Select genomic region:
Overview
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### Identified secondary metabolite regions using strictness 'relaxed'

NZ_CP014504.1 (Pedobacter cryoconitis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | hglE-KS,T1PKS | 155,141 | 206,514 |
Region 2 | NRPS,NRPS-like,T1PKS | 211,232 | 261,849 |
Region 3 | phosphonate | 484,246 | 508,046 |
Region 4 | NI-siderophore | 1,021,622 | 1,055,293 | Low | fulvivirgamide A2/fulvivirgamide B2/fulvivirgamide B3/fulvivirgamide B4 | other:other
Region 5 | NRPS,T1PKS | 1,147,973 | 1,218,904 | Low | pinensins | ribosomal:RiPP
Region 6 | terpene | 1,316,775 | 1,337,611 |
Region 7 | lanthipeptide-class-i | 1,670,093 | 1,694,299 |
Region 8 | linaridin | 1,744,722 | 1,765,264 |
Region 9 | terpene | 1,886,940 | 1,909,953 | Low | carotenoid | terpene
Region 10 | NAPAA | 2,232,484 | 2,266,953 |  |
Region 11 | NRPS | 2,453,457 | 2,510,560 |
Region 12 | NRPS | 2,540,187 | 2,688,175 |
Region 13 | T3PKS,terpene-precursor | 2,945,371 | 2,994,101 |
Region 14 | lanthipeptide-class-i,NRPS,T1PKS,NRPS-like | 3,225,965 | 3,315,507 |  |
Region 15 | NI-siderophore | 3,354,291 | 3,384,060 |
Region 16 | NRPS | 3,387,875 | 3,472,745 |
Region 17 | NI-siderophore | 4,285,508 | 4,317,799 | Low | berninamycin K/berninamycin J/berninamycin A/berninamycin B | ribosomal:RiPP
Region 18 | lanthipeptide-class-i | 5,148,519 | 5,172,871 |
Region 19 | lanthipeptide-class-i | 5,777,973 | 5,803,586 | Low | pinensins | ribosomal:RiPP

NZ_CP014504.1 - Region 1 - 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: 155,141 - 206,514 nt. (total: 51,374 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: oxidoreductase
AY601_RS00895: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: glycosyltransferase
AY601_RS00860: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

AY601_RS00865: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

AY601_RS00955: sugar transferase

smcogs
  SMCOG1146: sugar transferase

Hydrolases: dehalogenase hydrolase
AY601_RS00770: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

AY601_RS00855: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: dehydratase
AY601_RS00765: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
AY601_RS00840: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AY601_RS00845: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001244.3 |  |  | 0.57 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  |  | 0.57 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  |  | 0.57 | PKS | asperlactone | Aspergillus ochraceus
BGC0001284.4 |  |  | 0.56 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  |  | 0.55 | PKS | FR901512 | fungal sp. No.14919
BGC0001160.5 |  |  | 0.53 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  | 0.53 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001258.3 |  |  | 0.51 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0001254.3 |  |  | 0.50 | PKS | ACT-Toxin II | Alternaria alternata
BGC0000041.3 |  |  | 0.49 | PKS | oronofacic acid | Pseudomonas syringae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001244.3 |  | 0.62 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.62 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.62 | PKS | asperlactone | Aspergillus ochraceus
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001258.3 |  | 0.59 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0001254.3 |  | 0.58 | PKS | ACT-Toxin II | Alternaria alternata
BGC0000041.3 |  | 0.58 | PKS | oronofacic acid | Pseudomonas syringae

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:
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: 19.60 out of 21.55
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.40 out of 20.97
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.28 out of 27.55
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.93 out of 28.19
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.47 out of 32.93
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 15.96 out of 18.16
Confidence: strong
Additional weak hits (1):
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 24.53 out of 33.14
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 1, location 155140 - 206514:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk)
Non-colinear ordering:
  AY601_RS00845 + AY601_RS00850

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 155140 - 202178:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk)
Non-colinear ordering:
  AY601_RS00845 + AY601_RS00850

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 162203 - 206514:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk)
Non-colinear ordering:
  AY601_RS00845 + AY601_RS00850

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).
AY601_RS00840: mal
PKS_AT (1186..1474): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 61.3
  Methoxymalonyl-CoA: 28.1
  Methylmalonyl-CoA: 25.0
  CHC-CoA: 17.2
  fatty_acid: 16.6
  Ethylmalonyl-CoA: 14.9
  Propionyl-CoA: 12.3
  inactive: 10.5
  2-Methylbutyryl-CoA: 9.5
  trans-1,2-CPDA: 0.0
  Isobutyryl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

AY601_RS00845: pk
PKS_AT (590..800): 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
--- | ---
AbrC3 | Antibiotic production activator
ArcA | Repressor of carbon oxidation
CcpA | Catabolite control protein A
GnfM | Regulator of nitrogen-fixation genes
LexA variant 3 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes
ZuR variant 1 | Zinc-responsive repressor

NZ_CP014504.1 - Region 2 - NRPS,NRPS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 211,232 - 261,849 nt. (total: 50,618 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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))

#### 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 glycosyltransferase transferase
AY601_RS01055: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

AY601_RS01130: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

AY601_RS01135: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Ligases: ligase
AY601_RS01080: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AY601_RS01085: 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 | NRPS-like | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001132.4 |  |  |  | 1.09 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  | 1.07 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  |  | 1.04 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  |  | 1.04 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  |  | 1.00 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  |  |  | 0.98 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  |  | 0.97 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  |  |  | 0.97 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  |  |  | 0.96 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  |  | 0.89 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.68 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.66 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  | 0.66 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

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:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.15 out of 18.46
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.28 out of 26.33
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.96 out of 32.93
Confidence: medium
Additional weak hits (3):
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 15.87 out of 18.46
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.59 out of 29.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 24.07 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 4, location 211231 - 261849:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Pro - mal) + (Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 211231 - 255284:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Pro - mal) + (Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 215291 - 261849:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Pro - mal) + (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).
AY601_RS01080: Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (499..896): 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:
    LWQAFDVSFQECYLMTAGEYNQYGPTECHVVTQL
  Nearest Stachelhaus code(s):
    Pro DVQFMAQVVK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AY601_RS01085: Pro - mal
Search NORINE for peptide: strict or relaxed
AMP-binding (21..421): 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:
    LWQAFDVSFQECFLMTAGEFNQYGPTECHVVTEL
  Nearest Stachelhaus code(s):
    Pro DVQFMAQVVK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

PKS_AT (1131..1425): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 79.2%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 156.5
  inactive: 107.1
  Methoxymalonyl-CoA: 73.1
  Methylmalonyl-CoA: 58.5
  Isobutyryl-CoA: 39.0
  Propionyl-CoA: 33.2
  Ethylmalonyl-CoA: 32.5
  CHC-CoA: 18.1
  2-Methylbutyryl-CoA: 15.2
  Benzoyl-CoA: 14.5
  trans-1,2-CPDA: 13.1
  3-Methylbutyryl-CoA: 10.1
  fatty_acid: 0.0
  Acetyl-CoA: 0.0

