Select genomic region:
Overview
13.1
16.1

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

NZ_CYYA01000013 (original name was: NZ_CYYA01000013.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 13.1 | ranthipeptide | 37,088 | 58,733 |

NZ_CYYA01000016 (original name was: NZ_CYYA01000016.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 16.1 | NRPS-like | 3,052 | 46,252 |

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 13.1 | ranthipeptide | 37,088 | 58,733 |
Region 16.1 | NRPS-like | 3,052 | 46,252 |

No secondary metabolite regions were found in these records:
  NZ_CYYA01000001 (original name was: NZ_CYYA01000001.1)
  NZ_CYYA01000002 (original name was: NZ_CYYA01000002.1)
  NZ_CYYA01000003 (original name was: NZ_CYYA01000003.1)
  NZ_CYYA01000004 (original name was: NZ_CYYA01000004.1)
  NZ_CYYA01000005 (original name was: NZ_CYYA01000005.1)
  NZ_CYYA01000006 (original name was: NZ_CYYA01000006.1)
  NZ_CYYA01000007 (original name was: NZ_CYYA01000007.1)
  NZ_CYYA01000008 (original name was: NZ_CYYA01000008.1)
  NZ_CYYA01000009 (original name was: NZ_CYYA01000009.1)
  NZ_CYYA01000010 (original name was: NZ_CYYA01000010.1)
  NZ_CYYA01000011 (original name was: NZ_CYYA01000011.1)
  NZ_CYYA01000012 (original name was: NZ_CYYA01000012.1)
  NZ_CYYA01000014 (original name was: NZ_CYYA01000014.1)
  NZ_CYYA01000015 (original name was: NZ_CYYA01000015.1)
  NZ_CYYA01000017 (original name was: NZ_CYYA01000017.1)
  NZ_CYYA01000018 (original name was: NZ_CYYA01000018.1)
  NZ_CYYA01000019 (original name was: NZ_CYYA01000019.1)
  NZ_CYYA01000020 (original name was: NZ_CYYA01000020.1)
  NZ_CYYA01000021 (original name was: NZ_CYYA01000021.1)
  NZ_CYYA01000022 (original name was: NZ_CYYA01000022.1)
  NZ_CYYA01000023 (original name was: NZ_CYYA01000023.1)
  NZ_CYYA01000024 (original name was: NZ_CYYA01000024.1)
  NZ_CYYA01000025 (original name was: NZ_CYYA01000025.1)
  NZ_CYYA01000026 (original name was: NZ_CYYA01000026.1)
  NZ_CYYA01000027 (original name was: NZ_CYYA01000027.1)
  NZ_CYYA01000028 (original name was: NZ_CYYA01000028.1)
  NZ_CYYA01000029 (original name was: NZ_CYYA01000029.1)
  NZ_CYYA01000030 (original name was: NZ_CYYA01000030.1)
  NZ_CYYA01000031 (original name was: NZ_CYYA01000031.1)
  NZ_CYYA01000032 (original name was: NZ_CYYA01000032.1)
  NZ_CYYA01000033 (original name was: NZ_CYYA01000033.1)
  NZ_CYYA01000034 (original name was: NZ_CYYA01000034.1)
  NZ_CYYA01000035 (original name was: NZ_CYYA01000035.1)
  NZ_CYYA01000036 (original name was: NZ_CYYA01000036.1)
  NZ_CYYA01000037 (original name was: NZ_CYYA01000037.1)
  NZ_CYYA01000038 (original name was: NZ_CYYA01000038.1)
  NZ_CYYA01000039 (original name was: NZ_CYYA01000039.1)
  NZ_CYYA01000040 (original name was: NZ_CYYA01000040.1)
  NZ_CYYA01000041 (original name was: NZ_CYYA01000041.1)
  NZ_CYYA01000042 (original name was: NZ_CYYA01000042.1)
  NZ_CYYA01000043 (original name was: NZ_CYYA01000043.1)
  NZ_CYYA01000044 (original name was: NZ_CYYA01000044.1)
  NZ_CYYA01000045 (original name was: NZ_CYYA01000045.1)
  NZ_CYYA01000046 (original name was: NZ_CYYA01000046.1)
  NZ_CYYA01000047 (original name was: NZ_CYYA01000047.1)

