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1.5

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

NZ_CP036170.1 ([Clostridium] scindens ATCC 35704)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | RRE-containing,lanthipeptide-class-ii,sactipeptide | 1,735,044 | 1,777,272 |
Region 2 | terpene-precursor | 3,028,544 | 3,049,428 |  |
Region 3 | NRPS | 3,181,636 | 3,228,991 |
Region 4 | ranthipeptide | 3,338,913 | 3,360,570 |
Region 5 | t3nrps-iterative | 3,575,745 | 3,619,770 |  |

NZ_CP036170.1 - Region 1 - RRE-containing,lanthipeptide-class-ii,sactipeptide
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: 1,735,044 - 1,777,272 nt. (total: 42,229 nt) Show pHMM detection rules used
RRE-containing: 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])
lanthipeptide-class-ii: cds(LANC_like and DUF4135)
sactipeptide: (subtilosin or thuricin or TIGR04404 or Subtilosin_A or skfc)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acetyltransferase
HDCHBGLK_RS08970: Chloramphenicol acetyltransferase

smcogs
  SMCOG1156: Chloramphenicol acetyltransferase

Lyases: cyclase
HDCHBGLK_RS09055: 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 | RRE-containing | lanthipeptide-class-ii | sactipeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001210.5 |  |  |  | 0.34 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000554.4 |  |  |  | 0.33 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000525.5 |  |  |  | 0.29 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000600.3 |  |  |  | 0.28 | ribosomal | thurincin H | Bacillus thuringiensis
BGC0000602.5 |  |  |  | 0.27 | ribosomal | subtilosin A | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000502.5 |  |  |  | 0.27 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0002700.2 |  |  |  | 0.26 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000517.4 |  |  |  | 0.25 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125
BGC0000500.5 |  |  |  | 0.25 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0000516.4 |  |  |  | 0.25 | ribosomal | geobacillin II | Geobacillus thermodenitrificans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0001210.5 |  | 0.48 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002116.3 |  | 0.48 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0000600.3 |  | 0.47 | ribosomal | thurincin H | Bacillus thuringiensis
BGC0000554.4 |  | 0.47 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002700.2 |  | 0.46 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000602.5 |  | 0.45 | ribosomal | subtilosin A | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000500.5 |  | 0.45 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0002663.2 |  | 0.44 | ribosomal | amyloliquecidin GF610 | Bacillus amyloliquefaciens UMAF6639
BGC0002144.3 |  | 0.44 | ribosomal | phazolicin | Rhizobium sp. Pop5

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 HDCHBGLK_RS09055

HDCHBGLK_RS18795
Leader:
MQEKQEHYLAGDLEVELEEFKSLAQNEEYA
Core:
E G F L S T T I K C G T F L T I Y C C
Core with dehydrations:
E G F L Dha Dhb Dhb I K Cys G Dhb F L Dhb I Y Cys Cys

