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Overview
1.1
1.2
1.3

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

NZ_CP102290.1

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1 | NRPS-like | 1,146,400 | 1,189,124 |
Region 2 | NRPS | 3,267,723 | 3,315,078 |
Region 3 | ranthipeptide | 3,666,176 | 3,687,790 |

NZ_CP102290.1 - Region 1 - NRPS-like
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: 1,146,400 - 1,189,124 nt. (total: 42,725 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) 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 | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000375.1 |  | 0.21 | NRP | indigoidine | Streptomyces chromofuscus
BGC0000427.1 |  | 0.21 | NRP | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413
BGC0001399.1 |  | 0.20 | NRP | fellutamide B | Aspergillus nidulans FGSC A4
BGC0001132.1 |  | 0.18 | NRP | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001873.1 |  | 0.18 | NRP | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0001131.1 |  | 0.18 | NRP | ambactin | Xenorhabdus miraniensis
BGC0001825.1 |  | 0.18 | NRP | xenematide | Xenorhabdus nematophila AN6/1
BGC0001844.1 |  | 0.18 | NRP | holrhizin | Paraburkholderia rhizoxinica HKI 454
BGC0001833.1 |  | 0.18 | NRP | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.1 |  | 0.18 | NRP | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000375.1 |  | 0.54 | NRP | indigoidine | Streptomyces chromofuscus
BGC0000427.1 |  | 0.54 | NRP | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413
BGC0001399.1 |  | 0.52 | NRP | fellutamide B | Aspergillus nidulans FGSC A4
BGC0001132.1 |  | 0.49 | NRP | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001873.1 |  | 0.49 | NRP | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0001131.1 |  | 0.49 | NRP | ambactin | Xenorhabdus miraniensis
BGC0001825.1 |  | 0.49 | NRP | xenematide | Xenorhabdus nematophila AN6/1
BGC0001844.1 |  | 0.49 | NRP | holrhizin | Paraburkholderia rhizoxinica HKI 454
BGC0001833.1 |  | 0.49 | NRP | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.1 |  | 0.49 | NRP | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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 1, location 1146399 - 1189124:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (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).

ctg1_1113: X
  Search NORINE for peptide: strict or relaxed
  AMP-binding (229..607): X
  NRPSPredictor2: asp, asn
  SVM prediction details:
    Predicted physicochemical class:
      hydrophilic
    Large clusters prediction:
      asp, asn, glu, gln, aad
    Small clusters prediction:
      asp, asn
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DVeqIGhVDK
    Nearest Stachelhaus code:
      orn
    Stachelhaus code match:
      70% (weak)

NZ_CP102290.1 - Region 2 - NRPS
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: 3,267,723 - 3,315,078 nt. (total: 47,356 nt) Show pHMM detection rules used
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 | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000343.1 |  | 0.25 | NRP | enterobactin | Pseudomonas sp. J465
BGC0000308.1 |  | 0.24 | NRP | aureusimine | Staphylococcus aureus subsp. aureus str. JKD6008
BGC0001771.1 |  | 0.23 | NRP | scleric acid | Streptomyces sclerotialus
BGC0001575.1 |  | 0.22 | NRP | dipeptide aldehydes | Ruminococcus sp. 5_1_39BFAA
BGC0001686.1 |  | 0.21 | NRP | N-octanoyl-Met-Phe-H | Clostridium sp. CAG:567
BGC0000352.1 |  | 0.21 | NRP | fimsbactin A | Acinetobacter sp. ADP1
BGC0001131.1 |  | 0.21 | NRP | ambactin | Xenorhabdus miraniensis
BGC0001591.1 |  | 0.21 | Other | fatty acid enol ester | uncultured bacterium CSLC2
BGC0001688.1 |  | 0.21 | Other | N-tetradecanoyl tyrosine | uncultured bacterium CSLC2
BGC0001767.1 |  | 0.20 | NRP | salinichelins | Salinispora pacifica CNY331

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000343.1 |  | 0.59 | NRP | enterobactin | Pseudomonas sp. J465
BGC0000308.1 |  | 0.57 | NRP | aureusimine | Staphylococcus aureus subsp. aureus str. JKD6008
BGC0001771.1 |  | 0.56 | NRP | scleric acid | Streptomyces sclerotialus
BGC0001575.1 |  | 0.55 | NRP | dipeptide aldehydes | Ruminococcus sp. 5_1_39BFAA
BGC0001686.1 |  | 0.54 | NRP | N-octanoyl-Met-Phe-H | Clostridium sp. CAG:567
BGC0000352.1 |  | 0.54 | NRP | fimsbactin A | Acinetobacter sp. ADP1
BGC0001131.1 |  | 0.53 | NRP | ambactin | Xenorhabdus miraniensis
BGC0001591.1 |  | 0.53 | Other | fatty acid enol ester | uncultured bacterium CSLC2
BGC0001688.1 |  | 0.53 | Other | N-tetradecanoyl tyrosine | uncultured bacterium CSLC2
BGC0001767.1 |  | 0.53 | NRP | salinichelins | Salinispora pacifica CNY331

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 3267722 - 3315078:
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).

ctg1_3053: X - X
  Search NORINE for peptide: strict or relaxed
  AMP-binding (465..856): X
  NRPSPredictor2: phe, trp, phg, tyr, bht
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aromatic
    Large clusters prediction:
      phe, trp, phg, tyr, bht
    Small clusters prediction:
      N/A
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DAiSVGqVgK
    Nearest Stachelhaus code:
      tyr
    Stachelhaus code match:
      70% (weak)
  AMP-binding (1497..1887): X
  NRPSPredictor2: tyr, bht
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aromatic
    Large clusters prediction:
      phe, trp, phg, tyr, bht
    Small clusters prediction:
      tyr, bht
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DivqIGmVCK
    Nearest Stachelhaus code:
      lys
    Stachelhaus code match:
      60% (weak)
ctg1_3056: X
  Search NORINE for peptide: strict or relaxed
  AMP-binding (22..444): X
  NRPSPredictor2: (unknown)
  SVM prediction details:
    NOTE: outside applicability domain
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      N/A
    Small clusters prediction:
      N/A
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      tycliGGPLK
    Nearest Stachelhaus code:
      ala
    Stachelhaus code match:
      50% (weak)

NZ_CP102290.1 - Region 3 - 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: 3,666,176 - 3,687,790 nt. (total: 21,615 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 |  | 0.16 | Other | nucleocidin | Streptomyces calvus
BGC0000622.1 |  | 0.15 | RiPP | megacin | Bacillus megaterium
BGC0001887.1 |  | 0.14 | RiPP | huazacin | Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0001860.1 |  | 0.09 | RiPP | thiomuracin | Thermobispora bispora DSM 43833
BGC0000613.1 |  | 0.09 | RiPP | thiomuracin A | Nonomuraea sp. Bp3714-39
BGC0001591.1 |  | 0.09 | Other | fatty acid enol ester | uncultured bacterium CSLC2
BGC0001688.1 |  | 0.09 | Other | N-tetradecanoyl tyrosine | uncultured bacterium CSLC2
BGC0000604.1 |  | 0.08 | RiPP | GE2270A | Nonomuraea sp. WU8817
BGC0001686.1 |  | 0.08 | NRP | N-octanoyl-Met-Phe-H | Clostridium sp. CAG:567
BGC0001155.1 |  | 0.08 | RiPP | GE2270 | Planobispora rosea

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001387.1 |  | 0.47 | Other | nucleocidin | Streptomyces calvus
BGC0000622.1 |  | 0.45 | RiPP | megacin | Bacillus megaterium
BGC0001887.1 |  | 0.43 | RiPP | huazacin | Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0001860.1 |  | 0.33 | RiPP | thiomuracin | Thermobispora bispora DSM 43833
BGC0000613.1 |  | 0.33 | RiPP | thiomuracin A | Nonomuraea sp. Bp3714-39
BGC0001591.1 |  | 0.32 | Other | fatty acid enol ester | uncultured bacterium CSLC2
BGC0001688.1 |  | 0.32 | Other | N-tetradecanoyl tyrosine | uncultured bacterium CSLC2
BGC0000604.1 |  | 0.31 | RiPP | GE2270A | Nonomuraea sp. WU8817
BGC0001686.1 |  | 0.30 | NRP | N-octanoyl-Met-Phe-H | Clostridium sp. CAG:567
BGC0001155.1 |  | 0.30 | RiPP | GE2270 | Planobispora rosea

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