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Overview
1.1
1.2
1.3
1.4
1.5

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

NZ_SOCO01000001.1 (Stenotrophomonas sp. CC22-02)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | RiPP-like | 958,060 | 968,935 |
Region 1.2 | lanthipeptide-class-ii | 1,175,373 | 1,198,273 |
Region 1.3 | lassopeptide | 1,724,308 | 1,746,863 |
Region 1.4 | NRP-metallophore,NRPS | 2,027,200 | 2,075,567 | High | 2,3-dihydroxybenzoylserine | NRPS:Type I
Region 1.5 | terpene-precursor | 2,665,152 | 2,686,030 |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | RiPP-like | 958,060 | 968,935 |
Region 1.2 | lanthipeptide-class-ii | 1,175,373 | 1,198,273 |
Region 1.3 | lassopeptide | 1,724,308 | 1,746,863 |
Region 1.4 | NRP-metallophore,NRPS | 2,027,200 | 2,075,567 | High | 2,3-dihydroxybenzoylserine | NRPS:Type I
Region 1.5 | terpene-precursor | 2,665,152 | 2,686,030 |

No secondary metabolite regions were found in these records:
  NZ_SOCO01000002.1 (Stenotrophomonas sp. CC22-02)
  NZ_SOCO01000003.1 (Stenotrophomonas sp. CC22-02)
  NZ_SOCO01000004.1 (Stenotrophomonas sp. CC22-02)
  NZ_SOCO01000005.1 (Stenotrophomonas sp. CC22-02)
  NZ_SOCO01000006.1 (Stenotrophomonas sp. CC22-02)
  NZ_SOCO01000007.1 (Stenotrophomonas sp. CC22-02)

Compact view
NZ_SOCO01000001.1 - Region 1 - RiPP-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: 958,060 - 968,935 nt. (total: 10,876 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
No tailoring functions detected.
Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001962.3 |  | 0.27 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0000188.5 |  | 0.23 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0001650.4 |  | 0.23 | NRPS | Le-pyrrolopyrazines | Lysobacter enzymogenes
BGC0000452.5 |  | 0.21 | NRPS | tyrocidine | Brevibacillus brevis NBRC 100599
BGC0000651.5 |  | 0.20 | terpene | KS-505a | Streptomyces argenteolus
BGC0001283.3 |  | 0.18 | PKS | Bisenarsan | Streptomyces lividans 1326

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001962.3 |  | 0.27 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0000188.5 |  | 0.23 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0001650.4 |  | 0.23 | NRPS | Le-pyrrolopyrazines | Lysobacter enzymogenes
BGC0000452.5 |  | 0.21 | NRPS | tyrocidine | Brevibacillus brevis NBRC 100599
BGC0000651.5 |  | 0.20 | terpene | KS-505a | Streptomyces argenteolus
BGC0001283.3 |  | 0.18 | PKS | Bisenarsan | Streptomyces lividans 1326

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: 19.00 out of 20.47
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.19 out of 19.26
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.64 out of 26.85
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47
Confidence: medium
Additional weak hits (2):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.71 out of 39.62
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_SOCO01000001.1 - Region 2 - lanthipeptide-class-ii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,175,373 - 1,198,273 nt. (total: 22,901 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase
N440_RS05695: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

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

Reference | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000528.5 |  | 0.52 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002346.3 |  | 0.47 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000503.5 |  | 0.46 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0002698.2 |  | 0.43 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001576.3 |  | 0.43 | ribosomal | divamide A | Prochloron didemni
BGC0000500.5 |  | 0.41 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0002316.2 |  | 0.41 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0002704.2 |  | 0.41 | ribosomal | archalan β | Halorussus salinus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000528.5 |  | 0.52 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002346.3 |  | 0.47 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000503.5 |  | 0.46 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0002698.2 |  | 0.43 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001576.3 |  | 0.43 | ribosomal | divamide A | Prochloron didemni
BGC0000500.5 |  | 0.41 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0002316.2 |  | 0.41 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0002704.2 |  | 0.41 | ribosomal | archalan β | Halorussus salinus

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

No significant matches found.

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

No significant matches found.

