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Overview
11.1
17.1

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

NZ_SMMX01000001 (original name was: NZ_SMMX01000001.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 11.1 | ranthipeptide | 271,830 | 293,601 |

NZ_SMMX01000025 (original name was: NZ_SMMX01000025.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 17.1 | lanthipeptide-class-ii | 5,348 | 28,473 |

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 11.1 | ranthipeptide | 271,830 | 293,601 |
Region 17.1 | lanthipeptide-class-ii | 5,348 | 28,473 |

No secondary metabolite regions were found in these records:
  NZ_SMMX01000010 (original name was: NZ_SMMX01000010.1)
  NZ_SMMX01000011 (original name was: NZ_SMMX01000011.1)
  NZ_SMMX01000012 (original name was: NZ_SMMX01000012.1)
  NZ_SMMX01000013 (original name was: NZ_SMMX01000013.1)
  NZ_SMMX01000014 (original name was: NZ_SMMX01000014.1)
  NZ_SMMX01000015 (original name was: NZ_SMMX01000015.1)
  NZ_SMMX01000016 (original name was: NZ_SMMX01000016.1)
  NZ_SMMX01000017 (original name was: NZ_SMMX01000017.1)
  NZ_SMMX01000018 (original name was: NZ_SMMX01000018.1)
  NZ_SMMX01000019 (original name was: NZ_SMMX01000019.1)
  NZ_SMMX01000020 (original name was: NZ_SMMX01000020.1)
  NZ_SMMX01000021 (original name was: NZ_SMMX01000021.1)
  NZ_SMMX01000022 (original name was: NZ_SMMX01000022.1)
  NZ_SMMX01000023 (original name was: NZ_SMMX01000023.1)
  NZ_SMMX01000024 (original name was: NZ_SMMX01000024.1)
  NZ_SMMX01000026 (original name was: NZ_SMMX01000026.1)
  NZ_SMMX01000027 (original name was: NZ_SMMX01000027.1)
  NZ_SMMX01000028 (original name was: NZ_SMMX01000028.1)
  NZ_SMMX01000029 (original name was: NZ_SMMX01000029.1)
  NZ_SMMX01000002 (original name was: NZ_SMMX01000002.1)
  NZ_SMMX01000030 (original name was: NZ_SMMX01000030.1)
  NZ_SMMX01000031 (original name was: NZ_SMMX01000031.1)
  NZ_SMMX01000032 (original name was: NZ_SMMX01000032.1)
  NZ_SMMX01000033 (original name was: NZ_SMMX01000033.1)
  NZ_SMMX01000034 (original name was: NZ_SMMX01000034.1)
  NZ_SMMX01000035 (original name was: NZ_SMMX01000035.1)
  NZ_SMMX01000036 (original name was: NZ_SMMX01000036.1)
  NZ_SMMX01000037 (original name was: NZ_SMMX01000037.1)
  NZ_SMMX01000038 (original name was: NZ_SMMX01000038.1)
  NZ_SMMX01000039 (original name was: NZ_SMMX01000039.1)
  NZ_SMMX01000003 (original name was: NZ_SMMX01000003.1)
  NZ_SMMX01000040 (original name was: NZ_SMMX01000040.1)
  NZ_SMMX01000041 (original name was: NZ_SMMX01000041.1)
  NZ_SMMX01000042 (original name was: NZ_SMMX01000042.1)
  NZ_SMMX01000043 (original name was: NZ_SMMX01000043.1)
  NZ_SMMX01000044 (original name was: NZ_SMMX01000044.1)
  NZ_SMMX01000045 (original name was: NZ_SMMX01000045.1)
  NZ_SMMX01000046 (original name was: NZ_SMMX01000046.1)
  NZ_SMMX01000047 (original name was: NZ_SMMX01000047.1)
  NZ_SMMX01000048 (original name was: NZ_SMMX01000048.1)
  NZ_SMMX01000049 (original name was: NZ_SMMX01000049.1)
  NZ_SMMX01000004 (original name was: NZ_SMMX01000004.1)
  NZ_SMMX01000050 (original name was: NZ_SMMX01000050.1)
  NZ_SMMX01000051 (original name was: NZ_SMMX01000051.1)
  NZ_SMMX01000052 (original name was: NZ_SMMX01000052.1)
  NZ_SMMX01000005 (original name was: NZ_SMMX01000005.1)
  NZ_SMMX01000006 (original name was: NZ_SMMX01000006.1)
  NZ_SMMX01000007 (original name was: NZ_SMMX01000007.1)
  NZ_SMMX01000008 (original name was: NZ_SMMX01000008.1)
  NZ_SMMX01000009 (original name was: NZ_SMMX01000009.1)