#### antiSMASH-DB 4.0 matches for HDCHBGLK_RS18795

100.0%
NZ_CP036170.1:
Lanthipeptides: HDCHBGLK_RS18795_lanthipeptide
1
E G F L S T T I K C G T F L T I Y C C
19
E G F L S T T I K C G T F L T I Y C C
1
E G F L S T T I K C G T F L T I Y C C
19
47.4%
NZ_WWSD01000018.1:
Lanthipeptides: GT593_RS11715_lanthipeptide
7
T I K C G T F L T I Y C C
19
T I C L T I Y C C
3
T I G C A A L L T I Y C C
15
42.9%
NZ_CP061274.1 and 1 other:
NZ_JADKRR010000001.1 Lanthipeptides: ITJ40_RS10085_lanthipeptide
Lanthipeptides: H9X71_RS09850_lanthipeptide
1
E G F L S T-T I K C G T F L
14
G+L T T I+C G T F+
3
S G W L C T L T I E C G T F I
17
with 20 more sequence matches
Only the first 10 are displayed here.
38.5%
NZ_CP070036.1 and 3 others:
NZ_JADMPO010000043.1 Lanthipeptides: I2I27_RS16805_lanthipeptide NZ_JADNGF010000061.1 Lanthipeptides: I2E06_RS15650_lanthipeptide NZ_JAQMLK010000037.1 Lanthipeptides: PNW18_RS16660_lanthipeptide
Lanthipeptides: I6K72_RS03970_lanthipeptide
5
S T T I K C G T F L T I Y C C
19
S T+ C F L T I Y C C
12
S H T V G C S A F L T I Y C C
26
36.8%
NZ_CP036524.1:
Lanthipeptides: LAJLEIBI_RS18025_lanthipeptide
10
C G T F L T I Y C C
19
C T F T I C C
6
C T T F F T I I C C
15
36.8%
NZ_CP113781.1:
Lanthipeptides: GGADHKLB_RS14125_lanthipeptide
8
I K C G T F L T I Y C C
19
+ C F L T I C C
1
L N C T H F L T I L C C
12
36.8%
NZ_KE159748.1:
Lanthipeptides: C817_RS31970_lanthipeptide
7
T I K C G T F L T I Y C C
19
T C T L T+ C C
2
T K M C A T L L T L L C C
14
36.8%
NZ_KE159770.1:
Lanthipeptides: C817_RS32100_lanthipeptide
5
S T T I K C G T F L T I Y C C
19
++T+ C G T+ T+ C C
2
T S T L M C G T Y F T L I C C
16
33.3%
NZ_AUBN01000022.1:
Lanthipeptides: G448_RS16025_lanthipeptide
3
F L S T T I K C G T F L
14
F + T I+C G T F+
6
F C T L T I E C G T F I
17
31.6%
NZ_CP102267.1 and 2 others:
NZ_JADMOE010000006.1 Lanthipeptides: I2G55_RS05425_lanthipeptide NZ_LT635469.1 Lanthipeptides: BQ7352_RS14540_lanthipeptide
Lanthipeptides: NQ550_RS10225_lanthipeptide
11
G T F L T I Y C C
19
+F L T I C C
4
S S F L T I V C C
12
28.9%
NZ_CYZG01000001.1:
Lanthipeptides: ARA00_RS15445_lanthipeptide
5
S T T I K C G T F L T I Y C C
19
S T+ C G F L T I Y C C
24
S H T V G C G A F L T I Y C C
38
26.1%
NZ_AP014703.1 and 7 others:
NZ_CP031648.1 Lanthipeptides: DZG01_RS30720_lanthipeptide NZ_CP048607.1 Lanthipeptides: GZ982_RS30490_lanthipeptide NZ_CP048810.1 Lanthipeptides: GN234_RS22585_lanthipeptide NZ_CP072913.1 Lanthipeptides: J9870_RS25175_lanthipeptide NZ_CP097108.1 Lanthipeptides: M3M50_RS26395_lanthipeptide NZ_JAJQKS010000013.1 Lanthipeptides: LT249_RS28350_lanthipeptide NZ_QGDM01000020.1 Lanthipeptides: ATJ40_RS31250_lanthipeptide
Lanthipeptides: PBDP_RS25585_lanthipeptide
4
L S T T I K C G T F
13
L+T T++C T F
1
L A T T M E C N T F
10
25.0%
NZ_CP022413.2 and 20 others:
NZ_JAQDBP010000004.1 Lanthipeptides: PGY07_RS07085_lanthipeptide NZ_JAQDBP010000004.1 Lanthipeptides: PGY07_RS07085_lanthipeptide NZ_JAQEAL010000002.1 Lanthipeptides: PGU65_RS02165_lanthipeptide NZ_JAQESL010000010.1 Lanthipeptides: PG840_RS09145_lanthipeptide NZ_JAQEUC010000007.1 Lanthipeptides: PG788_RS06860_lanthipeptide NZ_JAQEYW010000009.1 Lanthipeptides: PG422_RS09400_lanthipeptide NZ_QRHW01000005.1 Lanthipeptides: DW641_RS05035_lanthipeptide NZ_QROS01000011.1 Lanthipeptides: DW021_RS13630_lanthipeptide NZ_QRPQ01000001.1 Lanthipeptides: DWZ74_RS02490_lanthipeptide NZ_QRZZ01000003.1 Lanthipeptides: DWV87_RS03165_lanthipeptide NZ_QRZZ01000003.1 Lanthipeptides: DWV87_RS03165_lanthipeptide NZ_QSJW01000012.1 Lanthipeptides: DW767_RS16350_lanthipeptide NZ_QSJW01000012.1 Lanthipeptides: DW767_RS16350_lanthipeptide NZ_QSKF01000004.1 Lanthipeptides: DW740_RS06305_lanthipeptide NZ_QSKF01000004.1 Lanthipeptides: DW740_RS06305_lanthipeptide NZ_QTZB01000014.1 Lanthipeptides: DXC15_RS13895_lanthipeptide NZ_QUCI01000011.1 Lanthipeptides: DW648_RS10830_lanthipeptide NZ_QUJJ01000004.1 Lanthipeptides: DW748_RS03630_lanthipeptide NZ_QUJJ01000004.1 Lanthipeptides: DW748_RS03630_lanthipeptide NZ_QUKU01000006.1 Lanthipeptides: DXC27_RS05470_lanthipeptide
Lanthipeptides: CGC63_RS01420_lanthipeptide
7
T I K C G T F L T I Y C C
19
+++C G+ T+ C C
8
S V E C G S I F T L A C C
20