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

#### Lanthipeptide(s) for N440_RS05695

N440_RS05690
Leader:
MDLNDDVVSGWLNGSDDVDGCANPAGSLFIYGA
Core:
A A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
Core with dehydrations:
A A Dhb E Dha A L Dhb Dha A Dha D Dhb L I Dhb G G G Dhb E Cys Dhb Dhb Dhb M Dha V V N H Cys L Cys Cys

#### antiSMASH-DB 4.0 matches for N440_RS05690

100.0%
NZ_CP015612.1 and 17 others:
NZ_CP027562.1 Lanthipeptides: C6Y55_RS08375_lanthipeptide NZ_CP028358.1 Lanthipeptides: C9J74_RS08630_lanthipeptide NZ_CP040435.1 Lanthipeptides: FEO92_RS08800_lanthipeptide NZ_CP040438.1 Lanthipeptides: FEO89_RS08350_lanthipeptide NZ_CP040439.1 Lanthipeptides: FEO88_RS08780_lanthipeptide NZ_CP056088.1 Lanthipeptides: HUZ96_RS08220_lanthipeptide NZ_CP090418.1 Lanthipeptides: LYZ64_RS08310_lanthipeptide NZ_CP109812.1 Lanthipeptides: FQS62_RS08595_lanthipeptide NZ_DS999412.1 Lanthipeptides: SSKA14_RS15505_lanthipeptide NZ_JAEDUZ010000008.1 Lanthipeptides: JAK52_RS03215_lanthipeptide NZ_JAEDWK010000010.1 Lanthipeptides: JAK51_RS04155_lanthipeptide NZ_JAJNMF010000022.1 Lanthipeptides: LQ423_RS11465_lanthipeptide NZ_JVUI01000059.1 Lanthipeptides: ADG58_RS15825_lanthipeptide NZ_LR134301.1 Lanthipeptides: EL200_RS07985_lanthipeptide NZ_OBEE01000002.1 Lanthipeptides: CRO53_RS02030_lanthipeptide NZ_RHQE01000015.1 Lanthipeptides: EGJ89_RS13150_lanthipeptide NZ_SOCO01000001.1 Lanthipeptides: N440_RS05690_lanthipeptide
Lanthipeptides: A7326_RS08120_lanthipeptide
1
A A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
A A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
1
A A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
97.1%
NZ_CP011010.1:
Lanthipeptides: VN11_RS08230_lanthipeptide
1
A A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
A A T E S A L T+A S D T L I T G G G T E C T T T M S V V N H C L C C
1
A A T E S A L T A A S D T L I T G G G T E C T T T M S V V N H C L C C
35
97.1%
NZ_CP043578.1 and 3 others:
NZ_CP067993.1 Lanthipeptides: JJL50_RS07700_lanthipeptide NZ_JVHP01000063.1 Lanthipeptides: ADI44_RS21105_lanthipeptide NZ_OU943334.1 Lanthipeptides: LNN95_RS09005_lanthipeptide
Lanthipeptides: F0Q13_RS08255_lanthipeptide
1
A A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
1
G A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
with 16 more sequence matches
Only the first 10 are displayed here.
72.3%
NZ_CP047310.1 and 4 others:
NZ_CP104169.1 Lanthipeptides: NDR96_RS06465_lanthipeptide NZ_JABDRV010000001.1 Lanthipeptides: HRL60_RS01085_lanthipeptide NZ_JAEDVS010000025.1 Lanthipeptides: JAK50_RS15965_lanthipeptide NZ_JVPM01000038.1 Lanthipeptides: ADH50_RS19075_lanthipeptide
Lanthipeptides: GS396_RS07720_lanthipeptide
2
A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
14
A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
47
37.1%
NZ_CP011305.1 and 19 others:
