Select genomic region:
Overview
1.1
1.2
1.3
1.4
1.5
1.6
1.7
1.8
1.9
1.10
1.11
1.12
1.13
1.14
1.15
1.16

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

NZ_CP051206.1 (Dolichospermum flos-aquae CCAP 1403/13F)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | lanthipeptide-class-v | 264,333 | 306,745 |
Region 1.2 | NRPS | 352,778 | 399,081 | Low | hassallidin C/hassallidin D | NRPS:Type I+saccharide:hybrid/tailoring
Region 1.3 | lanthipeptide-class-v | 839,780 | 882,038 |
Region 1.4 | NRPS-like,NRPS,betalactone | 1,131,575 | 1,200,771 | High | anabaenopeptin | NRPS:Type I
Region 1.5 | terpene-precursor | 1,258,195 | 1,279,133 |
Region 1.6 | hglE-KS,T1PKS | 1,454,658 | 1,506,746 | High | heterocyst glycolipids | other:other
Region 1.7 | terpene | 1,529,360 | 1,551,273 |
Region 1.8 | hglE-KS | 2,461,504 | 2,508,220 | Medium | heterocyst glycolipids | other:other
Region 1.9 | lanthipeptide-class-ii | 2,895,747 | 2,918,929 |
Region 1.10 | NRPS | 3,017,461 | 3,066,760 |
Region 1.11 | cyanobactin | 3,228,883 | 3,259,952 | High | anacyclamide A10 | ribosomal:RiPP:Cyanobactin
Region 1.12 | NRPS-like,T1PKS,NRPS | 4,221,094 | 4,292,052 | Low | puwainaphycin F/minutissamide A/minutissamide B/minutissamide C/minutissamide D | NRPS:Type I
Region 1.13 | azole-containing-RiPP | 4,350,671 | 4,372,769 |
Region 1.14 | terpene | 4,573,676 | 4,594,608 |
Region 1.15 | terpene | 4,861,069 | 4,881,899 |
Region 1.16 | NRPS-like | 5,018,746 | 5,079,167 | High | micropeptin K139 | NRPS:Type I

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | lanthipeptide-class-v | 264,333 | 306,745 |
Region 1.2 | NRPS | 352,778 | 399,081 | Low | hassallidin C/hassallidin D | NRPS:Type I+saccharide:hybrid/tailoring
Region 1.3 | lanthipeptide-class-v | 839,780 | 882,038 |
Region 1.4 | NRPS-like,NRPS,betalactone | 1,131,575 | 1,200,771 | High | anabaenopeptin | NRPS:Type I
Region 1.5 | terpene-precursor | 1,258,195 | 1,279,133 |
Region 1.6 | hglE-KS,T1PKS | 1,454,658 | 1,506,746 | High | heterocyst glycolipids | other:other
Region 1.7 | terpene | 1,529,360 | 1,551,273 |
Region 1.8 | hglE-KS | 2,461,504 | 2,508,220 | Medium | heterocyst glycolipids | other:other
Region 1.9 | lanthipeptide-class-ii | 2,895,747 | 2,918,929 |
Region 1.10 | NRPS | 3,017,461 | 3,066,760 |
Region 1.11 | cyanobactin | 3,228,883 | 3,259,952 | High | anacyclamide A10 | ribosomal:RiPP:Cyanobactin
Region 1.12 | NRPS-like,T1PKS,NRPS | 4,221,094 | 4,292,052 | Low | puwainaphycin F/minutissamide A/minutissamide B/minutissamide C/minutissamide D | NRPS:Type I
Region 1.13 | azole-containing-RiPP | 4,350,671 | 4,372,769 |
Region 1.14 | terpene | 4,573,676 | 4,594,608 |
Region 1.15 | terpene | 4,861,069 | 4,881,899 |
Region 1.16 | NRPS-like | 5,018,746 | 5,079,167 | High | micropeptin K139 | NRPS:Type I

No secondary metabolite regions were found in these records:
  NZ_CP051207.1 (Dolichospermum flos-aquae CCAP 1403/13F)

Compact view
NZ_CP051206.1 - Region 1 - lanthipeptide-class-v
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: 264,333 - 306,745 nt. (total: 42,413 nt) Show pHMM detection rules used
lanthipeptide-class-v: (APH and HopA1)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lanthipeptides
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: dehydratase
HGD76_RS01580: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Isomerases: isomerase racemase
HGD76_RS01465: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

HGD76_RS01475: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase
HGD76_RS01480: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters
Shows areas 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 | lanthipeptide-class-v | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000343.5 |  | 0.44 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0000913.3 |  | 0.41 | other (other) | MK-8 | Enterobacter cloacae
BGC0000649.3 |  | 0.39 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002007.2 |  | 0.38 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0000393.5 |  | 0.38 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622
BGC0000883.5 |  | 0.38 | other (other) | arginomycin | Streptomyces arginensis
BGC0002473.3 |  | 0.37 | NRPS | propanochelin, butanochelin, pentanochelin | Acinetobacter bouvetii DSM 14964 = CIP 107468
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0001148.5 |  | 0.36 | NRPS, ribosomal | pheganomycin | Streptomyces cirratus
BGC0001221.5 |  | 0.35 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000343.5 |  | 0.44 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0000913.3 |  | 0.41 | other (other) | MK-8 | Enterobacter cloacae
BGC0000649.3 |  | 0.39 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002007.2 |  | 0.38 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0000393.5 |  | 0.38 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622
BGC0000883.5 |  | 0.38 | other (other) | arginomycin | Streptomyces arginensis
BGC0002473.3 |  | 0.37 | NRPS | propanochelin, butanochelin, pentanochelin | Acinetobacter bouvetii DSM 14964 = CIP 107468
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0001148.5 |  | 0.36 | NRPS, ribosomal | pheganomycin | Streptomyces cirratus
BGC0001221.5 |  | 0.35 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.28 out of 27.55
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.82 out of 25.88
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.09 out of 21.55
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.80 out of 29.72
Confidence: medium
Additional weak hits (7):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.28 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.28 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.28 out of 28.14
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 25.75
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 25.65 out of 31.73
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 25.16 out of 35.63
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 18.76 out of 30.11
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
GnfM | Regulator of nitrogen-fixation genes
NtrC | Nitrogen regulatory protein C
PsrA | Oleic acid responsive regulator