Compact view
c00011_NZ_SMMX.. - 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: 271,830 - 293,601 nt. (total: 21,772 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
--- | --- | --- | --- | --- | ---
BGC0001387.1 |  | 0.17 | Other | nucleocidin | Streptomyces calvus
BGC0001540.1 |  | 0.16 | Other | CC-1065 | Streptomyces zelensis
BGC0001607.1 |  | 0.15 | Other | gilvusmycin | Streptomyces sp. NRRL B-1347
BGC0000466.1 |  | 0.15 | NRP | yatakemycin | Streptomyces sp. TP-A2060
BGC0000703.1 |  | 0.14 | Saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001985.1 |  | 0.14 | Other | pyrazomycin | Streptomyces candidus
BGC0002009.1 |  | 0.13 | Polyketide | kanglemycin A, kanglemycin V1, kanglemycin V2 | Amycolatopsis vancoresmycina
BGC0000842.1 |  | 0.13 | Other (Non-NRP beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0000807.1 |  | 0.11 | Saccharide | phosphonoglycans | Stackebrandtia nassauensis DSM 44728
BGC0001510.1 |  | 0.09 | Other | anisomycin | Streptomyces hygrospinosus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001387.1 |  | 0.48 | Other | nucleocidin | Streptomyces calvus
BGC0001540.1 |  | 0.46 | Other | CC-1065 | Streptomyces zelensis
BGC0001607.1 |  | 0.46 | Other | gilvusmycin | Streptomyces sp. NRRL B-1347
BGC0000466.1 |  | 0.45 | NRP | yatakemycin | Streptomyces sp. TP-A2060
BGC0000703.1 |  | 0.44 | Saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001985.1 |  | 0.43 | Other | pyrazomycin | Streptomyces candidus
BGC0002009.1 |  | 0.42 | Polyketide | kanglemycin A, kanglemycin V1, kanglemycin V2 | Amycolatopsis vancoresmycina
BGC0000842.1 |  | 0.41 | Other (Non-NRP beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0000807.1 |  | 0.37 | Saccharide | phosphonoglycans | Stackebrandtia nassauensis DSM 44728
BGC0001510.1 |  | 0.32 | Other | anisomycin | Streptomyces hygrospinosus

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
c00017_NZ_SMMX.. - Region 1 - lanthipeptide-class-ii
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: 5,348 - 28,473 nt. (total: 23,126 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### 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-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000525.1 |  | 0.25 | RiPP | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000516.1 |  | 0.19 | RiPP | geobacillin II | Geobacillus thermodenitrificans
BGC0001660.1 |  | 0.19 | RiPP | mathermycin | Marinactinospora thermotolerans
BGC0000554.1 |  | 0.18 | RiPP | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000703.1 |  | 0.17 | Saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001210.1 |  | 0.16 | RiPP | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000502.1 |  | 0.15 | RiPP | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001412.1 |  | 0.15 | Saccharide | polysaccharide C | Bacteroides fragilis
BGC0002009.1 |  | 0.15 | Polyketide | kanglemycin A, kanglemycin V1, kanglemycin V2 | Amycolatopsis vancoresmycina
BGC0001225.1 |  | 0.14 | NRP | celesticetin | Streptomyces caelestis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000525.1 |  | 0.59 | RiPP | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000516.1 |  | 0.52 | RiPP | geobacillin II | Geobacillus thermodenitrificans
BGC0001660.1 |  | 0.51 | RiPP | mathermycin | Marinactinospora thermotolerans
BGC0000554.1 |  | 0.49 | RiPP | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000703.1 |  | 0.48 | Saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001210.1 |  | 0.46 | RiPP | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000502.1 |  | 0.45 | RiPP | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001412.1 |  | 0.45 | Saccharide | polysaccharide C | Bacteroides fragilis
BGC0002009.1 |  | 0.45 | Polyketide | kanglemycin A, kanglemycin V1, kanglemycin V2 | Amycolatopsis vancoresmycina
BGC0001225.1 |  | 0.43 | NRP | celesticetin | Streptomyces caelestis

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.

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 ctg17_16 - Putative Class II

allorf_18579_18656 leader / core peptide
  VHPIDHVEYGT - PIDha Dha Dha Dhb DhaLC Dhb Dha DhaNDha
allorf_18548_18700 leader / core peptide
  MHIEDRNIELS - GDLLHEFEEVQRLVDEEIGVPYDha DhbWDhaIGC Dhb DhaFFDhbLIC C Dha
allorf_21699_21764 leader / core peptide
  LRNNSTYA - NRYCFDhaGDhbVIIDha Dhb

#### 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.

allorf_18579_18656 - Class II
  Cleavage pHMM score: -5.70
  RODEO score: 0
  Monoisotopic mass: 1207.6 Da
  Molecular weight: 1208.3 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1226.3 Da N = 1
    1244.3 Da N = 2
    1262.3 Da N = 3
    1280.3 Da N = 4
    1298.4 Da N = 5
    1316.4 Da N = 6
    1334.4 Da N = 7
    1352.4 Da N = 8
allorf_18548_18700 - Class II
  Cleavage pHMM score: -4.60
  RODEO score: 0
  Monoisotopic mass: 4296.1 Da
  Molecular weight: 4298.8 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4316.8 Da N = 1
    4334.8 Da N = 2
    4352.9 Da N = 3
    4370.9 Da N = 4
allorf_21699_21764 - Class II
  Cleavage pHMM score: -6.70
  RODEO score: 0
  Monoisotopic mass: 1387.7 Da
  Molecular weight: 1388.6 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1406.6 Da N = 1
    1424.6 Da N = 2
    1442.6 Da N = 3