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Overview
1.1
1.2
1.3

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

NZ_LR134378.1

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1 | arylpolyene,RiPP-like | 33,188 | 77,053 | APE Vf | Other | 25%
Region 2 | NRPS,T1PKS,NRPS-like | 1,916,845 | 1,992,767 | streptobactin | NRP | 11%
Region 3 | terpene | 2,276,976 | 2,298,798 |

NZ_LR134378.1 - Region 1 - RiPP-like,arylpolyene
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: 33,188 - 77,053 nt. (total: 43,866 nt) Show pHMM detection rules used
arylpolyene: (APE_KS1 or APE_KS2)
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
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 | arylpolyene | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000836.1 |  |  | 0.42 | Other | APE Ec | Escherichia coli CFT073
BGC0002008.1 |  |  | 0.39 | Other | aryl polyenes | Xenorhabdus doucetiae
BGC0000840.1 |  |  | 0.29 | Other | xanthomonadin I | Xanthomonas oryzae pv. oryzae
BGC0000837.1 |  |  | 0.27 | Other | APE Vf | Aliivibrio fischeri ES114
BGC0001895.1 |  |  | 0.27 | Polyketide | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001
BGC0002000.1 |  |  | 0.26 | Polyketide | setomimycin | Streptomyces aurantiacus JA 4570
BGC0001343.1 |  |  | 0.25 | Polyketide | aurachin A, aurachin D | Stigmatella aurantiaca Sg a15
BGC0001723.1 |  |  | 0.25 | Polyketide | oviedomycin | Streptomyces antibioticus
BGC0000231.1 |  |  | 0.25 | Polyketide | griseusin | Streptomyces griseus
BGC0000839.1 |  |  | 0.24 | Other | flexirubin | Chitinophaga pinensis DSM 2588

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000836.1 |  | 0.62 | Other | APE Ec | Escherichia coli CFT073
BGC0001895.1 |  | 0.60 | Polyketide | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001
BGC0002000.1 |  | 0.60 | Polyketide | setomimycin | Streptomyces aurantiacus JA 4570
BGC0002008.1 |  | 0.59 | Other | aryl polyenes | Xenorhabdus doucetiae
BGC0001343.1 |  | 0.58 | Polyketide | aurachin A, aurachin D | Stigmatella aurantiaca Sg a15
BGC0001723.1 |  | 0.58 | Polyketide | oviedomycin | Streptomyces antibioticus
BGC0000231.1 |  | 0.58 | Polyketide | griseusin | Streptomyces griseus
BGC0000234.1 |  | 0.56 | Polyketide | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000228.1 |  | 0.56 | Polyketide | granaticin | Streptomyces violaceoruber
BGC0002012.1 |  | 0.55 | Polyketide | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772

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.
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_LR134378.1 - Region 2 - NRPS,NRPS-like,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: 1,916,845 - 1,992,767 nt. (total: 75,923 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX))
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
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
TTA codons
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 | T1PKS | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000427.1 |  |  |  |  | 1.19 | NRP | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413
BGC0000457.1 |  |  |  |  | 1.13 | NRP | vicibactin | Rhizobium etli CFN 42
BGC0001561.1 |  |  |  |  | 1.03 | NRP | curacomycin | Streptomyces curacoi
BGC0001132.1 |  |  |  |  | 1.03 | NRP | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001479.1 |  |  |  |  | 1.01 | NRP | anabaenopeptin NZ857, nostamide A | Nostoc punctiforme PCC 73102
BGC0000417.1 |  |  |  |  | 1.00 | NRP | rhodochelin | Rhodococcus jostii RHA1
BGC0000979.1 |  |  |  |  | 1.00 | NRP, Polyketide | cylindrospermopsin | Aphanizomenon sp. 10E9
BGC0000980.1 |  |  |  |  | 1.00 | NRP, Polyketide | cylindrospermopsin | Aphanizomenon sp. 22D11
BGC0000901.1 |  |  |  |  | 0.99 | Other | ferrichrome | Aspergillus niger
BGC0001128.1 |  |  |  |  | 0.99 | NRP | luminmide | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000375.1 |  | 0.68 | NRP | indigoidine | Streptomyces chromofuscus
BGC0000427.1 |  | 0.67 | NRP | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413
BGC0000417.1 |  | 0.65 | NRP | rhodochelin | Rhodococcus jostii RHA1
BGC0001615.1 |  | 0.65 | NRP | hexose-palythine-serine, hexose-shinorine | Heteroscytonema crispum UCFS10
BGC0001437.1 |  | 0.65 | NRP | obafluorin | Pseudomonas fluorescens
BGC0001710.1 |  | 0.65 | NRP | obafluorin | Pseudomonas fluorescens
BGC0001249.1 |  | 0.65 | NRP | dimethylcoprogen | Alternaria alternata
BGC0000900.1 |  | 0.65 | Other | ferrichrome | Aspergillus oryzae
BGC0000457.1 |  | 0.65 | NRP | vicibactin | Rhizobium etli CFN 42
BGC0000348.1 |  | 0.65 | NRP | ergovaline | Epichloe festucae var. lolii

