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Overview
1.1
1.2

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

NZ_LR698967.1

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1 | terpene,NAPAA | 2,407,759 | 2,459,335 | carotenoid | Terpene | 25%
Region 2 | T1PKS | 2,543,869 | 2,588,740 | kanamycin | Saccharide | 1%

NZ_LR698967.1 - Region 1 - NAPAA,terpene
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: 2,407,759 - 2,459,335 nt. (total: 51,577 nt) Show pHMM detection rules used
terpene: (Terpene_synth or Terpene_synth_C or phytoene_synt or Lycopene_cycl or terpene_cyclase or NapT7 or fung_ggpps or fung_ggpps2 or trichodiene_synth or TRI5)
NAPAA: (AMP-binding and PP-binding and TIGR02353)

#### 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 | terpene | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000647.1 |  |  | 0.32 | Terpene | carotenoid | Rhodobacter sphaeroides
BGC0000650.1 |  |  | 0.27 | Terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000466.1 |  |  | 0.26 | NRP | yatakemycin | Streptomyces sp. TP-A2060
BGC0000648.1 |  |  | 0.23 | Terpene | carotenoid | Myxococcus xanthus
BGC0001122.1 |  |  | 0.21 | NRP, Polyketide | dihydroisoflavipucine, isoflavipucine | Aspergillus terreus NIH2624
BGC0000427.1 |  |  | 0.21 | NRP | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413
BGC0001128.1 |  |  | 0.18 | NRP | luminmide | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.1 |  |  | 0.18 | NRP | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001844.1 |  |  | 0.18 | NRP | holrhizin | Paraburkholderia rhizoxinica HKI 454
BGC0001521.1 |  |  | 0.18 | NRP | auriculamide | Herpetosiphon aurantiacus DSM 785

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000650.1 |  | 0.67 | Terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000648.1 |  | 0.65 | Terpene | carotenoid | Myxococcus xanthus
BGC0000647.1 |  | 0.65 | Terpene | carotenoid | Rhodobacter sphaeroides
BGC0000640.1 |  | 0.56 | Terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000643.1 |  | 0.56 | Terpene | carotenoid | Brevundimonas vesicularis
BGC0000634.1 |  | 0.56 | Terpene | carotenoid | Brevundimonas sp. SD212
BGC0000656.1 |  | 0.56 | Terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000637.1 |  | 0.55 | Terpene | carotenoid | Corynebacterium glutamicum
BGC0000375.1 |  | 0.54 | NRP | indigoidine | Streptomyces chromofuscus
BGC0000888.1 |  | 0.53 | Other | bacilysin | Bacillus sp. CS93

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.
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 2407758 - 2459335:
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

For candidate cluster 3, location 2425477 - 2459335:
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_2226: X
  Search NORINE for peptide: strict or relaxed
  AMP-binding (28..399): X
  NRPSPredictor2: (unknown)
  SVM prediction details:
    Predicted physicochemical class:
      hydrophilic
    Large clusters prediction:
      N/A
    Small clusters prediction:
      N/A
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DAESIGtVvK
    Nearest Stachelhaus code:
      lys
    Stachelhaus code match:
      80% (moderate)

NZ_LR698967.1 - Region 2 - T1PKS
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: 2,543,869 - 2,588,740 nt. (total: 44,872 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001909.1 |  | 0.31 | Polyketide | strobilurin | Strobilurus tenacellus
BGC0001281.1 |  | 0.24 | Polyketide | ustilagic acid | Ustilago maydis 521
BGC0001831.1 |  | 0.24 | Polyketide | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001163.1 |  | 0.21 | Polyketide | 1-heptadecene | Moorea producens 3L
BGC0001162.1 |  | 0.21 | Polyketide | 1-heptadecene | Moorea producens JHB
BGC0001161.1 |  | 0.21 | Polyketide | 1-heptadecene | Moorea bouillonii PNG
BGC0000044.1 |  | 0.20 | Polyketide | dawenol | Stigmatella aurantiaca DW4/3-1
BGC0001927.1 |  | 0.20 | Other | A-94964 | Streptomyces sp.
BGC0001264.1 |  | 0.19 | Polyketide | betaenone A, betaenone B, betaenone C | Phoma betae
BGC0001280.1 |  | 0.19 | Polyketide | betaenone C, betaenone A | Phoma betae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001909.1 |  | 0.65 | Polyketide | strobilurin | Strobilurus tenacellus
BGC0001281.1 |  | 0.58 | Polyketide | ustilagic acid | Ustilago maydis 521
BGC0001831.1 |  | 0.57 | Polyketide | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001163.1 |  | 0.54 | Polyketide | 1-heptadecene | Moorea producens 3L
BGC0001162.1 |  | 0.54 | Polyketide | 1-heptadecene | Moorea producens JHB
BGC0001161.1 |  | 0.54 | Polyketide | 1-heptadecene | Moorea bouillonii PNG
BGC0000044.1 |  | 0.53 | Polyketide | dawenol | Stigmatella aurantiaca DW4/3-1
BGC0001927.1 |  | 0.52 | Other | A-94964 | Streptomyces sp.
BGC0001264.1 |  | 0.51 | Polyketide | betaenone A, betaenone B, betaenone C | Phoma betae
BGC0001280.1 |  | 0.51 | Polyketide | betaenone C, betaenone A | Phoma betae

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.
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 4, location 2543868 - 2588740:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal)

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_2337: mal
  PKS_AT (647..946): mal
  ATSignature: Malonyl-CoA
  Top 3 matches:
    Malonyl-CoA: 62.5%
  minowa: fatty_acid
  Prediction, score:
    fatty_acid: 112.4
    Methylmalonyl-CoA: 64.5
    Methoxymalonyl-CoA: 63.5
    Malonyl-CoA: 56.9
    Ethylmalonyl-CoA: 39.6
    Propionyl-CoA: 38.5
    Acetyl-CoA: 31.6
    trans-1,2-CPDA: 27.9
    CHC-CoA: 24.8
    Isobutyryl-CoA: 21.5
    2-Methylbutyryl-CoA: 18.1
    inactive: 11.7
    Benzoyl-CoA: 0.0
    3-Methylbutyryl-CoA: 0.0
ctg1_2338: pk
  CAL_domain (200..535): pk
  minowa: Acetyl-CoA
  Prediction, score:
    Acetyl-CoA: 13.1
    shikimic_acid: 0.0
    fatty_acid: 0.0
    AHBA: 0.0
    NH2: -2.5