NZ_CP031058.1 Lanthipeptides: DUW70_RS15590_lanthipeptide NZ_CP031167.1 Lanthipeptides: MG068_RS07815_lanthipeptide NZ_CP040436.1 Lanthipeptides: FEO91_RS08085_lanthipeptide NZ_CP046588.1 Lanthipeptides: GOC52_RS08100_lanthipeptide NZ_CP060259.1 Lanthipeptides: H7F32_RS08235_lanthipeptide NZ_CP071784.1 Lanthipeptides: J3U96_RS13765_lanthipeptide NZ_CP077679.1 Lanthipeptides: KS456_RS07940_lanthipeptide NZ_CP096975.1 Lanthipeptides: M1L61_RS08375_lanthipeptide NZ_CP104071.1 Lanthipeptides: K7565_RS07800_lanthipeptide NZ_CP104287.1 Lanthipeptides: K7567_RS07875_lanthipeptide NZ_CP104324.1 Lanthipeptides: K7569_RS08320_lanthipeptide NZ_JACLBK010000002.1 Lanthipeptides: ID844_RS05155_lanthipeptide NZ_JAEDVP010000027.1 Lanthipeptides: JAK38_RS15550_lanthipeptide NZ_JAEDVW010000007.1 Lanthipeptides: JAK53_RS03160_lanthipeptide NZ_JAEDWD010000009.1 Lanthipeptides: JAK45_RS02000_lanthipeptide NZ_JAFLWT010000006.1 Lanthipeptides: J1F00_RS06425_lanthipeptide NZ_JAQQGI010000014.1 Lanthipeptides: PQS91_RS16925_lanthipeptide NZ_KB907502.1 Lanthipeptides: G370_RS0114170_lanthipeptide NZ_RHPZ01000014.1 Lanthipeptides: EGJ03_RS16365_lanthipeptide
Lanthipeptides: YH67_RS07965_lanthipeptide
21
E C T T T M S V V N H C L C C
35
E C T T T+S V+N H C L C C
3
E C T T T V S V I N H C L C C
17
36.2%
NZ_CP007597.1:
Lanthipeptides: DX03_RS09815_lanthipeptide
2
A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
A T++A L T+ + T++T G G C T T T M S V+N H C+C C
25
A T D A A L T A M A P T M V T G G T G N C T T T M S V I N H C M C C
58
29.3%
NZ_CP069396.1:
Lanthipeptides: JRI60_RS03735_lanthipeptide
1
A A T E S A L T S A S D T L I T
16
A A T E+A L T A S D L+T
12
A A T E N A L T D A S D A L V T
27
28.8%
NZ_CP069338.1:
Lanthipeptides: JQX13_RS07220_lanthipeptide
2
A T E S A L T S A S D T L I T G G G T E C T T T M S V V N H C L C C
35
A T E+A L T+++D L T G + C T ++ H C C
24
A T E A A L T N S T D A L Y T-G C S S C T G S L----H S Y C C
52
26.4%
NZ_CP093340.1:
Lanthipeptides: MNO14_RS04685_lanthipeptide
1
A A T E S A L T S A S D T L I T G G G T E C T T-T M S V V N H C
32
A A T E+A+T S L+ T+C++ T S+ H C
24
A A T E A A M T D K S F L L L----T Q C S S C T A S I P A H C
52
24.4%
NZ_CP029194.1 and 1 other:
NZ_CP059991.1 Lanthipeptides: H4W23_RS35675_lanthipeptide
Lanthipeptides: DEJ46_RS04155_lanthipeptide
1
A A T E S A L T S A S D T L I T G
17
A A E+A L T A++ L+T G
12
A A G E A A L T D A T E A L L T G
28
24.4%
NZ_JH941044.1:
Lanthipeptides: Y19_RS0126875_lanthipeptide
1
A A T E S A L T S A S D T L I T G
17
A A E+A L T A++ L T G
12
A A G E A A L T D A T E A L F T G
28
22.9%
NZ_CP089924.1:
Lanthipeptides: LVB77_RS02735_lanthipeptide
16
T G G G T E C T T T M S V V N H C
32
+G C T+ S V N H C
2
S G A S V N C T S G S S V S N H C
18
22.0%
NZ_CP010407.1 and 4 others:
NZ_CP010407.1 Lanthipeptides: SVTN_RS37515_lanthipeptide NZ_CP010407.1 Lanthipeptides: SVTN_RS37515_lanthipeptide NZ_CP010407.1 Lanthipeptides: SVTN_RS37515_lanthipeptide NZ_JACHJY010000017.1 Lanthipeptides: GGE06_RS39715_lanthipeptide
Lanthipeptides: SVTN_RS37515_lanthipeptide
1
A A T E S A L T S A S D T L I T G
17
A A E+A L T ++ L+T G
12
A A G E A A L T D G T E A L L T G
28
allorf_1178234_1178455
Leader:
MAPSMAPTVLERAACPLLTVSWCVRTRRSAGRLLPGFAGNRPEAVGSPRA
Core:
G P L A P W M A P S S P H G W V H G V S C P G
Core with dehydrations:
G P L A P W M A P Dha Dha P H G W V H G V Dha Cys P G

