Select genomic region:
Overview
31.1
35.1
38.1

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

NZ_JPMD01000031 (original name was: NZ_JPMD01000031.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 31.1 | RRE-containing | 7,598 | 27,993 |

NZ_JPMD01000035 (original name was: NZ_JPMD01000035.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 35.1 | ranthipeptide,thiopeptide | 54,001 | 93,860 |

NZ_JPMD01000038 (original name was: NZ_JPMD01000038.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 38.1 | cyclic-lactone-autoinducer | 34,935 | 55,654 |

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 31.1 | RRE-containing | 7,598 | 27,993 |
Region 35.1 | ranthipeptide,thiopeptide | 54,001 | 93,860 |
Region 38.1 | cyclic-lactone-autoinducer | 34,935 | 55,654 |

No secondary metabolite regions were found in these records:
  NZ_JPMD01000001 (original name was: NZ_JPMD01000001.1)
  NZ_JPMD01000002 (original name was: NZ_JPMD01000002.1)
  NZ_JPMD01000003 (original name was: NZ_JPMD01000003.1)
  NZ_JPMD01000004 (original name was: NZ_JPMD01000004.1)
  NZ_JPMD01000005 (original name was: NZ_JPMD01000005.1)
  NZ_JPMD01000006 (original name was: NZ_JPMD01000006.1)
  NZ_JPMD01000007 (original name was: NZ_JPMD01000007.1)
  NZ_JPMD01000008 (original name was: NZ_JPMD01000008.1)
  NZ_JPMD01000009 (original name was: NZ_JPMD01000009.1)
  NZ_JPMD01000010 (original name was: NZ_JPMD01000010.1)
  NZ_JPMD01000011 (original name was: NZ_JPMD01000011.1)
  NZ_JPMD01000012 (original name was: NZ_JPMD01000012.1)
  NZ_JPMD01000013 (original name was: NZ_JPMD01000013.1)
  NZ_JPMD01000014 (original name was: NZ_JPMD01000014.1)
  NZ_JPMD01000015 (original name was: NZ_JPMD01000015.1)
  NZ_JPMD01000016 (original name was: NZ_JPMD01000016.1)
  NZ_JPMD01000017 (original name was: NZ_JPMD01000017.1)
  NZ_JPMD01000018 (original name was: NZ_JPMD01000018.1)
  NZ_JPMD01000019 (original name was: NZ_JPMD01000019.1)
  NZ_JPMD01000020 (original name was: NZ_JPMD01000020.1)
  NZ_JPMD01000021 (original name was: NZ_JPMD01000021.1)
  NZ_JPMD01000022 (original name was: NZ_JPMD01000022.1)
  NZ_JPMD01000023 (original name was: NZ_JPMD01000023.1)
  NZ_JPMD01000024 (original name was: NZ_JPMD01000024.1)
  NZ_JPMD01000025 (original name was: NZ_JPMD01000025.1)
  NZ_JPMD01000026 (original name was: NZ_JPMD01000026.1)
  NZ_JPMD01000027 (original name was: NZ_JPMD01000027.1)
  NZ_JPMD01000028 (original name was: NZ_JPMD01000028.1)
  NZ_JPMD01000029 (original name was: NZ_JPMD01000029.1)
  NZ_JPMD01000030 (original name was: NZ_JPMD01000030.1)
  NZ_JPMD01000032 (original name was: NZ_JPMD01000032.1)
  NZ_JPMD01000033 (original name was: NZ_JPMD01000033.1)
  NZ_JPMD01000034 (original name was: NZ_JPMD01000034.1)
  NZ_JPMD01000036 (original name was: NZ_JPMD01000036.1)