Compact view
c00013_NZ_CYYA.. - 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: 37,088 - 58,733 nt. (total: 21,646 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
--- | --- | --- | --- | --- | ---
BGC0001120.1 |  | 0.17 | NRP, Polyketide | burkholderic acid | Burkholderia thailandensis E264
BGC0000488.1 |  | 0.16 | RiPP | circularin A | Clostridium beijerinckii
BGC0000487.1 |  | 0.16 | RiPP | carnocyclin | Carnobacterium maltaromaticum
BGC0000542.1 |  | 0.16 | RiPP | paenicidin B | Paenibacillus terrae
BGC0000571.1 |  | 0.16 | RiPP | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0000504.1 |  | 0.16 | RiPP | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0001551.1 |  | 0.16 | RiPP | citrulassin E | Streptomyces glaucescens
BGC0001765.1 |  | 0.16 | Saccharide | salecan | Agrobacterium tumefaciens
BGC0000551.1 |  | 0.16 | RiPP | SapB | Streptomyces coelicolor A3(2)
BGC0000541.1 |  | 0.16 | RiPP | paenicidin A | Paenibacillus polymyxa

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001120.1 |  | 0.48 | NRP, Polyketide | burkholderic acid | Burkholderia thailandensis E264
BGC0000488.1 |  | 0.47 | RiPP | circularin A | Clostridium beijerinckii
BGC0000487.1 |  | 0.47 | RiPP | carnocyclin | Carnobacterium maltaromaticum
BGC0000542.1 |  | 0.46 | RiPP | paenicidin B | Paenibacillus terrae
BGC0000571.1 |  | 0.46 | RiPP | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0000504.1 |  | 0.46 | RiPP | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0001551.1 |  | 0.46 | RiPP | citrulassin E | Streptomyces glaucescens
BGC0001765.1 |  | 0.46 | Saccharide | salecan | Agrobacterium tumefaciens
BGC0000551.1 |  | 0.46 | RiPP | SapB | Streptomyces coelicolor A3(2)
BGC0000541.1 |  | 0.46 | RiPP | paenicidin A | Paenibacillus polymyxa

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
c00016_NZ_CYYA.. - Region 1 - 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: 3,052 - 46,252 nt. (total: 43,201 nt) Show pHMM detection rules used
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-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001168.1 |  | 0.32 | NRP | livipeptin | Streptomyces lividans 1326
BGC0001516.1 |  | 0.28 | NRP | aspergillic acid | Aspergillus flavus NRRL3357
BGC0001831.1 |  | 0.19 | Polyketide | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0000895.1 |  | 0.19 | Other | citrulline | Lactobacillus plantarum subsp. plantarum
BGC0001897.1 |  | 0.16 | Polyketide | cepacin A | Burkholderia ambifaria IOP40-10
BGC0000712.1 |  | 0.15 | Saccharide | paromomycin | Streptomyces rimosus subsp. paromomycinus
BGC0000393.1 |  | 0.14 | NRP, Polyketide | myxoprincomide-c506 | Myxococcus xanthus DK 1622
BGC0001160.1 |  | 0.14 | Polyketide | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000180.1 |  | 0.13 | Polyketide | legioliulin | Legionella parisiensis
BGC0000892.1 |  | 0.13 | Other | caryoynencin | Burkholderia gladioli BSR3

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001168.1 |  | 0.65 | NRP | livipeptin | Streptomyces lividans 1326
BGC0001516.1 |  | 0.61 | NRP | aspergillic acid | Aspergillus flavus NRRL3357
BGC0001831.1 |  | 0.52 | Polyketide | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0000895.1 |  | 0.52 | Other | citrulline | Lactobacillus plantarum subsp. plantarum
BGC0001897.1 |  | 0.47 | Polyketide | cepacin A | Burkholderia ambifaria IOP40-10
BGC0000712.1 |  | 0.45 | Saccharide | paromomycin | Streptomyces rimosus subsp. paromomycinus
BGC0000393.1 |  | 0.43 | NRP, Polyketide | myxoprincomide-c506 | Myxococcus xanthus DK 1622
BGC0001160.1 |  | 0.43 | Polyketide | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000180.1 |  | 0.42 | Polyketide | legioliulin | Legionella parisiensis
BGC0000892.1 |  | 0.42 | Other | caryoynencin | Burkholderia gladioli BSR3

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 3051 - 46252:
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).

ctg16_23: X
  Search NORINE for peptide: strict or relaxed
  AMP-binding (12..461): 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:
      nLvvmGGcLK
    Nearest Stachelhaus code:
      ala
    Stachelhaus code match:
      50% (weak)