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Overview
2.1
2.2

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

NZ_UFSY01000001 (original name was: NZ_UFSY01000001.1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 2.1 | ranthipeptide,lanthipeptide-class-iii,NRPS | 848,481 | 914,864 | equibactin | NRP | 35%
Region 2.2 | ranthipeptide | 1,185,709 | 1,207,350 |

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 2.1 | ranthipeptide,lanthipeptide-class-iii,NRPS | 848,481 | 914,864 | equibactin | NRP | 35%
Region 2.2 | ranthipeptide | 1,185,709 | 1,207,350 |

No secondary metabolite regions were found in these records:
  NZ_UFSY01000002 (original name was: NZ_UFSY01000002.1)

Compact view
c00002_NZ_UFSY.. - Region 1 - NRPS,lanthipeptide-class-iii,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: 848,481 - 914,864 nt. (total: 66,384 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)))
lanthipeptide-class-iii: (micKC and not PKS_KS)
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
Lanthipeptides
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 | ranthipeptide | lanthipeptide-class-iii | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000519.1 |  |  |  | 0.78 | RiPP | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000551.1 |  |  |  | 0.72 | RiPP | SapB | Streptomyces coelicolor A3(2)
BGC0000496.1 |  |  |  | 0.67 | RiPP | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000553.1 |  |  |  | 0.66 | RiPP | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000554.1 |  |  |  | 0.58 | RiPP | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000513.1 |  |  |  | 0.57 | RiPP | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000500.1 |  |  |  | 0.56 | RiPP | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0000504.1 |  |  |  | 0.55 | RiPP | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000938.1 |  |  |  | 0.55 | Other (Aminocoumarin) | fosfomycin | Streptomyces fradiae
BGC0000517.1 |  |  |  | 0.54 | RiPP | haloduracin β, haloduracin α | Bacillus halodurans C-125

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000553.1 |  | 0.66 | RiPP | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000501.1 |  | 0.65 | RiPP | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000347.1 |  | 0.63 | NRP | equibactin | Streptococcus equi subsp. equi
BGC0000551.1 |  | 0.62 | RiPP | SapB | Streptomyces coelicolor A3(2)
BGC0000518.1 |  | 0.62 | RiPP | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000373.1 |  | 0.61 | NRP | holomycin | Streptomyces clavuligerus ATCC 27064
BGC0001343.1 |  | 0.60 | Polyketide | aurachin A, aurachin D | Stigmatella aurantiaca Sg a15
BGC0000496.1 |  | 0.60 | RiPP | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001399.1 |  | 0.59 | NRP | fellutamide B | Aspergillus nidulans FGSC A4
BGC0000343.1 |  | 0.58 | NRP | enterobactin | Pseudomonas sp. J465

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 ctg2_769 - Putative Class III

ctg2_771 leader / core peptide
  MTNDILNLQRMQPREDITVMAAS - DhbYDha DhbNCKNDha DhaGVDhaLFIC
ctg2_772 leader / core peptide
  MTNDILNLQKMQPREDITVMAAS - DhbFDha DhbNCKNDha DhaGIDhaLFVC
ctg2_773 leader / core peptide
  MTNDILNLQKMQPREDIAV - MAADha DhbYDha DhbNCKNDha DhaGVDhaLFIC

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
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
Lanthipeptides
NRPS/PKS products
NRPS/PKS monomers
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.

ctg2_771 - Class III
  Cleavage pHMM score: -3.40
  RODEO score: 0
  Monoisotopic mass: 1714.8 Da
  Molecular weight: 1715.9 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1733.9 Da N = 1
    1752.0 Da N = 2
    1770.0 Da N = 3
    1788.0 Da N = 4
ctg2_772 - Class III
  Cleavage pHMM score: -2.90
  RODEO score: 0
  Monoisotopic mass: 1698.8 Da
  Molecular weight: 1699.9 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1717.9 Da N = 1
    1736.0 Da N = 2
    1754.0 Da N = 3
    1772.0 Da N = 4
ctg2_773 - Class III
  Cleavage pHMM score: -2.90
  RODEO score: 0
  Monoisotopic mass: 2057.0 Da
  Molecular weight: 2058.3 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2076.3 Da N = 1
    2094.4 Da N = 2
    2112.4 Da N = 3
    2130.4 Da N = 4
    2148.4 Da N = 5

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 848480 - 914864:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (cys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 870370 - 914864:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (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).

ctg2_787: X
  Search NORINE for peptide: strict or relaxed
  AMP-binding (27..433): X
  NRPSPredictor2: dhb, sal
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      N/A
    Small clusters prediction:
      dhb, sal
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      PLPgQGiimK
    Nearest Stachelhaus code:
      dhb
    Stachelhaus code match:
      60% (weak)
ctg2_788: cys
  Search NORINE for peptide: strict or relaxed
  AMP-binding (556..956): 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:
      DLYdMSMIWK
    Nearest Stachelhaus code:
      cys
    Stachelhaus code match:
      90% (moderate)

c00002_NZ_UFSY.. - Region 2 - 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: 1,185,709 - 1,207,350 nt. (total: 21,642 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
BGC0001887.1 |  | 0.13 | RiPP | huazacin | Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0000700.1 |  | 0.13 | Saccharide | istamycin | Streptomyces tenjimariensis
BGC0001521.1 |  | 0.13 | NRP | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0001122.1 |  | 0.10 | NRP, Polyketide | dihydroisoflavipucine, isoflavipucine | Aspergillus terreus NIH2624
BGC0001591.1 |  | 0.07 | Other | fatty acid enol ester | uncultured bacterium CSLC2
BGC0001688.1 |  | 0.07 | Other | N-tetradecanoyl tyrosine | uncultured bacterium CSLC2
BGC0000337.1 |  | 0.05 | NRP | destruxin A | Metarhizium robertsii ARSEF 23
BGC0001195.1 |  | 0.05 | NRP, Polyketide | nocardiopsin A, nocardiopsin B, nocardiopsin C, nocardiopsin D | Nocardiopsis sp. CMB-M0232
BGC0001281.1 |  | 0.04 | Polyketide | ustilagic acid | Ustilago maydis 521

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001387.1 |  | 0.49 | Other | nucleocidin | Streptomyces calvus
BGC0001887.1 |  | 0.42 | RiPP | huazacin | Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0000700.1 |  | 0.41 | Saccharide | istamycin | Streptomyces tenjimariensis
BGC0001521.1 |  | 0.41 | NRP | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0001122.1 |  | 0.35 | NRP, Polyketide | dihydroisoflavipucine, isoflavipucine | Aspergillus terreus NIH2624
BGC0001591.1 |  | 0.29 | Other | fatty acid enol ester | uncultured bacterium CSLC2
BGC0001688.1 |  | 0.29 | Other | N-tetradecanoyl tyrosine | uncultured bacterium CSLC2
BGC0000337.1 |  | 0.23 | NRP | destruxin A | Metarhizium robertsii ARSEF 23
BGC0001195.1 |  | 0.21 | NRP, Polyketide | nocardiopsin A, nocardiopsin B, nocardiopsin C, nocardiopsin D | Nocardiopsis sp. CMB-M0232
BGC0001281.1 |  | 0.20 | Polyketide | ustilagic acid | Ustilago maydis 521

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