#### MIBiG 4.0 matches for HDCHBGLK_RS18795

9.8%
BGC0002120.3 (NQE92413.1):
Lanthipeptide: nocathioamide A
1
E G F L S T T I K C G T F L T I Y C C
19
E C T ++ C C
31
E S S R P A A P A C H T L S S L P C C
49
allorf_1754275_1754343
Leader:
MIRIATIGGS
Core:
I L G V N R C V F F S S
Core with dehydrations:
I L G V N R Cys V F F Dha Dha

#### antiSMASH-DB 4.0 matches for allorf_1754275_1754343

100.0%
NZ_CP036170.1:
Lanthipeptides: allorf_1754275_1754343_lanthipeptide
1
I L G V N R C V F F S S
12
I L G V N R C V F F S S
1
I L G V N R C V F F S S
12
allorf_1760547_1760705
Leader:
MDIPAMDLFMGMLILGG
allorf_1772186_1772344
Leader:
MDIPAMDLFMGMLILGG
Shared core:
C H S S A T P F L S A S S E C L A T F S N L E M Q H S P I P V C N F R
Core with dehydrations:
Cys H Dha Dha A Dhb P F L Dha A Dha Dha E Cys L A Dhb F Dha N L E M Q H Dha P I P V Cys N F R

#### antiSMASH-DB 4.0 matches for allorf_1760547_1760705

100.0%
NZ_CP036170.1 and 1 other:
NZ_CP036170.1 Lanthipeptides: allorf_1760547_1760705_lanthipeptide
Lanthipeptides: allorf_1772186_1772344_lanthipeptide
1
C H S S A T P F L S A S S E C L A T F S N L E M Q H S P I P V C N F R
35
C H S S A T P F L S A S S E C L A T F S N L E M Q H S P I P V C N F R
1
C H S S A T P F L S A S S E C L A T F S N L E M Q H S P I P V C N F R
35
17.4%
NZ_QVFA01000004.1:
Lanthipeptides: DW882_RS14120_lanthipeptide
3
S S A T P F L S A S S E C L A T F S N L E M Q H S P I P V C N F R
35
++ T +S A S ++ S N+ + +P C +
13
A T T T A I I S A I S S V V S A I S N I S A A M T K V P A C K P K
45

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Sactipeptide 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.