  NZ_JPMD01000037 (original name was: NZ_JPMD01000037.1)
  NZ_JPMD01000039 (original name was: NZ_JPMD01000039.1)
  NZ_JPMD01000040 (original name was: NZ_JPMD01000040.1)
  NZ_JPMD01000041 (original name was: NZ_JPMD01000041.1)
  NZ_JPMD01000042 (original name was: NZ_JPMD01000042.1)
  NZ_JPMD01000043 (original name was: NZ_JPMD01000043.1)
  NZ_JPMD01000044 (original name was: NZ_JPMD01000044.1)
  NZ_JPMD01000045 (original name was: NZ_JPMD01000045.1)
  NZ_JPMD01000046 (original name was: NZ_JPMD01000046.1)
  NZ_JPMD01000047 (original name was: NZ_JPMD01000047.1)
  NZ_JPMD01000048 (original name was: NZ_JPMD01000048.1)
  NZ_JPMD01000049 (original name was: NZ_JPMD01000049.1)
  NZ_JPMD01000050 (original name was: NZ_JPMD01000050.1)
  NZ_JPMD01000051 (original name was: NZ_JPMD01000051.1)
  NZ_JPMD01000052 (original name was: NZ_JPMD01000052.1)
  NZ_JPMD01000053 (original name was: NZ_JPMD01000053.1)
  NZ_JPMD01000054 (original name was: NZ_JPMD01000054.1)
  NZ_JPMD01000055 (original name was: NZ_JPMD01000055.1)
  NZ_JPMD01000056 (original name was: NZ_JPMD01000056.1)
  NZ_JPMD01000057 (original name was: NZ_JPMD01000057.1)
  NZ_JPMD01000058 (original name was: NZ_JPMD01000058.1)
  NZ_JPMD01000059 (original name was: NZ_JPMD01000059.1)
  NZ_JPMD01000060 (original name was: NZ_JPMD01000060.1)
  NZ_JPMD01000061 (original name was: NZ_JPMD01000061.1)
  NZ_JPMD01000062 (original name was: NZ_JPMD01000062.1)
  NZ_JPMD01000063 (original name was: NZ_JPMD01000063.1)
  NZ_JPMD01000064 (original name was: NZ_JPMD01000064.1)
  NZ_JPMD01000065 (original name was: NZ_JPMD01000065.1)
  NZ_JPMD01000066 (original name was: NZ_JPMD01000066.1)
  NZ_JPMD01000067 (original name was: NZ_JPMD01000067.1)
  NZ_JPMD01000068 (original name was: NZ_JPMD01000068.1)
  NZ_JPMD01000069 (original name was: NZ_JPMD01000069.1)
  NZ_JPMD01000070 (original name was: NZ_JPMD01000070.1)
  NZ_JPMD01000071 (original name was: NZ_JPMD01000071.1)
  NZ_JPMD01000072 (original name was: NZ_JPMD01000072.1)
  NZ_JPMD01000073 (original name was: NZ_JPMD01000073.1)
  NZ_JPMD01000078 (original name was: NZ_JPMD01000078.1)
  NZ_JPMD01000079 (original name was: NZ_JPMD01000079.1)
  NZ_JPMD01000081 (original name was: NZ_JPMD01000081.1)
  NZ_JPMD01000082 (original name was: NZ_JPMD01000082.1)
  NZ_JPMD01000083 (original name was: NZ_JPMD01000083.1)
  NZ_JPMD01000089 (original name was: NZ_JPMD01000089.1)

Compact view
c00031_NZ_JPMD.. - 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: 7,598 - 27,993 nt. (total: 20,396 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
--- | --- | --- | --- | --- | ---
BGC0000813.1 |  | 0.09 | Alkaloid | K-252a | Nonomuraea longicatena
BGC0001435.1 |  | 0.06 | NRP, Polyketide | ikarugamycin | Streptomyces sp. ZJ306
BGC0000814.1 |  | 0.05 | Alkaloid | K-252a | Nonomuraea longicatena