NZ_CP051206.1 - 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: 352,778 - 399,081 nt. (total: 46,304 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: glycosyltransferase
HGD76_RS01885: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: esterase glucosidase
HGD76_RS01890: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

smcogs
  SMCOG1283: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

HGD76_RS01945: putative esterase

smcogs
  SMCOG1104: putative esterase

HGD76_RS01985: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

Ligases: ligase synthase
HGD76_RS01910: 1-deoxy-D-xylulose-5-phosphate synthase

smcogs
  SMCOG1110: 1-deoxy-D-xylulose-5-phosphate synthase

HGD76_RS01925: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

HGD76_RS01930: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

HGD76_RS01960: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

HGD76_RS01975: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

Similar gene clusters
Shows areas 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
--- | --- | --- | --- | --- | ---
BGC0000357.5 |  | 0.69 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001825.4 |  | 0.66 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001133.4 |  | 0.65 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001240.4 |  | 0.65 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000426.5 |  | 0.63 | NRPS | sevadicin | Paenibacillus larvae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000357.5 |  | 0.69 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001825.4 |  | 0.66 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001133.4 |  | 0.65 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001240.4 |  | 0.65 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000426.5 |  | 0.63 | NRPS | sevadicin | Paenibacillus larvae

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.34 out of 27.55
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.98 out of 29.38
Confidence: medium
Additional weak hits (1):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 24.87 out of 31.73
Confidence: weak
Module view
Shows module structures for each candidate cluster 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, and an explanation of the visualisation is available here.
Legend
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 domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
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 352777 - 399081:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Tyr)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation 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).
HGD76_RS01925: Tyr
Search NORINE for peptide: strict or relaxed
AMP-binding (614..1003): Tyr
nrpys: Tyr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    Polar aromatic ring (Tyr, bOH-Tyr)
  Single AA prediction:
    tyr (Tyr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNQAFDAAVSEMTLIVAGEFNAYGPTEATVCASL
  Nearest Stachelhaus code(s):
    Tyr DASTIAAVCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

HGD76_RS01960: X
AMP-binding (9..371): X
nrpys: 2,3-dohHda

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    MKFLHIGGINTHPTTYGTEHQTYGLTELGIMRSK
  Nearest Stachelhaus code(s):
    2,3-dohHda IGNPTGTIMK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
FuR variant 1 | Ferric Uptake Regulator
GnfM | Regulator of nitrogen-fixation genes
ToxT | Regulator of MSHA biosynthesis

NZ_CP051206.1 - Region 3 - lanthipeptide-class-v
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: 839,780 - 882,038 nt. (total: 42,259 nt) Show pHMM detection rules used
lanthipeptide-class-v: (APH and HopA1)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lanthipeptides
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: back translocase
HGD76_RS04535: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

Similar gene clusters
Shows areas 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 | lanthipeptide-class-v | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001685.3 |  | 0.47 | other (other) | N-acyloxyacyl lysine | Raoultella ornithinolytica 10-5246
BGC0000563.4 |  | 0.42 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  | 0.42 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000556.5 |  | 0.39 | ribosomal | streptin | Streptococcus pyogenes
BGC0002698.2 |  | 0.39 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0002346.3 |  | 0.39 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0002635.2 |  | 0.37 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0002303.3 |  | 0.37 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0001789.3 |  | 0.37 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000537.3 |  | 0.37 | ribosomal | nisin U | Streptococcus uberis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001685.3 |  | 0.47 | other (other) | N-acyloxyacyl lysine | Raoultella ornithinolytica 10-5246
BGC0000563.4 |  | 0.42 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  | 0.42 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000556.5 |  | 0.39 | ribosomal | streptin | Streptococcus pyogenes
BGC0002698.2 |  | 0.39 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0002346.3 |  | 0.39 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0002635.2 |  | 0.37 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0002303.3 |  | 0.37 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0001789.3 |  | 0.37 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000537.3 |  | 0.37 | ribosomal | nisin U | Streptococcus uberis

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.69 out of 26.06
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 23.25 out of 25.31
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.57 out of 25.31
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.02 out of 20.97
Confidence: medium
Additional weak hits (1):
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.75 out of 30.98
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
CcpA | Catabolite control protein A
MogR | Repressor of flagellar motility genes

NZ_CP051206.1 - Region 4 - NRPS,NRPS-like,betalactone
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: 1,131,575 - 1,200,771 nt. (total: 69,197 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
betalactone: (HMGL-like and AMP-binding)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase transketolase
HGD76_RS05815: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

HGD76_RS05970: transketolase

smcogs
  SMCOG1204: transketolase

Hydrolases: deformylase
HGD76_RS05950: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Ligases: ligase synthase
HGD76_RS05900: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

HGD76_RS05905: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

HGD76_RS05910: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

HGD76_RS05920: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

HGD76_RS05925: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

HGD76_RS05930: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

HGD76_RS05965: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HGD76_RS25150: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters
Shows areas 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 | NRPS | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000302.5 |  |  |  | 1.29 | NRPS | anabaenopeptin | Anabaena sp. 90
BGC0001132.4 |  |  |  | 1.24 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000342.4 |  |  |  | 1.23 | NRPS | enniatin | Fusarium equiseti
BGC0001128.4 |  |  |  | 1.19 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  |  | 1.18 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  |  | 1.18 | NRPS | AM-toxin | Alternaria alternata
BGC0002286.3 |  |  |  | 1.17 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  |  | 1.17 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  |  |  | 1.16 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  |  |  | 1.15 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000302.5 |  | 0.89 | NRPS | anabaenopeptin | Anabaena sp. 90
BGC0001132.4 |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000342.4 |  | 0.74 | NRPS | enniatin | Fusarium equiseti
BGC0002286.3 |  | 0.74 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.06 out of 19.26
Confidence: strong
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.25 out of 29.38
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.00 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.70 out of 26.06
Confidence: medium
Additional weak hits (9):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 27.05 out of 39.62
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 24.50 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.69 out of 29.38
Confidence: weak
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 16.71 out of 20.47
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.60 out of 30.97
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.37 out of 32.38
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.27 out of 36.53
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.04 out of 27.55
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 18.17 out of 30.12
Confidence: weak
Module view
Shows module structures for each candidate cluster 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, and an explanation of the visualisation is available here.
Legend
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 domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
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 1131574 - 1200771:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (D-Lys) + (Tyr - D-Lys) + (Val) + (X - NMe-Ala) + (Phe)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 1131574 - 1173479:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (D-Lys) + (Tyr - D-Lys) + (Val) + (X - NMe-Ala)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 1133481 - 1200771:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (D-Lys) + (Tyr - D-Lys) + (Val) + (X - NMe-Ala) + (Phe)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation 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).
HGD76_RS25150: X
AMP-binding (11..424): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FMASFDVAAEEPDLIIGGEINCYGPTETTVAASI
  Nearest Stachelhaus code(s):
    Lys or Arg DVEDIGSVAK (97% 8Å match)
  Stachelhaus code match:
    90% (moderate)

HGD76_RS05900: Lys
Search NORINE for peptide: strict or relaxed
AMP-binding (150..556): Lys
nrpys: Lys

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FTAAFDTAAEEPDLIIGGEVNSYGPTETTVIATL
  Nearest Stachelhaus code(s):
    Lys DTEDIGSVIK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

HGD76_RS05905: Tyr - Lys
Search NORINE for peptide: strict or relaxed
AMP-binding (46..438): Tyr
nrpys: Tyr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    Polar aromatic ring (Tyr, bOH-Tyr)
  Single AA prediction:
    tyr (Tyr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDASVSEMTLIVAGEFNAYGPTESTVCATV
  Nearest Stachelhaus code(s):
    Tyr DASTIAAVCK (100% 8Å match)
    Tyr or Pro DASTIAAVCK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1108..1513): Lys
nrpys: Lys

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FTAAFDTSIEEPDLIIGGEFNSYGPTEATVVTTL
  Nearest Stachelhaus code(s):
    Lys DTEDIGSVVK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

HGD76_RS05910: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (462..860): Val
nrpys: Val

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    val (Val)

Stachelhaus prediction details:
  Stachelhaus sequence:
    FEVSWDALTLEPWLLIGGEINGYGPSECTVFTCC
  Nearest Stachelhaus code(s):
    Val DALWLGGVFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

HGD76_RS05920: X - Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (462..856): X
nrpys: Hty

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAWGFDLSIGETFLTVGGEYNCYGPTESTVTAAI
  Nearest Stachelhaus code(s):
    Hty DLGFTGCVTK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1516..1915): Ala
nrpys: Ala

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
  Single AA prediction:
    ala (Ala)

Stachelhaus prediction details:
  Stachelhaus sequence:
    FWATFDLSIFEVNTNLAGEYNLYGPSEDTTYSTF
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

HGD76_RS05925: Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (551..955): Phe
nrpys: Phe

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    Unpolar aromatic ring (Phe, Trp)
  Single AA prediction:
    phe (Phe)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAVAFDASIWEPTIITAGEFNGYGPTESTVCTSI
  Nearest Stachelhaus code(s):
    Phe DAWTIAGVCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
FuR variant 1 | Ferric Uptake Regulator
MogR | Repressor of flagellar motility genes

NZ_CP051206.1 - Region 5 - terpene-precursor
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: 1,258,195 - 1,279,133 nt. (total: 20,939 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
HGD76_RS06315: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: transferase
HGD76_RS06320: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Ligases: synthetase
HGD76_RS06365: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Similar gene clusters
Shows areas 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-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.48 | terpene | astallatene | Arabidopsis thaliana
BGC0000894.4 |  | 0.46 | other (other) | citrinin | Monascus aurantiacus
BGC0000866.5 |  | 0.45 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0002400.2 |  | 0.45 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000867.3 |  | 0.44 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0001605.3 |  | 0.43 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000231.5 |  | 0.42 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002508.2 |  | 0.41 | other (other) | 8-azaguanine | Streptomyces pathocidini
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000234.5 |  | 0.39 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.48 | terpene | astallatene | Arabidopsis thaliana
BGC0000894.4 |  | 0.46 | other (other) | citrinin | Monascus aurantiacus
BGC0000866.5 |  | 0.45 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0002400.2 |  | 0.45 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000867.3 |  | 0.44 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0001605.3 |  | 0.43 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000231.5 |  | 0.42 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002508.2 |  | 0.41 | other (other) | 8-azaguanine | Streptomyces pathocidini
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000234.5 |  | 0.39 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
HGD76_RS06365: PT_FPPS_like
Domain 1 (47 - 312): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: Farnesyl diphosphate synthase, bacterial or Geranylgeranyl diphosphate synthase or geranylfarnesyl diphosphate synthase, bacterial
Terpene
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
NZ_CP051206.1 - Region 6 - T1PKS,hglE-KS
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: 1,454,658 - 1,506,746 nt. (total: 52,089 nt) Show pHMM detection rules used
hglE-KS: (hglE or hglD)
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
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
HGD76_RS07355: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase glycosyltransferase
HGD76_RS07295: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

HGD76_RS07345: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Lyases: dehydratase
HGD76_RS07310: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

HGD76_RS07350: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
HGD76_RS07250: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

HGD76_RS07325: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HGD76_RS07335: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HGD76_RS07340: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

Similar gene clusters
Shows areas 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 | hglE-KS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000869.5 |  |  | 0.96 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0001284.4 |  |  | 0.55 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0000863.3 |  |  | 0.54 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12
BGC0002276.2 |  |  | 0.54 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000862.3 |  |  | 0.53 | other (other) | eicosapentaenoic acid | Shewanella pneumatophori
BGC0001244.3 |  |  | 0.52 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000107.3 |  |  | 0.51 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0001276.3 |  |  | 0.51 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002154.2 |  |  | 0.51 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001258.3 |  |  | 0.51 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000869.5 |  | 0.77 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0000863.3 |  | 0.61 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12
BGC0002276.2 |  | 0.60 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000862.3 |  | 0.60 | other (other) | eicosapentaenoic acid | Shewanella pneumatophori
BGC0001244.3 |  | 0.60 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000107.3 |  | 0.59 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0001276.3 |  | 0.59 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002154.2 |  | 0.59 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001258.3 |  | 0.59 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.90 out of 20.47
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.52 out of 26.85
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 25.55 out of 30.25
Confidence: medium
Additional weak hits (3):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.60 out of 30.22
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 19.73 out of 30.11
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.62 out of 29.25
Confidence: weak
Module view
Shows module structures for each candidate cluster 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, and an explanation of the visualisation is available here.
Legend
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 domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
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 8, location 1454657 - 1506746:
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

For candidate cluster 9, location 1454657 - 1503439:
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

For candidate cluster 10, location 1463443 - 1506746:
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 substrate predictions
Shows the predicted substrates for each adenylation 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).
HGD76_RS07325: mal
PKS_AT (637..935): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 88.0
  Methoxymalonyl-CoA: 35.9
  inactive: 31.2
  Methylmalonyl-CoA: 18.6
  Isobutyryl-CoA: 10.5
  CHC-CoA: 9.5
  fatty_acid: 9.2
  trans-1,2-CPDA: 0.0
  Propionyl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

HGD76_RS07340: pk
PKS_AT (583..902): pk
ATSignature: (unknown)
No matches above 50%
minowa: trans-1,2-CPDA

Prediction, score:
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Malonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ColR | Phenol-responsive regulator
RutR | Regulator of the pyrimidine and purine metabolism
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP051206.1 - Region 7 - 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: 1,529,360 - 1,551,273 nt. (total: 21,914 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
No tailoring functions detected.
Similar gene clusters
Shows areas 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
--- | --- | --- | --- | --- | ---
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0002701.2 |  | 0.44 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0000663.5 |  | 0.35 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0002152.2 |  | 0.34 | other (other) | toxoflavin | Pseudomonas protegens Pf-5
BGC0002542.2 |  | 0.31 | NRPS, PKS | apratoxin A | Moorena bouillonii bAprat14
BGC0001733.3 |  | 0.30 | ribosomal | PcpA | Pleurocapsa sp. PCC 7327
BGC0001790.4 |  | 0.29 | NRPS | sulfazecin | Pseudomonas acidophila
BGC0002126.3 |  | 0.28 | NRPS | hypeptin | Lysobacter sp. K5869
BGC0001207.5 |  | 0.27 | NRPS | teixobactin | Eleftheria terrae
BGC0001186.4 |  | 0.27 | PKS | misakinolide A | Candidatus Entotheonella serta

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0002701.2 |  | 0.44 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0000663.5 |  | 0.35 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0002152.2 |  | 0.34 | other (other) | toxoflavin | Pseudomonas protegens Pf-5
BGC0002542.2 |  | 0.31 | NRPS, PKS | apratoxin A | Moorena bouillonii bAprat14
BGC0001733.3 |  | 0.30 | ribosomal | PcpA | Pleurocapsa sp. PCC 7327
BGC0001790.4 |  | 0.29 | NRPS | sulfazecin | Pseudomonas acidophila
BGC0002126.3 |  | 0.28 | NRPS | hypeptin | Lysobacter sp. K5869
BGC0001207.5 |  | 0.27 | NRPS | teixobactin | Eleftheria terrae
BGC0001186.4 |  | 0.27 | PKS | misakinolide A | Candidatus Entotheonella serta

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
triterpene | hopanoid |  | C30 | hopanoid skeleton | unknown
triterpene | polypodane |  | C30 | polypodane skeleton | unknown

Genes with terpene domains:
HGD76_RS07565: T2TS
Domain 1 (4 - 636): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.80 out of 29.72
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.78 out of 27.18
Confidence: medium
Additional weak hits (2):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.53 out of 29.38
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.00 out of 32.38
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NrdR | Represses ribonucleotide reductase encoding genes
NtrC | Nitrogen regulatory protein C

NZ_CP051206.1 - Region 8 - hglE-KS
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: 2,461,504 - 2,508,220 nt. (total: 46,717 nt) Show pHMM detection rules used
hglE-KS: (hglE or hglD)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acylase
HGD76_RS12320: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: ligase synthase
HGD76_RS12315: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

HGD76_RS12330: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas 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 | hglE-KS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001244.3 |  | 0.60 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001257.3 |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.60 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001276.3 |  | 0.59 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.59 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001258.3 |  | 0.59 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0000869.5 |  | 0.59 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0000107.3 |  | 0.59 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0001164.3 |  | 0.58 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001244.3 |  | 0.60 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001257.3 |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.60 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001276.3 |  | 0.59 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.59 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001258.3 |  | 0.59 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0000869.5 |  | 0.59 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0000107.3 |  | 0.59 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0001164.3 |  | 0.58 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.00 out of 21.55
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.64 out of 26.06
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.05 out of 21.55
Confidence: medium
Additional weak hits (5):
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.56 out of 36.53
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.21 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.73 out of 39.62
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.68 out of 26.12
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 25.06 out of 30.98
Confidence: weak
Module view
Shows module structures for each candidate cluster 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, and an explanation of the visualisation is available here.
Legend
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 domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
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 12, location 2461503 - 2508220:
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 substrate predictions
Shows the predicted substrates for each adenylation 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).
HGD76_RS12325: pk
PKS_AT (456..777): pk
ATSignature: (unknown)
No matches above 50%
minowa: trans-1,2-CPDA

Prediction, score:
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Malonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

HGD76_RS12330: mal
PKS_AT (624..922): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 66.7%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 98.3
  Methoxymalonyl-CoA: 37.1
  inactive: 35.2
  Methylmalonyl-CoA: 28.0
  CHC-CoA: 16.8
  fatty_acid: 16.3
  Isobutyryl-CoA: 9.1
  trans-1,2-CPDA: 0.0
  Propionyl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
ArcA | Repressor of carbon oxidation
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis

NZ_CP051206.1 - Region 9 - lanthipeptide-class-ii
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: 2,895,747 - 2,918,929 nt. (total: 23,183 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lanthipeptides
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase
HGD76_RS14150: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Similar gene clusters
Shows areas 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 | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000554.4 |  | 0.57 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001210.5 |  | 0.54 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0001579.4 |  | 0.53 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000527.5 |  | 0.48 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000558.5 |  | 0.48 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0002699.2 |  | 0.47 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0000503.5 |  | 0.47 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0001660.3 |  | 0.46 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000528.5 |  | 0.45 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000554.4 |  | 0.57 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001210.5 |  | 0.54 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0001579.4 |  | 0.53 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000527.5 |  | 0.48 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000558.5 |  | 0.48 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0002699.2 |  | 0.47 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0000503.5 |  | 0.47 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0001660.3 |  | 0.46 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000528.5 |  | 0.45 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.

#### Lanthipeptide(s) for HGD76_RS14150

HGD76_RS14160
Leader:
MSNLDIIRAWKDEEYRNSLSAEQQEQLPANPAGLVELNDEDMSSVSGG
Core:
C T T C G N P L H T L F W T C K A V S S P F D T I A
Core with dehydrations:
Cys Dhb Dhb Cys G N P L H Dhb L F W Dhb Cys K A V Dha Dha P F D Dhb I A

#### antiSMASH-DB 4.0 matches for HGD76_RS14160

100.0%
NZ_CP051206.1:
Lanthipeptides: HGD76_RS14160_lanthipeptide
1
C T T C G N P L H T L F W T C K A V S S P F D T I A
26
C T T C G N P L H T L F W T C K A V S S P F D T I A
1
C T T C G N P L H T L F W T C K A V S S P F D T I A
26
55.6%
NC_019684.1:
Lanthipeptides: NOS7524_RS02390_lanthipeptide
1
C T T C G N P L H T L F W T C K A V S S P F D T I A
26
C T T C G N P L H T C K A V I+
1
C T T C G N P L H T P I I K C K A V F G E L G D I S
26
51.9%
NZ_CP034058.1:
Lanthipeptides: EH233_RS23850_lanthipeptide
1
C T T C G N P L H T L F W T C K A V S S P F D T I A
26
C T T C G N P L H T C K V + I+
1
C T T C G N P L H T P I I K C K P V F G A L E D I S
26
with 7 more sequence matches
42.3%
NZ_VIKW01000003.1:
Lanthipeptides: FJR04_RS03310_lanthipeptide
1
C T T C G N P L H T L F W T C K A V S S
20
C T T C G+P H T L+ C K + +
1
C T T C G D P F H T L W V G C K P I G A
20
38.5%
NZ_CP060140.1:
Lanthipeptides: BDGGKGIB_RS05565_lanthipeptide
1
C T T C G N P L H T L F W T C K A V S S
20
C T T C G+P H T C K + +
1
C T T C G D P F H T W S V G C K P I G A
20
34.6%
NC_019738.1:
Lanthipeptides: MIC7113_RS14485_lanthipeptide
1
C T T C G N P L H T
10
C T C G N P L H T
1
C T P C G N P L H T
10
34.6%
NZ_CP011130.1:
Lanthipeptides: allorf_5346585_5346695_lanthipeptide
3
T C G N--P L H T L F W T C K A V S
19
T G N P + W T C K A +
2
T I G N S G P C A S R A W T C K A A A
20
23.3%
NZ_CP059734.1:
Lanthipeptides: allorf_0384683_0384871_lanthipeptide
8
L H T L F W T C K A V S S P
21
L H F T C+ V++P
1
L H I Y F L T C Q P V A N P
14
19.2%
NZ_CP026498.1:
Lanthipeptides: C2142_RS01030_lanthipeptide
6
N P L H T L F W T C K
16
+P T+ W T C+
8
D P W E T M T W T C R
18
15.2%
NZ_MKZS01000001.1:
Lanthipeptides: allorf_3081872_3082018_lanthipeptide
7
P L H T L F W
13
P L H+L W
27
P L H S L L W
33

#### MIBiG 4.0 matches for HGD76_RS14160

10.3%
BGC0001229.4 (SBI_06990):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
20
S P F D T I A
26
S P D T+
3
S P I D T V K
9

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 28.57 out of 29.38
Confidence: strong
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.84 out of 29.38
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.82 out of 29.38
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.30 out of 29.38
Confidence: medium
Additional weak hits (4):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 24.50 out of 28.14
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 25.75
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 23.32 out of 35.63
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.54 out of 20.01
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

HGD76_RS14160 - Class II
  Cleavage pHMM score: -4.10
  RODEO score: 0
  Monoisotopic mass: 2686.3 Da
  Molecular weight: 2688.1 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2706.1 Da N = 1
    2724.1 Da N = 2
    2742.1 Da N = 3
    2760.2 Da N = 4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
FuR variant 1 | Ferric Uptake Regulator

NZ_CP051206.1 - Region 10 - 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: 3,017,461 - 3,066,760 nt. (total: 49,300 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
HGD76_RS14740: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

HGD76_RS14750: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

Transferases: aminotransferase methyltransferase
HGD76_RS14660: aminotransferase

smcogs
  SMCOG1019: aminotransferase

HGD76_RS14675: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: amidase
HGD76_RS14760: amidase

smcogs
  SMCOG1105: amidase

Isomerases: isomerase mutase
HGD76_RS14655: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

HGD76_RS14700: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
HGD76_RS14705: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

HGD76_RS14825: pseudouridine synthase

smcogs
  SMCOG1279: pseudouridine synthase

Similar gene clusters
Shows areas 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
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.66 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.65 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.66 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.65 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 26.22 out of 29.25
Confidence: strong
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.30 out of 28.19
Confidence: medium
Additional weak hits (7):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.96 out of 32.74
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.91 out of 30.22
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.71 out of 30.97
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.38 out of 29.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.25 out of 30.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.25 out of 30.97
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.07 out of 32.38
Confidence: weak
Module view
Shows module structures for each candidate cluster 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, and an explanation of the visualisation is available here.
Legend
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 domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
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 14, location 3017460 - 3066760:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - D-X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation 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).
HGD76_RS14705: X - X
AMP-binding (501..916): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FTVAFDAAAEEPMMANGGEMNGYGPTEATVLSTV
  Nearest Stachelhaus code(s):
    3OH-Leu DALWWGGVLK (35% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1580..1996): X
nrpys: Val, Leu, Ile, Abu, Ival

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LTVAFDAAAEEPMVSTGGEMNGYGPTEATVLSTV
  Nearest Stachelhaus code(s):
    OH-Orn DGEGSGGVTK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
SypG | Regulator of biofilm formation and host colonization
ZuR variant 1 | Zinc-responsive repressor

NZ_CP051206.1 - Region 11 - cyanobactin
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: 3,228,883 - 3,259,952 nt. (total: 31,070 nt) Show pHMM detection rules used
cyanobactin: (cyanobactin_synth or TIGR03678 or cyanobactin_precursor)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
HGD76_RS15665: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

HGD76_RS15775: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: protease
HGD76_RS15705: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

HGD76_RS15765: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

Similar gene clusters
Shows areas 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 | cyanobactin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001505.4 |  | 0.82 | ribosomal | anacyclamide D8P, sphaerocyclamide | Sphaerospermopsis sp. LEGE 00249
BGC0000472.4 |  | 0.77 | ribosomal | anacyclamide A10 | Anabaena sp. 90
BGC0001880.3 |  | 0.60 | ribosomal | scytodecamide | Scytonema sp. UIC 10036
BGC0002629.2 |  | 0.55 | ribosomal | limnothamide | Limnothrix sp. CACIAM 69d
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001167.4 |  | 0.51 | ribosomal | piricyclamide 7005E1, piricyclamide 7005E2, piricyclamide 7005E3, piricyclamide 7005E4 | Microcystis aeruginosa PCC 7005
BGC0000483.5 |  | 0.50 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0001632.3 |  | 0.50 | ribosomal | kawaguchipeptin A | Microcystis aeruginosa NIES-88
BGC0000480.5 |  | 0.48 | ribosomal | tenuecyclamide A, tenuecyclamide C | Nostoc spongiaeforme var. tenue str. Carmeli
BGC0000475.5 |  | 0.48 | ribosomal | patellamide A, patellamide C | Prochloron didemni

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001505.4 |  | 0.82 | ribosomal | anacyclamide D8P, sphaerocyclamide | Sphaerospermopsis sp. LEGE 00249
BGC0000472.4 |  | 0.77 | ribosomal | anacyclamide A10 | Anabaena sp. 90
BGC0001880.3 |  | 0.60 | ribosomal | scytodecamide | Scytonema sp. UIC 10036
BGC0002629.2 |  | 0.55 | ribosomal | limnothamide | Limnothrix sp. CACIAM 69d
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001167.4 |  | 0.51 | ribosomal | piricyclamide 7005E1, piricyclamide 7005E2, piricyclamide 7005E3, piricyclamide 7005E4 | Microcystis aeruginosa PCC 7005
BGC0000483.5 |  | 0.50 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0001632.3 |  | 0.50 | ribosomal | kawaguchipeptin A | Microcystis aeruginosa NIES-88
BGC0000480.5 |  | 0.48 | ribosomal | tenuecyclamide A, tenuecyclamide C | Nostoc spongiaeforme var. tenue str. Carmeli
BGC0000475.5 |  | 0.48 | ribosomal | patellamide A, patellamide C | Prochloron didemni

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 18.15 out of 18.46
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.54 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.17 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.22 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.17 out of 27.78
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.23 out of 26.06
Confidence: medium
Additional weak hits (3):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 22.66 out of 26.12
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.05 out of 27.55
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.70 out of 25.75
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
MogR | Repressor of flagellar motility genes
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP051206.1 - Region 12 - 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: 4,221,094 - 4,292,052 nt. (total: 70,959 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
HGD76_RS20455: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase
HGD76_RS20410: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Ligases: ligase synthase
HGD76_RS20445: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