#### Sactipeptide(s) for allorf_1765734_1765871

allorf_1765734_1765871
Leader:
MEGGANMKTPK
Core:
I V A R G W T C V G C A G C T A C W A S A T A I S H V S A A N I F G

#### antiSMASH-DB 4.0 matches for allorf_1765734_1765871

100.0%
NZ_CP036170.1 and 1 other:
NZ_JAQDJC010000039.1 Sactipeptides: allorf_5599_5736_sactipeptide
Sactipeptides: allorf_1765734_1765871_sactipeptide
1
I V A R G W T C V G C A G C T A C W A S A T A I S H V S A A N I F G
34
I V A R G W T C V G C A G C T A C W A S A T A I S H V S A A N I F G
1
I V A R G W T C V G C A G C T A C W A S A T A I S H V S A A N I F G
34
29.4%
NZ_BMVL01000013.1 and 1 other:
NZ_BMVL01000013.1 Lanthipeptides: allorf_062892_063122_lanthipeptide
Lanthipeptides: allorf_062892_063122_lanthipeptide
7
T C V G C A G C T A C W A S A T A I S H V S A A N
31
T G A G C T A S A I + ++
2
T A R G N A G C T T V G A S A G P I R S I R G S D
26
26.5%
NZ_CP070973.1:
Lanthipeptides: allorf_2137977_2138177_lanthipeptide
4
R G W T C V G C A G C T A C W A S A T A I S H
26
R G + G C T C A+A +H
7
R G P S P A G C R V A T G C R T P A S A A A H
29
with 2 more sequence matches
20.6%
NZ_JACHJI010000006.1:
Lanthipeptides: FHS37_RS18610_lanthipeptide
6
W T C V G C A G C
14
W T C V C G C
15
W T C V T C W G C
23
13.0%
NZ_JAIQZM010000029.1:
Lanthipeptides: allorf_48291_48491_lanthipeptide
3
A R G W T C V G C-A G C T A C W A
19
++G+ +G C G C C W
12
S K G F K V L G C D R G C R N C W K
29
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.70 out of 26.06
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.86 out of 21.55
Confidence: medium
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 26.59 out of 33.14
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.38 out of 28.19
Confidence: medium
Additional weak hits (4):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.86 out of 36.54
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.08 out of 28.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 24.18 out of 30.98
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 24.18 out of 30.98
Confidence: weak
Lanthipeptides
RREFinder
Sactipeptides
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.

HDCHBGLK_RS18795 - Class II
  Cleavage pHMM score: -6.60
  RODEO score: 0
  Monoisotopic mass: 2009.0 Da
  Molecular weight: 2010.4 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2028.4 Da N = 1
    2046.4 Da N = 2
allorf_1754275_1754343 - Class II
  Cleavage pHMM score: -6.10
  RODEO score: 0
  Monoisotopic mass: 1304.7 Da
  Molecular weight: 1305.5 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1323.6 Da N = 1
allorf_1760547_1760705 - Class II
  Cleavage pHMM score: -6.10
  RODEO score: 0
  Monoisotopic mass: 3648.7 Da
  Molecular weight: 3651.1 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3669.1 Da N = 1
    3687.1 Da N = 2
    3705.2 Da N = 3
    3723.2 Da N = 4
    3741.2 Da N = 5
    3759.2 Da N = 6
allorf_1772186_1772344 - Class II
  Cleavage pHMM score: -6.10
  RODEO score: 0
  Monoisotopic mass: 3648.7 Da
  Molecular weight: 3651.1 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3669.1 Da N = 1
    3687.1 Da N = 2
    3705.2 Da N = 3
    3723.2 Da N = 4
    3741.2 Da N = 5
    3759.2 Da N = 6

RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (1735043...1755409)
HDCHBGLK_RS08955
  RRE type: Other_Sactipeptide_rSAM_RRE
  Location: 2 - 118
  Score: 63.3
lanthipeptide-class-ii protocluster (1752996...1775635)
HDCHBGLK_RS09065
  RRE type: Thurincin_rSAM_RRE
  Location: 33 - 89
  Score: 48.0
sactipeptide protocluster (1755949...1777272)
HDCHBGLK_RS09065
  RRE type: Thurincin_rSAM_RRE
  Location: 33 - 89
  Score: 48.0