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 1916844 - 1992767:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (gly) + (val - mal) + (ser)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 1916844 - 1960714:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (val - mal) + (gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 1922602 - 1970969:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (gly) + (val - mal) + (ser)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 1948639 - 1992767:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (val - mal) + (ser)

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_1533: X
  Search NORINE for peptide: strict or relaxed
  AMP-binding (120..450): 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:
      sLFsLSf-yK
    Nearest Stachelhaus code:
      cys
    Stachelhaus code match:
      50% (weak)
ctg1_1541: gly
  Search NORINE for peptide: strict or relaxed
  AMP-binding (503..908): gly
  NRPSPredictor2: gly
  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:
      gly
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DILQLGMvWK
    Nearest Stachelhaus code:
      gly
    Stachelhaus code match:
      90% (moderate)
ctg1_1542: val - mal
  Search NORINE for peptide: strict or relaxed
  AMP-binding (202..623): val
  NRPSPredictor2: val
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      gly, ala, val, leu, ile, abu, iva
    Small clusters prediction:
      val, leu, ile, abu, iva
    Single AA prediction:
      val
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DALWmGGTFK
    Nearest Stachelhaus code:
      val
    Stachelhaus code match:
      90% (moderate)
  PKS_AT (1514..1856): mal
  ATSignature: Malonyl-CoA
  Top 3 matches:
    Malonyl-CoA: 87.5%
    inactive: 83.3%
  minowa: Malonyl-CoA
  Prediction, score:
    Malonyl-CoA: 155.8
    inactive: 89.8
    Methoxymalonyl-CoA: 77.8
    Methylmalonyl-CoA: 66.5
    Ethylmalonyl-CoA: 46.4
    Propionyl-CoA: 46.0
    2-Methylbutyryl-CoA: 40.2
    Isobutyryl-CoA: 30.3
    Acetyl-CoA: 27.7
    Benzoyl-CoA: 23.6
    CHC-CoA: 22.6
    trans-1,2-CPDA: 17.1
    fatty_acid: 11.7
    3-Methylbutyryl-CoA: 0.0
ctg1_1554: ser
  Search NORINE for peptide: strict or relaxed
  AMP-binding (478..890): ser
  NRPSPredictor2: ser
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      ser, thr, dhpg, hpg
    Small clusters prediction:
      ser
    Single AA prediction:
      ser
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DVWHFSLVDK
    Nearest Stachelhaus code:
      ser
    Stachelhaus code match:
      100% (strong)
ctg1_1556: dhb
  Search NORINE for peptide: strict or relaxed
  AMP-binding (34..449): dhb
  NRPSPredictor2: dhb
  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:
      PMPAQGVVNK
    Nearest Stachelhaus code:
      dhb
    Stachelhaus code match:
      100% (strong)

NZ_LR134378.1 - Region 3 - 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: 2,276,976 - 2,298,798 nt. (total: 21,823 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)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000647.1 |  | 0.25 | Terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.1 |  | 0.19 | Terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0001120.1 |  | 0.18 | NRP, Polyketide | burkholderic acid | Burkholderia thailandensis E264
BGC0000643.1 |  | 0.18 | Terpene | carotenoid | Brevundimonas vesicularis
BGC0000634.1 |  | 0.18 | Terpene | carotenoid | Brevundimonas sp. SD212
BGC0000630.1 |  | 0.16 | Terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000640.1 |  | 0.16 | Terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000928.1 |  | 0.15 | Other | T3 toxin | Cylindrospermopsis raciborskii T3
BGC0000188.1 |  | 0.15 | Alkaloid | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0001456.1 |  | 0.15 | Terpene | isorenieratene | Streptomyces argillaceus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000647.1 |  | 0.58 | Terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.1 |  | 0.50 | Terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0001120.1 |  | 0.50 | NRP, Polyketide | burkholderic acid | Burkholderia thailandensis E264
BGC0000643.1 |  | 0.49 | Terpene | carotenoid | Brevundimonas vesicularis
BGC0000634.1 |  | 0.49 | Terpene | carotenoid | Brevundimonas sp. SD212
BGC0000630.1 |  | 0.47 | Terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000640.1 |  | 0.46 | Terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000928.1 |  | 0.46 | Other | T3 toxin | Cylindrospermopsis raciborskii T3
BGC0000188.1 |  | 0.46 | Alkaloid | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0001456.1 |  | 0.46 | Terpene | isorenieratene | Streptomyces argillaceus

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