HGD76_RS20450: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

HGD76_RS20460: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

HGD76_RS20470: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Similar gene clusters
Shows areas 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 | T1PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  |  | 1.35 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001164.3 |  |  |  | 1.26 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  | 1.24 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001833.4 |  |  |  | 1.22 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001163.3 |  |  |  | 1.21 | PKS | 1-heptadecene | Moorea producens 3L
BGC0001128.4 |  |  |  | 1.21 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  |  | 1.21 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  |  |  | 1.19 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000342.4 |  |  |  | 1.17 | NRPS | enniatin | Fusarium equiseti
BGC0001132.4 |  |  |  | 1.16 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.76 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001164.3 |  | 0.73 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.73 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001163.3 |  | 0.72 | PKS | 1-heptadecene | Moorea producens 3L
BGC0002286.3 |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 16.80 out of 18.16
Confidence: strong
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.64 out of 25.88
Confidence: medium
Additional weak hits (4):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.61 out of 28.14
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 24.07 out of 31.73
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 26.05 out of 30.97
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.00 out of 30.98
Confidence: weak
Module view
Shows module structures for each candidate cluster 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, and an explanation of the visualisation is available here.
Legend
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 domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
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 16, location 4221093 - 4292052:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2) + (ccmal) + (mal - Asp - X) + (Tyr - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 17, location 4223333 - 4292052:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2) + (ccmal) + (mal - Asp - X) + (Tyr - X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation 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).
HGD76_RS20445: NH2
CAL_domain (179..501): NH2
minowa: NH2

Prediction, score:
  NH2: 195.2
  Acetyl-CoA: 48.5
  fatty_acid: 20.9
  AHBA: 15.9
  shikimic_acid: 0.0

HGD76_RS20450: mal
PKS_AT (566..847): mal
ATSignature: Malonyl-CoA, inactive

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 95.8%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 192.2
  inactive: 183.5
  Methoxymalonyl-CoA: 57.2
  Methylmalonyl-CoA: 54.4
  Propionyl-CoA: 34.3
  Isobutyryl-CoA: 31.4
  Acetyl-CoA: 22.3
  Benzoyl-CoA: 22.2
  2-Methylbutyryl-CoA: 19.5
  3-Methylbutyryl-CoA: 12.3
  trans-1,2-CPDA: 11.7
  CHC-CoA: 10.7
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0

HGD76_RS20460: mal - Asp - X
Search NORINE for peptide: strict or relaxed
PKS_AT (572..858): mal
ATSignature: Malonyl-CoA, inactive

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 95.8%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 182.7
  inactive: 167.6
  Methoxymalonyl-CoA: 71.5
  Methylmalonyl-CoA: 60.9
  Propionyl-CoA: 45.1
  Isobutyryl-CoA: 31.0
  Benzoyl-CoA: 21.1
  Ethylmalonyl-CoA: 20.5
  fatty_acid: 18.6
  3-Methylbutyryl-CoA: 17.4
  2-Methylbutyryl-CoA: 15.2
  CHC-CoA: 15.1
  trans-1,2-CPDA: 14.8
  Acetyl-CoA: 12.0

AMP-binding (2507..2940): Asp
nrpys: Asp

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
  Small clusters prediction:
    asp,asn (Asp, Asn)
  Single AA prediction:
    asp (Asp)

Stachelhaus prediction details:
  Stachelhaus sequence:
    YSISADLGYTAPKIILGGDFNHYGPSETTVGVLT
  Nearest Stachelhaus code(s):
    Asp DLTKIGHVGK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3602..4001): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FWQIFDAILRDLHTFFSGEVNLYGATETTMVKCF
  Nearest Stachelhaus code(s):
    Asp DVRHFALMAK (71% 8Å match)
  Stachelhaus code match:
    70% (weak)

HGD76_RS20470: Tyr - X
Search NORINE for peptide: strict or relaxed
AMP-binding (478..872): Tyr
nrpys: Tyr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    Polar aromatic ring (Tyr, bOH-Tyr)
  Single AA prediction:
    tyr (Tyr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDASVSEMTLIVAGEFNAYGPSEATVCATV
  Nearest Stachelhaus code(s):
    Tyr DASTIAAVCK (94% 8Å match)
    Tyr or Pro DASTIAAVCK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

A-OX (1560..2336): X
No predictions made
Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
PsrA | Oleic acid responsive regulator

NZ_CP051206.1 - Region 13 - azole-containing-RiPP
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: 4,350,671 - 4,372,769 nt. (total: 22,099 nt) Show pHMM detection rules used
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Azole RiPPs
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
No tailoring functions detected.
Similar gene clusters
Shows areas 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 | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002144.3 |  | 0.48 | ribosomal | phazolicin | Rhizobium sp. Pop5
BGC0002115.3 |  | 0.45 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0001173.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus pumilus ATCC 7061
BGC0002013.4 |  | 0.43 | ribosomal | curacozole | Streptomyces curacoi
BGC0000569.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0000558.5 |  | 0.42 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0000571.3 |  | 0.42 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0001229.4 |  | 0.42 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0001555.4 |  | 0.42 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002144.3 |  | 0.48 | ribosomal | phazolicin | Rhizobium sp. Pop5
BGC0002115.3 |  | 0.45 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0001173.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus pumilus ATCC 7061
BGC0002013.4 |  | 0.43 | ribosomal | curacozole | Streptomyces curacoi
BGC0000569.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0000558.5 |  | 0.42 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0000571.3 |  | 0.42 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0001229.4 |  | 0.42 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0001555.4 |  | 0.42 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.15 out of 20.97
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.76 out of 29.38
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.64 out of 29.38
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.90 out of 26.06
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.87 out of 28.19
Confidence: medium
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
TFBS Finder
Azole RiPPs
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
FuR variant 1 | Ferric Uptake Regulator
MogR | Repressor of flagellar motility genes
ZuR variant 1 | Zinc-responsive repressor

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
NZ_CP051206.1 - Region 14 - 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: 4,573,676 - 4,594,608 nt. (total: 20,933 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
HGD76_RS21910: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Ligases: synthase
HGD76_RS21880: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

Similar gene clusters
Shows areas 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
--- | --- | --- | --- | --- | ---
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.5 |  | 0.47 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000646.5 |  | 0.41 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000641.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000643.3 |  | 0.40 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000639.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000642.3 |  | 0.39 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000634.3 |  | 0.39 | terpene | carotenoid | Brevundimonas sp. SD212
BGC0000638.3 |  | 0.39 | terpene | carotenoid | Pantoea ananatis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.5 |  | 0.47 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000646.5 |  | 0.41 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000641.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000643.3 |  | 0.40 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000639.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000642.3 |  | 0.39 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000634.3 |  | 0.39 | terpene | carotenoid | Brevundimonas sp. SD212
BGC0000638.3 |  | 0.39 | terpene | carotenoid | Pantoea ananatis

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
triterpene | C30 carotenoid | diapophytoene | C30 | acyclic | none
triterpene |  | PSPP | C30 | acyclic | PP
triterpene |  | squalene | C30 | acyclic | none
tetraterpene | C40 carotenoid | phytoene | C40 | acyclic | none
triterpene |  | hydroxysqualene | C30 | acyclic | OH

Genes with terpene domains:
HGD76_RS21905: PT_phytoene_like
Domain 1 (18 - 308): Prenyltransferase; Phytoene synthase like
Subtype: unknown

Reactions:
  FPP → diapophytoene
  FPP → PSPP
  FPP → squalene
  GGPP → phytoene
  PSPP → hydroxysqualene

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.44 out of 27.78
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.70 out of 23.79
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.54 out of 32.93
Confidence: medium
Additional weak hits (3):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.09 out of 26.85
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 25.17 out of 33.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.04 out of 29.38
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
PP | Diphosphate
PSPP | Presqualene diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
IolR | Regulator of the inositol catabolism
LexA variant 3 | Repressor of DNA damage response

NZ_CP051206.1 - Region 15 - 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: 4,861,069 - 4,881,899 nt. (total: 20,831 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: kinase
HGD76_RS23260: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

Similar gene clusters
Shows areas 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
--- | --- | --- | --- | --- | ---
BGC0001796.5 |  | 0.34 | NRPS | tauramamide | Brevibacillus laterosporus DSM 25
BGC0002436.2 |  | 0.34 | other (other) | coformycin | Streptomyces citricolor
BGC0000678.5 |  | 0.32 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001995.3 |  | 0.30 | terpene | heptelidic acid | Aspergillus oryzae RIB40
BGC0001291.3 |  | 0.29 | ribosomal | enterocin NKR-5-3B | Enterococcus faecium
BGC0000653.5 |  | 0.26 | terpene | pentalenolactone | Streptomyces arenae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001796.5 |  | 0.34 | NRPS | tauramamide | Brevibacillus laterosporus DSM 25
BGC0002436.2 |  | 0.34 | other (other) | coformycin | Streptomyces citricolor
BGC0000678.5 |  | 0.32 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001995.3 |  | 0.30 | terpene | heptelidic acid | Aspergillus oryzae RIB40
BGC0001291.3 |  | 0.29 | ribosomal | enterocin NKR-5-3B | Enterococcus faecium
BGC0000653.5 |  | 0.26 | terpene | pentalenolactone | Streptomyces arenae

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
triterpene |  | squalene | C30 | acyclic | none
triterpene | C30 carotenoid | diapophytoene | C30 | acyclic | none
triterpene |  | PSPP | C30 | acyclic | PP
tetraterpene | C40 carotenoid | phytoene | C40 | acyclic | none
triterpene |  | hydroxysqualene | C30 | acyclic | OH

Genes with terpene domains:
HGD76_RS23305: PT_phytoene_like
Domain 1 (10 - 206): Prenyltransferase; Phytoene synthase like
Subtype: unknown

Reactions:
  FPP → squalene
  FPP → diapophytoene
  FPP → PSPP
  GGPP → phytoene
  PSPP → hydroxysqualene

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.00 out of 29.72
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.63 out of 27.78
Confidence: medium
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 25.64 out of 29.25
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.95 out of 26.06
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.81 out of 28.19
Confidence: medium
Additional weak hits (1):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.53 out of 33.73
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
PP | Diphosphate
PSPP | Presqualene diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
MogR | Repressor of flagellar motility genes
NtrC | Nitrogen regulatory protein C
SypG | Regulator of biofilm formation and host colonization
ZuR variant 1 | Zinc-responsive repressor

NZ_CP051206.1 - Region 16 - 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: 5,018,746 - 5,079,167 nt. (total: 60,422 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
HGD76_RS24055: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: formyltransferase methyltransferase sulfotransferase
HGD76_RS24060: methyltransferase

smcogs
  SMCOG1089: methyltransferase

HGD76_RS24090: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

HGD76_RS24105: glutathione S-transferase

smcogs
  SMCOG1193: glutathione S-transferase

Ligases: ligase
HGD76_RS24070: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

HGD76_RS26350: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

HGD76_RS26355: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters
Shows areas 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 | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001249.5 |  |  | 0.87 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002164.2 |  |  | 0.70 | NRPS | peramine | Epichloe festucae
BGC0001641.4 |  |  | 0.70 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  |  | 0.66 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.74 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002164.2 |  | 0.68 | NRPS | peramine | Epichloe festucae
BGC0001641.4 |  | 0.68 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.66 | NRPS | AbT1 | Aureobasidium pullulans

Similar known clusters from MIBiG 4.0
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.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.07 out of 26.06
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.80 out of 29.72
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.28 out of 23.79
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.79 out of 24.78
Confidence: medium
Additional weak hits (3):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.31 out of 25.75
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.79 out of 31.73
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.93 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster 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, and an explanation of the visualisation is available here.
Legend
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 domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
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 21, location 5018745 - >5079167:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 22, location 5018745 - >5059720:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 23, location 5031086 - >5079167:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Pro)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation 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).
HGD76_RS26355: Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (83..488): Pro
nrpys: Pro

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    pro (Pro)
  Single AA prediction:
    pro (Pro)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQAFDVSFQESFLITAGEHNHYGPSESHVVTSF
  Nearest Stachelhaus code(s):
    Pro DVQFIAHVVK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
LexA variant 2 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes
NtrC | Nitrogen regulatory protein C
ToxT | Regulator of MSHA biosynthesis