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its RODEO score and predicted core sequence.

allorf_1765734_1765871
  Putative sactipeptide
  RODEO score: 26.0
  Core sequence, approximate: IVARGWTCVGCAGCTACWASATAISHVSAANIFG

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
MogR | Repressor of flagellar motility genes
ZuR variant 1 | Zinc-responsive repressor
ZuR variant 2 | Zinc-responsive repressor

NZ_CP036170.1 - Region 2 - 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: 3,028,544 - 3,049,428 nt. (total: 20,885 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: glycosyltransferase
HDCHBGLK_RS15600: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: back translocase
HDCHBGLK_RS15665: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

Ligases: synthase synthetase
HDCHBGLK_RS15635: 1-deoxy-D-xylulose-5-phosphate synthase

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

HDCHBGLK_RS15640: 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
--- | --- | --- | --- | --- | ---
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
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
BGC0001456.3 |  | 0.38 | terpene | isorenieratene | Streptomyces argillaceus
BGC0001605.3 |  | 0.37 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000665.5 |  | 0.37 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000633.3 |  | 0.36 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.36 | terpene | isorenieratene | Streptomyces collinus Tu 365

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
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
BGC0001456.3 |  | 0.38 | terpene | isorenieratene | Streptomyces argillaceus
BGC0001605.3 |  | 0.37 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000665.5 |  | 0.37 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000633.3 |  | 0.36 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.36 | terpene | isorenieratene | Streptomyces collinus Tu 365

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP

Genes with terpene domains:
HDCHBGLK_RS15640: PT_FPPS_like
Domain 1 (30 - 293): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:
  IPP, DMAPP → 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:
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.67 out of 28.19
Confidence: medium
Additional weak hits (2):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.98 out of 28.14
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.53 out of 33.73
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ZuR variant 1 | Zinc-responsive repressor

NZ_CP036170.1 - Region 3 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,181,636 - 3,228,991 nt. (total: 47,356 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
HDCHBGLK_RS16415: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Isomerases: mutase
HDCHBGLK_RS16450: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: ligase
HDCHBGLK_RS16465: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

HDCHBGLK_RS16480: 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
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.67 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
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
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.67 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
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
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.61 out of 27.78
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.14 out of 24.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.83 out of 28.19
Confidence: medium
Additional weak hits (6):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.28 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.36 out of 30.25
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.95 out of 39.62
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.32 out of 33.14
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.36 out of 27.18
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.58 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 6, location 3181635 - 3228991:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu - X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
HDCHBGLK_RS16465: X
AMP-binding (34..444): X
nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDLV--MIMENKHLPCGGAYQGYGITECSPLIGS
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

HDCHBGLK_RS16480: Leu - X
Search NORINE for peptide: strict or relaxed
AMP-binding (474..859): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAICFDAFLLEIALICGGEYNQYGPSEATVAVSH
  Nearest Stachelhaus code(s):
    Trp DALAVGQVVK (47% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1496..1882): 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:
    LHLSFDVFTTELQLILLGEFNIYGPTETSVHNCQ
  Nearest Stachelhaus code(s):
    Trp DVSQIGAVCK (53% 8Å match)
    Ser DVWSIAMVHK (44% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
LexA variant 2 | Repressor of DNA damage response
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_CP036170.1 - Region 4 - ranthipeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,338,913 - 3,360,570 nt. (total: 21,658 nt) Show pHMM detection rules used
ranthipeptide: (TIGR03973 or SCIFF or (cds(PF04055 and (TIGR04085 or SPASM)) 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]) and not (TIGR01716 or subtilosin or TIGR02111 or TIGR03966 or TIGR04103 or (YcaO or TIGR03604))))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
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
HDCHBGLK_RS17145: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