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
LexA variant 3 | Repressor of DNA damage response
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP014504.1 - Region 3 - phosphonate
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: 484,246 - 508,046 nt. (total: 23,801 nt) Show pHMM detection rules used
phosphonate: (phosphonates and minimum(1, [2-Hacid_dh_C, Aldedh, Aminotran_1_2, Aminotran_5, AurF, CTP_transf_like, DUF4992, Fe-ADH, HMGL-like, Metallophos_2, NTP_transf_3, NTP_transf_5, PALP, PEP_mutase, TPP_enzyme_C, TPP_enzyme_N, phosphonates]) and not (phosphonatesHydrolase or phosphonatesMeIsocitrateLyase))

#### 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: oxidase
AY601_RS02155: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

Transferases: aminotransferase
AY601_RS02165: aminotransferase

smcogs
  SMCOG1019: aminotransferase

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 | phosphonate | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000884.5 |  | 0.53 | other (other) | 3-methylarginine | Pseudomonas syringae pv. syringae
BGC0000623.3 |  | 0.48 | ribosomal | plantaricin W α, plantaricin W β | Lactobacillus plantarum
BGC0000590.5 |  | 0.46 | ribosomal | microcin N | Escherichia coli
BGC0002670.2 |  | 0.46 | other (other) | fosfonochlorin | Fusarium oxysporum f. sp. lycopersici 4287
BGC0000938.5 |  | 0.45 | other (aminocoumarin) | fosfomycin | Streptomyces fradiae
BGC0002577.2 |  | 0.43 | ribosomal | lactococcin G | Lactococcus lactis
BGC0000504.5 |  | 0.43 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0002586.2 |  | 0.42 | ribosomal | ASM1 | Lactiplantibacillus plantarum
BGC0000517.4 |  | 0.42 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125
BGC0000571.3 |  | 0.42 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000884.5 |  | 0.53 | other (other) | 3-methylarginine | Pseudomonas syringae pv. syringae
BGC0000623.3 |  | 0.48 | ribosomal | plantaricin W α, plantaricin W β | Lactobacillus plantarum
BGC0000590.5 |  | 0.46 | ribosomal | microcin N | Escherichia coli
BGC0002670.2 |  | 0.46 | other (other) | fosfonochlorin | Fusarium oxysporum f. sp. lycopersici 4287
BGC0000938.5 |  | 0.45 | other (aminocoumarin) | fosfomycin | Streptomyces fradiae
BGC0002577.2 |  | 0.43 | ribosomal | lactococcin G | Lactococcus lactis
BGC0000504.5 |  | 0.43 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0002586.2 |  | 0.42 | ribosomal | ASM1 | Lactiplantibacillus plantarum
BGC0000517.4 |  | 0.42 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125
BGC0000571.3 |  | 0.42 | ribosomal | burhizin | 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.

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:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.26 out of 26.06
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 19.13 out of 20.97
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.03 out of 26.06
Confidence: strong
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 26.70 out of 32.93
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.44 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.23 out of 26.06
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.61 out of 28.19
Confidence: medium
Additional weak hits (4):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.05 out of 23.43
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 24.04 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.03 out of 29.38
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 20.93 out of 29.72
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
LexA variant 3 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes
ZuR variant 1 | Zinc-responsive repressor

NZ_CP014504.1 - Region 4 - NI-siderophore
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: 1,021,622 - 1,055,293 nt. (total: 33,672 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### 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: oxygenase
AY601_RS04450: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Transferases: aminotransferase
AY601_RS04410: aminotransferase

smcogs
  SMCOG1019: aminotransferase

AY601_RS04460: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Lyases: decarboxylase
AY601_RS04440: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: synthase
AY601_RS04400: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate 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 | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001572.3 |  | 0.69 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002469.2 |  | 0.66 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0001478.5 |  | 0.62 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.61 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.60 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001453.5 |  | 0.60 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0000940.5 |  | 0.60 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001531.5 |  | 0.60 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0001499.5 |  | 0.59 | other (other) | aerobactin | Pantoea ananatis
BGC0000244.4 |  | 0.58 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001572.3 |  | 0.69 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002469.2 |  | 0.66 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0001478.5 |  | 0.62 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.61 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.60 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001453.5 |  | 0.60 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0000940.5 |  | 0.60 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001531.5 |  | 0.60 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0001499.5 |  | 0.59 | other (other) | aerobactin | Pantoea ananatis
BGC0000244.4 |  | 0.58 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus

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:
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.97 out of 21.55
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.24 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.58 out of 26.06
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 24.04 out of 30.25
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.99 out of 32.93
Confidence: medium
Additional weak hits (3):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.78 out of 26.12
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 23.05 out of 33.73
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
ColR | Phenol-responsive regulator
LexA variant 3 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes

NZ_CP014504.1 - Region 5 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,147,973 - 1,218,904 nt. (total: 70,932 nt) Show pHMM detection rules used
NRPS: cds(Condensation 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))

#### 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 oxygenase
AY601_RS04975: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

AY601_RS05045: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

AY601_RS05060: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

Transferases: acyltransferase aminotransferase
AY601_RS05040: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

AY601_RS05150: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Ligases: ligase synthase
AY601_RS05055: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AY601_RS05065: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AY601_RS05070: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AY601_RS05075: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AY601_RS05080: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AY601_RS05095: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001833.4 |  |  | 0.88 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.87 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  | 0.86 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.86 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  | 0.85 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001249.5 |  |  | 0.82 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001261.3 |  |  | 0.82 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  | 0.79 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  |  | 0.79 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001166.5 |  |  | 0.75 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.74 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae

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
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.82 out of 32.93
Confidence: medium
Additional weak hits (5):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.54 out of 32.74
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.45 out of 30.25
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.50 out of 36.53
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.69 out of 32.93
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 27.05 out of 39.62
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 9, location 1147972 - 1218904:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser - Asp) + (Asp - X) + (ohmal) + (X) + (Gly)

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).
AY601_RS05055: Ser - Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (233..624): Ser
nrpys: Ser

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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFFVSGEMNLYGPTEASIDVTF
  Nearest Stachelhaus code(s):
    Ser DVWHFSLIDK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1293..1688): 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:
    YGLSTDLGNTVSKVIFGGEINHYGPTETTIGKLL
  Nearest Stachelhaus code(s):
    Asp DLTKIGHIGK (68% 8Å match)
  Stachelhaus code match:
    100% (strong)

AY601_RS05065: Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (421..820): 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:
    YFLSFDLGYTSGKTILGGEINHYGPTETTIGTVF
  Nearest Stachelhaus code(s):
    Asp DLTKIGHIGK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AY601_RS05070: X
AMP-binding (310..687): X
nrpys: (unknown)

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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWYSFDLTQKNANVIFGGEYNSYGPSEASDVSSF
  Nearest Stachelhaus code(s):
    Hse DLKNVGSDVK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AY601_RS05075: mal
PKS_AT (528..806): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 71.0
  inactive: 36.8
  Methoxymalonyl-CoA: 25.8
  Methylmalonyl-CoA: 22.7
  Isobutyryl-CoA: 9.8
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Propionyl-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

