BGC0001128.1 |  | 0.65 | NRP | luminmide | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000426.1 |  | 0.65 | NRP | sevadicin | Paenibacillus larvae

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 2209602 - 2287433:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (asn) + (X) + (pro - phe - gly) + (D-X - gly - gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 2209602 - 2285500:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (asn) + (X) + (pro - phe - gly) + (D-X - gly - gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 2245528 - 2287433:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (asn) + (X) + (pro - phe - gly)

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).

ctg5_1951: X - gly - gly
  Search NORINE for peptide: strict or relaxed
  AMP-binding (765..1165): X
  NRPSPredictor2: val, leu, ile, abu, iva
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      N/A
    Small clusters prediction:
      val, leu, ile, abu, iva
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DvcYLGgiCK
    Nearest Stachelhaus code:
      leu
    Stachelhaus code match:
      60% (weak)
  AMP-binding (2280..2670): gly
  NRPSPredictor2: gly
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      gly, ala, val, leu, ile, abu, iva
    Small clusters prediction:
      gly, ala
    Single AA prediction:
      gly
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DItQmGVvWK
    Nearest Stachelhaus code:
      gly
    Stachelhaus code match:
      70% (weak)
  AMP-binding (3303..3699): gly
  NRPSPredictor2: gly
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      gly, ala, val, leu, ile, abu, iva
    Small clusters prediction:
      gly, ala
    Single AA prediction:
      gly
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DItQmGVvWK
    Nearest Stachelhaus code:
      gly
    Stachelhaus code match:
      70% (weak)
ctg5_1952: pro
  Search NORINE for peptide: strict or relaxed
  AMP-binding (0..347): pro
  NRPSPredictor2: pro
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      pro, pip
    Small clusters prediction:
      pro
    Single AA prediction:
      pro
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DVQFvAHVVK
    Nearest Stachelhaus code:
      pro
    Stachelhaus code match:
      90% (moderate)
ctg5_1953: pro - phe - gly - pro
  Search NORINE for peptide: strict or relaxed
  AMP-binding (0..347): pro
  NRPSPredictor2: pro
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      pro, pip
    Small clusters prediction:
      pro
    Single AA prediction:
      pro
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DVQFvAHVVK
    Nearest Stachelhaus code:
      pro
    Stachelhaus code match:
      90% (moderate)
  AMP-binding (981..1364): phe
  NRPSPredictor2: phe
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aromatic
    Large clusters prediction:
      phe, trp, phg, tyr, bht
    Small clusters prediction:
      phe, trp
    Single AA prediction:
      phe
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DGWAVAaVsK
    Nearest Stachelhaus code:
      trp
    Stachelhaus code match:
      80% (moderate)
  AMP-binding (1998..2394): gly
  NRPSPredictor2: gly
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      gly, ala, val, leu, ile, abu, iva
    Small clusters prediction:
      gly, ala
    Single AA prediction:
      gly
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DItQtGVvWK
    Nearest Stachelhaus code:
      gly
    Stachelhaus code match:
      70% (weak)
  AMP-binding (3028..3425): pro
  NRPSPredictor2: pro
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      pro, pip
    Small clusters prediction:
      pro
    Single AA prediction:
      pro
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DVQFvAHVVK
    Nearest Stachelhaus code:
      pro
    Stachelhaus code match:
      90% (moderate)
ctg5_1954: pro
  Search NORINE for peptide: strict or relaxed
  AMP-binding (0..347): pro
  NRPSPredictor2: pro
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      pro, pip
    Small clusters prediction:
      pro
    Single AA prediction:
      pro
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DVQFvAHVVK
    Nearest Stachelhaus code:
      pro
    Stachelhaus code match:
      90% (moderate)
ctg5_1955: X - pro
  Search NORINE for peptide: strict or relaxed
  AMP-binding (508..910): X
  NRPSPredictor2: (unknown)
  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:
      DAQDiGVVDK
    Nearest Stachelhaus code:
      gln
    Stachelhaus code match:
      90% (moderate)
  AMP-binding (1544..1941): pro
  NRPSPredictor2: pro
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      pro, pip
    Small clusters prediction:
      pro
    Single AA prediction:
      pro
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DVQFvAHVVK
    Nearest Stachelhaus code:
      pro
    Stachelhaus code match:
      90% (moderate)
ctg5_1956: asn
  Search NORINE for peptide: strict or relaxed
  AMP-binding (44..438): asn
  NRPSPredictor2: asn
  SVM prediction details:
    Predicted physicochemical class:
      hydrophilic
    Large clusters prediction:
      asp, asn, glu, gln, aad
    Small clusters prediction:
      asp, asn
    Single AA prediction:
      asn
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DLTKIGEVGK
    Nearest Stachelhaus code:
      asn
    Stachelhaus code match:
      100% (strong)