#### antiSMASH-DB 4.0 matches for allorf_1178234_1178455

88.5%
NZ_RHPZ01000014.1 and 1 other:
NZ_SOCO01000001.1 Lanthipeptides: allorf_1178234_1178455_lanthipeptide
Lanthipeptides: allorf_009576_009797_lanthipeptide
1
G P L A P W M A P S S P H G W V H G V S C P G
23
G P L A P W M A P S S P H G W V H G V S C P G
4
G P L A P W M A P S S P H G W V H G V S C P G
26
84.6%
NZ_CP046588.1 and 6 others:
NZ_CP056088.1 Lanthipeptides: allorf_1820746_1820967_lanthipeptide NZ_CP060259.1 Lanthipeptides: allorf_1747353_1747574_lanthipeptide NZ_CP104071.1 Lanthipeptides: allorf_1665125_1665346_lanthipeptide NZ_CP109812.1 Lanthipeptides: allorf_1794166_1794387_lanthipeptide NZ_JVPM01000038.1 Lanthipeptides: allorf_457583_457804_lanthipeptide NZ_OU943334.1 Lanthipeptides: allorf_1870884_1871105_lanthipeptide
Lanthipeptides: allorf_1742372_1742593_lanthipeptide
1
G P L A P W M A P S S P H G W V H G V S C P G
23
G P L A P M A P S S P H G W V H G V S C P G
4
G P L A P R M A P S S P H G W V H G V S C P G
26
80.8%
NZ_CP040435.1:
Lanthipeptides: allorf_1850191_1850412_lanthipeptide
1
G P L A P W M A P S S P H G W V H G V S C P G
23
G P L A P M A S S P H G W V H G V S C P G
4
G P L A P R M A S S S P H G W V H G V S C P G
26
with 7 more sequence matches
43.5%
NZ_CP101417.1:
Lanthipeptides: allorf_0369305_0369400_lanthipeptide
6
W M A P S S P H G W V H G V S C
21
W M P S H G G V S C
1
W M P P P S L H G R T C G V S C
16
30.8%
NZ_JABDRV010000001.1:
Lanthipeptides: allorf_0223350_0223580_lanthipeptide
8
A P S S P H G W V H G V S C P G
23
A P S S P H G W V H G V S C P G
37
A P S S P H G W V H G V S C P G
52
22.5%
NZ_PUPX01000001.1:
Lanthipeptides: allorf_1103640_1103849_lanthipeptide
6
W M A P S S P H G W V H G V S
20
W M S H G +H G V S
1
W M P L R S L H G R I H G V S
15
21.1%
NZ_JAEDVW010000007.1:
Lanthipeptides: allorf_22564_22716_lanthipeptide
7
M A P S S P H G W V
16
A P S S P H G V
15
K A P S S P H G E V
24
18.8%
NZ_MJGO01000037.1:
Lanthipeptides: BIU97_RS08315_lanthipeptide
3
L A P W M A P S S P H G
14
L+ +M P+S P+G
17
L S I Y M C P T S P N G
28
15.6%
NZ_CP023445.1:
Lanthipeptides: allorf_6233670_6233849_lanthipeptide
1
G P L A P W M A P S S P
12
G P A W P S P
23
G P A A G W R T P D S P
34
8.5%
NZ_CP035119.1:
Lanthipeptides: allorf_0912767_0912979_lanthipeptide
2
P L A P W M A P S S P H G W
15
P+A + +P+ P H +
42
P V A S F Y S P N R P H R F
55
allorf_1178421_1178636
Leader:
MDGFTACPALGDPTGSSRLQGS
Core:
A N A T N P T A T I G N P G K Q K S P R E A G F F G S C C G D W R S L G D S N P C F S L E R A T S
Core with dehydrations:
A N A Dhb N P Dhb A Dhb I G N P G K Q K Dha P R E A G F F G Dha Cys Cys G D W R Dha L G D Dha N P Cys F Dha L E R A Dhb Dha

#### antiSMASH-DB 4.0 matches for allorf_1178421_1178636

100.0%
NZ_SOCO01000001.1:
Lanthipeptides: allorf_1178421_1178636_lanthipeptide
1
A N A T N P T A T I G N P G K Q K S P R E A G F F G S C C G D W R S L G D S N P C F S L E R A T S
49
A N A T N P T A T I G N P G K Q K S P R E A G F F G S C C G D W R S L G D S N P C F S L E R A T S
1
A N A T N P T A T I G N P G K Q K S P R E A G F F G S C C G D W R S L G D S N P C F S L E R A T S
49
28.6%
NC_018485.1:
Lanthipeptides: allorf_3283390_3283524_lanthipeptide
32
W R S L G D S N P C F S L E R A T S
49
W R+ G D S N P C F E R A T S
14
W R A Q G D S N P C F R R E R A T S
31
24.5%
NZ_CP029354.1:
Lanthipeptides: allorf_108572_108748_lanthipeptide
3
A T N P T A T I G N P G K Q K S P R E A G F F G S C C G D W R S
34
A N P T I G R E F C +W S
24
A P N P I K T I G--------R E M T H F L C Q C N E W F S
47
with 2 more sequence matches
18.4%
NZ_CP046956.1:
Lanthipeptides: allorf_0712042_0712206_lanthipeptide
15
K Q K S P R E A G F F G S C C G D W
32
K Q K+ G F S C C W
11
K Q K T L-S C G I F S S C C S R W
27
16.3%
NZ_CP084541.1:
Lanthipeptides: LC193_RS09325_lanthipeptide
26
G S C C G D W R S L G D S N P C F
42
G S C C G W + + C F
4
G S C C G A W L P V P T A F T C F
20
allorf_1184819_1184995
Leader:
MPATGRPSLHLTSRPCTRPSVLRVPCIRVPAAAQLDAALNADAVCTGG
Core:
S T C H P V S L A A
Core with dehydrations:
Dha Dhb Cys H P V Dha L A A

#### antiSMASH-DB 4.0 matches for allorf_1184819_1184995

100.0%
NZ_CP011010.1 and 3 others:
NZ_DS999412.1 Lanthipeptides: allorf_3459447_3459623_lanthipeptide NZ_JAJNMF010000022.1 Lanthipeptides: allorf_02257_02373_lanthipeptide NZ_SOCO01000001.1 Lanthipeptides: allorf_1184819_1184995_lanthipeptide
Lanthipeptides: allorf_1772540_1772716_lanthipeptide
1
S T C H P V S L A A
10
S T C H P V S L A A
1
S T C H P V S L A A
10
45.0%
NZ_CP040436.1 and 11 others:
NZ_CP040438.1 Lanthipeptides: allorf_1797077_1797235_lanthipeptide NZ_CP040439.1 Lanthipeptides: allorf_1871764_1871973_lanthipeptide NZ_CP071784.1 Lanthipeptides: allorf_3040363_3040476_lanthipeptide NZ_CP104071.1 Lanthipeptides: allorf_1671217_1671393_lanthipeptide NZ_CP104287.1 Lanthipeptides: allorf_1684276_1684389_lanthipeptide NZ_CP104324.1 Lanthipeptides: allorf_1768103_1768216_lanthipeptide NZ_JACLBK010000002.1 Lanthipeptides: allorf_262851_262964_lanthipeptide NZ_JAEDWD010000009.1 Lanthipeptides: allorf_029791_029967_lanthipeptide NZ_JAFLWT010000006.1 Lanthipeptides: allorf_148855_148968_lanthipeptide NZ_JVUI01000059.1 Lanthipeptides: allorf_017163_017279_lanthipeptide NZ_KB907502.1 Lanthipeptides: allorf_016175_016288_lanthipeptide
Lanthipeptides: allorf_1728172_1728348_lanthipeptide
2
T C H P V S L A A
10
T C H P V S L A A
12
T C H P V S L A A
20
23.1%
NZ_AUFR01000008.1 and 1 other:
NZ_CP033719.1 Lanthipeptides: allorf_1493428_1493565_lanthipeptide
Lanthipeptides: allorf_101055_101192_lanthipeptide
2
T C H P V S L A A
10
T C+P V S A+
1
T C N P V S F A S
9
with 1 more sequence matches
12.2%
NZ_JACHJQ010000008.1:
Lanthipeptides: allorf_200802_200999_lanthipeptide
1
S T C H P V S L
8
S C H P V L
18
S A C H P V D L
25

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 27.95 out of 32.74
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.47 out of 28.19
Confidence: medium
Additional weak hits (7):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.42 out of 25.88
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.46 out of 32.74
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.79 out of 29.65
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.90 out of 20.01
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.61 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.18 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.00 out of 24.78
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

N440_RS05690 - Class II
  Cleavage pHMM score: -6.70
  RODEO score: 0
  Monoisotopic mass: 3231.5 Da
  Molecular weight: 3233.6 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3251.6 Da N = 1
    3269.6 Da N = 2
    3287.7 Da N = 3
    3305.7 Da N = 4
    3323.7 Da N = 5
    3341.7 Da N = 6
    3359.7 Da N = 7
    3377.8 Da N = 8
allorf_1178234_1178455 - Class II
  Cleavage pHMM score: -6.90
  RODEO score: 0
  Monoisotopic mass: 2272.1 Da
  Molecular weight: 2273.6 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2291.6 Da N = 1
    2309.6 Da N = 2
allorf_1178421_1178636 - Class II
  Cleavage pHMM score: -6.90
  RODEO score: 0
  Monoisotopic mass: 4922.3 Da
  Molecular weight: 4925.3 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4943.3 Da N = 1
    4961.4 Da N = 2
    4979.4 Da N = 3
    4997.4 Da N = 4
    5015.4 Da N = 5
    5033.4 Da N = 6
    5051.5 Da N = 7
allorf_1184819_1184995 - Class II
  Cleavage pHMM score: -6.70
  RODEO score: 0
  Monoisotopic mass: 930.5 Da
  Molecular weight: 931.1 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    949.1 Da N = 1
    967.1 Da N = 2

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
FuR variant 2 | Ferric Uptake Regulator
ZuR variant 1 | Zinc-responsive repressor

NZ_SOCO01000001.1 - Region 3 - 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: 1,724,308 - 1,746,863 nt. (total: 22,556 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
Hydrolases: hydrolase
N440_RS08105: 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
--- | --- | --- | --- | --- | ---
BGC0000576.3 |  | 0.52 | ribosomal | rubrivinodin | Rubrivivax gelatinosus IL144
BGC0000573.3 |  | 0.49 | ribosomal | caulonodin I, caulonodin II | Caulobacter sp. K31
BGC0000577.3 |  | 0.48 | ribosomal | sphingonodin II | Sphingobium japonicum UT26S
BGC0001786.3 |  | 0.46 | ribosomal | subterisin | Novosphingobium subterraneum
BGC0001779.5 |  | 0.44 | ribosomal | siamycin | Streptomyces nodosus
BGC0001645.3 |  | 0.44 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0002064.2 |  | 0.42 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0000519.4 |  | 0.41 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002015.4 |  | 0.41 | ribosomal | aborycin | Streptomyces sp. ZS0098

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000576.3 |  | 0.52 | ribosomal | rubrivinodin | Rubrivivax gelatinosus IL144
BGC0000573.3 |  | 0.49 | ribosomal | caulonodin I, caulonodin II | Caulobacter sp. K31
BGC0000577.3 |  | 0.48 | ribosomal | sphingonodin II | Sphingobium japonicum UT26S
BGC0001786.3 |  | 0.46 | ribosomal | subterisin | Novosphingobium subterraneum
BGC0001779.5 |  | 0.44 | ribosomal | siamycin | Streptomyces nodosus
BGC0001645.3 |  | 0.44 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0002064.2 |  | 0.42 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0000519.4 |  | 0.41 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002015.4 |  | 0.41 | ribosomal | aborycin | Streptomyces sp. ZS0098

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.

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 N440_RS20340

N440_RS20340
Leader:
MNELIELGVVAGEQNHEDQGELIELGSVVSETK
Full core:
A H N H G T L W D G V F P T T S P
Putative macrolactam:
A H N H G T L W D

#### antiSMASH-DB 4.0 matches for N440_RS20340

100.0%
NC_011071.1 and 41 others:
NZ_AP021867.1 Lassopeptides: GJU96_RS20605_lassopeptide NZ_CP011010.1 Lassopeptides: VN11_RS22530_lassopeptide NZ_CP011305.1 Lassopeptides: YH67_RS21020_lassopeptide NZ_CP015612.1 Lassopeptides: A7326_RS21600_lassopeptide NZ_CP027562.1 Lassopeptides: C6Y55_RS23185_lassopeptide NZ_CP029773.1 Lassopeptides: DM611_RS22725_lassopeptide NZ_CP031058.1 Lassopeptides: DUW70_RS11975_lassopeptide NZ_CP031167.1 Lassopeptides: MG068_RS21080_lassopeptide NZ_CP037858.1 Lassopeptides: EZ304_RS20935_lassopeptide NZ_CP040432.1 Lassopeptides: FEO95_RS22840_lassopeptide NZ_CP040438.1 Lassopeptides: FEO89_RS21625_lassopeptide NZ_CP040439.1 Lassopeptides: FEO88_RS23220_lassopeptide NZ_CP043578.1 Lassopeptides: F0Q13_RS11365_lassopeptide NZ_CP046588.1 Lassopeptides: GOC52_RS10870_lassopeptide NZ_CP047310.1 Lassopeptides: GS396_RS20180_lassopeptide NZ_CP060259.1 Lassopeptides: H7F32_RS11180_lassopeptide NZ_CP067993.1 Lassopeptides: JJL50_RS10815_lassopeptide NZ_CP077679.1 Lassopeptides: KS456_RS10490_lassopeptide NZ_CP080573.1 Lassopeptides: K1516_RS11235_lassopeptide NZ_CP090418.1 Lassopeptides: LYZ64_RS11980_lassopeptide NZ_CP096975.1 Lassopeptides: M1L61_RS12085_lassopeptide NZ_CP104169.1 Lassopeptides: NDR96_RS09175_lassopeptide NZ_CP106759.1 Lassopeptides: N8888_RS09665_lassopeptide NZ_CP120400.1 Lassopeptides: PVE91_RS09960_lassopeptide NZ_JABDRV010000002.1 Lassopeptides: HRL60_RS08285_lassopeptide NZ_JADCQA010000003.1 Lassopeptides: IMX13_RS03920_lassopeptide NZ_JAEDVS010000016.1 Lassopeptides: JAK50_RS09365_lassopeptide NZ_JAEDVW010000040.1 Lassopeptides: JAK53_RS10000_lassopeptide NZ_JAEDWA010000005.1 Lassopeptides: JAK63_RS01795_lassopeptide NZ_JAEDWK010000019.1 Lassopeptides: JAK51_RS11395_lassopeptide NZ_JAEDWU010000002.1 Lassopeptides: JAK37_RS06750_lassopeptide NZ_JAKJQX010000001.1 Lassopeptides: MT466_RS00850_lassopeptide NZ_JAQQGI010000001.1 Lassopeptides: PQS91_RS01155_lassopeptide NZ_JVHP01000037.1 Lassopeptides: ADI44_RS25485_lassopeptide NZ_JVPM01000019.1 Lassopeptides: ADH50_RS20965_lassopeptide NZ_JVUI01000038.1 Lassopeptides: ADG58_RS23065_lassopeptide NZ_OBEE01000001.1 Lassopeptides: CRO53_RS21815_lassopeptide NZ_OU943334.1 Lassopeptides: LNN95_RS11880_lassopeptide NZ_RHPZ01000001.1 Lassopeptides: EGJ03_RS21120_lassopeptide NZ_RHQE01000001.1 Lassopeptides: EGJ89_RS22430_lassopeptide NZ_SOCO01000001.1 Lassopeptides: N440_RS20340_lassopeptide
Lassopeptides: SMAL_RS21110_lassopeptide
1
A H N H G T L W D G V F P T T S P
17
A H N H G T L W D G V F P T T S P
1
A H N H G T L W D G V F P T T S P
17
88.2%
NZ_CP058243.1:
Lassopeptides: AD14011_RS10295_lassopeptide
1
A H N H G T L W D G V F P T T S P
17
A H H G T L W D G+F P T T S P
1
A H G H G T L W D G I F P T T S P
17
61.1%
NZ_CP049017.1:
Lassopeptides: G4Q83_RS07645_lassopeptide
1
A H N H G T L W D G V F-P T T S P
17
A H N H G T + F T T S P
1
A H N H G T F L E A S F I A T T S P
18
with 5 more sequence matches
29.2%
NZ_CP033362.1:
Lassopeptides: EB232_RS01185_lassopeptide
6
T L W D G V F P T T S P
17
T D G V F P +P
6
T A L D G V F P I H T P
17
22.2%
NZ_CP044492.1 and 1 other:
NZ_CP066294.2 Lanthipeptides: IGS65_RS08185_lanthipeptide
Lanthipeptides: FSA31_RS00605_lanthipeptide
8
W D G V F P T T S
16
W G V P T S
4
W Q G V V P T V S
12
22.2%
NZ_CP049223.1 and 4 others:
NZ_CP049225.1 Lanthipeptides: G6Z85_RS06555_lanthipeptide NZ_CP049228.1 Lanthipeptides: G6Z83_RS06555_lanthipeptide NZ_JAKWZB010000003.1 Lanthipeptides: MMO78_RS01405_lanthipeptide NZ_PNGO01000002.1 Lanthipeptides: CJ224_RS02730_lanthipeptide
Lanthipeptides: G6Z86_RS06445_lanthipeptide
8
W D G V F P T T S
16
W G V P T S
4
W Q G V L P T V S
12
22.2%
NZ_FNUH01000004.1 and 1 other:
NZ_FOGM01000011.1 Lanthipeptides: BMX20_RS07220_lanthipeptide
Lanthipeptides: BLU50_RS05815_lanthipeptide
7
L W D G V F P T T S
16
W G V P T S
3
F W Q G V V P T V S
12
13.9%
NZ_CP015883.1 and 1 other:
NZ_JAASJP010000011.1 Lanthipeptides: allorf_43013_43183_lanthipeptide
Lanthipeptides: allorf_0205278_0205448_lanthipeptide
3
N H G T L W D G V F
12
N+G +W+ V F
16
N N G C M W N T V F
25

#### 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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.83 out of 23.79
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.99 out of 27.55
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
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
Additional weak hits (12):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.07 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.01 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.96 out of 32.74
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.93 out of 32.74
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.23 out of 27.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.38 out of 29.65
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.40 out of 26.12
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.28 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 25.78 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 26.30 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 20.01 out of 33.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.60 out of 30.98
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.

N440_RS20340 - Class II
  Cleavage pHMM score: 10.60
  RODEO score: 23
  Monoisotopic mass: 1817.8 Da
  Molecular weight: 1818.9 Da
  Number of bridges: 0

RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (1724307...1746863)
N440_RS08110
  RRE type: Lasso_Fused_RRE
  Location: 5 - 76
  Score: 57.9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
GnfM | Regulator of nitrogen-fixation genes
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence

NZ_SOCO01000001.1 - Region 4 - NRP-metallophore,NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,027,200 - 2,075,567 nt. (total: 48,368 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
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 oxidoreductase
N440_RS09435: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

N440_RS09475: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

N440_RS09495: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

Hydrolases: hydrolase
N440_RS09450: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Isomerases: isomerase
N440_RS09460: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase
N440_RS09440: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

N440_RS09455: 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 | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002689.2 |  |  | 1.25 | NRPS | 2,3-dihydroxybenzoylserine | Stenotrophomonas maltophilia K279a
BGC0001132.4 |  |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  | 0.66 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  |  | 0.66 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000343.5 |  |  | 0.62 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001135.5 |  |  | 0.62 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002689.2 |  | 0.85 | NRPS | 2,3-dihydroxybenzoylserine | Stenotrophomonas maltophilia K279a
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.66 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.66 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000343.5 |  | 0.65 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

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:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 26.33 out of 26.33
Confidence: strong
Additional weak hits (22):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.87 out of 20.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.47 out of 30.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.63 out of 30.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.81 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.35 out of 30.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.98 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.08 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.16 out of 32.74
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.00 out of 20.01
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.59 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 26.18 out of 32.74
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.91 out of 30.97
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.81 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.77 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.02 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 28.48 out of 39.62
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.58 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.91 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.56 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.92 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 27.05 out of 39.62
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 26.35 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 4, location 2027199 - 2075567:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
N440_RS09440: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (457..845): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWELHFFTSGEHNLYGPTEAAVDVSY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

N440_RS09455: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (39..444): diOH-Bz
nrpys: diOH-Bz

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
  Small clusters prediction:
    Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
  Single AA prediction:
    dhb (diOH-Bz)

Stachelhaus prediction details:
  Stachelhaus sequence:
    SASLFPMSSPGGGLQVGGAQQVFGMAEGLVNYTR
  Nearest Stachelhaus code(s):
    diOH-Bz PMPAQGVVNK (94% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator

NZ_SOCO01000001.1 - Region 5 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,665,152 - 2,686,030 nt. (total: 20,879 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
N440_RS12365: 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
BGC0000634.3 |  | 0.32 | terpene | carotenoid | Brevundimonas sp. SD212
BGC0000640.3 |  | 0.32 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000630.3 |  | 0.31 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000641.3 |  | 0.30 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000639.3 |  | 0.30 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000642.3 |  | 0.30 | terpene | carotenoid | Enterobacteriaceae bacterium DC413

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
BGC0000634.3 |  | 0.32 | terpene | carotenoid | Brevundimonas sp. SD212
BGC0000640.3 |  | 0.32 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000630.3 |  | 0.31 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000641.3 |  | 0.30 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000639.3 |  | 0.30 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000642.3 |  | 0.30 | terpene | carotenoid | Enterobacteriaceae bacterium DC413

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:
N440_RS12365: PT_FPPS_like
Domain 1 (32 - 292): 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: 17.40 out of 19.26
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
Additional weak hits (7):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.45 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.46 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.63 out of 18.57
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: 14.54 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.11 out of 28.19
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
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein