Select genomic region:
Overview
1.1
2.1
2.2
2.3
5.1
5.2
6.1
10.1
13.1
14.1
15.1

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

NZ_JACICH010000001.1 (Xanthomonas euroxanthea)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | lassopeptide | 1,110,927 | 1,133,334 | High | xanthomonin II/xanthomonin I | ribosomal:RiPP:Lasso peptide

NZ_JACICH010000002.1 (Xanthomonas euroxanthea)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | terpene-precursor | 605,919 | 626,794 |
Region 2.2 | redox-cofactor | 978,179 | 1,000,306 |  |
Region 2.3 | NI-siderophore | 1,047,346 | 1,080,097 | High | xanthoferrin | other:other

NZ_JACICH010000005.1 (Xanthomonas euroxanthea)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 5.1 | t3nrps-iterative,NRPS | 7,246 | 54,009 |
Region 5.2 | arylpolyene | 174,808 | 216,004 | Medium | xanthomonadin I | other:other

NZ_JACICH010000006.1 (Xanthomonas euroxanthea)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 6.1 | NRPS-like | 1 | 20,755 | Low | myxovalargin A | NRPS:Type I

NZ_JACICH010000010.1 (Xanthomonas euroxanthea)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 10.1 | NRPS | 1 | 10,843 |

NZ_JACICH010000013.1 (Xanthomonas euroxanthea)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 13.1 | NRPS | 1 | 4,969 |

NZ_JACICH010000014.1 (Xanthomonas euroxanthea)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 14.1 | NRPS | 1 | 4,754 |

NZ_JACICH010000015.1 (Xanthomonas euroxanthea)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 15.1 | NRPS | 1 | 2,516 |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | lassopeptide | 1,110,927 | 1,133,334 | High | xanthomonin II/xanthomonin I | ribosomal:RiPP:Lasso peptide
Region 2.1 | terpene-precursor | 605,919 | 626,794 |
Region 2.2 | redox-cofactor | 978,179 | 1,000,306 |  |
Region 2.3 | NI-siderophore | 1,047,346 | 1,080,097 | High | xanthoferrin | other:other
Region 5.1 | t3nrps-iterative,NRPS | 7,246 | 54,009 |
Region 5.2 | arylpolyene | 174,808 | 216,004 | Medium | xanthomonadin I | other:other
Region 6.1 | NRPS-like | 1 | 20,755 | Low | myxovalargin A | NRPS:Type I
Region 10.1 | NRPS | 1 | 10,843 |
Region 13.1 | NRPS | 1 | 4,969 |
Region 14.1 | NRPS | 1 | 4,754 |
Region 15.1 | NRPS | 1 | 2,516 |

No secondary metabolite regions were found in these records:
  NZ_JACICH010000003.1 (Xanthomonas euroxanthea)
  NZ_JACICH010000004.1 (Xanthomonas euroxanthea)
  NZ_JACICH010000007.1 (Xanthomonas euroxanthea)
  NZ_JACICH010000008.1 (Xanthomonas euroxanthea)
  NZ_JACICH010000009.1 (Xanthomonas euroxanthea)
  NZ_JACICH010000011.1 (Xanthomonas euroxanthea)
  NZ_JACICH010000012.1 (Xanthomonas euroxanthea)
  NZ_JACICH010000016.1 (Xanthomonas euroxanthea)
  NZ_JACICH010000017.1 (Xanthomonas euroxanthea)
  NZ_JACICH010000018.1 (Xanthomonas euroxanthea)
  NZ_JACICH010000019.1 (Xanthomonas euroxanthea)
  NZ_JACICH010000020.1 (Xanthomonas euroxanthea)

Compact view
NZ_JACICH010000001.1 - Region 1 - lassopeptide
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: 1,110,927 - 1,133,334 nt. (total: 22,408 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
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
Lasso peptides
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
FHY13_RS04825: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase
FHY13_RS04830: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

FHY13_RS04855: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

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 | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000580.3 |  | 0.88 | ribosomal | xanthomonin II, xanthomonin I | Xanthomonas gardneri ATCC 19865
BGC0000570.3 |  | 0.63 | ribosomal | astexin-1 | Asticcacaulis excentricus CB 48
BGC0000573.3 |  | 0.60 | ribosomal | caulonodin I, caulonodin II | Caulobacter sp. K31
BGC0001786.3 |  | 0.60 | ribosomal | subterisin | Novosphingobium subterraneum
BGC0000574.3 |  | 0.58 | ribosomal | caulosegnin I, caulosegnin II, caulosegnin III | Caulobacter segnis ATCC 21756
BGC0000577.3 |  | 0.57 | ribosomal | sphingonodin II | Sphingobium japonicum UT26S
BGC0000576.3 |  | 0.57 | ribosomal | rubrivinodin | Rubrivivax gelatinosus IL144
BGC0002633.2 |  | 0.43 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002403.2 |  | 0.42 | PKS | β-Diketones | Hordeum vulgare subsp. vulgare
BGC0000820.5 |  | 0.40 | other (other) | physostigmine | Streptomyces griseofuscus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000580.3 |  | 0.88 | ribosomal | xanthomonin II, xanthomonin I | Xanthomonas gardneri ATCC 19865
BGC0000570.3 |  | 0.63 | ribosomal | astexin-1 | Asticcacaulis excentricus CB 48
BGC0000573.3 |  | 0.60 | ribosomal | caulonodin I, caulonodin II | Caulobacter sp. K31
BGC0001786.3 |  | 0.60 | ribosomal | subterisin | Novosphingobium subterraneum
BGC0000574.3 |  | 0.58 | ribosomal | caulosegnin I, caulosegnin II, caulosegnin III | Caulobacter segnis ATCC 21756
BGC0000577.3 |  | 0.57 | ribosomal | sphingonodin II | Sphingobium japonicum UT26S
BGC0000576.3 |  | 0.57 | ribosomal | rubrivinodin | Rubrivivax gelatinosus IL144
BGC0002633.2 |  | 0.43 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002403.2 |  | 0.42 | PKS | β-Diketones | Hordeum vulgare subsp. vulgare
BGC0000820.5 |  | 0.40 | other (other) | physostigmine | Streptomyces griseofuscus

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.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.

#### Lassopeptide(s) for FHY13_RS04840

FHY13_RS04840
Leader:
MNINDTTHSDASSEITVLGVASTDTK
Full core:
G G P L A G E E I G G F N V P G
Putative macrolactam:
G G P L A G E E
FHY13_RS04840
Cleaved off residues:
ISEE

#### antiSMASH-DB 4.0 matches for FHY13_RS04840

100.0%
NZ_CM002307.1 and 56 others:
NZ_CP011256.1 Lassopeptides: XB05_RS24520_lassopeptide NZ_CP012251.1 Lassopeptides: AKJ12_RS23425_lassopeptide NZ_CP016878.1 Lassopeptides: XJ27_RS23915_lassopeptide NZ_CP018728.1 Lassopeptides: BJD10_RS25145_lassopeptide NZ_CP029263.1 Lassopeptides: DGN21_RS02930_lassopeptide NZ_CP044334.1 Lassopeptides: F6Y24_RS09085_lassopeptide NZ_CP062164.1 Lassopeptides: ICA18_RS02860_lassopeptide NZ_CP076534.1 Lassopeptides: KPG65_RS08545_lassopeptide NZ_CP098604.1 Lassopeptides: NDY25_RS14310_lassopeptide NZ_CP101417.1 Lassopeptides: NMB96_RS02310_lassopeptide NZ_CP107241.1 Lassopeptides: OEG85_RS03720_lassopeptide NZ_HG999362.1 Lassopeptides: KHN93_RS03315_lassopeptide NZ_HG999363.1 Lassopeptides: KHN77_RS02995_lassopeptide NZ_HG999364.1 Lassopeptides: KHO05_RS03095_lassopeptide NZ_JAASRA010000001.1 Lassopeptides: FHY35_RS01405_lassopeptide NZ_JAASRB010000002.1 Lassopeptides: FHT12_RS12290_lassopeptide NZ_JAASRF010000002.1 Lassopeptides: FHR48_RS06095_lassopeptide NZ_JAASRG010000002.1 Lassopeptides: FHY20_RS09925_lassopeptide NZ_JAASRJ010000002.1 Lassopeptides: FHY12_RS12975_lassopeptide NZ_JAASRK010000002.1 Lassopeptides: FHY11_RS09760_lassopeptide NZ_JAASRL010000003.1 Lassopeptides: FHY10_RS16380_lassopeptide NZ_JAATIU010000002.1 Lassopeptides: GGR60_RS11030_lassopeptide NZ_JAATIV010000002.1 Lassopeptides: GGR63_RS15750_lassopeptide NZ_JAATIY010000001.1 Lassopeptides: GGR72_RS06800_lassopeptide NZ_JACHNM010000002.1 Lassopeptides: FHY34_RS11015_lassopeptide NZ_JACHNN010000001.1 Lassopeptides: FHT07_RS03800_lassopeptide NZ_JACHNO010000002.1 Lassopeptides: FHT09_RS10540_lassopeptide NZ_JACHNQ010000001.1 Lassopeptides: FHR57_RS03345_lassopeptide NZ_JACHNR010000001.1 Lassopeptides: FHR58_RS07330_lassopeptide NZ_JACHNS010000004.1 Lassopeptides: FHR60_RS13510_lassopeptide NZ_JACHNT010000007.1 Lassopeptides: FHR62_RS17675_lassopeptide NZ_JACHOE010000002.1 Lassopeptides: GGR59_RS09535_lassopeptide NZ_JACHOI010000001.1 Lassopeptides: GGR67_RS03770_lassopeptide NZ_JACICH010000001.1 Lassopeptides: FHY13_RS04840_lassopeptide NZ_JACICI010000001.1 Lassopeptides: FHY16_RS03570_lassopeptide NZ_JACICJ010000002.1 Lassopeptides: FHY17_RS09150_lassopeptide NZ_JACIIP010000002.1 Lassopeptides: FHR64_RS08920_lassopeptide NZ_JACIIQ010000008.1 Lassopeptides: FHR65_RS11870_lassopeptide NZ_JACIIT010000002.1 Lassopeptides: FHT05_RS08405_lassopeptide NZ_JACIJV010000001.1 Lassopeptides: FHR59_RS03435_lassopeptide NZ_JZEF01000002.1 Lassopeptides: XARJCFBP2528_RS23390_lassopeptide NZ_JZEG01000001.1 Lassopeptides: XARJCFBP7179_RS23550_lassopeptide NZ_JZEH01000001.1 Lassopeptides: XARJCFBP7634_RS22250_lassopeptide NZ_JZEI01000001.1 Lassopeptides: XARJCFBP7651_RS22545_lassopeptide NZ_KL638866.1 Lassopeptides: IA64_RS22220_lassopeptide NZ_KL638873.1 Lassopeptides: GW16_RS22410_lassopeptide NZ_LMOG01000002.1 Lassopeptides: ASF73_RS22605_lassopeptide NZ_LR861803.1 Lassopeptides: H7A86_RS02980_lassopeptide NZ_LR861807.1 Lassopeptides: H5027_RS18790_lassopeptide NZ_LR990736.1 Lassopeptides: LMG31887_RS03570_lassopeptide NZ_LR990739.1 Lassopeptides: KC661_RS03500_lassopeptide NZ_LR994544.1 Lassopeptides: XTG_RS03110_lassopeptide NZ_PUPR01000001.1 Lassopeptides: C0535_RS05675_lassopeptide NZ_QREQ01000002.1 Lassopeptides: C0538_RS11855_lassopeptide NZ_QRER01000001.1 Lassopeptides: C0539_RS04405_lassopeptide NZ_VCME01000014.1 Lassopeptides: FFY45_RS13360_lassopeptide
Lassopeptides: XHC_RS22885_lassopeptide
1
G G P L A G E E I G G F N V P G
16
G G P L A G E E I G G F N V P G
1
G G P L A G E E I G G F N V P G
16
68.8%
NZ_CM002307.1 and 32 others:
NZ_CP011256.1 Lassopeptides: XB05_RS24515_lassopeptide NZ_CP012251.1 Lassopeptides: AKJ12_RS23430_lassopeptide NZ_CP016878.1 Lassopeptides: XJ27_RS23910_lassopeptide NZ_CP018728.1 Lassopeptides: BJD10_RS25150_lassopeptide NZ_CP098604.1 Lassopeptides: NDY25_RS14305_lassopeptide NZ_CP101417.1 Lassopeptides: NMB96_RS02315_lassopeptide NZ_CP107241.1 Lassopeptides: OEG85_RS03715_lassopeptide NZ_HG999363.1 Lassopeptides: KHN77_RS02990_lassopeptide NZ_HG999364.1 Lassopeptides: KHO05_RS03090_lassopeptide NZ_JAASRB010000002.1 Lassopeptides: FHT12_RS12285_lassopeptide NZ_JAASRJ010000002.1 Lassopeptides: FHY12_RS12980_lassopeptide NZ_JAASRK010000002.1 Lassopeptides: FHY11_RS09765_lassopeptide NZ_JAATIU010000002.1 Lassopeptides: GGR60_RS11025_lassopeptide NZ_JAATIV010000002.1 Lassopeptides: GGR63_RS15745_lassopeptide NZ_JACHNM010000002.1 Lassopeptides: FHY34_RS11010_lassopeptide NZ_JACHNO010000002.1 Lassopeptides: FHT09_RS10545_lassopeptide NZ_JACHOE010000002.1 Lassopeptides: GGR59_RS09540_lassopeptide NZ_JACHOI010000001.1 Lassopeptides: GGR67_RS03765_lassopeptide NZ_JACICH010000001.1 Lassopeptides: FHY13_RS04845_lassopeptide NZ_JACICI010000001.1 Lassopeptides: FHY16_RS03565_lassopeptide NZ_JACICJ010000002.1 Lassopeptides: FHY17_RS09145_lassopeptide NZ_JACIIT010000002.1 Lassopeptides: FHT05_RS08410_lassopeptide NZ_JZEH01000001.1 Lassopeptides: XARJCFBP7634_RS22255_lassopeptide NZ_JZEI01000001.1 Lassopeptides: XARJCFBP7651_RS22540_lassopeptide NZ_KL638873.1 Lassopeptides: GW16_RS22405_lassopeptide NZ_LR861803.1 Lassopeptides: H7A86_RS02975_lassopeptide NZ_LR990736.1 Lassopeptides: LMG31887_RS03565_lassopeptide NZ_LR990739.1 Lassopeptides: KC661_RS03495_lassopeptide NZ_LR994544.1 Lassopeptides: XTG_RS03105_lassopeptide NZ_QREQ01000002.1 Lassopeptides: C0538_RS11850_lassopeptide NZ_QRER01000001.1 Lassopeptides: C0539_RS04400_lassopeptide NZ_VCME01000014.1 Lassopeptides: FFY45_RS13365_lassopeptide
Lassopeptides: XHC_RS22890_lassopeptide
1
G G P L A G E E I G G F N V P G
16
G G P L A G E E+G G G
1
G G P L A G E E M G G I T T L G
16
68.8%
NZ_CP029263.1 and 18 others:
NZ_CP044334.1 Lassopeptides: F6Y24_RS09090_lassopeptide NZ_CP062164.1 Lassopeptides: ICA18_RS02855_lassopeptide NZ_HG999362.1 Lassopeptides: KHN93_RS03310_lassopeptide NZ_JAASRA010000001.1 Lassopeptides: FHY35_RS01400_lassopeptide NZ_JAASRL010000003.1 Lassopeptides: FHY10_RS16375_lassopeptide NZ_JAATIY010000001.1 Lassopeptides: GGR72_RS06805_lassopeptide NZ_JACHNN010000001.1 Lassopeptides: FHT07_RS03795_lassopeptide NZ_JACHNQ010000001.1 Lassopeptides: FHR57_RS03340_lassopeptide NZ_JACHNR010000001.1 Lassopeptides: FHR58_RS07335_lassopeptide NZ_JACHNT010000007.1 Lassopeptides: FHR62_RS17680_lassopeptide NZ_JACIIP010000002.1 Lassopeptides: FHR64_RS08915_lassopeptide NZ_JACIIQ010000008.1 Lassopeptides: FHR65_RS11875_lassopeptide NZ_JACIJV010000001.1 Lassopeptides: FHR59_RS03430_lassopeptide NZ_JZEF01000002.1 Lassopeptides: XARJCFBP2528_RS23385_lassopeptide NZ_JZEG01000001.1 Lassopeptides: XARJCFBP7179_RS23555_lassopeptide NZ_KL638866.1 Lassopeptides: IA64_RS22225_lassopeptide NZ_LR861807.1 Lassopeptides: H5027_RS18795_lassopeptide NZ_PUPR01000001.1 Lassopeptides: C0535_RS05670_lassopeptide
Lassopeptides: DGN21_RS02925_lassopeptide
1
G G P L A G E E I G G F N V P G
16
G G P L A G E E+G G G
1
G G P L A G E E M G G S T T L G
16
with 9 more sequence matches
68.8%
NZ_LMOG01000002.1:
Lassopeptides: ASF73_RS22610_lassopeptide
1
G G P L A G E E I G G F N V P G
16
G G P L A G E E+G G G
1
G G P L A G E E M G G T T T L G
16
62.5%
NZ_CP076534.1:
Lassopeptides: KPG65_RS08540_lassopeptide
2
G P L A G E E I G G F N V P G
16
G P L A G E E+G G G
2
G P L A G E E M G G S T T L G
16
62.5%
NZ_JAASRF010000002.1 and 2 others:
NZ_JAASRG010000002.1 Lassopeptides: FHY20_RS09930_lassopeptide NZ_JACHNS010000004.1 Lassopeptides: FHR60_RS13505_lassopeptide
Lassopeptides: FHR48_RS06090_lassopeptide
1
G G P L A G E E I G G F N V P G
16
G G P L+G E E+G G G
1
G G P L S G E E M G G T A T L G
16
62.5%
NZ_JACHCO010000003.1:
Lassopeptides: HDE79_RS09305_lassopeptide
1
G G P L A G E E I G G F N V P G
16
G G P L E I G G F G
1
G G P L M N E V I G G F T T S G
16
62.5%
NZ_JACHCP010000001.1:
Lassopeptides: HDE80_RS00035_lassopeptide
1
G G P L A G E E I G G F N V P G
16
G G P L E I G G F G
1
G G P L M N E V I G G F T T A G
16
56.2%
NZ_CP089507.1:
Lassopeptides: LU699_RS12715_lassopeptide
1
G G P L A G E E I G G F N V P G
16
G G L G E+I G +P G
1
G G A L V G E D I G D P F I P G
16
50.0%
NZ_CP017074.1:
Lassopeptides: BGP89_RS14250_lassopeptide
1
G G P L A G E E I G G F N V P G
16
G L G E++G G P G
1
G S A L I G E D V G G R Y T P G
16
50.0%
NZ_CP042218.1:
Lassopeptides: FPZ22_RS13815_lassopeptide
1
G G P L A G E E I G G F
12
G G L G E++G G F
1
G G T L I G E D M G G F
12
50.0%
NZ_CP089507.1:
Lassopeptides: LU699_RS12710_lassopeptide
1
G G P L A G E E I G G F N V P G
16
G G L G E++G +P G
1
G G A L L G E D M G N T T M P G
16

#### MIBiG 4.0 matches for FHY13_RS04840

80.0%
BGC0000580.3 (EGD17354.1):
Lasso peptide: xanthomonin II or xanthomonin I
1
G G P L A G E E I G G F N V P G
16
G G P L A G E E I G G F N V P G
1
G G P L A G E E I G G F N V P G
16
55.0%
BGC0000580.3 (EGD17355.1):
Lasso peptide: xanthomonin II or xanthomonin I
1
G G P L A G E E I G G F N V P G
16
G G P L A G E E+G G G
1
G G P L A G E E M G G I T T L G
16

#### 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:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.22 out of 18.46
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.78 out of 29.72
Confidence: medium
Additional weak hits (6):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.67 out of 20.01
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.06 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.43 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.59 out of 26.06
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.81 out of 20.01
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.28 out of 36.54
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

FHY13_RS04840 - Class II
  Cleavage pHMM score: 9.50
  RODEO score: 22
  Monoisotopic mass: 1451.7 Da
  Molecular weight: 1452.6 Da
  Number of bridges: 0

Weights before cleavage:
  Monoisotopic mass: 1909.9 Da
  Molecular weight: 1911.0 Da

RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (1110926...1133334)
FHY13_RS04850
  RRE type: Lasso_Fused_RRE
  Location: 3 - 66
  Score: 64.9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NtrC | Nitrogen regulatory protein C
RpoN | Regulator of nitrogen assimilation and virulence

NZ_JACICH010000002.1 - Region 1 - 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: 605,919 - 626,794 nt. (total: 20,876 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
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
Ligases: synthetase
FHY13_RS10840: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000643.3 |  | 0.33 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000640.3 |  | 0.32 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000634.3 |  | 0.32 | terpene | carotenoid | Brevundimonas sp. SD212
BGC0000630.3 |  | 0.31 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.31 | terpene | β-carotein | uncultured bacterium
BGC0000639.3 |  | 0.30 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000641.3 |  | 0.30 | terpene | carotenoid | Enterobacteriaceae bacterium DC416

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000643.3 |  | 0.33 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000640.3 |  | 0.32 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000634.3 |  | 0.32 | terpene | carotenoid | Brevundimonas sp. SD212
BGC0000630.3 |  | 0.31 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.31 | terpene | β-carotein | uncultured bacterium
BGC0000639.3 |  | 0.30 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000641.3 |  | 0.30 | terpene | carotenoid | Enterobacteriaceae bacterium DC416

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

Genes with terpene domains:
FHY13_RS10840: PT_FPPS_like
Domain 1 (31 - 291): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:
  DMAPP, IPP → FPP

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: 19.26 out of 19.26
Confidence: strong
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.96 out of 30.25
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.01 out of 27.78
Confidence: medium
Additional weak hits (10):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.22 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.42 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.63 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.51 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.17 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.32 out of 27.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.43 out of 24.78
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.90 out of 20.01
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.13 out of 27.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.37 out of 29.65
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
IPP | Isopentenyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
ColR | Phenol-responsive regulator

NZ_JACICH010000002.1 - Region 2 - redox-cofactor
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: 978,179 - 1,000,306 nt. (total: 22,128 nt) Show pHMM detection rules used
redox-cofactor: (cds(PF04055 and (TIGR04085 or SPASM)) and (TIGR02111 or TIGR03966) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
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
FHY13_RS12395: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | redox-cofactor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001100.5 |  | 0.34 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0002713.2 |  | 0.30 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0000906.3 |  | 0.30 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000905.5 |  | 0.30 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000461.5 |  | 0.29 | NRPS | WAP-8294A2 | Lysobacter enzymogenes
BGC0000796.3 |  | 0.25 | saccharide | S-layer glycan | Paenibacillus alvei
BGC0000768.5 |  | 0.23 | saccharide | gellan polysaccharide | Sphingomonas elodea ATCC 31461

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001100.5 |  | 0.34 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0002713.2 |  | 0.30 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0000906.3 |  | 0.30 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000905.5 |  | 0.30 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000461.5 |  | 0.29 | NRPS | WAP-8294A2 | Lysobacter enzymogenes
BGC0000796.3 |  | 0.25 | saccharide | S-layer glycan | Paenibacillus alvei
BGC0000768.5 |  | 0.23 | saccharide | gellan polysaccharide | Sphingomonas elodea ATCC 31461

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.19 out of 20.47
Confidence: strong
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.02 out of 21.84
Confidence: medium
Additional weak hits (6):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.21 out of 20.01
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.08 out of 30.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.85 out of 26.12
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.45 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.65 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.87 out of 32.93
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (978178...1000306)
FHY13_RS20125
  RRE type: PqqD_RRE
  Location: 1 - 91
  Score: 116.6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MexT | Global virulence regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_JACICH010000002.1 - Region 3 - 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: 1,047,346 - 1,080,097 nt. (total: 32,752 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
TTA codons
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
FHY13_RS12685: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: sulfhydrylase
FHY13_RS12750: O-succinylhomoserine sulfhydrylase

smcogs
  SMCOG1168: O-succinylhomoserine sulfhydrylase

Lyases: decarboxylase
FHY13_RS12725: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

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
--- | --- | --- | --- | --- | ---
BGC0001408.5 |  | 0.87 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0002527.2 |  | 0.80 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0000946.5 |  | 0.79 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0000947.5 |  | 0.62 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0000844.5 |  | 0.49 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0000943.5 |  | 0.49 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002681.3 |  | 0.48 | other (other) | rhizoferrin | Francisella tularensis subsp. tularensis SCHU S4
BGC0002692.2 |  | 0.47 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000942.4 |  | 0.47 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0002683.2 |  | 0.45 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001408.5 |  | 0.87 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0002527.2 |  | 0.80 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0000946.5 |  | 0.79 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0000947.5 |  | 0.62 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0000844.5 |  | 0.49 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0000943.5 |  | 0.49 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002681.3 |  | 0.48 | other (other) | rhizoferrin | Francisella tularensis subsp. tularensis SCHU S4
BGC0002692.2 |  | 0.47 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000942.4 |  | 0.47 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0002683.2 |  | 0.45 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418

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:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.02 out of 21.84
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.00 out of 28.19
Confidence: medium
Additional weak hits (9):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.12 out of 26.06
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.29 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.46 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.56 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.50 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.21 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.78 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.38 out of 30.25
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MexT | Global virulence regulator
ZuR variant 1 | Zinc-responsive repressor

NZ_JACICH010000005.1 - Region 1 - NRPS,t3nrps-iterative
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: 7,246 - 54,009 nt. (total: 46,764 nt) Show pHMM detection rules used
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)
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
TTA codons
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
FHY13_RS15980: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acyltransferase glycosyltransferase
FHY13_RS15985: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

FHY13_RS15990: glycosyltransferase

smcogs
  SMCOG1102: glycosyltransferase

Lyases: decarboxylase dehydratase
FHY13_RS15925: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

FHY13_RS16000: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase
FHY13_RS15930: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

FHY13_RS15995: 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 | t3nrps-iterative | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002075.3 |  |  | 0.87 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  |  | 0.68 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  | 0.60 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  | 0.59 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 18.25 out of 18.46
Confidence: strong
Additional weak hits (22):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.34 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.62 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.52 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.52 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.90 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.89 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.35 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.33 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.98 out of 29.38
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.71 out of 33.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.99 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.23 out of 26.06
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.25 out of 30.97
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.04 out of 39.62
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.76 out of 26.06
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 26.33
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.31 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.34 out of 20.97
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.08 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.34 out of 32.93
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.45 out of 35.63
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.63 out of 30.98
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 7245 - 54009:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (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).
FHY13_RS15995: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (465..852): 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:
    FAMTFDIAGLELQALVGGETQLYGPTETTIWSTI
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_JACICH010000005.1 - Region 2 - arylpolyene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 174,808 - 216,004 nt. (total: 41,197 nt) Show pHMM detection rules used
arylpolyene: (APE_KS1 or APE_KS2)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
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 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
FHY13_RS16740: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acyltransferase halogenase
FHY13_RS16730: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

FHY13_RS16775: acyltransferase

smcogs
  SMCOG1141: acyltransferase

FHY13_RS16790: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

Ligases: ligase synthase
FHY13_RS16715: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

FHY13_RS16725: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

FHY13_RS16805: 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 | arylpolyene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002341.2 |  | 0.77 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0000840.5 |  | 0.76 | other (other) | xanthomonadin I | Xanthomonas oryzae pv. oryzae
BGC0000866.5 |  | 0.50 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0002643.2 |  | 0.48 | other (other) | aetokthonotoxin | Aetokthonos hydrillicola Thurmond2011
BGC0000867.3 |  | 0.48 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0001987.2 |  | 0.46 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0001366.5 |  | 0.44 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2
BGC0002008.3 |  | 0.44 | other (other) | aryl polyenes | Xenorhabdus doucetiae
BGC0001940.3 |  | 0.43 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0001075.5 |  | 0.43 | PKS, terpene | aurachin RE | Rhodococcus erythropolis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002341.2 |  | 0.77 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0000840.5 |  | 0.76 | other (other) | xanthomonadin I | Xanthomonas oryzae pv. oryzae
BGC0000866.5 |  | 0.50 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0002643.2 |  | 0.48 | other (other) | aetokthonotoxin | Aetokthonos hydrillicola Thurmond2011
BGC0000867.3 |  | 0.48 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0001987.2 |  | 0.46 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0001366.5 |  | 0.44 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2
BGC0002008.3 |  | 0.44 | other (other) | aryl polyenes | Xenorhabdus doucetiae
BGC0001940.3 |  | 0.43 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0001075.5 |  | 0.43 | PKS, terpene | aurachin RE | Rhodococcus erythropolis

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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.75 out of 23.79
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (6):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.87 out of 29.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 25.11 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.65 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.00 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.19 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.05 out of 24.78
Confidence: weak
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 substrates
TFBS Finder
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).
FHY13_RS16805: X
AMP-binding (39..308): 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:
    TPQV-------LVTVSATAREMFGSTETCVFAVR
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism

NZ_JACICH010000006.1 - Region 1 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 20,755 nt. (total: 20,755 nt) Show pHMM detection rules used
Region on contig edge.
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
TTA codons
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 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
FHY13_RS17355: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: phosphatase
FHY13_RS17320: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001166.5 |  | 0.63 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001261.3 |  | 0.63 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.63 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000308.5 |  | 0.46 | NRPS | aureusimine A, aureusimine B, aureusimine C | Staphylococcus aureus subsp. aureus str. JKD6008
BGC0001168.5 |  | 0.43 | NRPS | Livipeptin | Streptomyces lividans 1326
BGC0000393.5 |  | 0.43 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622
BGC0001768.4 |  | 0.41 | NRPS | sansalvamide | [Nectria] haematococca mpVI 77-13-4
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001166.5 |  | 0.63 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001261.3 |  | 0.63 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.63 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000308.5 |  | 0.46 | NRPS | aureusimine A, aureusimine B, aureusimine C | Staphylococcus aureus subsp. aureus str. JKD6008
BGC0001168.5 |  | 0.43 | NRPS | Livipeptin | Streptomyces lividans 1326
BGC0000393.5 |  | 0.43 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622
BGC0001768.4 |  | 0.41 | NRPS | sansalvamide | [Nectria] haematococca mpVI 77-13-4
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42

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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.60 out of 23.79
Confidence: medium
Additional weak hits (4):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.83 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.57 out of 27.78
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 23.05 out of 33.73
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.91 out of 35.63
Confidence: weak
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
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism

NZ_JACICH010000010.1 - Region 1 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 10,843 nt. (total: 10,843 nt) Show pHMM detection rules used
Region on contig edge.
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
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
FHY13_RS19945: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FHY13_RS19950: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

FHY13_RS19960: 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
--- | --- | --- | --- | --- | ---
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001166.5 |  | 0.63 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001166.5 |  | 0.63 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans

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

No significant matches found.

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

No significant matches found.

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
NZ_JACICH010000013.1 - Region 1 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 4,969 nt. (total: 4,969 nt) Show pHMM detection rules used
Region on contig edge.
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
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
FHY13_RS20005: 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 |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0000357.5 |  | 0.62 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0000357.5 |  | 0.62 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255

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.

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
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 0 - 4969:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Phe)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
FHY13_RS20005: Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (552..944): Phe
nrpys: Phe

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:
    LQQAFDASVFEMTLVSAGEFNAYGPTEATVWSTW
  Nearest Stachelhaus code(s):
    Phe DAFTVAAVWK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
NZ_JACICH010000014.1 - Region 1 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 4,754 nt. (total: 4,754 nt) Show pHMM detection rules used
Region on contig edge.
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
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
FHY13_RS20010: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

FHY13_RS20015: 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 |  | 0.70 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001166.5 |  | 0.68 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.66 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001758.4 |  | 0.66 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.70 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001166.5 |  | 0.68 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.66 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001758.4 |  | 0.66 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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

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.

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
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 0 - 4754:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr)

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).
FHY13_RS20010: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (6..416): 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:
    LAAHFDFSVWEGNQVFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
NZ_JACICH010000015.1 - Region 1 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 2,516 nt. (total: 2,516 nt) Show pHMM detection rules used
Region on contig edge.
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
TTA codons
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
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
FHY13_RS20020: 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
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  | 0.62 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.61 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.61 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002518.3 |  | 0.57 | NRPS | syringafactin A, syringafactin C | Pseudomonas sp. SZ57
BGC0001844.4 |  | 0.56 | NRPS | holrhizin A, holrhizin B, holrhizin C, holrhizin D | Paraburkholderia rhizoxinica HKI 454
BGC0001517.3 |  | 0.55 | NRPS | asperphenamate | Aspergillus terreus NIH2624
BGC0000393.5 |  | 0.54 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  | 0.62 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.61 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.61 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002518.3 |  | 0.57 | NRPS | syringafactin A, syringafactin C | Pseudomonas sp. SZ57
BGC0001844.4 |  | 0.56 | NRPS | holrhizin A, holrhizin B, holrhizin C, holrhizin D | Paraburkholderia rhizoxinica HKI 454
BGC0001517.3 |  | 0.55 | NRPS | asperphenamate | Aspergillus terreus NIH2624
BGC0000393.5 |  | 0.54 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622

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 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