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Overview
1.1
1.2
1.3

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

NC_014828.1

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1 | transAT-PKS,NRPS,NRPS-like | 258,423 | 319,666 | pellasoren | NRP + Polyketide:Modular type I | 25%
Region 2 | RRE-containing | 943,911 | 962,761 |
Region 3 | ranthipeptide | 1,539,227 | 1,560,834 |

NC_014828.1 - Region 1 - NRPS,NRPS-like,transAT-PKS
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: 258,423 - 319,666 nt. (total: 61,244 nt) Show pHMM detection rules used
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))
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 | transAT-PKS | NRPS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001050.1 |  |  |  | 0.99 | NRP, Polyketide | thalassospiramide A | Tistrella bauzanensis
BGC0001909.1 |  |  |  | 0.97 | Polyketide | strobilurin | Strobilurus tenacellus
BGC0001163.1 |  |  |  | 0.93 | Polyketide | 1-heptadecene | Moorea producens 3L
BGC0001162.1 |  |  |  | 0.93 | Polyketide | 1-heptadecene | Moorea producens JHB
BGC0000044.1 |  |  |  | 0.76 | Polyketide | dawenol | Stigmatella aurantiaca DW4/3-1
BGC0000412.1 |  |  |  | 0.74 | NRP | pyochelin | Pseudomonas aeruginosa PAO1
BGC0000258.1 |  |  |  | 0.71 | Polyketide | prodigiosin | Serratia sp.
BGC0000260.1 |  |  |  | 0.71 | Polyketide | prodigiosin | Hahella chejuensis KCTC 2396
BGC0000259.1 |  |  |  | 0.70 | Polyketide | prodigiosin | Serratia marcescens
BGC0000056.1 |  |  |  | 0.70 | Polyketide | esperamicin | Actinomadura verrucosospora

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001050.1 |  | 0.66 | NRP, Polyketide | thalassospiramide A | Tistrella bauzanensis
BGC0001909.1 |  | 0.66 | Polyketide | strobilurin | Strobilurus tenacellus
BGC0001163.1 |  | 0.64 | Polyketide | 1-heptadecene | Moorea producens 3L
BGC0001162.1 |  | 0.64 | Polyketide | 1-heptadecene | Moorea producens JHB
BGC0000373.1 |  | 0.62 | NRP | holomycin | Streptomyces clavuligerus ATCC 27064
BGC0000258.1 |  | 0.61 | Polyketide | prodigiosin | Serratia sp.
BGC0000259.1 |  | 0.61 | Polyketide | prodigiosin | Serratia marcescens
BGC0000260.1 |  | 0.61 | Polyketide | prodigiosin | Hahella chejuensis KCTC 2396
BGC0000044.1 |  | 0.60 | Polyketide | dawenol | Stigmatella aurantiaca DW4/3-1
BGC0001983.1 |  | 0.60 | Other | triacsins | Kitasatospora aureofaciens

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 1, location 258422 - 319666:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal) + (ccmal - cys - cys)

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_264: mal
  PKS_AT (6..289): mal
  ATSignature: Malonyl-CoA
  Top 3 matches:
    Malonyl-CoA: 54.2%
  minowa: Malonyl-CoA
  Prediction, score:
    Malonyl-CoA: 66.7
    Methoxymalonyl-CoA: 43.8
    Methylmalonyl-CoA: 35.9
    inactive: 33.1
    Benzoyl-CoA: 16.6
    Propionyl-CoA: 13.5
    Ethylmalonyl-CoA: 12.7
    Acetyl-CoA: 9.3
    fatty_acid: 9.1
    trans-1,2-CPDA: 0.0
    Isobutyryl-CoA: 0.0
    CHC-CoA: 0.0
    3-Methylbutyryl-CoA: 0.0
    2-Methylbutyryl-CoA: 0.0
ctg1_265: cys - cys
  Search NORINE for peptide: strict or relaxed
  AMP-binding (1726..2109): cys
  NRPSPredictor2: cys
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      cys
    Small clusters prediction:
      cys
    Single AA prediction:
      cys
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DLYNLSLIWK
    Nearest Stachelhaus code:
      cys
    Stachelhaus code match:
      100% (strong)
  AMP-binding (2767..2994): cys
  NRPSPredictor2: cys
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      cys
    Small clusters prediction:
      cys
    Single AA prediction:
      cys
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DLYN-----K
    Nearest Stachelhaus code:
      cys
    Stachelhaus code match:
      50% (weak)
ctg1_267: pk
  CAL_domain (157..469): pk
  minowa: fatty_acid
  Prediction, score:
    fatty_acid: 95.5
    shikimic_acid: 0.0
    NH2: 0.0
    Acetyl-CoA: 0.0
    AHBA: 0.0

NC_014828.1 - Region 2 - RRE-containing
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: 943,911 - 962,761 nt. (total: 18,851 nt) Show pHMM detection rules used
RRE-containing: 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])

#### 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
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 | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000575.1 |  | 0.15 | RiPP | lariatin | Rhodococcus jostii
BGC0000554.1 |  | 0.15 | RiPP | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001634.1 |  | 0.15 | RiPP | keywimysin | Streptomyces sp. NRRL F-5702
BGC0000794.1 |  | 0.15 | Saccharide | S-layer glycan | Geobacillus stearothermophilus
BGC0000584.1 |  | 0.14 | RiPP | colicin V | Escherichia coli
BGC0001356.1 |  | 0.14 | RiPP | paeninodin | Paenibacillus dendritiformis C454
BGC0001779.1 |  | 0.14 | RiPP | siamycin | Streptomyces nodosus
BGC0001889.1 |  | 0.14 | RiPP | fusilassin | Thermobifida fusca YX
BGC0000792.1 |  | 0.14 | Saccharide | polysaccharide | Enterococcus faecalis OG1RF
BGC0001120.1 |  | 0.14 | NRP, Polyketide | burkholderic acid | Burkholderia thailandensis E264

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000575.1 |  | 0.46 | RiPP | lariatin | Rhodococcus jostii
BGC0000554.1 |  | 0.45 | RiPP | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001634.1 |  | 0.45 | RiPP | keywimysin | Streptomyces sp. NRRL F-5702
BGC0000794.1 |  | 0.45 | Saccharide | S-layer glycan | Geobacillus stearothermophilus
BGC0000584.1 |  | 0.44 | RiPP | colicin V | Escherichia coli
BGC0001356.1 |  | 0.44 | RiPP | paeninodin | Paenibacillus dendritiformis C454
BGC0001779.1 |  | 0.43 | RiPP | siamycin | Streptomyces nodosus
BGC0001889.1 |  | 0.43 | RiPP | fusilassin | Thermobifida fusca YX
BGC0000792.1 |  | 0.43 | Saccharide | polysaccharide | Enterococcus faecalis OG1RF
BGC0001120.1 |  | 0.43 | NRP, Polyketide | burkholderic acid | Burkholderia thailandensis E264

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
NC_014828.1 - Region 3 - 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: 1,539,227 - 1,560,834 nt. (total: 21,608 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
--- | --- | --- | --- | --- | ---
BGC0001733.1 |  | 0.25 | RiPP | PcpA | Pleurocapsa sp. PCC 7327
BGC0000323.1 |  | 0.11 | NRP | cichofactin A, cichofactin B | Pseudomonas cichorii
BGC0000607.1 |  | 0.09 | RiPP | micrococcin P1 | Macrococcus caseolyticus
BGC0001692.1 |  | 0.06 | NRP | nematophin | Xenorhabdus nematophila ATCC 19061
BGC0000689.1 |  | 0.05 | Saccharide | 2-deoxystreptamine | Micromonospora echinospora
BGC0000260.1 |  | 0.04 | Polyketide | prodigiosin | Hahella chejuensis KCTC 2396
BGC0000714.1 |  | 0.04 | Saccharide | sisomicin | Micromonospora inyonensis
BGC0001603.1 |  | 0.04 | Saccharide | gentamicin | Micromonospora echinospora
BGC0000304.1 |  | 0.04 | NRP | apicidin | Fusarium incarnatum
BGC0000413.1 |  | 0.04 | NRP | pyoverdin | Pseudomonas protegens Pf-5

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001733.1 |  | 0.59 | RiPP | PcpA | Pleurocapsa sp. PCC 7327
BGC0000323.1 |  | 0.37 | NRP | cichofactin A, cichofactin B | Pseudomonas cichorii
BGC0000607.1 |  | 0.33 | RiPP | micrococcin P1 | Macrococcus caseolyticus
BGC0001692.1 |  | 0.24 | NRP | nematophin | Xenorhabdus nematophila ATCC 19061
BGC0000689.1 |  | 0.21 | Saccharide | 2-deoxystreptamine | Micromonospora echinospora
BGC0000260.1 |  | 0.20 | Polyketide | prodigiosin | Hahella chejuensis KCTC 2396
BGC0000714.1 |  | 0.19 | Saccharide | sisomicin | Micromonospora inyonensis
BGC0001603.1 |  | 0.19 | Saccharide | gentamicin | Micromonospora echinospora
BGC0000304.1 |  | 0.19 | NRP | apicidin | Fusarium incarnatum
BGC0000413.1 |  | 0.18 | NRP | pyoverdin | Pseudomonas protegens Pf-5

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