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Overview
1.1
1.2
1.3

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

NC_013790.1

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1 | NRPS | 84,290 | 129,886 |
Region 2 | NRPS | 486,386 | 538,949 |
Region 3 | thioamitides | 859,886 | 881,786 |

NC_013790.1 - Region 1 - 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: 84,290 - 129,886 nt. (total: 45,597 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
--- | --- | --- | --- | --- | ---
BGC0000308.1 |  | 0.23 | NRP | aureusimine | Staphylococcus aureus subsp. aureus str. JKD6008
BGC0001833.1 |  | 0.20 | NRP | icosalide A, icosalide B | Burkholderia gladioli
BGC0001844.1 |  | 0.20 | NRP | holrhizin | Paraburkholderia rhizoxinica HKI 454
BGC0001479.1 |  | 0.20 | NRP | anabaenopeptin NZ857, nostamide A | Nostoc punctiforme PCC 73102
BGC0001131.1 |  | 0.20 | NRP | ambactin | Xenorhabdus miraniensis
BGC0001758.1 |  | 0.20 | NRP | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.1 |  | 0.20 | NRP | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.1 |  | 0.20 | NRP | luminmide | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001168.1 |  | 0.20 | NRP | livipeptin | Streptomyces lividans 1326
BGC0001641.1 |  | 0.20 | NRP | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000308.1 |  | 0.56 | NRP | aureusimine | Staphylococcus aureus subsp. aureus str. JKD6008
BGC0001833.1 |  | 0.53 | NRP | icosalide A, icosalide B | Burkholderia gladioli
BGC0001844.1 |  | 0.53 | NRP | holrhizin | Paraburkholderia rhizoxinica HKI 454
BGC0001479.1 |  | 0.53 | NRP | anabaenopeptin NZ857, nostamide A | Nostoc punctiforme PCC 73102
BGC0001131.1 |  | 0.53 | NRP | ambactin | Xenorhabdus miraniensis
BGC0001758.1 |  | 0.53 | NRP | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.1 |  | 0.53 | NRP | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.1 |  | 0.53 | NRP | luminmide | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001168.1 |  | 0.53 | NRP | livipeptin | Streptomyces lividans 1326
BGC0001641.1 |  | 0.53 | NRP | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

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 84289 - 129886:
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_71: X - X
  Search NORINE for peptide: strict or relaxed
  AMP-binding (655..1094): X
  NRPSPredictor2: (unknown)
  SVM prediction details:
    NOTE: outside applicability domain
    Predicted physicochemical class:
      hydrophilic
    Large clusters prediction:
      orn, lys, arg
    Small clusters prediction:
      N/A
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      iVrgIGSIaK
    Nearest Stachelhaus code:
      orn
    Stachelhaus code match:
      60% (weak)
  AMP-binding (1702..2102): X
  NRPSPredictor2: hydrophobic-aliphatic
  SVM prediction details:
    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:
      DVQiIAmVyK
    Nearest Stachelhaus code:
      pro
    Stachelhaus code match:
      70% (weak)

NC_013790.1 - 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: 486,386 - 538,949 nt. (total: 52,564 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
--- | --- | --- | --- | --- | ---
BGC0001686.1 |  | 0.29 | NRP | N-octanoyl-Met-Phe-H | Clostridium sp. CAG:567
BGC0000308.1 |  | 0.29 | NRP | aureusimine | Staphylococcus aureus subsp. aureus str. JKD6008
BGC0001479.1 |  | 0.26 | NRP | anabaenopeptin NZ857, nostamide A | Nostoc punctiforme PCC 73102
BGC0001132.1 |  | 0.25 | NRP | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001873.1 |  | 0.25 | NRP | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0001135.1 |  | 0.24 | NRP | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.1 |  | 0.24 | NRP | luminmide | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000404.1 |  | 0.24 | NRP | penicillin | Penicillium chrysogenum
BGC0001575.1 |  | 0.23 | NRP | dipeptide aldehydes | Ruminococcus sp. 5_1_39BFAA
BGC0001825.1 |  | 0.23 | NRP | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001686.1 |  | 0.63 | NRP | N-octanoyl-Met-Phe-H | Clostridium sp. CAG:567
BGC0000308.1 |  | 0.62 | NRP | aureusimine | Staphylococcus aureus subsp. aureus str. JKD6008
BGC0001479.1 |  | 0.59 | NRP | anabaenopeptin NZ857, nostamide A | Nostoc punctiforme PCC 73102
BGC0001132.1 |  | 0.59 | NRP | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001873.1 |  | 0.59 | NRP | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0001135.1 |  | 0.58 | NRP | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.1 |  | 0.58 | NRP | luminmide | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000404.1 |  | 0.57 | NRP | penicillin | Penicillium chrysogenum
BGC0001575.1 |  | 0.56 | NRP | dipeptide aldehydes | Ruminococcus sp. 5_1_39BFAA
BGC0001825.1 |  | 0.56 | NRP | xenematide | Xenorhabdus nematophila AN6/1

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 486385 - 538949:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - X - leu - 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_350: X - X - leu - X
  Search NORINE for peptide: strict or relaxed
  AMP-binding (228..605): X
  NRPSPredictor2: orn, lys, arg
  SVM prediction details:
    Predicted physicochemical class:
      hydrophilic
    Large clusters prediction:
      orn, lys, arg
    Small clusters prediction:
      N/A
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DVdEfGSItK
    Nearest Stachelhaus code:
      orn
    Stachelhaus code match:
      70% (weak)
  AMP-binding (1226..1603): X
  NRPSPredictor2: orn, horn
  SVM prediction details:
    Predicted physicochemical class:
      hydrophilic
    Large clusters prediction:
      orn, lys, arg
    Small clusters prediction:
      orn, horn
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DVddfGSItK
    Nearest Stachelhaus code:
      orn
    Stachelhaus code match:
      60% (weak)
  AMP-binding (2229..2614): leu
  NRPSPredictor2: leu
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      gly, ala, val, leu, ile, abu, iva
    Small clusters prediction:
      N/A
    Single AA prediction:
      leu
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DALFgGiVtK
    Nearest Stachelhaus code:
      leu
    Stachelhaus code match:
      70% (weak)
  AMP-binding (3233..3610): X
  NRPSPredictor2: orn, lys, arg
  SVM prediction details:
    Predicted physicochemical class:
      hydrophilic
    Large clusters prediction:
      orn, lys, arg
    Small clusters prediction:
      N/A
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DVdEfGSItK
    Nearest Stachelhaus code:
      orn
    Stachelhaus code match:
      70% (weak)

NC_013790.1 - Region 3 - thioamitides
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: 859,886 - 881,786 nt. (total: 21,901 nt) Show pHMM detection rules used
thioamitides: ((YcaO or TIGR03882) and TfuA)

#### 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 | thioamitides | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001849.1 |  | 0.22 | RiPP | thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D | Streptomyces varsoviensis
BGC0001120.1 |  | 0.15 | NRP, Polyketide | burkholderic acid | Burkholderia thailandensis E264
BGC0001925.1 |  | 0.14 | Alkaloid | altemicidin, SB-203207, SB-203208 | Streptomyces sp.
BGC0001696.1 |  | 0.13 | RiPP | neothioviridamide | Streptomyces sp.
BGC0001802.1 |  | 0.13 | RiPP | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0000483.1 |  | 0.13 | RiPP | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0000193.1 |  | 0.13 | Polyketide | aclacinomycin | Streptomyces galilaeus
BGC0000625.1 |  | 0.11 | RiPP | thioviridamide | Streptomyces olivoviridis
BGC0001803.1 |  | 0.11 | RiPP | thioviridamide | Streptomyces olivoviridis
BGC0000473.1 |  | 0.10 | RiPP | microcyclamide | Microcystis aeruginosa NIES-298

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001849.1 |  | 0.55 | RiPP | thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D | Streptomyces varsoviensis
BGC0001120.1 |  | 0.45 | NRP, Polyketide | burkholderic acid | Burkholderia thailandensis E264
BGC0001925.1 |  | 0.43 | Alkaloid | altemicidin, SB-203207, SB-203208 | Streptomyces sp.
BGC0001696.1 |  | 0.42 | RiPP | neothioviridamide | Streptomyces sp.
BGC0001802.1 |  | 0.42 | RiPP | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0000483.1 |  | 0.42 | RiPP | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0000193.1 |  | 0.42 | Polyketide | aclacinomycin | Streptomyces galilaeus
BGC0000625.1 |  | 0.38 | RiPP | thioviridamide | Streptomyces olivoviridis
BGC0001803.1 |  | 0.38 | RiPP | thioviridamide | Streptomyces olivoviridis
BGC0000473.1 |  | 0.35 | RiPP | microcyclamide | Microcystis aeruginosa NIES-298

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