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000813.1 |  | 0.33 | Alkaloid | K-252a | Nonomuraea longicatena
BGC0001435.1 |  | 0.25 | NRP, Polyketide | ikarugamycin | Streptomyces sp. ZJ306
BGC0000814.1 |  | 0.22 | Alkaloid | K-252a | Nonomuraea longicatena

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
c00035_NZ_JPMD.. - Region 1 - ranthipeptide,thiopeptide
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: 54,001 - 93,860 nt. (total: 39,860 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)))
thiopeptide: ((YcaO or TIGR03882) and ((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or PF07366 or PF06968 or PF04055) or thiostrepton)

#### 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
Thiopeptides
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 | thiopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001387.1 |  |  | 0.34 | Other | nucleocidin | Streptomyces calvus
BGC0001285.1 |  |  | 0.34 | Other (Fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0001889.1 |  |  | 0.32 | RiPP | fusilassin | Thermobifida fusca YX
BGC0001356.1 |  |  | 0.31 | RiPP | paeninodin | Paenibacillus dendritiformis C454
BGC0001634.1 |  |  | 0.31 | RiPP | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001645.1 |  |  | 0.31 | RiPP | lagmysin | Streptomyces sp. NRRL S-118
BGC0000540.1 |  |  | 0.31 | RiPP | paenibacillin | Paenibacillus polymyxa OSY-DF
BGC0001412.1 |  |  | 0.31 | Saccharide | polysaccharide C | Bacteroides fragilis
BGC0000538.1 |  |  | 0.31 | RiPP | nisin Z | Lactococcus lactis
BGC0001494.1 |  |  | 0.30 | RiPP | acinetodin | Acinetobacter gyllenbergii CIP 110306

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001387.1 |  | 0.49 | Other | nucleocidin | Streptomyces calvus
BGC0001285.1 |  | 0.48 | Other (Fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0001889.1 |  | 0.46 | RiPP | fusilassin | Thermobifida fusca YX
BGC0001356.1 |  | 0.46 | RiPP | paeninodin | Paenibacillus dendritiformis C454
BGC0001634.1 |  | 0.46 | RiPP | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001645.1 |  | 0.46 | RiPP | lagmysin | Streptomyces sp. NRRL S-118
BGC0000540.1 |  | 0.46 | RiPP | paenibacillin | Paenibacillus polymyxa OSY-DF
BGC0001412.1 |  | 0.46 | Saccharide | polysaccharide C | Bacteroides fragilis
BGC0000538.1 |  | 0.46 | RiPP | nisin Z | Lactococcus lactis
BGC0001494.1 |  | 0.45 | RiPP | acinetodin | Acinetobacter gyllenbergii CIP 110306

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.

Thiopeptide 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. Predicted tail sequences are also shown.
No core peptides 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
Thiopeptides
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
c00038_NZ_JPMD.. - Region 1 - cyclic-lactone-autoinducer
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: 34,935 - 55,654 nt. (total: 20,720 nt) Show pHMM detection rules used
cyclic-lactone-autoinducer: (TIGR04223 or AgrB)

#### 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 | cyclic-lactone-autoinducer | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000844.1 |  | 0.13 | Other | clavulanic acid | Streptomyces clavuligerus
BGC0000488.1 |  | 0.11 | RiPP | circularin A | Clostridium beijerinckii
BGC0000453.1 |  | 0.08 | NRP | valinomycin | Streptomyces tsusimaensis
BGC0000845.1 |  | 0.06 | Other (Non-NRP beta-lactam) | clavulanic acid | Streptomyces clavuligerus ATCC 27064

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000844.1 |  | 0.42 | Other | clavulanic acid | Streptomyces clavuligerus
BGC0000488.1 |  | 0.38 | RiPP | circularin A | Clostridium beijerinckii
BGC0000453.1 |  | 0.31 | NRP | valinomycin | Streptomyces tsusimaensis
BGC0000845.1 |  | 0.26 | Other (Non-NRP beta-lactam) | clavulanic acid | Streptomyces clavuligerus ATCC 27064

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