AY601_RS05080: X
AMP-binding (504..900): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    GYLIFSPSIRNESLEVRGEVSRYGSTEAS--STA
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

AY601_RS05095: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (457..860): Gly
nrpys: Gly

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:
    gly (Gly)

Stachelhaus prediction details:
  Stachelhaus sequence:
    FSITFDISILETQALCGGDWNMYGPTETTIWSSA
  Nearest Stachelhaus code(s):
    Gly DILQLGMIWK (82% 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
LexA variant 3 | Repressor of DNA damage response

NZ_CP014504.1 - Region 6 - 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: 1,316,775 - 1,337,611 nt. (total: 20,837 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
--- | --- | --- | --- | --- | ---
BGC0000650.3 |  | 0.42 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000636.3 |  | 0.31 | terpene | carotenoid | Brevibacterium linens
BGC0000527.5 |  | 0.30 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000637.3 |  | 0.30 | terpene | carotenoid | Corynebacterium glutamicum
BGC0000536.3 |  | 0.28 | ribosomal | nisin Q | Lactococcus lactis
BGC0000545.5 |  | 0.27 | ribosomal | ruminococcin A | [Ruminococcus] gnavus E1
BGC0000549.3 |  | 0.26 | ribosomal | salivaricin D | Streptococcus salivarius
BGC0002007.2 |  | 0.26 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0000080.5 |  | 0.22 | PKS | jerangolid A, jerangolid D | Sorangium cellulosum
BGC0001377.5 |  | 0.22 | PKS | uncialamycin | Streptomyces uncialis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000650.3 |  | 0.42 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000636.3 |  | 0.31 | terpene | carotenoid | Brevibacterium linens
BGC0000527.5 |  | 0.30 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000637.3 |  | 0.30 | terpene | carotenoid | Corynebacterium glutamicum
BGC0000536.3 |  | 0.28 | ribosomal | nisin Q | Lactococcus lactis
BGC0000545.5 |  | 0.27 | ribosomal | ruminococcin A | [Ruminococcus] gnavus E1
BGC0000549.3 |  | 0.26 | ribosomal | salivaricin D | Streptococcus salivarius
BGC0002007.2 |  | 0.26 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0000080.5 |  | 0.22 | PKS | jerangolid A, jerangolid D | Sorangium cellulosum
BGC0001377.5 |  | 0.22 | PKS | uncialamycin | Streptomyces uncialis

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:
AY601_RS05690: PT_phytoene_like
Domain 1 (14 - 273): 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:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.21 out of 26.06
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.23 out of 26.06
Confidence: medium
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 23.46 out of 29.25
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 21.14 out of 23.79
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.64 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.64 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.82 out of 26.06
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.20 out of 28.19
Confidence: medium
Additional weak hits (3):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.38 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.78 out of 26.12
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.38 out of 29.25
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
--- | ---
IolR | Regulator of the inositol catabolism
MogR | Repressor of flagellar motility genes
SypG | Regulator of biofilm formation and host colonization
ZuR variant 1 | Zinc-responsive repressor

NZ_CP014504.1 - Region 7 - lanthipeptide-class-i
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: 1,670,093 - 1,694,299 nt. (total: 24,207 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### 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 dehydratase
AY601_RS07165: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

AY601_RS07170: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: 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-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0001429.4 |  | 0.28 | NRPS, PKS | myxochromide S1 | Stigmatella aurantiaca DW4/3-1
BGC0001431.4 |  | 0.28 | NRPS, PKS | myxochromide S | Stigmatella aurantiaca
BGC0000988.5 |  | 0.24 | NRPS, PKS | epothilone B | Sorangium cellulosum
BGC0000990.3 |  | 0.23 | NRPS, PKS | epothilone | Sorangium cellulosum
BGC0001564.4 |  | 0.23 | NRPS, PKS | cusperin | Cuspidothrix issatschenkoi CHARLIE-1
BGC0000184.5 |  | 0.20 | PKS | sorangicin A | Sorangium cellulosum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0001429.4 |  | 0.28 | NRPS, PKS | myxochromide S1 | Stigmatella aurantiaca DW4/3-1
BGC0001431.4 |  | 0.28 | NRPS, PKS | myxochromide S | Stigmatella aurantiaca
BGC0000988.5 |  | 0.24 | NRPS, PKS | epothilone B | Sorangium cellulosum
BGC0000990.3 |  | 0.23 | NRPS, PKS | epothilone | Sorangium cellulosum
BGC0001564.4 |  | 0.23 | NRPS, PKS | cusperin | Cuspidothrix issatschenkoi CHARLIE-1
BGC0000184.5 |  | 0.20 | PKS | sorangicin A | Sorangium cellulosum

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 AY601_RS07165

AY601_RS07160
Leader:
MKEEKKQFKFSLNKKVISSMANSQ
Core:
P T N L G Q G A N Q L V D S S T C Q V Q S C H Q C I T V P I P T I S F
Core with dehydrations:
P Dhb N L G Q G A N Q L V D Dha Dha Dhb Cys Q V Q Dha Cys H Q Cys I Dhb V P I P Dhb I Dha F

#### antiSMASH-DB 4.0 matches for AY601_RS07160

100.0%
NZ_CP014504.1:
Lanthipeptides: AY601_RS07160_lanthipeptide
1
P T N L G Q G A N Q L V D S S T C Q V Q S C H Q C I T V P I P T I S F
35
P T N L G Q G A N Q L V D S S T C Q V Q S C H Q C I T V P I P T I S F
1
P T N L G Q G A N Q L V D S S T C Q V Q S C H Q C I T V P I P T I S F
35
20.0%
NZ_JACHIN010000006.1:
Lanthipeptides: HNR40_RS24335_lanthipeptide
13
D S S T C Q V Q S C H Q C
25
D S S T + C H C
9
D S S T L S I M L C H G C
21
17.1%
NZ_PVZV01000003.1 and 1 other:
NZ_PVZV01000003.1 Lanthipeptides: C2865_RS14135_lanthipeptide
Lanthipeptides: C2865_RS14135_lanthipeptide
15
S T C Q V Q S C H Q C I T V P I
30
S T C Q +C+ + P+
12
S T C Q T S A C N S G V A N P V
27
with 3 more sequence matches
14.6%
NZ_CP026498.1:
Lanthipeptides: C2142_RS40575_lanthipeptide
13
D S S T C Q V Q S C H Q
24
D S S +V S C++
23
D S S I A R V M S C Y R
34
14.3%
NZ_SDLS01000012.1:
Lanthipeptides: EIZ45_RS46150_lanthipeptide
15
S T C Q V Q S C H
23
S T C++ +C H
12
S T C E I S A C H
20
12.2%
NZ_CP120210.1:
Lanthipeptides: P3102_RS20320_lanthipeptide
13
D S S T C Q V Q S C H Q C I T V P I P T I
33
D + C V++ +T+P+ I
12
D D A E C T V E T K R G L V T I P L A D I
32

#### MIBiG 4.0 matches for AY601_RS07160

11.4%
BGC0000477.3 (ACA04491.1 (core 1)):
Cyanobactin: patellin 2 or patellin 3
27
T V P I P T I
33
T+P+P T+
1
T L P V P T L
7

#### 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:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.48 out of 26.06
Confidence: medium
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 24.68 out of 28.14
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.70 out of 26.06
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 24.01 out of 28.19
Confidence: medium
Additional weak hits (2):
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 15.87 out of 18.46
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.62 out of 30.22
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.

AY601_RS07160 - Class I
  Cleavage pHMM score: -3.60
  RODEO score: 14
  Monoisotopic mass: 3541.8 Da
  Molecular weight: 3544.0 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3562.0 Da N = 1
    3580.0 Da N = 2
    3598.0 Da N = 3
    3616.0 Da N = 4
    3634.1 Da N = 5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MogR | Repressor of flagellar motility genes
PerR | Peroxide regulator
ZuR variant 1 | Zinc-responsive repressor

NZ_CP014504.1 - Region 8 - linaridin
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: 1,744,722 - 1,765,264 nt. (total: 20,543 nt) Show pHMM detection rules used
linaridin: (cypemycin or cypI)

#### 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
Ligases: synthase
AY601_RS07510: 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 | linaridin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000528.5 |  | 0.39 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002346.3 |  | 0.37 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000502.5 |  | 0.36 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0000503.5 |  | 0.36 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0002316.2 |  | 0.36 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0002152.2 |  | 0.34 | other (other) | toxoflavin | Pseudomonas protegens Pf-5
BGC0001920.4 |  | 0.34 | ribosomal | siamycin I | Streptomyces sp.
BGC0002015.4 |  | 0.34 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001674.5 |  | 0.34 | ribosomal | MS-271 | Streptomyces mirabilis
BGC0002307.3 |  | 0.34 | ribosomal | humidimycin | Streptomyces humidus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000528.5 |  | 0.39 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002346.3 |  | 0.37 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000502.5 |  | 0.36 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0000503.5 |  | 0.36 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0002316.2 |  | 0.36 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0002152.2 |  | 0.34 | other (other) | toxoflavin | Pseudomonas protegens Pf-5
BGC0001920.4 |  | 0.34 | ribosomal | siamycin I | Streptomyces sp.
BGC0002015.4 |  | 0.34 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001674.5 |  | 0.34 | ribosomal | MS-271 | Streptomyces mirabilis
BGC0002307.3 |  | 0.34 | ribosomal | humidimycin | Streptomyces humidus

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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
Additional weak hits (1):
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 25.00 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein

NZ_CP014504.1 - Region 9 - 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: 1,886,940 - 1,909,953 nt. (total: 23,014 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 oxidoreductase
AY601_RS08055: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

AY601_RS08075: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Hydrolases: hydrolase
AY601_RS25905: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

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
--- | --- | --- | --- | --- | ---
BGC0000650.3 |  | 0.63 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000644.3 |  | 0.49 | terpene | carotenoid | Dietzia sp. CQ4
BGC0002283.2 |  | 0.43 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.43 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0000648.3 |  | 0.43 | terpene | carotenoid | Myxococcus xanthus
BGC0000636.3 |  | 0.40 | terpene | carotenoid | Brevibacterium linens
BGC0001903.3 |  | 0.37 | other (other) | neocarazostatin A | Streptomyces sp. MA37
BGC0000595.3 |  | 0.32 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0002409.3 |  | 0.27 | NRPS | frankobactin A1, frankobactin A2, frankobactin A3, frankobactin B1, frankobactin B2, frankobactin B3, frankobactin C1 | Frankia sp. CH37
BGC0000333.5 |  | 0.27 | NRPS | cyclomarin D | Salinispora arenicola CNS-205

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000650.3 |  | 0.63 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000644.3 |  | 0.49 | terpene | carotenoid | Dietzia sp. CQ4
BGC0002283.2 |  | 0.43 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.43 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0000648.3 |  | 0.43 | terpene | carotenoid | Myxococcus xanthus
BGC0000636.3 |  | 0.40 | terpene | carotenoid | Brevibacterium linens
BGC0001903.3 |  | 0.37 | other (other) | neocarazostatin A | Streptomyces sp. MA37
BGC0000595.3 |  | 0.32 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0002409.3 |  | 0.27 | NRPS | frankobactin A1, frankobactin A2, frankobactin A3, frankobactin B1, frankobactin B2, frankobactin B3, frankobactin C1 | Frankia sp. CH37
BGC0000333.5 |  | 0.27 | NRPS | cyclomarin D | Salinispora arenicola CNS-205

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.

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
--- | --- | --- | --- | --- | ---
tetraterpene | C40 carotenoid |  | C40 | unknown | unknown

Genes with terpene domains:
AY601_RS08080: PT_phytoene_like
Domain 1 (11 - 271): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

AY601_RS08100: Lycopene_cycl + Lycopene_cycl
Domain 1 (3 - 91): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

Domain 2 (136 - 218): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

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
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 25.52 out of 28.14
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 22.73 out of 25.88
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.98 out of 29.72
Confidence: medium
Additional weak hits (1):
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.99 out of 29.51
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NtrC | Nitrogen regulatory protein C
PerR | Peroxide regulator
PsrA | Oleic acid responsive regulator
ToxT | Regulator of MSHA biosynthesis

NZ_CP014504.1 - Region 10 - NAPAA
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: 2,232,484 - 2,266,953 nt. (total: 34,470 nt) Show pHMM detection rules used
NAPAA: (AMP-binding and TIGR02353)

#### 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: methyltransferase
AY601_RS09670: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: ligase
AY601_RS09620: 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 | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.73 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001249.5 |  | 0.60 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002286.3 |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.60 | NRPS | AM-toxin | Alternaria alternata
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.73 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001249.5 |  | 0.60 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002286.3 |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.60 | NRPS | AM-toxin | Alternaria alternata
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae

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:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.98 out of 27.78
Confidence: medium
Additional weak hits (3):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.83 out of 30.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 25.87 out of 36.54
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.59 out of 39.62
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 2232483 - 2266953:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Lys)

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).
AY601_RS09620: Lys
Search NORINE for peptide: strict or relaxed
AMP-binding (190..583): Lys
nrpys: Lys

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGEFFDASLEELSTILGGEVNTYGPTEATVIATY
  Nearest Stachelhaus code(s):
    Lys DAESIGTVIK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria

NZ_CP014504.1 - Region 11 - 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: 2,453,457 - 2,510,560 nt. (total: 57,104 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
Ligases: ligase synthase
AY601_RS10555: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

AY601_RS10610: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AY601_RS10615: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001133.4 |  | 0.72 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001133.4 |  | 0.72 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004

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:
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.74 out of 25.88
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 15.94 out of 18.46
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 15.94 out of 18.46
Confidence: medium
Additional weak hits (3):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 25.17 out of 33.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.78 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.09 out of 30.25
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 15, location 2453456 - 2510560:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - Val - X) + (Val - Val)

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).
AY601_RS10610: Val - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (540..940): 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:
    LGAGFDATTFEGWFMVGGEINGYGPTENTTFSLT
  Nearest Stachelhaus code(s):
    Val DAFWVGGTFK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1637..2032): 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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    val (Val)

Stachelhaus prediction details:
  Stachelhaus sequence:
    MGWSFDAAVEQMLATAGGEYNAYGPTECTVFATT
  Nearest Stachelhaus code(s):
    Leu or Val DAALIGAVFK (47% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AY601_RS10615: X - Val - X
Search NORINE for peptide: strict or relaxed
AMP-binding (484..884): X
nrpys: (unknown)

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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRTFDPFVEQMLNMVGGEYVAYGPTECTVTSTI
  Nearest Stachelhaus code(s):
    Arg DVELIGAVTK (50% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1537..1936): 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:
    LGAGFDATTFESWFMVGGEINGYGPTENTTFSIC
  Nearest Stachelhaus code(s):
    Val DAFWIGGTFK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2621..3016): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    Polar aromatic ring (Tyr, bOH-Tyr)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRSFDPFVEQMDVIAGGEYNAYGPTECTITATV
  Nearest Stachelhaus code(s):
    Arg DAEDIGAITK (59% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
PsrA | Oleic acid responsive regulator
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP014504.1 - Region 12 - 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: 2,540,187 - 2,688,175 nt. (total: 147,989 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: oxygenase
AY601_RS10960: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

Transferases: aminotransferase
AY601_RS10935: aminotransferase

smcogs
  SMCOG1019: aminotransferase

AY601_RS11060: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Lyases: decarboxylase
AY601_RS10955: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: ligase synthase
AY601_RS10915: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AY601_RS10940: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AY601_RS10945: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AY601_RS10950: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AY601_RS10965: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AY601_RS10980: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AY601_RS11000: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AY601_RS11005: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AY601_RS11010: 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 | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.74 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.74 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.74 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.74 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
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.

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:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 25.42 out of 26.06
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.21 out of 26.06
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.08 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.97 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.06 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.93 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.41 out of 26.06
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.09 out of 21.55
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 24.33 out of 28.19
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.16 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.69 out of 30.11
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.23 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.88 out of 26.06
Confidence: medium
Additional weak hits (4):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.89 out of 26.06
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.16 out of 27.55
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.67 out of 30.22
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.95 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 16, location 2540186 - 2688175:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-X - D-Val - D-X - D-Leu - D-Asp - Phe - D-X - X) + (D-Val - D-X - D-X - X) + (X - Gly - Asp) + (Val) + (X - X - Thr) + (D-Gly - X) + (Leu) + (Gly)

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).
AY601_RS10915: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (458..846): Gly
nrpys: Gly

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:
    gly (Gly)

Stachelhaus prediction details:
  Stachelhaus sequence:
    FSMTFDISILEGQALCGGDWNMYGPTETTVWSAL
  Nearest Stachelhaus code(s):
    Gly DILQLGMVWK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AY601_RS10940: Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (542..922): Leu
nrpys: Leu

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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FNLTFDLSILEGLAIAGGELNAYGPTETTIYSTV
  Nearest Stachelhaus code(s):
    Leu DAWLIGAIYK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AY601_RS10945: Gly - X
Search NORINE for peptide: strict or relaxed
AMP-binding (534..921): Gly
nrpys: Gly

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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    HVIAFDISLFEPQIHIGGDHELYGPTETTIWCTK
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (53% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2039..2434): 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:
    RWMTFVDHICEGLLSCSGEINIYGSTEVTADATY
  Nearest Stachelhaus code(s):
    bAla VDALVSLADK (59% 8Å match)
  Stachelhaus code match:
    70% (weak)

AY601_RS10950: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (28..411): Thr
nrpys: Thr

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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAPHFDFSVWECSQFFGGELNLYGTTETTIHVTA
  Nearest Stachelhaus code(s):
    Thr DFWSFGLVHK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AY601_RS10955: X - X
AMP-binding (19..417): 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:
    FWETFDPSLRDVHIFFAGEINLYGPTETTLAKFH
  Nearest Stachelhaus code(s):
    Asp DPRHLALLAK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1101..1405): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    phe (Phe)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFVDHLWEGVLTSSGELNIYGSTEVTADATC
  Nearest Stachelhaus code(s):
    bAla VDWVTSLADK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AY601_RS10965: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (537..919): 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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LHSVFDTTNTETWLISGGDINGYGPTENTTFSTF
  Nearest Stachelhaus code(s):
    Val DAFWIGGTFK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AY601_RS10980: X - Gly - Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (246..637): X
nrpys: Tyr, Pro

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:
    MDQAFDASISEMTFITAGEFNAYGPTEYAVCATI
  Nearest Stachelhaus code(s):
    Tyr or Pro DASTIAAVCK (82% 8Å match)
    Tyr DASTIAAVCK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1324..1716): Gly
nrpys: Gly

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:
    gly (Gly)

Stachelhaus prediction details:
  Stachelhaus sequence:
    VSVTFDVSVVDLQAVCGGDWHLYGPTETTIWSTG
  Nearest Stachelhaus code(s):
    Gly DILQFGLIWK (71% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (2411..2807): 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:
    YGLSTDLGNTVSKIIFGGEVNHYGPTETTIGKLL
  Nearest Stachelhaus code(s):
    Asp DLTKIGHIGK (71% 8Å match)
  Stachelhaus code match:
    100% (strong)

AY601_RS11000: Val - X - X - X
Search NORINE for peptide: strict or relaxed
AMP-binding (546..942): 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:
    LNVGFDATTFESWFMAGGEINGYGPTENTTFSLT
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2066..2468): X
nrpys: Dpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    HAKAFDISVWQSELLVTGEVNAYGPTEASDDICH
  Nearest Stachelhaus code(s):
    Dpr DIWELTADDK (85% 8Å match)
    Dab DIWELTADDK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3592..3985): X
nrpys: Leu, Tyr

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:
    leu (Leu)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHAFDAFGWEPFLLAGGDINNYGPTENSVVTTS
  Nearest Stachelhaus code(s):
    Leu or Tyr DAWFLGNVVK (91% 8Å match)
    Leu DAWFLGNVVK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5108..5507): X
nrpys: Dpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    HAKAFDISVWQSELLVTGEVNAYGPTEASDDICH
  Nearest Stachelhaus code(s):
    Dpr DIWELTADDK (85% 8Å match)
    Dab DIWELTADDK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AY601_RS11005: X - Val - X - Leu - Asp - Phe - X - X
Search NORINE for peptide: strict or relaxed
AMP-binding (465..866): X
nrpys: Dpr

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    HSKAFDISVWQSEVLVTGEVNAYGPTEASDDICH
  Nearest Stachelhaus code(s):
    Dpr DIWELTADDK (85% 8Å match)
    Dab DIWELTADDK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1988..2390): 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:
    LDIGFDATTFEGWFLAGGEINGYGPTENTTFSLT
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3532..3925): X
nrpys: Asp, Asn, Glu, Gln, Aad

