Select genomic region:
Overview
7.1
9.1
11.1

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

c00007_NZ_JAGZ.. (original name was: NZ_JAGZDX010000003.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 7.1 | ranthipeptide | 81,798 | 103,405 |

c00009_NZ_JAGZ.. (original name was: NZ_JAGZDX010000004.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 9.1 | RRE-containing | 326,434 | 346,697 | kijanimicin | Polyketide | 4%

c00011_NZ_JAGZ.. (original name was: NZ_JAGZDX010000005.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 11.1 | ladderane,NRPS | 1 | 73,407 | heme D1 | Other | 11%

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 7.1 | ranthipeptide | 81,798 | 103,405 |
Region 9.1 | RRE-containing | 326,434 | 346,697 | kijanimicin | Polyketide | 4%
Region 11.1 | ladderane,NRPS | 1 | 73,407 | heme D1 | Other | 11%

No secondary metabolite regions were found in these records:
  c00001_NZ_JAGZ.. (original name was: NZ_JAGZDX010000007.1)
  c00002_NZ_JAGZ.. (original name was: NZ_JAGZDX010000008.1)
  c00003_NZ_JAGZ.. (original name was: NZ_JAGZDX010000010.1)
  c00004_NZ_JAGZ.. (original name was: NZ_JAGZDX010000011.1)
  c00005_NZ_JAGZ.. (original name was: NZ_JAGZDX010000001.1)
  c00006_NZ_JAGZ.. (original name was: NZ_JAGZDX010000012.1)
  c00008_NZ_JAGZ.. (original name was: NZ_JAGZDX010000013.1)
  c00010_NZ_JAGZ.. (original name was: NZ_JAGZDX010000014.1)
  c00012_NZ_JAGZ.. (original name was: NZ_JAGZDX010000009.1)
  c00013_NZ_JAGZ.. (original name was: NZ_JAGZDX010000002.1)
  c00014_NZ_JAGZ.. (original name was: NZ_JAGZDX010000006.1)

Compact view
c00007_NZ_JAGZ.. - 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: 81,798 - 103,405 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
--- | --- | --- | --- | --- | ---
BGC0000599.1 |  | 0.18 | RiPP | thuricin CD α, thuricin CD β | Bacillus thuringiensis
BGC0000560.1 |  | 0.15 | RiPP | subtilomycin | Bacillus subtilis
BGC0000466.1 |  | 0.14 | NRP | yatakemycin | Streptomyces sp. TP-A2060
BGC0001607.1 |  | 0.14 | Other | gilvusmycin | Streptomyces sp. NRRL B-1347
BGC0001120.1 |  | 0.13 | NRP, Polyketide | burkholderic acid | Burkholderia thailandensis E264
BGC0001391.1 |  | 0.12 | RiPP | thusin | Bacillus thuringiensis serovar rongseni
BGC0000552.1 |  | 0.12 | RiPP | SmbA, SmbB | Streptococcus mutans
BGC0000608.1 |  | 0.12 | RiPP | nocathiacin | Actinokineospora fastidiosa
BGC0000807.1 |  | 0.12 | Saccharide | phosphonoglycans | Stackebrandtia nassauensis DSM 44728
BGC0000539.1 |  | 0.12 | RiPP | nukacin ISK-1 | Staphylococcus warneri

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000599.1 |  | 0.49 | RiPP | thuricin CD α, thuricin CD β | Bacillus thuringiensis
BGC0000560.1 |  | 0.46 | RiPP | subtilomycin | Bacillus subtilis
BGC0000466.1 |  | 0.44 | NRP | yatakemycin | Streptomyces sp. TP-A2060
BGC0001607.1 |  | 0.43 | Other | gilvusmycin | Streptomyces sp. NRRL B-1347
BGC0001120.1 |  | 0.41 | NRP, Polyketide | burkholderic acid | Burkholderia thailandensis E264
BGC0001391.1 |  | 0.41 | RiPP | thusin | Bacillus thuringiensis serovar rongseni
BGC0000552.1 |  | 0.41 | RiPP | SmbA, SmbB | Streptococcus mutans
BGC0000608.1 |  | 0.40 | RiPP | nocathiacin | Actinokineospora fastidiosa
BGC0000807.1 |  | 0.40 | Saccharide | phosphonoglycans | Stackebrandtia nassauensis DSM 44728
BGC0000539.1 |  | 0.39 | RiPP | nukacin ISK-1 | Staphylococcus warneri

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
c00009_NZ_JAGZ.. - Region 1 - 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: 326,434 - 346,697 nt. (total: 20,264 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
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 | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001410.1 |  | 0.17 | Saccharide | polysaccharide A | Bacteroides fragilis
BGC0000868.1 |  | 0.16 | Other | teichuronic acid | Bacillus subtilis subsp. subtilis str. 168
BGC0001588.1 |  | 0.16 | Saccharide | exopolysaccharides | Burkholderia pseudomallei 1026b
BGC0000732.1 |  | 0.15 | Saccharide | capsular polysaccharide | Raoultella planticola
BGC0000733.1 |  | 0.15 | Saccharide | capsular polysaccharide | Klebsiella pneumoniae
BGC0001589.1 |  | 0.15 | Saccharide | exopolysaccharides | Burkholderia cenocepacia J2315
BGC0000794.1 |  | 0.15 | Saccharide | S-layer glycan | Geobacillus stearothermophilus
BGC0000730.1 |  | 0.15 | Saccharide | capsular polysaccharide | Klebsiella pneumoniae
BGC0000731.1 |  | 0.15 | Saccharide | capsular polysaccharide | Klebsiella pneumoniae
BGC0000800.1 |  | 0.15 | Saccharide | xanthan | Xanthomonas campestris

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001410.1 |  | 0.48 | Saccharide | polysaccharide A | Bacteroides fragilis
BGC0000868.1 |  | 0.47 | Other | teichuronic acid | Bacillus subtilis subsp. subtilis str. 168
BGC0001588.1 |  | 0.46 | Saccharide | exopolysaccharides | Burkholderia pseudomallei 1026b
BGC0000732.1 |  | 0.46 | Saccharide | capsular polysaccharide | Raoultella planticola
BGC0000733.1 |  | 0.46 | Saccharide | capsular polysaccharide | Klebsiella pneumoniae
BGC0001589.1 |  | 0.45 | Saccharide | exopolysaccharides | Burkholderia cenocepacia J2315
BGC0000794.1 |  | 0.45 | Saccharide | S-layer glycan | Geobacillus stearothermophilus
BGC0000730.1 |  | 0.45 | Saccharide | capsular polysaccharide | Klebsiella pneumoniae
BGC0000731.1 |  | 0.45 | Saccharide | capsular polysaccharide | Klebsiella pneumoniae
BGC0000800.1 |  | 0.45 | Saccharide | xanthan | Xanthomonas campestris

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
c00011_NZ_JAGZ.. - Region 1 - NRPS,ladderane
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 - 73,407 nt. (total: 73,407 nt) Show pHMM detection rules used
Region on contig edge.
ladderane: ladderane
NRPS: cds(Condensation 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 | ladderane | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000886.1 |  |  | 0.40 | Other | allylmalonyl-CoA | Streptomyces tsukubensis
BGC0001575.1 |  |  | 0.31 | NRP | dipeptide aldehydes | Ruminococcus sp. 5_1_39BFAA
BGC0000259.1 |  |  | 0.31 | Polyketide | prodigiosin | Serratia marcescens
BGC0000812.1 |  |  | 0.29 | Alkaloid | huperzine A | Shiraia sp. slf14
BGC0000698.1 |  |  | 0.29 | Saccharide | hygromycin A | Streptomyces hygroscopicus
BGC0000207.1 |  |  | 0.28 | Polyketide | chartreusin | Streptomyces chartreusis
BGC0001002.1 |  |  | 0.27 | NRP, Polyketide | jawsamycin | Streptomyces roseoverticillatus
BGC0000308.1 |  |  | 0.26 | NRP | aureusimine | Staphylococcus aureus subsp. aureus str. JKD6008
BGC0000245.1 |  |  | 0.25 | Polyketide | medermycin | Streptomyces sp. AM-7161
BGC0000384.1 |  |  | 0.25 | NRP | lyngbyatoxin | Lyngbya majuscula

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001897.1 |  | 0.61 | Polyketide | cepacin A | Burkholderia ambifaria IOP40-10
BGC0001184.1 |  | 0.61 | Other | bacilysin | Bacillus velezensis FZB42
BGC0000888.1 |  | 0.60 | Other | bacilysin | Bacillus sp. CS93
BGC0001197.1 |  | 0.59 | Polyketide | frankiamicin | Frankia sp. EAN1pec
BGC0000308.1 |  | 0.59 | NRP | aureusimine | Staphylococcus aureus subsp. aureus str. JKD6008
BGC0000253.1 |  | 0.58 | Polyketide | oviedomycin | Streptomyces antibioticus
BGC0001723.1 |  | 0.57 | Polyketide | oviedomycin | Streptomyces antibioticus
BGC0000715.1 |  | 0.57 | Saccharide | actinospectacin | Streptomyces spectabilis
BGC0000859.1 |  | 0.57 | Other | ectoine | Methylomicrobium alcaliphilum
BGC0000854.1 |  | 0.57 | Other | ectoine | Methylomicrobium alcaliphilum 20Z

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 0 - 73407:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 26075 - 73407:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - 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).

ctg11_51: X - X
  Search NORINE for peptide: strict or relaxed
  AMP-binding (457..845): 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:
      DAsFLGgVyK
    Nearest Stachelhaus code:
      leu
    Stachelhaus code match:
      70% (weak)
  AMP-binding (1479..1869): X
  NRPSPredictor2: asp, asn, glu, gln, aad
  SVM prediction details:
    Predicted physicochemical class:
      hydrophilic
    Large clusters prediction:
      asp, asn, glu, gln, aad
    Small clusters prediction:
      N/A
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DMKnLGtVsK
    Nearest Stachelhaus code:
      asp
    Stachelhaus code match:
      70% (weak)