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Overview
1.1
1.2

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

NZ_CP073280.1

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1.1 | ranthipeptide | 1,360,226 | 1,381,998 |
Region 1.2 | NRPS,cyclic-lactone-autoinducer | 2,557,457 | 2,608,611 |

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1.1 | ranthipeptide | 1,360,226 | 1,381,998 |
Region 1.2 | NRPS,cyclic-lactone-autoinducer | 2,557,457 | 2,608,611 |

No secondary metabolite regions were found in these records:
  NZ_CP073281.1
  NZ_CP073282.1

Compact view
NZ_CP073280.1 - 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: 1,360,226 - 1,381,998 nt. (total: 21,773 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
BGC0000386.1 |  | 0.14 | NRP | malleobactin A, malleobactin B, malleobactin C, malleobactin D | Burkholderia thailandensis E264
BGC0001985.1 |  | 0.13 | Other | pyrazomycin | Streptomyces candidus
BGC0001664.1 |  | 0.13 | Terpene | merosterol | Scytonema sp. PCC 10023
BGC0001221.1 |  | 0.07 | Other (Phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0001501.1 |  | 0.06 | Alkaloid | ambiguine P | Fischerella sp. TAU
BGC0001126.1 |  | 0.06 | Terpene, Alkaloid | 12-epi-hapalindole J isonitrile, ambiguine A isonitrile, ambiguine B isonitrile, ambiguine C isonitrile, ambiguine D isonitrile, ambiguine E isonitrile, ambiguine K isonitrile, ambiguine L isonitrile, ambiguine I isonitrile, ambiguine J isonitrile | Fischerella ambigua UTEX 1903
BGC0001612.1 |  | 0.06 | Alkaloid | ambiguine H isonitrile | Fischerella ambigua UTEX 1903
BGC0001595.1 |  | 0.05 | Alkaloid | fischerindole | Fischerella sp. SAG 46.79
BGC0001594.1 |  | 0.05 | Alkaloid | fischerindole L | Fischerella muscicola UTEX 1829

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001387.1 |  | 0.48 | Other | nucleocidin | Streptomyces calvus
BGC0000386.1 |  | 0.44 | NRP | malleobactin A, malleobactin B, malleobactin C, malleobactin D | Burkholderia thailandensis E264
BGC0001985.1 |  | 0.42 | Other | pyrazomycin | Streptomyces candidus
BGC0001664.1 |  | 0.41 | Terpene | merosterol | Scytonema sp. PCC 10023
BGC0001221.1 |  | 0.28 | Other (Phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0001501.1 |  | 0.26 | Alkaloid | ambiguine P | Fischerella sp. TAU
BGC0001126.1 |  | 0.25 | Terpene, Alkaloid | 12-epi-hapalindole J isonitrile, ambiguine A isonitrile, ambiguine B isonitrile, ambiguine C isonitrile, ambiguine D isonitrile, ambiguine E isonitrile, ambiguine K isonitrile, ambiguine L isonitrile, ambiguine I isonitrile, ambiguine J isonitrile | Fischerella ambigua UTEX 1903
BGC0001612.1 |  | 0.25 | Alkaloid | ambiguine H isonitrile | Fischerella ambigua UTEX 1903
BGC0001595.1 |  | 0.23 | Alkaloid | fischerindole | Fischerella sp. SAG 46.79
BGC0001594.1 |  | 0.23 | Alkaloid | fischerindole L | Fischerella muscicola UTEX 1829

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
NZ_CP073280.1 - Region 2 - NRPS,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: 2,557,457 - 2,608,611 nt. (total: 51,155 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX))
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
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 | NRPS | cyclic-lactone-autoinducer | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000426.1 |  |  | 0.42 | NRP | sevadicin | Paenibacillus larvae
BGC0000427.1 |  |  | 0.42 | NRP | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413
BGC0000373.1 |  |  | 0.42 | NRP | holomycin | Streptomyces clavuligerus ATCC 27064
BGC0001479.1 |  |  | 0.42 | NRP | anabaenopeptin NZ857, nostamide A | Nostoc punctiforme PCC 73102
BGC0000389.1 |  |  | 0.41 | NRP | massetolide A | Pseudomonas fluorescens SS101
BGC0001135.1 |  |  | 0.41 | NRP | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000347.1 |  |  | 0.41 | NRP | equibactin | Streptococcus equi subsp. equi
BGC0001615.1 |  |  | 0.41 | NRP | hexose-palythine-serine, hexose-shinorine | Heteroscytonema crispum UCFS10
BGC0001261.1 |  |  | 0.41 | NRP | AM-toxin | Alternaria alternata
BGC0001873.1 |  |  | 0.40 | NRP | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000426.1 |  | 0.59 | NRP | sevadicin | Paenibacillus larvae
BGC0000389.1 |  | 0.58 | NRP | massetolide A | Pseudomonas fluorescens SS101
BGC0000488.1 |  | 0.57 | RiPP | circularin A | Clostridium beijerinckii
BGC0000347.1 |  | 0.56 | NRP | equibactin | Streptococcus equi subsp. equi
BGC0000373.1 |  | 0.56 | NRP | holomycin | Streptomyces clavuligerus ATCC 27064
BGC0001192.1 |  | 0.55 | NRP | colistin A, colistin B | Paenibacillus alvei
BGC0000331.1 |  | 0.54 | NRP | cyanopeptin | Planktothrix agardhii NIVA-CYA 116
BGC0000351.1 |  | 0.54 | NRP | exochelin | Mycolicibacterium smegmatis
BGC0000427.1 |  | 0.54 | NRP | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413
BGC0001479.1 |  | 0.54 | NRP | anabaenopeptin NZ857, nostamide A | Nostoc punctiforme PCC 73102

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.

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 2, location 2557456 - 2608611:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (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_2236: cys
  Search NORINE for peptide: strict or relaxed
  AMP-binding (524..918): 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)
ctg1_2238: cys
  Search NORINE for peptide: strict or relaxed
  AMP-binding (553..948): 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:
      DLYNMSMIWK
    Nearest Stachelhaus code:
      cys
    Stachelhaus code match:
      100% (strong)
ctg1_2239: X
  Search NORINE for peptide: strict or relaxed
  AMP-binding (25..431): X
  NRPSPredictor2: (unknown)
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aromatic
    Large clusters prediction:
      dhb, sal
    Small clusters prediction:
      dhb, sal
    Single AA prediction:
      dhb
  Stachelhaus prediction details:
    Stachelhaus sequence:
      PLPAQGVLsK
    Nearest Stachelhaus code:
      sal
    Stachelhaus code match:
      90% (moderate)