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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LYQSFDAAVEQLHAISGGEYNEYGPTETTVTALE
  Nearest Stachelhaus code(s):
    Lys DIESIGTVTK (59% 8Å match)
    Arg DAEDIGAITK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (5051..5445): Leu
nrpys: Leu

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:
    leu (Leu)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHAFDAFGWEPFLLAGGDVNNYGPTENSVVTTS
  Nearest Stachelhaus code(s):
    Leu DAWFLGNVVK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (6564..6962): 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:
    YGLSTDLGNTVTKIIFGGEVNHYGPTETTIGKLL
  Nearest Stachelhaus code(s):
    Asp DLTKIGHIGK (71% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (8086..8475): 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:
    LSQAFDASCYENTLVSAGEVNAYGPTENTVCTSL
  Nearest Stachelhaus code(s):
    Tyr DASTVAAVCK (79% 8Å match)
    Phe DAWTVAAVCK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (9127..9529): X
nrpys: Dpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    HAKAFDISVWQSELLVTGEVNAYGPTEASDDICH
  Nearest Stachelhaus code(s):
    Dpr DIWELTADDK (85% 8Å match)
    Dab DIWELTADDK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (10649..11043): X
nrpys: (unknown)

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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LYLSFDASVEQLDAVSGGEYNEYGPTETSIVAIR
  Nearest Stachelhaus code(s):
    Arg DAEDVGVIGK (53% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
CelR | Cellobiose uptake repressor
MogR | Repressor of flagellar motility genes
ZuR variant 1 | Zinc-responsive repressor

NZ_CP014504.1 - Region 13 - T3PKS,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: 2,945,371 - 2,994,101 nt. (total: 48,731 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
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
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
AY601_RS12260: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

AY601_RS12280: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

Ligases: synthase synthetase
AY601_RS12290: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

AY601_RS12300: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AY601_RS12375: 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 | T3PKS | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000486.4 |  |  | 0.25 | ribosomal | butyrivibriocin AR10 | Butyrivibrio fibrisolvens
BGC0002309.2 |  |  | 0.23 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000678.5 |  |  | 0.21 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000665.5 |  |  | 0.20 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001863.4 |  |  | 0.20 | ribosomal, terpene | bacillicn CER074 | Bacillus mycoides
BGC0000664.5 |  |  | 0.20 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000498.5 |  |  | 0.20 | ribosomal | bovicin HJ50 | Streptococcus equinus
BGC0001911.3 |  |  | 0.19 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  |  | 0.19 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000561.5 |  |  | 0.19 | ribosomal | thermophilin 1277 | Streptococcus thermophilus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002127.3 |  | 0.50 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000280.5 |  | 0.50 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0000281.3 |  | 0.49 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0001962.3 |  | 0.49 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0000902.4 |  | 0.49 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.46 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0002332.2 |  | 0.44 | PKS | 4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A | Candidatus Entotheonella sp.
BGC0001077.4 |  | 0.44 | PKS | 6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone | Actinoplanes missouriensis 431
BGC0000255.5 |  | 0.43 | PKS | pederin | Uncultured bacterium
BGC0001285.5 |  | 0.42 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida

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
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP
diterpene precursor |  | GGPP | C20 | acyclic | PP
sesterterpene precursor |  | GFPP | C25 | acyclic | PP
triterpene precursor |  | HPP | C30 | acyclic | PP

Genes with terpene domains:
AY601_RS12375: PT_FPPS_like
Domain 1 (27 - 320): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

Reactions:
  IPP, DMAPP → FPP
  IPP, DMAPP → GGPP
  IPP, DMAPP → GFPP
  IPP, DMAPP → HPP

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:
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.55 out of 21.55
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.79 out of 23.43
Confidence: medium
Additional weak hits (1):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.68 out of 26.12
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
Terpene
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 17, location 2945370 - 2994101:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal)
Non-colinear ordering:
  AY601_RS12300 + AY601_RS12305

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 18, location 2945370 - 2986423:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal)
Non-colinear ordering:
  AY601_RS12300 + AY601_RS12305

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
GFPP | Geranylfarnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
HPP | Hexaprenyl diphosphate
IPP | Isopentenyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
BldD | Development and antibiotic global regulator
ToxT | Regulator of MSHA biosynthesis

NZ_CP014504.1 - Region 14 - NRPS,NRPS-like,T1PKS,lanthipeptide-class-i
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: 3,225,965 - 3,315,507 nt. (total: 89,543 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))
NRPS: cds(Condensation 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-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
Lanthipeptides
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: oxygenase
AY601_RS13570: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: carbamoyltransferase
AY601_RS13660: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

Hydrolases: deaminase esterase hydrolase
AY601_RS13580: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

AY601_RS13610: thioesterase

smcogs
  SMCOG1004: thioesterase

AY601_RS13645: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Lyases: cyclase dehydratase
AY601_RS13500: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

AY601_RS13505: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

Ligases: ligase synthase
AY601_RS13615: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AY601_RS13620: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AY601_RS13625: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AY601_RS13630: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AY601_RS13635: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AY601_RS13650: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

Translocases: permease
AY601_RS13460: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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-i | NRPS | T1PKS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  |  |  | 1.18 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  |  |  | 1.11 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  |  |  |  | 1.11 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  |  | 1.05 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  |  |  | 1.05 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  |  |  |  | 1.05 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  |  |  |  | 1.05 | NRPS | enniatin | Fusarium equiseti
BGC0001758.4 |  |  |  |  | 1.04 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  |  |  |  | 1.04 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  |  | 1.04 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.73 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002576.2 |  | 0.70 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.70 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | 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.

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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.74 out of 26.06
Confidence: medium
Additional weak hits (3):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 25.41 out of 36.54
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.28 out of 28.14
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.08 out of 32.74
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
Lanthipeptides
NRPS/PKS products
NRPS/PKS substrates
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.
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 20, location 3225964 - 3315507:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk) + (fatty_acid) + (pk - Gln - Gln) + (Leu - X - Ser)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 22, location 3244918 - 3315507:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk) + (fatty_acid) + (pk - Gln - Gln) + (Leu - X - Ser)

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).
AY601_RS13615: Leu - X - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (524..922): Leu
nrpys: Leu

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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNDHFDFSVWEGNQIFGGEVNMYGITEVTVHATY
  Nearest Stachelhaus code(s):
    Leu DFWNIGMVHK (94% 8Å match)
    Thr DFWNIGMVHK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1598..1996): 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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNDHFDVSVWEGNQIFAGEVNMYGITEVTVHTTY
  Nearest Stachelhaus code(s):
    Ser DVWSIAMVHK (94% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2683..3079): Ser
nrpys: Ser

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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWELHFIASGEYNLYGPTEAAIDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHISLIDK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AY601_RS13625: pk - Gln - Gln
Search NORINE for peptide: strict or relaxed
PKS_AT (528..778): pk
ATSignature: (unknown)
No matches above 50%
minowa: inactive

Prediction, score:
  inactive: 25.2
  Malonyl-CoA: 23.5
  Methoxymalonyl-CoA: 10.3
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-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

AMP-binding (1938..2341): Gln
nrpys: Gln

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:
    N/A
  Single AA prediction:
    gln (Gln)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGLAFDASVQQGDGILAGEYNFYGPTETCVDSTS
  Nearest Stachelhaus code(s):
    Gln DAQDLGVVDK (76% 8Å match)
    Ile DAQDLGVVDK (74% 8Å match)
    Glu DAKDIGVVDK (68% 8Å match)
    Dpr DAQDLAVVNK (65% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (2979..3381): Gln
nrpys: Gln

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    gln (Gln)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGLAFDASCQQGDGLLAGEYNLYGPTETCVDSTY
  Nearest Stachelhaus code(s):
    Ile DAQDLGVVDK (74% 8Å match)
    Dpr DAQDLAVVNK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AY601_RS13630: fatty_acid
CAL_domain (151..471): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 70.6
  NH2: 23.8
  shikimic_acid: 0.0
  Acetyl-CoA: 0.0
  AHBA: 0.0

AY601_RS13635: pk
PKS_AT (538..829): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 70.8%
  Methylmalonyl-CoA: 62.5%
  CE-Malonyl-CoA: 58.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 110.1
  Malonyl-CoA: 107.0
  Methoxymalonyl-CoA: 100.9
  Isobutyryl-CoA: 85.5
  Ethylmalonyl-CoA: 74.3
  2-Methylbutyryl-CoA: 53.7
  trans-1,2-CPDA: 44.9
  Propionyl-CoA: 44.6
  Benzoyl-CoA: 40.5
  CHC-CoA: 39.7
  inactive: 33.8
  fatty_acid: 32.2
  3-Methylbutyryl-CoA: 31.5
  Acetyl-CoA: 30.1

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

Regulator | Description
--- | ---
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis

NZ_CP014504.1 - Region 15 - NI-siderophore
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: 3,354,291 - 3,384,060 nt. (total: 29,770 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### 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
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 | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002681.3 |  | 0.43 | other (other) | rhizoferrin | Francisella tularensis subsp. tularensis SCHU S4
BGC0000944.5 |  | 0.43 | other (non-nrp siderophore) | staphyloferrin A | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002489.2 |  | 0.37 | other (other) | pseudopaline | Pseudomonas aeruginosa PAO1
BGC0002470.2 |  | 0.37 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0002133.3 |  | 0.36 | ribosomal | group 1 methanobactin | Methylosinus sp. LW3
BGC0001556.5 |  | 0.30 | NRPS, PKS | combamide | Streptomyces sp.
BGC0002571.2 |  | 0.29 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0002691.2 |  | 0.29 | NRPS | amphibactin B, amphibactin C, amphibactin D, amphibactin E, amphibactin H, amphibactin S, amphibactin T, amphibactin V | Vibrio neptunius
BGC0001417.4 |  | 0.28 | NRPS, PKS | myxochromide D | Cystobacterineae bacterium
BGC0002123.3 |  | 0.28 | NRPS, PKS | pseudovibriamide A1, pseudovibriamide B1, pseudovibriamide A2, pseudovibriamide A3, pseudovibriamide A4, pseudovibriamide B2, pseudovibriamide A5, pseudovibriamide A6, pseudovibriamide B3, pseudovibriamide B4, pseudovibriamide B6, pseudovibriamide B5 | Pseudovibrio brasiliensis Ab134

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002681.3 |  | 0.43 | other (other) | rhizoferrin | Francisella tularensis subsp. tularensis SCHU S4
BGC0000944.5 |  | 0.43 | other (non-nrp siderophore) | staphyloferrin A | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002489.2 |  | 0.37 | other (other) | pseudopaline | Pseudomonas aeruginosa PAO1
BGC0002470.2 |  | 0.37 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0002133.3 |  | 0.36 | ribosomal | group 1 methanobactin | Methylosinus sp. LW3
BGC0001556.5 |  | 0.30 | NRPS, PKS | combamide | Streptomyces sp.
BGC0002571.2 |  | 0.29 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0002691.2 |  | 0.29 | NRPS | amphibactin B, amphibactin C, amphibactin D, amphibactin E, amphibactin H, amphibactin S, amphibactin T, amphibactin V | Vibrio neptunius
BGC0001417.4 |  | 0.28 | NRPS, PKS | myxochromide D | Cystobacterineae bacterium
BGC0002123.3 |  | 0.28 | NRPS, PKS | pseudovibriamide A1, pseudovibriamide B1, pseudovibriamide A2, pseudovibriamide A3, pseudovibriamide A4, pseudovibriamide B2, pseudovibriamide A5, pseudovibriamide A6, pseudovibriamide B3, pseudovibriamide B4, pseudovibriamide B6, pseudovibriamide B5 | Pseudovibrio brasiliensis Ab134

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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.56 out of 20.47
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.64 out of 26.33
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.76 out of 21.55
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.06 out of 20.01
Confidence: medium
Additional weak hits (4):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.33 out of 30.22
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.75 out of 36.54
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.99 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 24.33 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
ArcA | Repressor of carbon oxidation
ArgR | Regulator of arginine biosynthesis genes
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP014504.1 - Region 16 - 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: 3,387,875 - 3,472,745 nt. (total: 84,871 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: oxidoreductase oxygenase
AY601_RS14035: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

AY601_RS14125: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: aminotransferase
AY601_RS13985: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: esterase
AY601_RS14010: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: cyclase dehydratase
AY601_RS13965: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

AY601_RS14045: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Ligases: ligase
AY601_RS14025: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AY601_RS14030: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AY601_RS14040: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AY601_RS14055: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.71 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0002286.3 |  | 0.70 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.71 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0002286.3 |  | 0.70 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

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:
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.85 out of 29.38
Confidence: medium
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 27.53 out of 30.97
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.44 out of 27.18
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.44 out of 27.18
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 27.05 out of 32.93
Confidence: medium
Additional weak hits (5):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.82 out of 32.74
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 28.48 out of 39.62
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 18.02 out of 30.12
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.55 out of 28.14
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.58 out of 19.52
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 24, location 3387874 - 3472745:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ala - Tyr - Ser - Ser) + (Val - Val - Asp) + (Asn - D-Asn) + (Ser - Asp - 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).
AY601_RS14025: Ser - Asp - X
Search NORINE for peptide: strict or relaxed
AMP-binding (466..854): Ser
nrpys: Ser

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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWELHFFTSGEHNLYGPTEASIDVTY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLIDK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1517..1910): 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:
    YGISADLGNTITKIILGGEYNHYGPTETTIGKLI
  Nearest Stachelhaus code(s):
    Asp DLTKIGHIGK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2574..2954): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    TAHFFDASIYETSLLTGGEFNAYGPTEICVAATI
  Nearest Stachelhaus code(s):
    Leu DAWILGAVAK (59% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AY601_RS14030: Asn - Asn
Search NORINE for peptide: strict or relaxed
AMP-binding (540..935): Asn
nrpys: Asn

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:
    asn (Asn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWATFDLTVTSCKLIVGGEYNEYGPTETTVGCTV
  Nearest Stachelhaus code(s):
    Asn DLTKIGEVGK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1596..1991): Asn
nrpys: Asn

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:
    asn (Asn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWATFDLTVTSCKLIVGGEYNEYGPTETTVGCTV
  Nearest Stachelhaus code(s):
    Asn DLTKIGEVGK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AY601_RS14040: Val - Val - Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (538..934): 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:
    LSSGFDAVTFEGWFITGGDINGYGPTENTTFSLT
  Nearest Stachelhaus code(s):
    Val DAFWIGGTFK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1597..1976): 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:
    LSSGFDAVTFEGWFITGGDINGYGPTENTTFSLT
  Nearest Stachelhaus code(s):
    Val DAFWIGGTFK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2639..3018): 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:
    YGISADLGNTVTKIIFGGEYNHYGPSETTIGKLL
  Nearest Stachelhaus code(s):
    Asp DLTKIGHIGK (71% 8Å match)
  Stachelhaus code match:
    100% (strong)

AY601_RS14055: Ala - Tyr - Ser - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (457..831): 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:
    FWCTFDLSIFEYNTNMAGERNLYGPSEDTTYSTF
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1494..1888): 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:
    TSQAFDASVSEVTIVTAGEFNAYGPSESSICATA
  Nearest Stachelhaus code(s):
    Cl-Tyr or Tyr DASTVAAIGK (74% 8Å match)
    Tyr DASTVAAVCK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2551..2939): Ser
nrpys: Ser

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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWELHFFTSGEHNLYGPTEASIDVTY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLIDK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3602..3990): Ser
nrpys: Ser

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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWELHFFTSGEHNLYGPTEASIDVTY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLIDK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
CopR | Copper-responsive regulator
FuR variant 1 | Ferric Uptake Regulator
LexA variant 3 | Repressor of DNA damage response
NrdR | Represses ribonucleotide reductase encoding genes

NZ_CP014504.1 - Region 17 - NI-siderophore
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: 4,285,508 - 4,317,799 nt. (total: 32,292 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### 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
Hydrolases: back translocase
AY601_RS17905: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

Ligases: ligase
AY601_RS17935: 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 | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000942.4 |  | 0.59 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001499.5 |  | 0.55 | other (other) | aerobactin | Pantoea ananatis
BGC0001572.3 |  | 0.53 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002469.2 |  | 0.53 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0001478.5 |  | 0.53 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0001498.5 |  | 0.53 | other (other) | aerobactin | Xenorhabdus szentirmaii DSM 16338
BGC0000941.3 |  | 0.52 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.52 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001531.5 |  | 0.52 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002464.3 |  | 0.51 | other (other) | alcaligin | Bordetella pertussis Tohama I

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000942.4 |  | 0.59 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001499.5 |  | 0.55 | other (other) | aerobactin | Pantoea ananatis
BGC0001572.3 |  | 0.53 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002469.2 |  | 0.53 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0001478.5 |  | 0.53 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0001498.5 |  | 0.53 | other (other) | aerobactin | Xenorhabdus szentirmaii DSM 16338
BGC0000941.3 |  | 0.52 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.52 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001531.5 |  | 0.52 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002464.3 |  | 0.51 | other (other) | alcaligin | Bordetella pertussis Tohama I

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
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 28.14 out of 28.14
Confidence: strong
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 25.44 out of 28.14
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.45 out of 26.06
Confidence: strong
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: 22.87 out of 26.06
Confidence: medium
Additional weak hits (3):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.25 out of 30.97
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.59 out of 32.93
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.54 out of 28.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
MogR | Repressor of flagellar motility genes
PerR | Peroxide regulator
ToxT | Regulator of MSHA biosynthesis

NZ_CP014504.1 - Region 18 - lanthipeptide-class-i
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: 5,148,519 - 5,172,871 nt. (total: 24,353 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### 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
Oxidoreductases: oxygenase
AY601_RS21900: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: glycosyltransferase
AY601_RS21840: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Lyases: cyclase dehydratase
AY601_RS21885: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

AY601_RS21890: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: 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-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.71 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002099.3 |  | 0.56 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0002084.4 |  | 0.56 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0000948.5 |  | 0.47 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000542.3 |  | 0.44 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0002668.2 |  | 0.41 | ribosomal | cesin A | Clostridium estertheticum
BGC0000556.5 |  | 0.41 | ribosomal | streptin | Streptococcus pyogenes
BGC0001727.3 |  | 0.41 | ribosomal | paenilan | Paenibacillus polymyxa E681

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.71 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002099.3 |  | 0.56 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0002084.4 |  | 0.56 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0000948.5 |  | 0.47 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000542.3 |  | 0.44 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0002668.2 |  | 0.41 | ribosomal | cesin A | Clostridium estertheticum
BGC0000556.5 |  | 0.41 | ribosomal | streptin | Streptococcus pyogenes
BGC0001727.3 |  | 0.41 | ribosomal | paenilan | Paenibacillus polymyxa E681

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:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
Additional weak hits (2):
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.37 out of 32.38
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.95 out of 39.62
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
--- | ---
MexT | Global virulence regulator

NZ_CP014504.1 - Region 19 - lanthipeptide-class-i
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: 5,777,973 - 5,803,586 nt. (total: 25,614 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### 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 dehydratase
AY601_RS24520: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

AY601_RS24530: 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-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001392.5 |  | 0.56 | ribosomal | pinensins | Chitinophaga pinensis DSM 2588
BGC0000590.5 |  | 0.51 | ribosomal | microcin N | Escherichia coli
BGC0002005.2 |  | 0.50 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0000588.5 |  | 0.48 | ribosomal | microcin L | Escherichia coli
BGC0002698.2 |  | 0.47 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001289.5 |  | 0.46 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002577.2 |  | 0.43 | ribosomal | lactococcin G | Lactococcus lactis
BGC0001210.5 |  | 0.43 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002579.2 |  | 0.43 | ribosomal | carnobacteriocin XY | Carnobacterium maltaromaticum
BGC0001727.3 |  | 0.42 | ribosomal | paenilan | Paenibacillus polymyxa E681

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001392.5 |  | 0.56 | ribosomal | pinensins | Chitinophaga pinensis DSM 2588
BGC0000590.5 |  | 0.51 | ribosomal | microcin N | Escherichia coli
BGC0002005.2 |  | 0.50 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0000588.5 |  | 0.48 | ribosomal | microcin L | Escherichia coli
BGC0002698.2 |  | 0.47 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001289.5 |  | 0.46 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002577.2 |  | 0.43 | ribosomal | lactococcin G | Lactococcus lactis
BGC0001210.5 |  | 0.43 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002579.2 |  | 0.43 | ribosomal | carnobacteriocin XY | Carnobacterium maltaromaticum
BGC0001727.3 |  | 0.42 | ribosomal | paenilan | Paenibacillus polymyxa E681

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.

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.
No hits above weak threshold.
Weak hits (3):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 25.75
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 20.42 out of 22.40
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.88 out of 30.98
Confidence: weak
Lanthipeptides
RREFinder
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.
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (5777972...5803586)
AY601_RS24520
  RRE type: Lanthipeptide_LanB_RRE
  Location: 251 - 339
  Score: 27.8

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---