HDCHBGLK_RS17225: HAD-superfamily hydrolase, subfamily IA, variant

smcogs
  SMCOG1115: HAD-superfamily hydrolase, subfamily IA, variant

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 | ranthipeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002306.2 |  | 0.47 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0002436.2 |  | 0.34 | other (other) | coformycin | Streptomyces citricolor
BGC0000678.5 |  | 0.34 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001995.3 |  | 0.34 | terpene | heptelidic acid | Aspergillus oryzae RIB40
BGC0001387.5 |  | 0.33 | other (other) | nucleocidin | Streptomyces calvus
BGC0000604.4 |  | 0.31 | ribosomal | GE2270A | Nonomuraea sp. WU8817
BGC0001155.5 |  | 0.30 | ribosomal | GE2270 | Planobispora rosea
BGC0001607.5 |  | 0.30 | other (other) | gilvusmycin | Streptomyces sp. NRRL B-1347
BGC0002713.2 |  | 0.30 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0001591.4 |  | 0.29 | other (other) | fatty acid enol ester, N-tetradecanoyl tyrosine | uncultured bacterium CSLC2

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002306.2 |  | 0.47 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0002436.2 |  | 0.34 | other (other) | coformycin | Streptomyces citricolor
BGC0000678.5 |  | 0.34 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001995.3 |  | 0.34 | terpene | heptelidic acid | Aspergillus oryzae RIB40
BGC0001387.5 |  | 0.33 | other (other) | nucleocidin | Streptomyces calvus
BGC0000604.4 |  | 0.31 | ribosomal | GE2270A | Nonomuraea sp. WU8817
BGC0001155.5 |  | 0.30 | ribosomal | GE2270 | Planobispora rosea
BGC0001607.5 |  | 0.30 | other (other) | gilvusmycin | Streptomyces sp. NRRL B-1347
BGC0002713.2 |  | 0.30 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0001591.4 |  | 0.29 | other (other) | fatty acid enol ester, N-tetradecanoyl tyrosine | uncultured bacterium CSLC2

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:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.79 out of 27.78
Confidence: medium
Additional weak hits (1):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 25.59 out of 36.54
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

ranthipeptide protocluster (3338912...3360570)
HDCHBGLK_RS17170
  RRE type: Ranthipeptide_rSAM_RRE
  Location: 0 - 111
  Score: 99.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP036170.1 - Region 5 - 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: 3,575,745 - 3,619,770 nt. (total: 44,026 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)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS 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
Lyases: decarboxylase
HDCHBGLK_RS18415: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase
HDCHBGLK_RS18420: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001240.4 |  | 0.59 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001166.5 |  | 0.59 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001250.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001641.4 |  | 0.58 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.58 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002164.2 |  | 0.58 | NRPS | peramine | Epichloe festucae
BGC0001268.4 |  | 0.54 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002518.3 |  | 0.45 | NRPS | syringafactin A, syringafactin C | Pseudomonas sp. SZ57
BGC0002171.2 |  | 0.45 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger ATCC 1015

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001240.4 |  | 0.59 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001166.5 |  | 0.59 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001250.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001641.4 |  | 0.58 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.58 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002164.2 |  | 0.58 | NRPS | peramine | Epichloe festucae
BGC0001268.4 |  | 0.54 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002518.3 |  | 0.45 | NRPS | syringafactin A, syringafactin C | Pseudomonas sp. SZ57
BGC0002171.2 |  | 0.45 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger ATCC 1015

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 24.43 out of 24.78
Confidence: strong
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.72 out of 24.78
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 21.07 out of 25.31
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.42 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.03 out of 26.06
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.55 out of 21.55
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.51 out of 27.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.26 out of 28.19
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.97 out of 32.93
Confidence: medium
Additional weak hits (5):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.11 out of 28.14
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.23 out of 33.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.33 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.86 out of 30.25
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 24.18 out of 30.98
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).
HDCHBGLK_RS18420: X
AMP-binding (9..413): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FDFAFDVSVKDSWAIFSGEANVYGPTEITCNCTY
  Nearest Stachelhaus code(s):
    Ser DVNEISVIEK (35% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
ArcA | Repressor of carbon oxidation
CatR | H2O2-responsive repressor
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
LexA variant 2 | Repressor of DNA damage response
LexA variant 3 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor