Select genomic region:
Overview
12.1
12.2
19.1

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

NZ_PKIB01000002 (original name was: NZ_PKIB01000002.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 12.1 | T3PKS | 94,907 | 136,085 |
Region 12.2 | lanthipeptide-class-i | 262,886 | 288,920 | suicin 90-1330 | RiPP | 100%

NZ_PKIB01000007 (original name was: NZ_PKIB01000007.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 19.1 | RiPP-like | 93,585 | 107,497 |

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 12.1 | T3PKS | 94,907 | 136,085 |
Region 12.2 | lanthipeptide-class-i | 262,886 | 288,920 | suicin 90-1330 | RiPP | 100%
Region 19.1 | RiPP-like | 93,585 | 107,497 |

No secondary metabolite regions were found in these records:
  NZ_PKIB01000001 (original name was: NZ_PKIB01000001.1)
  NZ_PKIB01000010 (original name was: NZ_PKIB01000010.1)
  NZ_PKIB01000011 (original name was: NZ_PKIB01000011.1)
  NZ_PKIB01000012 (original name was: NZ_PKIB01000012.1)
  NZ_PKIB01000013 (original name was: NZ_PKIB01000013.1)
  NZ_PKIB01000014 (original name was: NZ_PKIB01000014.1)
  NZ_PKIB01000015 (original name was: NZ_PKIB01000015.1)
  NZ_PKIB01000016 (original name was: NZ_PKIB01000016.1)
  NZ_PKIB01000017 (original name was: NZ_PKIB01000017.1)
  NZ_PKIB01000018 (original name was: NZ_PKIB01000018.1)
  NZ_PKIB01000019 (original name was: NZ_PKIB01000019.1)
  NZ_PKIB01000020 (original name was: NZ_PKIB01000020.1)
  NZ_PKIB01000021 (original name was: NZ_PKIB01000021.1)
  NZ_PKIB01000003 (original name was: NZ_PKIB01000003.1)
  NZ_PKIB01000004 (original name was: NZ_PKIB01000004.1)
  NZ_PKIB01000005 (original name was: NZ_PKIB01000005.1)
  NZ_PKIB01000006 (original name was: NZ_PKIB01000006.1)
  NZ_PKIB01000008 (original name was: NZ_PKIB01000008.1)
  NZ_PKIB01000009 (original name was: NZ_PKIB01000009.1)

Compact view
c00012_NZ_PKIB.. - Region 1 - T3PKS
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: 94,907 - 136,085 nt. (total: 41,179 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### 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
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 | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001521.1 |  | 0.17 | NRP | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0001937.1 |  | 0.17 | Other | tubercidin | Streptomyces tubercidicus
BGC0000487.1 |  | 0.17 | RiPP | carnocyclin | Carnobacterium maltaromaticum
BGC0001526.1 |  | 0.16 | Other | bartolosides E, bartolosides F, bartolosides G, bartolosides H, bartolosides I, bartolosides J, bartolosides K | Synechocystis salina LEGE 06099
BGC0001525.1 |  | 0.16 | Other | bartoloside 2, bartoloside 3, bartoloside 4 | Synechocystis salina LEGE 06155
BGC0000554.1 |  | 0.16 | RiPP | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001210.1 |  | 0.16 | RiPP | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000527.1 |  | 0.16 | RiPP | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000504.1 |  | 0.16 | RiPP | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000500.1 |  | 0.16 | RiPP | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001521.1 |  | 0.49 | NRP | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0001937.1 |  | 0.48 | Other | tubercidin | Streptomyces tubercidicus
BGC0000487.1 |  | 0.48 | RiPP | carnocyclin | Carnobacterium maltaromaticum
BGC0001526.1 |  | 0.47 | Other | bartolosides E, bartolosides F, bartolosides G, bartolosides H, bartolosides I, bartolosides J, bartolosides K | Synechocystis salina LEGE 06099
BGC0001525.1 |  | 0.47 | Other | bartoloside 2, bartoloside 3, bartoloside 4 | Synechocystis salina LEGE 06155
BGC0000554.1 |  | 0.47 | RiPP | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001210.1 |  | 0.47 | RiPP | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000527.1 |  | 0.47 | RiPP | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000504.1 |  | 0.47 | RiPP | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000500.1 |  | 0.47 | RiPP | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum

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
c00012_NZ_PKIB.. - Region 2 - lanthipeptide-class-i
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: 262,886 - 288,920 nt. (total: 26,035 nt) Show pHMM detection rules used
lanthipeptide-class-i: ((LANC_like and (Lant_dehydr_N or Lant_dehydr_C)) and not (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
Lanthipeptides
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 | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001789.1 |  | 0.93 | RiPP | suicin 90-1330 | Streptococcus suis
BGC0000537.1 |  | 0.66 | RiPP | nisin U | Streptococcus uberis
BGC0000536.1 |  | 0.49 | RiPP | nisin Q | Lactococcus lactis
BGC0000535.1 |  | 0.49 | RiPP | nisin A | Lactococcus lactis subsp. lactis
BGC0000538.1 |  | 0.44 | RiPP | nisin Z | Lactococcus lactis
BGC0001289.1 |  | 0.33 | RiPP | penisin | Paenibacillus ehimensis
BGC0000544.1 |  | 0.30 | RiPP | planosporicin | Planomonospora alba
BGC0000560.1 |  | 0.28 | RiPP | subtilomycin | Bacillus subtilis
BGC0000543.1 |  | 0.28 | RiPP | pep5 | Staphylococcus epidermidis
BGC0000549.1 |  | 0.26 | RiPP | salivaricin D | Streptococcus salivarius

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001789.1 |  | 0.98 | RiPP | suicin 90-1330 | Streptococcus suis
BGC0000537.1 |  | 0.87 | RiPP | nisin U | Streptococcus uberis
BGC0000536.1 |  | 0.78 | RiPP | nisin Q | Lactococcus lactis
BGC0000535.1 |  | 0.78 | RiPP | nisin A | Lactococcus lactis subsp. lactis
BGC0000538.1 |  | 0.75 | RiPP | nisin Z | Lactococcus lactis
BGC0001289.1 |  | 0.67 | RiPP | penisin | Paenibacillus ehimensis
BGC0000544.1 |  | 0.64 | RiPP | planosporicin | Planomonospora alba
BGC0000560.1 |  | 0.61 | RiPP | subtilomycin | Bacillus subtilis
BGC0000543.1 |  | 0.61 | RiPP | pep5 | Staphylococcus epidermidis
BGC0000549.1 |  | 0.59 | RiPP | salivaricin D | Streptococcus salivarius

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.
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.

#### Lanthipeptide(s) for ctg12_262 - Putative Class I

ctg12_263 leader / core peptide
  MNNEDFNLDLVTISKENNSGASPR - VDhb DhaKDhaLC DhbPGCKDhbGILMDhb CAIKDhbADhb CGCHFG

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
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
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.

ctg12_263 - Class I
  Cleavage pHMM score: 27.40
  RODEO score: 28
  Monoisotopic mass: 2987.5 Da
  Molecular weight: 2989.6 Da
  Number of bridges: 5
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3007.6 Da N = 1
    3025.7 Da N = 2
    3043.7 Da N = 3

c00019_NZ_PKIB.. - Region 1 - RiPP-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: 93,585 - 107,497 nt. (total: 13,913 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193)

#### 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 | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000617.1 |  | 0.38 | RiPP | coagulin | Bacillus coagulans
BGC0001863.1 |  | 0.16 | RiPP, Terpene | bacillicn CER074 | Bacillus mycoides
BGC0000558.1 |  | 0.15 | RiPP | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0000624.1 |  | 0.15 | RiPP | salivaricin CRL1328 α peptide, salivaricin CRL1328 β peptide | Lactobacillus salivarius
BGC0001388.1 |  | 0.14 | RiPP | gassericin E | Lactobacillus gasseri
BGC0000619.1 |  | 0.14 | RiPP | gassericin T | Lactobacillus gasseri
BGC0001602.1 |  | 0.14 | RiPP | gassericin-T | Lactobacillus gasseri
BGC0000554.1 |  | 0.13 | RiPP | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001225.1 |  | 0.13 | NRP | celesticetin | Streptomyces caelestis
BGC0000561.1 |  | 0.11 | RiPP | thermophilin 1277 | Streptococcus thermophilus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000617.1 |  | 0.71 | RiPP | coagulin | Bacillus coagulans
BGC0001863.1 |  | 0.46 | RiPP, Terpene | bacillicn CER074 | Bacillus mycoides
BGC0000558.1 |  | 0.46 | RiPP | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0000624.1 |  | 0.46 | RiPP | salivaricin CRL1328 α peptide, salivaricin CRL1328 β peptide | Lactobacillus salivarius
BGC0001388.1 |  | 0.43 | RiPP | gassericin E | Lactobacillus gasseri
BGC0000619.1 |  | 0.43 | RiPP | gassericin T | Lactobacillus gasseri
BGC0001602.1 |  | 0.43 | RiPP | gassericin-T | Lactobacillus gasseri
BGC0000554.1 |  | 0.42 | RiPP | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001225.1 |  | 0.42 | NRP | celesticetin | Streptomyces caelestis
BGC0000561.1 |  | 0.37 | RiPP | thermophilin 1277 | Streptococcus thermophilus

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