Select genomic region:
Overview
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1.20

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

NZ_CP025957.1 (Paenibacillus polymyxa)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | NRPS | 67,680 | 131,409 | High | fusaricidin B | NRPS:Type I+PKS
Region 2 | RRE-containing | 351,637 | 373,091 |
Region 3 | transAT-PKS,NRPS | 1,032,222 | 1,109,603 |
Region 4 | proteusin | 1,221,960 | 1,242,196 |
Region 5 | NRPS,transAT-PKS | 1,275,474 | 1,375,450 |
Region 6 | lassopeptide | 1,410,683 | 1,434,750 |
Region 7 | NRPS | 1,490,947 | 1,552,036 | Low | marthiapeptide A | NRPS:Type I
Region 8 | lanthipeptide-class-i | 1,740,631 | 1,767,640 | High | paenilan | ribosomal:RiPP
Region 9 | NRPS-like,cyclic-lactone-autoinducer | 2,041,678 | 2,103,902 |
Region 10 | NRPS | 2,449,151 | 2,542,888 | High | tridecaptin | NRPS:Type I
Region 11 | NRPS | 2,699,827 | 2,782,052 |  |
Region 12 | NRPS,T1PKS | 2,787,734 | 2,861,701 | Low | brevicidine | NRPS:Type I
Region 13 | betalactone | 2,987,148 | 3,018,081 | High | bovienimide A | NRPS:Type I
Region 14 | cyclic-lactone-autoinducer | 3,059,109 | 3,079,657 |
Region 15 | terpene-precursor | 3,406,246 | 3,427,169 |  |
Region 16 | transAT-PKS,NRPS,T3PKS,PKS-like | 3,584,674 | 3,686,609 | Low | aurantinin B/aurantinin C/aurantinin D | PKS
Region 17 | terpene-precursor | 3,969,948 | 3,992,335 |
Region 18 | NRPS | 4,910,605 | 4,990,177 | High | polymyxin | NRPS:Type I
Region 19 | lanthipeptide-class-i | 5,081,333 | 5,105,881 | Low | S-layer glycan | saccharide
Region 20 | lanthipeptide-class-i | 5,420,805 | 5,447,095 | High | paenicidin A | ribosomal:RiPP:Lanthipeptide

NZ_CP025957.1 - Region 1 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 67,680 - 131,409 nt. (total: 63,730 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 oxidase synthase
C1A50_RS00385: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

C1A50_RS00395: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

C1A50_RS00400: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

C1A50_RS00490: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

Transferases: acetyltransferase
C1A50_RS00485: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: synthase
C1A50_RS00490: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

Isomerases: isomerase
C1A50_RS00325: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
C1A50_RS00320: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

C1A50_RS00330: carbamoyl phosphate synthase small subunit

smcogs
  SMCOG1249: carbamoyl phosphate synthase small subunit

C1A50_RS00390: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C1A50_RS00405: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C1A50_RS00415: 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
--- | --- | --- | --- | --- | ---
BGC0001152.5 |  | 0.88 | NRPS, PKS | fusaricidin B | Paenibacillus polymyxa
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.71 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.70 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001152.5 |  | 0.88 | NRPS, PKS | fusaricidin B | Paenibacillus polymyxa
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.71 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.70 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
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.
Location:
Identifier
Identity
Coverage
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: 21.28 out of 26.33
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.47 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.99 out of 26.06
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.60 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
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.14 out of 18.16
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 24.03 out of 27.78
Confidence: strong
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.67 out of 21.55
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.06 out of 23.79
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.04 out of 32.93
Confidence: medium
Additional weak hits (13):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.46 out of 36.54
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.15 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.53 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.45 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.60 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.09 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.46 out of 26.06
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.64 out of 30.97
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.79 out of 25.88
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.71 out of 33.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.23 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.07 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.72 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 1, location 67679 - 131409:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - D-Val - X - D-Thr - D-Asn - 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).
C1A50_RS00390: X
AMP-binding (15..386): 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:
    NHSVHFYGISLSDACVGGSLNGYGLSELGNVTLG
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

C1A50_RS00415: Thr - Val - X - Thr - Asn - X
Search NORINE for peptide: strict or relaxed
AMP-binding (465..864): Thr
nrpys: Thr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNDHFDFSVWEGNQIFGGEINMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1505..1899): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LETGFDASTFEGWLLVGGDINGYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3016..3406): X
nrpys: Ile, Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LVYAFDASVSETTLLTAGSFNGYGPTEDSVCTTM
  Nearest Stachelhaus code(s):
    Ile or Tyr DASTLAGVCK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4047..4446): Thr
nrpys: Thr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNDHFDFSVWEGNQIFGGEINMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5563..5958): Asn
nrpys: Asn

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

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

AMP-binding (7078..7478): X
nrpys: Ala, D-Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TQLTFDFSVPECNLFACGEENIYGPTEAAVYATR
  Nearest Stachelhaus code(s):
    Ala or D-Ala DFPNFCIVYK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AbrC3 | Antibiotic production activator
ArcA | Repressor of carbon oxidation
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
IolR | Regulator of the inositol catabolism
LexA variant 3 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes

NZ_CP025957.1 - Region 2 - RRE-containing
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: 351,637 - 373,091 nt. (total: 21,455 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])

#### 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: protease
C1A50_RS01570: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

Translocases: transporter
C1A50_RS01520: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002306.2 |  | 0.57 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000551.5 |  | 0.41 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0001638.4 |  | 0.41 | ribosomal | klebsazolicin | Klebsiella pneumoniae subsp. ozaenae
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0002698.2 |  | 0.40 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000802.5 |  | 0.39 | saccharide | succinoglycan | Sinorhizobium meliloti
BGC0000521.3 |  | 0.39 | ribosomal | lacticin 481 | Lactococcus lactis subsp. lactis
BGC0002323.2 |  | 0.39 | ribosomal | nisin J | Staphylococcus capitis
BGC0000539.5 |  | 0.39 | ribosomal | nukacin ISK-1 | Staphylococcus warneri

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002306.2 |  | 0.57 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000551.5 |  | 0.41 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0001638.4 |  | 0.41 | ribosomal | klebsazolicin | Klebsiella pneumoniae subsp. ozaenae
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0002698.2 |  | 0.40 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000802.5 |  | 0.39 | saccharide | succinoglycan | Sinorhizobium meliloti
BGC0000521.3 |  | 0.39 | ribosomal | lacticin 481 | Lactococcus lactis subsp. lactis
BGC0002323.2 |  | 0.39 | ribosomal | nisin J | Staphylococcus capitis
BGC0000539.5 |  | 0.39 | ribosomal | nukacin ISK-1 | Staphylococcus warneri

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:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.04 out of 27.04
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.72 out of 26.06
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.52 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.85 out of 28.19
Confidence: medium
Additional weak hits (4):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.71 out of 26.85
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.42 out of 28.14
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.68 out of 26.12
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (351636...373091)
C1A50_RS01550
  RRE type: Other_Sactipeptide_rSAM_RRE
  Location: 0 - 126
  Score: 48.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
MogR | Repressor of flagellar motility genes
ZuR variant 1 | Zinc-responsive repressor

NZ_CP025957.1 - Region 3 - NRPS,transAT-PKS
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: 1,032,222 - 1,109,603 nt. (total: 77,382 nt) Show pHMM detection rules used
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
C1A50_RS04650: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Transferases: acylase
C1A50_RS04730: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase
C1A50_RS04720: hydrolase

smcogs
  SMCOG1179: hydrolase

Ligases: ligase synthase
C1A50_RS04735: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C1A50_RS04740: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C1A50_RS04745: 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 | transAT-PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  | 0.81 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  | 0.77 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001133.4 |  |  | 0.73 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001166.5 |  |  | 0.72 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001128.4 |  |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  | 0.69 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001133.4 |  | 0.71 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000402.4 |  | 0.69 | NRPS | paenilarvin A, paenilarvin B, paenilarvin C | Paenibacillus larvae subsp. larvae DSM 25430
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | 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: 18.31 out of 18.57
Confidence: strong
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.80 out of 25.88
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.73 out of 27.78
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.87 out of 21.55
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.86 out of 21.84
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.40 out of 26.06
Confidence: medium
Additional weak hits (11):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 25.21 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.06 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.93 out of 26.06
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 20.52 out of 30.11
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.53 out of 33.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.19 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.16 out of 31.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.65 out of 31.73
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.88 out of 24.78
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.28 out of 39.62
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.06 out of 25.88
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 3, location 1032221 - 1109603:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid - mal - Tyr - D-X) + (Ser - D-Ser) + (Ser - D-Ile - 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).
C1A50_RS04730: mal
PKS_AT (6..293): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 66.7%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 86.9
  inactive: 36.9
  Methoxymalonyl-CoA: 25.0
  Propionyl-CoA: 13.5
  Methylmalonyl-CoA: 12.7
  Acetyl-CoA: 10.4
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

C1A50_RS04735: fatty_acid - Tyr - X
Search NORINE for peptide: strict or relaxed
CAL_domain (36..482): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 310.8
  NH2: 17.2
  shikimic_acid: 0.0
  Acetyl-CoA: 0.0
  AHBA: 0.0

AMP-binding (3153..3549): Tyr
nrpys: Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TWRLFDAFVGATVCTLGGEFNEYGPTENSVVTTM
  Nearest Stachelhaus code(s):
    Tyr DALTTGEVVK (71% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (4193..4596): X
nrpys: Asp, Asn, Glu, Gln, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTYDSAVWQWDFILGGETNLYGPTEASIGCVA
  Nearest Stachelhaus code(s):
    Glu DVWHIGSIGK (65% 8Å match)
    Orn DVWNIGLIHK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

C1A50_RS04740: Ser - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (469..873): 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:
    RWMTFDVSVWEWHFFASGEHNLYGPTEATVDATW
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1523..1934): 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:
    RWMTFDVSLWESHFFASGEHNLYGPTEATVEVAY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

C1A50_RS04745: Ser - Ile - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (470..881): 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:
    RWMTFDVSLWESHFFASGEHNLYGPTEATVEVAY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1533..1939): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNSSFDGSVFDGFILFGGELHMYGPTESTVFATC
  Nearest Stachelhaus code(s):
    Ile DGFFLGVVFK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (3061..3470): 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:
    RWMTFDVSLWESHFFASGEHNLYGPTEATVEVAY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
MexT | Global virulence regulator
MogR | Repressor of flagellar motility genes
PsrA | Oleic acid responsive regulator
ToxT | Regulator of MSHA biosynthesis

NZ_CP025957.1 - Region 4 - proteusin
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: 1,221,960 - 1,242,196 nt. (total: 20,237 nt) Show pHMM detection rules used
proteusin: (PoyD or TIGR03793)

#### 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
Transferases: acyltransferase
C1A50_RS05350: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

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 | proteusin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000889.5 |  | 0.32 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.31 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001594.3 |  | 0.29 | other (other) | fischerindole L | Fischerella muscicola UTEX 1829
BGC0001126.4 |  | 0.28 | other (other), terpene | 12-epi-hapalindole J isonitrile, ambiguine A isonitrile, ambiguine B isonitrile, ambiguine C isonitrile, ambiguine D isonitrile, ambiguine E isonitrile, ambiguine K isonitrile, ambiguine L isonitrile, ambiguine I isonitrile, ambiguine J isonitrile | Fischerella ambigua UTEX 1903
BGC0001501.5 |  | 0.28 | other (other) | ambiguine P | Fischerella sp. TAU
BGC0001612.3 |  | 0.28 | other (other) | ambiguine H isonitrile | Fischerella ambigua UTEX 1903
BGC0002443.3 |  | 0.27 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0002713.2 |  | 0.26 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0000668.5 |  | 0.25 | other (other), terpene | 12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole | Hapalosiphon welwitschii UTEX B 1830
BGC0002637.3 |  | 0.24 | NRPS | rimomycin A, rimomycin B, rimomycin C | Streptomyces sp. WAC 06783

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000889.5 |  | 0.32 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.31 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001594.3 |  | 0.29 | other (other) | fischerindole L | Fischerella muscicola UTEX 1829
BGC0001126.4 |  | 0.28 | other (other), terpene | 12-epi-hapalindole J isonitrile, ambiguine A isonitrile, ambiguine B isonitrile, ambiguine C isonitrile, ambiguine D isonitrile, ambiguine E isonitrile, ambiguine K isonitrile, ambiguine L isonitrile, ambiguine I isonitrile, ambiguine J isonitrile | Fischerella ambigua UTEX 1903
BGC0001501.5 |  | 0.28 | other (other) | ambiguine P | Fischerella sp. TAU
BGC0001612.3 |  | 0.28 | other (other) | ambiguine H isonitrile | Fischerella ambigua UTEX 1903
BGC0002443.3 |  | 0.27 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0002713.2 |  | 0.26 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0000668.5 |  | 0.25 | other (other), terpene | 12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole | Hapalosiphon welwitschii UTEX B 1830
BGC0002637.3 |  | 0.24 | NRPS | rimomycin A, rimomycin B, rimomycin C | Streptomyces sp. WAC 06783

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46
Confidence: strong
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.33 out of 27.55
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.98 out of 20.97
Confidence: strong
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: 18.04 out of 18.57
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.16 out of 20.97
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.68 out of 28.19
Confidence: medium
Additional weak hits (3):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.60 out of 32.74
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 20.23 out of 30.11
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
GnfM | Regulator of nitrogen-fixation genes
RpoN | Regulator of nitrogen assimilation and virulence
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_CP025957.1 - Region 5 - NRPS,transAT-PKS
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: 1,275,474 - 1,375,450 nt. (total: 99,977 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
C1A50_RS05740: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

C1A50_RS05750: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

Transferases: acylase acyltransferase aminotransferase
C1A50_RS05680: aminotransferase

smcogs
  SMCOG1019: aminotransferase

C1A50_RS05700: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

C1A50_RS05705: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase
C1A50_RS05645: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase synthase
C1A50_RS05640: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C1A50_RS05660: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

C1A50_RS05670: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C1A50_RS05675: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C1A50_RS05685: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C1A50_RS05690: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C1A50_RS05710: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C1A50_RS05715: 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 | transAT-PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002286.3 |  |  | 0.90 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.90 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  | 0.90 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  | 0.88 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  | 0.88 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.87 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002075.3 |  |  | 0.84 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001825.4 |  |  | 0.83 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  |  | 0.83 | NRPS | AM-toxin | Alternaria alternata
BGC0001249.5 |  |  | 0.82 | NRPS | dimethylcoprogen | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001825.4 |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.31 out of 26.06
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.44 out of 30.25
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.55 out of 19.26
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 24.59 out of 24.78
Confidence: strong
Additional weak hits (10):
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.67 out of 29.72
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.85 out of 39.62
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.34 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.21 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.98 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.45 out of 26.06
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 24.27 out of 32.74
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.71 out of 33.73
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.68 out of 24.78
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.36 out of 27.18
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 5, location 1275473 - 1375450:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Asn) + (Gln - Me-ohmal) + (mal) + (X) + (ohmal) + (X - Gly) + (ccmal - Lys - X) + (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).
C1A50_RS05640: Asn
Search NORINE for peptide: strict or relaxed
AMP-binding (457..852): Asn
nrpys: Asn

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

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

C1A50_RS05670: Gln
Search NORINE for peptide: strict or relaxed
AMP-binding (269..665): Gln
nrpys: Gln

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    QGLAFDPSVQQLNTIMAGEFNIYGPTEAAINTTL
  Nearest Stachelhaus code(s):
    Gln DAQNIAVINK (53% 8Å match)
    bOH-Gln DAQNIASINK (50% 8Å match)
  Stachelhaus code match:
    80% (moderate)

C1A50_RS05685: X
AMP-binding (39..457): X
nrpys: Asp, Asn, Glu, Gln, Aad

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 with H-bond donor (Asp, Asn, Glu, Gln, Aad)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    TWLTFTDSVWEWQFLNGGEANIYGMTESAIYATC
  Nearest Stachelhaus code(s):
    Ile DFWNIGIIYK (53% 8Å match)
  Stachelhaus code match:
    60% (weak)

C1A50_RS05700: X - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (472..903): X
nrpys: Asp, Asn, Glu, Gln, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TWLTFTDSVWEWQFFNGGEANLYGMTESAIYATQ
  Nearest Stachelhaus code(s):
    Gln DAWQFGLIDK (65% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1559..1953): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGITFDIFVLELQMMVGGEFNMYGPTETTVWSTV
  Nearest Stachelhaus code(s):
    Gly DILQMGMVWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

C1A50_RS05705: mal
PKS_AT (6..293): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 62.5%
  inactive: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 125.2
  Methoxymalonyl-CoA: 46.3
  inactive: 44.9
  Methylmalonyl-CoA: 37.9
  Ethylmalonyl-CoA: 17.3
  fatty_acid: 13.9
  Isobutyryl-CoA: 13.2
  Propionyl-CoA: 11.8
  Acetyl-CoA: 7.9
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

C1A50_RS05710: Lys - X
Search NORINE for peptide: strict or relaxed
AMP-binding (2062..2459): Lys
nrpys: Lys

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:
    YAFAFDASVEEPSAISGGDYNTYGPTEATVCATY
  Nearest Stachelhaus code(s):
    Lys DAESIGSVCK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (3046..3447): 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:
    RWLAFDGSIVESFFMSGGELNLYGPTEASVFATA
  Nearest Stachelhaus code(s):
    Val DGYFLGVVFK (59% 8Å match)
    Ile DGFFLGVVFK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

C1A50_RS05715: X
AMP-binding (459..851): X
nrpys: Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LEPCFDVSVYEGWFMTGGDVNAYGPSENTIFTSF
  Nearest Stachelhaus code(s):
    Ala DVFWTGGIFK (65% 8Å match)
    norCMA DPYWWGATFK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
ColR | Phenol-responsive regulator
LexA variant 2 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes

NZ_CP025957.1 - Region 6 - 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: 1,410,683 - 1,434,750 nt. (total: 24,068 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
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
C1A50_RS05995: 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
--- | --- | --- | --- | --- | ---
BGC0001356.4 |  | 0.67 | ribosomal | paeninodin | Paenibacillus dendritiformis C454
BGC0002150.2 |  | 0.55 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0002151.2 |  | 0.55 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0001552.3 |  | 0.53 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001634.3 |  | 0.53 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001549.3 |  | 0.52 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001164.3 |  | 0.52 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000575.5 |  | 0.52 | ribosomal | lariatin | Rhodococcus jostii
BGC0002298.2 |  | 0.51 | ribosomal | lassomycin-like peptide | Sanguibacter keddieii DSM 10542
BGC0001645.3 |  | 0.51 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001356.4 |  | 0.67 | ribosomal | paeninodin | Paenibacillus dendritiformis C454
BGC0002150.2 |  | 0.55 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0002151.2 |  | 0.55 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0001552.3 |  | 0.53 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001634.3 |  | 0.53 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001549.3 |  | 0.52 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001164.3 |  | 0.52 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000575.5 |  | 0.52 | ribosomal | lariatin | Rhodococcus jostii
BGC0002298.2 |  | 0.51 | ribosomal | lassomycin-like peptide | Sanguibacter keddieii DSM 10542
BGC0001645.3 |  | 0.51 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118

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.
Lassopeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.30 out of 26.06
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.35 out of 27.55
Confidence: medium
Additional weak hits (5):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.86 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.61 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.22 out of 28.14
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.03 out of 30.22
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.71 out of 25.75
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.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (1410682...1434750)
C1A50_RS06005
  RRE type: Stand_Alone_Lasso_RRE
  Location: 16 - 94
  Score: 84.3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
GnfM | Regulator of nitrogen-fixation genes
MogR | Repressor of flagellar motility genes

NZ_CP025957.1 - Region 7 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,490,947 - 1,552,036 nt. (total: 61,090 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
Hydrolases: hydrolase
C1A50_RS06355: hydrolase

smcogs
  SMCOG1179: hydrolase

Ligases: ligase
C1A50_RS06460: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C1A50_RS06465: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

C1A50_RS06470: 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
--- | --- | --- | --- | --- | ---
BGC0000426.5 |  | 0.73 | NRPS | sevadicin | Paenibacillus larvae
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.68 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  | 0.68 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001133.4 |  | 0.67 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000426.5 |  | 0.73 | NRPS | sevadicin | Paenibacillus larvae
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.68 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  | 0.68 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001133.4 |  | 0.67 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | 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.
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: 21.93 out of 26.33
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.28 out of 26.06
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.82 out of 21.84
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.16 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.49 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.26 out of 28.19
Confidence: medium
Additional weak hits (7):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.92 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 24.19 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.60 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.44 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.11 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 24.74 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 7, location 1490946 - 1552036:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Phe) + (Ile) + (D-Ser - Cys - Cys - Cys)

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).
C1A50_RS06460: Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (6..396): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LIWAFDASVWEMTLITAGSVNAYGPTEASICASL
  Nearest Stachelhaus code(s):
    Phe DAWTIAAICK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

C1A50_RS06465: Ile
Search NORINE for peptide: strict or relaxed
AMP-binding (474..877): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VGSSFDGSVFDGFVLFGGEIHMYGPTESTVYAMY
  Nearest Stachelhaus code(s):
    Ile DGFFLGVVYK (85% 8Å match)
    Leu DGFFLGVVYK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

C1A50_RS06470: Ser - Cys - Cys - Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (469..875): 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:
    N/A
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

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

AMP-binding (1977..2358): Cys
nrpys: Cys

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:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Small clusters prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Single AA prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDISFDLSVYDGNSLLSGDISLGGATEASIWSIY
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3009..3390): Cys
nrpys: Cys

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:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Small clusters prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Single AA prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDISFDLSVYDGNSLLSGDISLGGATEASIWSIY
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4047..4446): Cys
nrpys: Cys

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:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Small clusters prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Single AA prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDISFDLSVYDGNSILSGDVSMGGATEASIWSIY
  Nearest Stachelhaus code(s):
    Cys DLYNFSMIWK (85% 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
MexT | Global virulence regulator
MogR | Repressor of flagellar motility genes
ZuR variant 1 | Zinc-responsive repressor

NZ_CP025957.1 - Region 8 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,740,631 - 1,767,640 nt. (total: 27,010 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: PPTase
C1A50_RS07585: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Lyases: cyclase dehydratase
C1A50_RS07525: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

C1A50_RS07535: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

C1A50_RS07545: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001727.3 |  | 0.88 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0002576.2 |  | 0.76 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.57 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0000556.5 |  | 0.54 | ribosomal | streptin | Streptococcus pyogenes
BGC0002635.2 |  | 0.54 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000560.5 |  | 0.54 | ribosomal | subtilomycin | Bacillus subtilis
BGC0000541.5 |  | 0.53 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000542.3 |  | 0.53 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000506.4 |  | 0.52 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001727.3 |  | 0.88 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0002576.2 |  | 0.76 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.57 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0000556.5 |  | 0.54 | ribosomal | streptin | Streptococcus pyogenes
BGC0002635.2 |  | 0.54 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000560.5 |  | 0.54 | ribosomal | subtilomycin | Bacillus subtilis
BGC0000541.5 |  | 0.53 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000542.3 |  | 0.53 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000506.4 |  | 0.52 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii

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

No significant matches found.

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

#### Lanthipeptide(s) for C1A50_RS07545

C1A50_RS07530
Leader:
MKNQFDLDLQVAKNEVAPKEVQPA
Core:
SGLICTPSCATGTLNCQVSLSFCKTC
Core with dehydrations:
DhaGLICysDhbPDhaCysADhbGDhbLNCysQVDhaLDhaFCysKDhbCys

#### antiSMASH-DB 4.0 matches for C1A50_RS07530

100.0%
NC_014483.2 and 17 others:
NC_014622.2 Lanthipeptides: PPSC2_RS36205_lanthipeptide NC_017542.1 Lanthipeptides: PPM_RS07465_lanthipeptide NZ_CP006872.1 Lanthipeptides: PPSQR21_RS07740_lanthipeptide NZ_CP023711.1 Lanthipeptides: CPY53_RS22235_lanthipeptide NZ_CP025957.1 Lanthipeptides: C1A50_RS07530_lanthipeptide NZ_CP029370.1 Lanthipeptides: DI243_RS07495_lanthipeptide NZ_CP040829.1 Lanthipeptides: FGY93_RS00500_lanthipeptide NZ_CP049598.1 Lanthipeptides: G7L40_RS00115_lanthipeptide NZ_CP073682.1 Lanthipeptides: KAI36_RS07745_lanthipeptide NZ_CP084033.1 Lanthipeptides: LAZ93_RS07550_lanthipeptide NZ_CP085682.1 Lanthipeptides: LJR53_RS07370_lanthipeptide NZ_CP086373.1 Lanthipeptides: LMH85_RS07780_lanthipeptide NZ_CP092779.1 Lanthipeptides: MJ749_RS07440_lanthipeptide NZ_CP097766.1 Lanthipeptides: MF620_RS07485_lanthipeptide NZ_CP102865.1 Lanthipeptides: NWS42_RS21195_lanthipeptide NZ_JWJJ01000002.1 Lanthipeptides: U707_RS10390_lanthipeptide NZ_POVT01000009.1 Lanthipeptides: C1T20_RS05900_lanthipeptide
Lanthipeptides: PPE_RS07020_lanthipeptide
1
SGLICTPSCATGTLNCQVSLSFCKTC
26
SGLICTPSCATGTLNCQVSLSFCKTC
1
SGLICTPSCATGTLNCQVSLSFCKTC
26
96.2%
NZ_CP061172.1 and 5 others:
NZ_CP109848.1 Lanthipeptides: OF859_RS22650_lanthipeptide NZ_CP113973.1 Lanthipeptides: OYT09_RS07785_lanthipeptide NZ_JAAMNR010000001.1 Lanthipeptides: G9G54_RS03500_lanthipeptide NZ_PNXQ01000013.1 Lanthipeptides: C1I60_RS14430_lanthipeptide NZ_POVS01000009.1 Lanthipeptides: C1T21_RS10630_lanthipeptide
Lanthipeptides: IAQ67_RS07480_lanthipeptide
1
SGLICTPSCATGTLNCQVSLSFCKTC
26
SGLICTPSCATGTLNCQVSL+FCKTC
1
SGLICTPSCATGTLNCQVSLTFCKTC
26
96.2%
NZ_JAKVDC010000001.1:
Lanthipeptides: MKN04_RS02755_lanthipeptide
1
SGLICTPSCATGTLNCQVSLSFCKTC
26
SG+ICTPSCATGTLNCQVSLSFCKTC
1
SGIICTPSCATGTLNCQVSLSFCKTC
26
with 59 more sequence matches
Only the first 10 are displayed here.
92.3%
NC_023037.2 and 5 others:
NZ_CP017967.2 Lanthipeptides: PPYC1_RS07755_lanthipeptide NZ_CP017968.3 Lanthipeptides: PPYC2_RS08330_lanthipeptide NZ_CP073683.1 Lanthipeptides: KAI37_RS07495_lanthipeptide NZ_FOYG01000001.1 Lanthipeptides: BM358_RS03525_lanthipeptide NZ_PTJM01000020.1 Lanthipeptides: C5G87_RS02825_lanthipeptide
Lanthipeptides: X809_RS07820_lanthipeptide
1
SGLICTPSCATGTLNCQVSLSFCKTC
26
SG+ICTPSCATGTLNCQVSL+FCKTC
1
SGIICTPSCATGTLNCQVSLTFCKTC
26
84.6%
NZ_JAIFIS010000001.1:
Lanthipeptides: K1X09_RS26315_lanthipeptide
1
SGLICTPSCATGTLNCQVSLSFCKTC
26
SGLICTPSC TGTLNC++SLSFC+TC
1
SGLICTPSCLTGTLNCKISLSFCRTC
26
80.8%
NZ_WTWY01000020.1:
Lanthipeptides: GQY55_RS27090_lanthipeptide
1
SGLICTPSCATGTLNCQVSLSFCKTC
26
SG ICTPSC TGTLNC++SLSFC+TC
1
SGFICTPSCLTGTLNCKISLSFCRTC
26
76.9%
NZ_NIST01000001.1:
Lanthipeptides: CD001_RS09870_lanthipeptide
1
SGLICTPSCATGTLNCQVSLSFCKTC
26
+G ICTPSC TGTLNC+VSL+FC+TC
1
TGGICTPSCLTGTLNCRVSLTFCRTC
26
57.7%
NZ_CP029370.1:
Lanthipeptides: DI243_RS07485_lanthipeptide
1
SGLICTPSCATGTLNCQVSLSFCKTC
26
SG+ICTP+C T LNC S+S C C
1
SGIICTPTCLTSILNCYTSISHCGPC
26
38.5%
NZ_CP090942.1:
Lanthipeptides: LZT96_RS12010_lanthipeptide
1
SGLICTPSCA-TGTLN
15
S ICTP CA TG+ N
3
SKFICTPGCAKTGSFN
18
35.3%
NC_022237.1 and 1 other:
NZ_JUZI01000019.1 Lanthipeptides: ADI02_RS09325_lanthipeptide
Lanthipeptides: SII_RS05025_lanthipeptide
1
SGLICTPSCATGTL----------NCQVSLS
21
S +CTP C TG L NC V +S
3
SVFMCTPGCVTGALMGCNLQTATCNCHVHIS
33
34.6%
NZ_CP094805.1:
Lanthipeptides: MUA37_RS13310_lanthipeptide
1
SGLICTPSCA-TGTLN
15
S +CTP CA TG+ N
3
SKFLCTPGCAKTGSFN
18
34.6%
NZ_NBBB01000022.1 and 1 other:
NZ_NUOG01000083.1 Lanthipeptides: COE07_RS24905_lanthipeptide
Lanthipeptides: B6F67_RS25205_lanthipeptide
1
SGLICTPSCATGTLNCQVSLSFC
23
SG+ICTP T C+++ ++C
1
SGIICTP--GTCQTLCRITENWC
21
30.8%
NC_003923.1 and 11 others:
NC_009641.1 Lanthipeptides: NWMN_RS09635_lanthipeptide NZ_AP019791.1 Lanthipeptides: RxyAA322_RS06460_lanthipeptide NZ_CP023076.1 Lanthipeptides: CJ017_RS08945_lanthipeptide NZ_CP054876.1 Lanthipeptides: HUW54_RS09150_lanthipeptide NZ_CP077098.1 Lanthipeptides: KSF82_RS09475_lanthipeptide NZ_CP092781.1 Lanthipeptides: ML436_RS08940_lanthipeptide NZ_CP102959.1 Lanthipeptides: NW979_RS08780_lanthipeptide NZ_CP102962.1 Lanthipeptides: NW971_RS09555_lanthipeptide NZ_LR133917.1 Lanthipeptides: ELZ45_RS09155_lanthipeptide NZ_LS483317.1 Lanthipeptides: DQL75_RS09700_lanthipeptide NZ_VKCY01000012.1 Lanthipeptides: FNK43_RS09020_lanthipeptide
Lanthipeptides: MW_RS09420_lanthipeptide
4
ICTPSCA-TGTLN
15
+CTP CA TG+ N
7
LCTPGCAKTGSFN
19

#### MIBiG 4.0 matches for C1A50_RS07530

21.6%
BGC0001229.4 (SBI_06989):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
1
SGLICTPSCATGTLNCQVSLSFCKT
25
+GLI + VS +FC T
6
TGLILGIVAIQAGVAVGVSAAFCPT
30
20.6%
BGC0000535.4 (ADJ56352.1):
Lanthipeptide: nisin A
4
ICTPSCATGTL
14
+CTP C TG L
6
LCTPGCKTGAL
16
14.3%
BGC0000517.4 (BAB04173.1):
Lanthipeptide: haloduracin β or haloduracin α
5
CTPSC
9
C PSC
23
CMPSC
27
with 1 more sequence matches
10.7%
BGC0000517.4 (BAB04173.1):
Lanthipeptide: haloduracin β or haloduracin α
9
CATGTLNCQV
18
CA ++C++
1
CAWYNISCRL
10

#### 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:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.33 out of 18.16
Confidence: strong
Additional weak hits (5):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 23.88 out of 33.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.91 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.91 out of 28.14
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.02 out of 30.22
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 20.57 out of 30.12
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

C1A50_RS07530 - Class I
  Cleavage pHMM score: 5.70
  RODEO score: 23
  Monoisotopic mass: 2492.2 Da
  Molecular weight: 2493.9 Da
  Number of bridges: 5
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2511.9 Da N = 1
    2530.0 Da N = 2
    2548.0 Da N = 3

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (1740630...1767640)
C1A50_RS07545
  RRE type: Lanthipeptide_LanB_RRE
  Location: 182 - 277
  Score: 60.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator

NZ_CP025957.1 - Region 9 - NRPS-like,cyclic-lactone-autoinducer
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: 2,041,678 - 2,103,902 nt. (total: 62,225 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
cyclic-lactone-autoinducer: (TIGR04223 or AgrB)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acetyltransferase acyltransferase
C1A50_RS09130: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

C1A50_RS25975: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

Hydrolases: hydrolase
C1A50_RS09015: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase synthase
C1A50_RS09060: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C1A50_RS09260: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs
  SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

Translocases: permease transporter
C1A50_RS08985: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

C1A50_RS09185: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | NRPS-like | cyclic-lactone-autoinducer | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002164.2 |  |  | 0.27 | NRPS | peramine | Epichloe festucae
BGC0002135.2 |  |  | 0.27 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  | 0.27 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001249.5 |  |  | 0.26 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0000357.5 |  |  | 0.26 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0000307.4 |  |  | 0.26 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001250.4 |  |  | 0.26 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  |  | 0.26 | NRPS | epichloenin A | Epichloe festucae
BGC0001240.4 |  |  | 0.26 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001758.4 |  |  | 0.26 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002164.2 |  | 0.61 | NRPS | peramine | Epichloe festucae
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.60 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001249.5 |  | 0.60 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0000357.5 |  | 0.60 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001240.4 |  | 0.59 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001758.4 |  | 0.59 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 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
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46
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: 22.13 out of 27.78
Confidence: medium
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 24.68 out of 28.14
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 26.52 out of 33.14
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.22 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.02 out of 28.19
Confidence: medium
Additional weak hits (15):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.68 out of 26.12
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.98 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.18 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.25 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.48 out of 21.55
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.50 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.81 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.47 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.74 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.27 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.78 out of 21.55
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.53 out of 33.73
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.59 out of 33.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.76 out of 23.43
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.59 out of 36.54
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 9, location 2041677 - 2103902:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 10, location 2041677 - 2085373:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (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).
C1A50_RS09060: X
AMP-binding (224..633): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    Unpolar aromatic ring (Phe, Trp)
  Single AA prediction:
    phe (Phe)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LVVAFDASVWDGTLTVAGEVNVYGPTECTVATTT
  Nearest Stachelhaus code(s):
    bMe-Phe DAWTTAVAAK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
PerR | Peroxide regulator
RpoN | Regulator of nitrogen assimilation and virulence
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor
ZuR variant 2 | Zinc-responsive repressor

NZ_CP025957.1 - Region 10 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,449,151 - 2,542,888 nt. (total: 93,738 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acyltransferase aminotransferase glycosyltransferase
C1A50_RS10855: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

C1A50_RS10970: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

C1A50_RS11020: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: esterase hydrolase
C1A50_RS10920: thioesterase

smcogs
  SMCOG1004: thioesterase

C1A50_RS10945: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase
C1A50_RS10935: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C1A50_RS10940: 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
--- | --- | --- | --- | --- | ---
BGC0001843.2 |  | 0.86 | NRPS | tridecaptin M | Paenibacillus sp. M-152
BGC0000449.5 |  | 0.85 | NRPS | tridecaptin | Paenibacillus terrae
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.73 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001843.2 |  | 0.86 | NRPS | tridecaptin M | Paenibacillus sp. M-152
BGC0000449.5 |  | 0.85 | NRPS | tridecaptin | Paenibacillus terrae
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.73 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.72 | 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.42 out of 20.47
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.55 out of 21.55
Confidence: strong
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.87 out of 21.55
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.14 out of 25.31
Confidence: medium
Additional weak hits (4):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.68 out of 26.12
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 28.80 out of 39.62
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.46 out of 21.55
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.82 out of 20.01
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 12, location 2449150 - 2542888:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Val - D-Dab - D-Gly - D-Ser - D-Trp - Ser - Dab - D-Dab - Trp - Val) + (D-Ile - Ala)

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).
C1A50_RS10935: Val - Dab - Gly - Ser - Trp - Ser - Dab - Dab - Trp
Search NORINE for peptide: strict or relaxed
AMP-binding (464..896): Val
nrpys: Val

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

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

AMP-binding (2026..2485): Dab
nrpys: Dab

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TAYAFDVFVGDRESITSSDINSYGVTEAAIDSSF
  Nearest Stachelhaus code(s):
    Dab DVGEISSIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3618..4015): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FGMTFDIFVLELQMMVGGEYNMYGPTETTVWSTV
  Nearest Stachelhaus code(s):
    Gly DILQMGMVWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5165..5583): 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:
    RWMTFDVSVWEWHFFASGEVNLYGPTEATVDVSY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (6704..7099): Trp
nrpys: Trp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LYFAFDAACWEQALFTAGSYNGYGPTENSVATSI
  Nearest Stachelhaus code(s):
    Trp DAWAFAGVAK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (8243..8661): 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:
    RWMTFDVSVWEWHFFASGEVNLYGPTEATVDVSY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (9333..9792): Dab
nrpys: Dab

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TAYAFDVFVGDRESITSSDINSYGVTEAAIDSSF
  Nearest Stachelhaus code(s):
    Dab DVGEISSIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (10438..10897): Dab
nrpys: Dab

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TAYAFDVFVGDRESITSSDINSYGVTEAAIDSSF
  Nearest Stachelhaus code(s):
    Dab DVGEISSIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (12015..12410): Trp
nrpys: Trp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LYFAFDAACWEQALVTAGSYNGYGPTENSVATSI
  Nearest Stachelhaus code(s):
    Trp DAWAFAGVAK (97% 8Å match)
  Stachelhaus code match:
    90% (moderate)

C1A50_RS10940: Val - Ile - Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (268..716): Val
nrpys: Val

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

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

AMP-binding (1363..1770): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSTGFDASTFEGFMLVGGDSNVYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTFK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2905..3298): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNTCFDVSTFEGWLLVGGDINGYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Ala DVFWLGGTFK (100% 8Å match)
    Val DVFWLGGTFK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
CatR | H2O2-responsive repressor
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025957.1 - Region 11 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,699,827 - 2,782,052 nt. (total: 82,226 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
Hydrolases: amidase hydrolase
C1A50_RS11770: amidase

smcogs
  SMCOG1105: amidase

C1A50_RS11895: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase synthase
C1A50_RS11835: carbamoyl phosphate synthase small subunit

smcogs
  SMCOG1249: carbamoyl phosphate synthase small subunit

C1A50_RS25615: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C1A50_RS25625: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C1A50_RS26090: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0000307.4 |  | 0.68 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001240.4 |  | 0.68 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0000307.4 |  | 0.68 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001240.4 |  | 0.68 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

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: 18.04 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.91 out of 19.26
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.64 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.29 out of 26.06
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.71 out of 27.78
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
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.32 out of 30.25
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.74 out of 27.78
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 20.97 out of 20.97
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 20.97 out of 20.97
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.06 out of 19.26
Confidence: strong
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.59 out of 23.05
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.86 out of 28.19
Confidence: medium
Additional weak hits (16):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.75 out of 26.06
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 27.57 out of 39.62
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 21.62 out of 30.97
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.98 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.86 out of 30.25
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.62 out of 32.93
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.77 out of 32.38
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.23 out of 33.73
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.53 out of 29.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.89 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.02 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.96 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 29.16 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 27.30 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.41 out of 26.06
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.99 out of 32.93
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 13, location 2699826 - 2782052:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Gly - D-Dab - D-Gly - D-Ser) + (Dab) + (D-Dab - Ile - Glu)

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).
C1A50_RS25615: Gly - Dab - Gly - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (464..861): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FGMTFDIFVLELQMMVGGEYNMYGPTETTVWSTV
  Nearest Stachelhaus code(s):
    Gly DILQMGMVWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1992..2435): Dab
nrpys: Dab

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TAYAFDVFVGDRESITSSDINSYGVTEAAIDSSF
  Nearest Stachelhaus code(s):
    Dab DVGEISSIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3568..3965): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FGMTFDIFVLELQMMVGGEYNMYGPTETTVWSTV
  Nearest Stachelhaus code(s):
    Gly DILQMGMVWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5116..5529): 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:
    RWMTFDVSVWEWHFFASGEVNLYGPTEATVDVSY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

C1A50_RS25625: Dab - Dab - Ile - Glu
Search NORINE for peptide: strict or relaxed
AMP-binding (120..579): Dab
nrpys: Dab

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TAYAFDVFVGDRESITSSDINSYGVTEAAIDSSF
  Nearest Stachelhaus code(s):
    Dab DVGEISSIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1225..1684): Dab
nrpys: Dab

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TEYAFDVFVGDRESITSSDINSYGVTEAAIDSSF
  Nearest Stachelhaus code(s):
    Dab DVGEISSIDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2802..3196): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNTGFDASTFEGFLLVGGDSNIYGPTENTTFSTV
  Nearest Stachelhaus code(s):
    Ile DAFFLGITFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3860..4285): Glu
nrpys: Glu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LALSFDASVKQADGLIGGETNVYGPTEATVDTTA
  Nearest Stachelhaus code(s):
    Glu DAKDLGVVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AfsR | Pleiotropic regulatory for antibiotic production
ArcA | Repressor of carbon oxidation
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
ColR | Phenol-responsive regulator
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_CP025957.1 - Region 12 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,787,734 - 2,861,701 nt. (total: 73,968 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
C1A50_RS12015: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: esterase
C1A50_RS12040: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase synthase
C1A50_RS12025: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

C1A50_RS12030: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C1A50_RS12035: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

C1A50_RS25390: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  | 0.87 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.83 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  |  | 0.82 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  |  | 0.82 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  |  | 0.79 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.77 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  | 0.75 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001641.4 |  |  | 0.73 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002071.2 |  |  | 0.71 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.75 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4 |  | 0.73 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001641.4 |  | 0.72 | 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.
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:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.13 out of 26.85
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.56 out of 20.47
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 18.25 out of 18.46
Confidence: strong
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.83 out of 26.33
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.79 out of 23.79
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.54 out of 20.97
Confidence: medium
Additional weak hits (6):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.82 out of 27.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.00 out of 30.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.83 out of 29.65
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 25.75
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.06 out of 25.88
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 14, location 2787733 - 2861701:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk - X) + (Thr - Ser - Orn - Ser - D-Ala) + (Phe - Gln - Glu)

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).
C1A50_RS12025: pk - X
PKS_AT (536..823): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 66.7%
  Methylmalonyl-CoA: 62.5%
  Isobutyryl-CoA: 58.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 124.4
  Methoxymalonyl-CoA: 114.4
  Malonyl-CoA: 108.3
  Isobutyryl-CoA: 96.1
  trans-1,2-CPDA: 87.6
  Ethylmalonyl-CoA: 85.7
  Propionyl-CoA: 72.0
  2-Methylbutyryl-CoA: 65.3
  CHC-CoA: 55.3
  3-Methylbutyryl-CoA: 46.4
  Benzoyl-CoA: 46.3
  Acetyl-CoA: 45.6
  inactive: 35.1
  fatty_acid: 19.3

AMP-binding (2281..2686): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HAESFDVSVWQAEVLITGEVNAYGPAEAADDITL
  Nearest Stachelhaus code(s):
    Dab DIWELTADDK (74% 8Å match)
    Ser DVWEMTADDK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

C1A50_RS12030: Thr - Ser - Orn - Ser - Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (501..900): Thr
nrpys: Thr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNSHFDFSVWEGNQIFGGEINMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1542..1947): 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:
    RWMTFDVSVWEWHFFASGEHNLYGPTEATVDVSY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2591..2993): Orn
nrpys: Orn

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    IAWAFDVFVGDRESILGSDVNSYGVTESTIDSSY
  Nearest Stachelhaus code(s):
    Orn DVGEIGSIDK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3635..4040): 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:
    RWMTFDVSVWEWHFFASGEHNLYGPTEATVDVSY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4722..5122): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    IALTFDVSVAEGNFFAAGEENIYGPTESTIYAAG
  Nearest Stachelhaus code(s):
    Ala DVANFAIIYK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

C1A50_RS12035: Phe - Gln
Search NORINE for peptide: strict or relaxed
AMP-binding (471..861): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LFFAFDAAVWEMTLIAAGSINAYGPTETTVCATV
  Nearest Stachelhaus code(s):
    Phe DAWTIAAVCK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1505..1907): Gln
nrpys: Gln

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGLAFDASVQQADGIIGGDTNVYGPTECCVDSTE
  Nearest Stachelhaus code(s):
    Gln DAQDLGVVDK (82% 8Å match)
    Glu DAKDIGVVDK (82% 8Å match)
    Ile DAQDLGVVDK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

C1A50_RS25390: Glu
Search NORINE for peptide: strict or relaxed
AMP-binding (34..308): Glu
nrpys: Glu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGLSFDASVKQADGIIGGETNVYGPTECCVDSTY
  Nearest Stachelhaus code(s):
    Glu DAKDIGVVDK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AfsR | Pleiotropic regulatory for antibiotic production
CcpA | Catabolite control protein A
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025957.1 - Region 13 - betalactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,987,148 - 3,018,081 nt. (total: 30,934 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
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
C1A50_RS12770: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

Hydrolases: hydrolase
C1A50_RS12750: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

Ligases: synthase
C1A50_RS12735: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

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

Reference | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.59 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.59 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.59 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.58 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.58 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.58 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001844.4 |  | 0.44 | NRPS | holrhizin A, holrhizin B, holrhizin C, holrhizin D | Paraburkholderia rhizoxinica HKI 454
BGC0002518.3 |  | 0.44 | NRPS | syringafactin A, syringafactin C | Pseudomonas sp. SZ57
BGC0000426.5 |  | 0.44 | NRPS | sevadicin | Paenibacillus larvae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.59 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.59 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.59 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.58 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.58 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.58 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001844.4 |  | 0.44 | NRPS | holrhizin A, holrhizin B, holrhizin C, holrhizin D | Paraburkholderia rhizoxinica HKI 454
BGC0002518.3 |  | 0.44 | NRPS | syringafactin A, syringafactin C | Pseudomonas sp. SZ57
BGC0000426.5 |  | 0.44 | NRPS | sevadicin | Paenibacillus larvae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 28.14 out of 28.14
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57
Confidence: strong
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 25.44 out of 28.14
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.01 out of 32.93
Confidence: medium
Additional weak hits (5):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.50 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.39 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.20 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.42 out of 36.54
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.39 out of 32.93
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
LexA variant 3 | Repressor of DNA damage response
PerR | Peroxide regulator
ToxT | Regulator of MSHA biosynthesis

NZ_CP025957.1 - Region 14 - cyclic-lactone-autoinducer
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: 3,059,109 - 3,079,657 nt. (total: 20,549 nt) Show pHMM detection rules used
cyclic-lactone-autoinducer: (TIGR04223 or AgrB)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
C1A50_RS13040: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

Hydrolases: deacetylase hydrolase
C1A50_RS12965: amidohydrolase

smcogs
  SMCOG1244: amidohydrolase

C1A50_RS13045: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

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 | cyclic-lactone-autoinducer | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000504.5 |  | 0.41 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000916.5 |  | 0.39 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0000772.5 |  | 0.38 | saccharide | lipopolysaccharide | Brucella melitensis
BGC0002442.3 |  | 0.36 | ribosomal | toyoncin | Bacillus toyonensis
BGC0001304.3 |  | 0.36 | PKS | aflavarin | Aspergillus flavus NRRL3357
BGC0000551.5 |  | 0.36 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000518.3 |  | 0.35 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002698.2 |  | 0.35 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001636.4 |  | 0.34 | NRPS | KK-1 | Curvularia clavata
BGC0000541.5 |  | 0.33 | ribosomal | paenicidin A | Paenibacillus polymyxa

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000504.5 |  | 0.41 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000916.5 |  | 0.39 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0000772.5 |  | 0.38 | saccharide | lipopolysaccharide | Brucella melitensis
BGC0002442.3 |  | 0.36 | ribosomal | toyoncin | Bacillus toyonensis
BGC0001304.3 |  | 0.36 | PKS | aflavarin | Aspergillus flavus NRRL3357
BGC0000551.5 |  | 0.36 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000518.3 |  | 0.35 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002698.2 |  | 0.35 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001636.4 |  | 0.34 | NRPS | KK-1 | Curvularia clavata
BGC0000541.5 |  | 0.33 | ribosomal | paenicidin A | Paenibacillus polymyxa

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.99 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 20.47
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.30 out of 27.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 24.68 out of 28.19
Confidence: strong
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.31 out of 24.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.08 out of 28.19
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 19.49 out of 20.01
Confidence: strong
Additional weak hits (4):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.04 out of 30.22
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.48 out of 32.38
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.31 out of 25.75
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.71 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArgR | Regulator of arginine biosynthesis genes
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
LexA variant 2 | Repressor of DNA damage response
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NZ_CP025957.1 - Region 15 - 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: 3,406,246 - 3,427,169 nt. (total: 20,924 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: carboxylase
C1A50_RS14730: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Ligases: synthase synthetase
C1A50_RS14685: 1-deoxy-D-xylulose-5-phosphate synthase

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

C1A50_RS14690: 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
--- | --- | --- | --- | --- | ---
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
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
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002284.3 |  | 0.38 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0001594.3 |  | 0.37 | other (other) | fischerindole L | Fischerella muscicola UTEX 1829
BGC0000666.5 |  | 0.36 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0001501.5 |  | 0.36 | other (other) | ambiguine P | Fischerella sp. TAU

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
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
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002284.3 |  | 0.38 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0001594.3 |  | 0.37 | other (other) | fischerindole L | Fischerella muscicola UTEX 1829
BGC0000666.5 |  | 0.36 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0001501.5 |  | 0.36 | other (other) | ambiguine P | Fischerella sp. TAU

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:
C1A50_RS14690: PT_FPPS_like
Domain 1 (41 - 307): 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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.38 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.03 out of 26.06
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.60 out of 25.88
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.22 out of 28.19
Confidence: medium
Additional weak hits (5):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.78 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.13 out of 30.25
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.89 out of 24.78
Confidence: weak
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.08 out of 20.47
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
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
--- | ---
MogR | Repressor of flagellar motility genes
PsrA | Oleic acid responsive regulator
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_CP025957.1 - Region 16 - NRPS,PKS-like,T3PKS,transAT-PKS
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: 3,584,674 - 3,686,609 nt. (total: 101,936 nt) Show pHMM detection rules used
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
PKS-like: (t2pks2 or ksIII)

#### 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
C1A50_RS15580: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

C1A50_RS15585: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

C1A50_RS15595: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

C1A50_RS15710: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

Transferases: PPTase acetyltransferase acylase
C1A50_RS15570: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

C1A50_RS15575: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

C1A50_RS15630: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

C1A50_RS15715: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: hydrolase
C1A50_RS15640: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

Lyases: hydratase
C1A50_RS15590: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

C1A50_RS15605: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

C1A50_RS15610: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
C1A50_RS15600: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

C1A50_RS15615: hydroxymethylglutaryl-CoA synthase

smcogs
  SMCOG1043: hydroxymethylglutaryl-CoA synthase

C1A50_RS15620: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C1A50_RS15720: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs
  SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

Translocases: transporter
C1A50_RS15515: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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 | transAT-PKS | NRPS | T3PKS | PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  |  |  | 1.45 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  |  |  |  | 1.33 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  |  | 1.31 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  |  |  | 1.31 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  |  |  |  | 1.28 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  |  |  |  | 1.27 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  |  |  |  | 1.24 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000205.3 |  |  |  |  | 1.12 | PKS | bryostatin | Candidatus Endobugula sertula
BGC0001164.3 |  |  |  |  | 1.07 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001268.4 |  |  |  |  | 1.04 | NRPS, PKS | fusarin C | Fusarium fujikuroi

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.66 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000205.3 |  | 0.65 | PKS | bryostatin | Candidatus Endobugula sertula
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.65 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001244.3 |  | 0.63 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002276.2 |  | 0.62 | NRPS | choline | Aspergillus nidulans FGSC A4

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 24.98 out of 27.55
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 26.06 out of 26.06
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.79 out of 20.97
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.09 out of 27.78
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.96 out of 30.25
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.30 out of 27.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.75 out of 28.19
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.84 out of 32.93
Confidence: medium
Additional weak hits (20):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.92 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.29 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.68 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 21.73 out of 30.97
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.53 out of 33.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.28 out of 21.55
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.62 out of 25.75
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.22 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.32 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.11 out of 29.38
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.51 out of 32.93
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.18 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.11 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.14 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.56 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.96 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.79 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.98 out of 28.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.96 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.84 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 18, location 3584673 - 3686609:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid - Gly - ohmal - Me-mal) + (ohmal - mal - ccmal - ccmal - mal) + (ccmal - Me-ccmal - ohmal) + (ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 19, location 3584673 - 3682297:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid - Gly - ohmal - Me-mal) + (ohmal - mal - ccmal - ccmal - mal) + (ccmal - Me-ccmal - ohmal) + (ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 20, location 3644083 - 3685346:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid - Gly - ohmal - Me-mal) + (ohmal - mal - ccmal - ccmal - mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 21, location 3645361 - 3686609:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid - Gly - ohmal - Me-mal) + (ohmal - mal - ccmal - ccmal - mal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
C1A50_RS15570: mal
PKS_AT (4..283): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 66.7%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 95.9
  inactive: 35.5
  Methoxymalonyl-CoA: 25.7
  Methylmalonyl-CoA: 22.6
  fatty_acid: 13.6
  Propionyl-CoA: 13.0
  2-Methylbutyryl-CoA: 12.4
  CHC-CoA: 9.9
  Isobutyryl-CoA: 9.4
  trans-1,2-CPDA: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

C1A50_RS15575: mal
PKS_AT (7..298): mal
ATSignature: (unknown)
No matches above 50%
minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 41.7
  inactive: 29.1
  Methoxymalonyl-CoA: 14.1
  Methylmalonyl-CoA: 9.4
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

C1A50_RS15600: fatty_acid - Gly
Search NORINE for peptide: strict or relaxed
CAL_domain (66..485): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 13.4
  NH2: 8.4
  AHBA: 8.2
  Acetyl-CoA: 5.0
  shikimic_acid: 0.0

AMP-binding (1159..1555): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FSMTFDIAGLELQALCGGEWNMFGPTETTIWSTI
  Nearest Stachelhaus code(s):
    Gly DILQLGMIWK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
ColR | Phenol-responsive regulator
GnfM | Regulator of nitrogen-fixation genes
LexA variant 3 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes
RpoN | Regulator of nitrogen assimilation and virulence
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_CP025957.1 - Region 17 - 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: 3,969,948 - 3,992,335 nt. (total: 22,388 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
Ligases: synthetase
C1A50_RS17120: 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
--- | --- | --- | --- | --- | ---
BGC0001910.4 |  | 0.29 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0002007.2 |  | 0.24 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001910.4 |  | 0.29 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0002007.2 |  | 0.24 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina

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

No significant matches found.

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP
diterpene precursor |  | GGPP | C20 | acyclic | PP
sesterterpene precursor |  | GFPP | C25 | acyclic | PP
triterpene precursor |  | HPP | C30 | acyclic | PP

Genes with terpene domains:
C1A50_RS17120: PT_FPPS_like
Domain 1 (536 - 761): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.02 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.57 out of 26.06
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.61 out of 24.78
Confidence: medium
Additional weak hits (9):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 25.02 out of 36.54
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.01 out of 29.51
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.85 out of 32.74
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 25.81 out of 31.73
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.33 out of 30.22
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.53 out of 30.25
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.27 out of 30.12
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 20.22 out of 30.12
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.85 out of 36.53
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
LexA variant 2 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes

NZ_CP025957.1 - Region 18 - 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: 4,910,605 - 4,990,177 nt. (total: 79,573 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
C1A50_RS21485: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: glycosyltransferase
C1A50_RS21340: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

Hydrolases: deacetylase
C1A50_RS21390: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

Ligases: ligase
C1A50_RS21440: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C1A50_RS21455: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

C1A50_RS21460: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter
C1A50_RS21360: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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
--- | --- | --- | --- | --- | ---
BGC0001153.5 |  | 0.87 | NRPS | polymyxin B | Paenibacillus polymyxa
BGC0001192.5 |  | 0.86 | NRPS | colistin A, colistin B | Paenibacillus alvei
BGC0000408.5 |  | 0.86 | NRPS | polymyxin | Paenibacillus polymyxa
BGC0002653.2 |  | 0.84 | NRPS | macolacin | Paenibacillus xylanexedens
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000426.5 |  | 0.73 | NRPS | sevadicin | Paenibacillus larvae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001153.5 |  | 0.87 | NRPS | polymyxin B | Paenibacillus polymyxa
BGC0001192.5 |  | 0.86 | NRPS | colistin A, colistin B | Paenibacillus alvei
BGC0000408.5 |  | 0.86 | NRPS | polymyxin | Paenibacillus polymyxa
BGC0002653.2 |  | 0.84 | NRPS | macolacin | Paenibacillus xylanexedens
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000426.5 |  | 0.73 | NRPS | sevadicin | Paenibacillus larvae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.26 out of 26.06
Confidence: strong
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: 18.04 out of 18.57
Confidence: strong
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.83 out of 21.55
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.67 out of 25.31
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.06 out of 20.97
Confidence: medium
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
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.15 out of 27.78
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 23.92 out of 27.55
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.46 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.99 out of 26.06
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.50 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.50 out of 28.19
Confidence: medium
Additional weak hits (23):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.70 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.64 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.73 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.52 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.34 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.85 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.86 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.00 out of 26.06
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.58 out of 32.93
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.22 out of 28.14
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.63 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.49 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.34 out of 30.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 26.61 out of 36.54
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.45 out of 21.55
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.74 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.46 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.47 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.06 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.28 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.18 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.52 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.60 out of 30.98
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 23, location 4910604 - 4990177:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Leu - Leu - Dab - Dab - Thr) + (Dab - Thr - Dab - Dab - Dab)

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).
C1A50_RS21440: Dab - Thr - Dab - Dab - Dab
Search NORINE for peptide: strict or relaxed
AMP-binding (466..878): Dab
nrpys: Dab

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TAYAFDVFVGDRESITSSDINSYGVTEAAIDSSF
  Nearest Stachelhaus code(s):
    Dab DVGEISSIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1520..1927): Thr
nrpys: Thr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNDHFDFSVWEGNQIFGGEINMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2585..3039): Dab
nrpys: Dab

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TGYAFDVFVGDRESITSSDINSYGVTEAAIDSSF
  Nearest Stachelhaus code(s):
    Dab DVGEISSIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3681..4093): Dab
nrpys: Dab

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TGYAFDVFVGDRESITSSDINAYGVTEAAIDSSF
  Nearest Stachelhaus code(s):
    Dab DVGEISAIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4735..5152): Dab
nrpys: Dab

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TGYAFDVFVGDRESITSSDINAYGVTEAAIDSSF
  Nearest Stachelhaus code(s):
    Dab DVGEISAIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

C1A50_RS21455: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (269..676): Thr
nrpys: Thr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNDHFDFSVWEGNQIFGGEINMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

C1A50_RS21460: Leu - Leu - Dab - Dab
Search NORINE for peptide: strict or relaxed
AMP-binding (293..683): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LMFAFDASCWEKILVTGGSFNAYGPTEASIVTTL
  Nearest Stachelhaus code(s):
    Leu DAWIVGAIVK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1800..2195): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    INTSFDGAIFDGLILFGGENHLYGPSESTVYTTY
  Nearest Stachelhaus code(s):
    Leu DGFLLGLVYK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2837..3275): Dab
nrpys: Dab

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TGYAFDVFVGDRESITSSDINAYGVTEAAIDSSF
  Nearest Stachelhaus code(s):
    Dab DVGEISAIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3920..4355): Dab
nrpys: Dab

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TGYAFDVFVGDRESITSSDINAYGVTEAAIDSSF
  Nearest Stachelhaus code(s):
    Dab DVGEISAIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
CatR | H2O2-responsive repressor
CcpA | Catabolite control protein A
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
GnfM | Regulator of nitrogen-fixation genes
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_CP025957.1 - Region 19 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,081,333 - 5,105,881 nt. (total: 24,549 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: transferase
C1A50_RS22130: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Hydrolases: hydrolase
C1A50_RS22095: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: cyclase dehydratase
C1A50_RS22120: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

C1A50_RS22125: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

Ligases: synthase
C1A50_RS22135: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0000560.5 |  | 0.56 | ribosomal | subtilomycin | Bacillus subtilis
BGC0000749.3 |  | 0.55 | saccharide | capsular polysaccharide | Escherichia coli
BGC0002635.2 |  | 0.53 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0001289.5 |  | 0.53 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000508.3 |  | 0.52 | ribosomal | epidermin | Staphylococcus epidermidis
BGC0000556.5 |  | 0.48 | ribosomal | streptin | Streptococcus pyogenes
BGC0000514.5 |  | 0.48 | ribosomal | gallidermin | Staphylococcus gallinarum
BGC0002668.2 |  | 0.47 | ribosomal | cesin A | Clostridium estertheticum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0000560.5 |  | 0.56 | ribosomal | subtilomycin | Bacillus subtilis
BGC0000749.3 |  | 0.55 | saccharide | capsular polysaccharide | Escherichia coli
BGC0002635.2 |  | 0.53 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0001289.5 |  | 0.53 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000508.3 |  | 0.52 | ribosomal | epidermin | Staphylococcus epidermidis
BGC0000556.5 |  | 0.48 | ribosomal | streptin | Streptococcus pyogenes
BGC0000514.5 |  | 0.48 | ribosomal | gallidermin | Staphylococcus gallinarum
BGC0002668.2 |  | 0.47 | ribosomal | cesin A | Clostridium estertheticum

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

No significant matches found.

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

#### Lanthipeptide(s) for C1A50_RS22125

C1A50_RS26135
Leader:
MNSPELVFFEQEDTLDLDLQINDLTLKQA
Core:
KNPCTSTVTCSVSRCLGTHVTCECWC
Core with dehydrations:
KNPCysDhbDhaDhbVDhbCysDhaVDhaRCysLGDhbHVDhbCysECysWCys

#### antiSMASH-DB 4.0 matches for C1A50_RS26135

100.0%
NZ_CP006872.1 and 4 others:
NZ_CP025957.1 Lanthipeptides: allorf_5095957_5096169_lanthipeptide NZ_CP049598.1 Lanthipeptides: allorf_2509002_2509214_lanthipeptide NZ_CP084033.1 Lanthipeptides: allorf_5103763_5103975_lanthipeptide NZ_FNYX01000002.1 Lanthipeptides: allorf_035057_035269_lanthipeptide
Lanthipeptides: allorf_5187783_5187995_lanthipeptide
1
KNPCTSTVTCSVSRCLGTHVTCECWC
26
KNPCTSTVTCSVSRCLGTHVTCECWC
1
KNPCTSTVTCSVSRCLGTHVTCECWC
26
53.8%
NZ_CP029370.1 and 2 others:
NZ_JAFJXZ010000017.1 Lanthipeptides: JYU28_RS14110_lanthipeptide NZ_JAOYTP010000003.1 Lanthipeptides: OIU26_RS10605_lanthipeptide
Lanthipeptides: DI243_RS22305_lanthipeptide
3
PCTSTVTCSVSRCLGTHVTCEC
24
CT TVTC+VS C T+VTC C
1
ACTGTVTCAVSACYDTYVTCNC
22
46.2%
NZ_JAKOBS010000017.1:
Lanthipeptides: allorf_241159_241323_lanthipeptide
4
CTSTVTCSVSRCLGTHVTCEC
24
CT+ VTC+VS CL T+ +C+C
3
CTNNVTCNVSACLNTYKSCDC
23
with 1 more sequence matches
23.7%
NZ_JANVAG010000003.1:
Lanthipeptides: allorf_436904_437122_lanthipeptide
5
TSTVTCSVSRCLGTHVTCEC
24
T+TV +V+ C+GT C C
19
TTTVCGTVAPCVGTQRVCGC
38

#### MIBiG 4.0 matches for C1A50_RS26135

21.4%
BGC0000517.4 (BAB04173.1):
Lanthipeptide: haloduracin β or haloduracin α
4
CTSTVTCSVS
13
CT TV C S
17
CTLTVECMPS
26
15.4%
BGC0000563.4 (AEA03263.1):
Lanthipeptide: venezuelin
21
TCEC
24
TCEC
2
TCEC
5

#### 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.
No hits above weak threshold.
Weak hits (1):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.70 out of 25.75
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

C1A50_RS26135 - Class I
  Cleavage pHMM score: -7.10
  RODEO score: 19
  Monoisotopic mass: 2673.2 Da
  Molecular weight: 2675.1 Da
  Number of bridges: 6
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2693.1 Da N = 1
    2711.1 Da N = 2

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (5081332...5105881)
C1A50_RS22125
  RRE type: Lanthipeptide_LanB_RRE
  Location: 175 - 252
  Score: 56.9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP025957.1 - Region 20 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,420,805 - 5,447,095 nt. (total: 26,291 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
C1A50_RS23530: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Lyases: cyclase dehydratase
C1A50_RS23560: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

C1A50_RS23570: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

Translocases: transporter
C1A50_RS23555: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000541.5 |  | 0.99 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000542.3 |  | 0.85 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0002576.2 |  | 0.76 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.60 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000538.3 |  | 0.57 | ribosomal | nisin Z | Lactococcus lactis
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0000506.4 |  | 0.56 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000556.5 |  | 0.54 | ribosomal | streptin | Streptococcus pyogenes
BGC0000560.5 |  | 0.54 | ribosomal | subtilomycin | Bacillus subtilis
BGC0002635.2 |  | 0.53 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000541.5 |  | 0.99 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000542.3 |  | 0.85 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0002576.2 |  | 0.76 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.60 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000538.3 |  | 0.57 | ribosomal | nisin Z | Lactococcus lactis
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0000506.4 |  | 0.56 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000556.5 |  | 0.54 | ribosomal | streptin | Streptococcus pyogenes
BGC0000560.5 |  | 0.54 | ribosomal | subtilomycin | Bacillus subtilis
BGC0002635.2 |  | 0.53 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa

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

No significant matches found.

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

#### Lanthipeptide(s) for C1A50_RS23570

C1A50_RS25095
Leader:
MAENLFDLDIQVNKSQGSVEPQ
Core:
VLSIVACSSGCGSGKTAASCVETCGNRCFTNVGSLC
Core with dehydrations:
VLDhaIVACysDhaDhaGCysGDhaGKDhbAADhaCysVEDhbCysGNRCysFDhbNVGDhaLCys

#### antiSMASH-DB 4.0 matches for C1A50_RS25095

100.0%
NZ_CP015423.1 and 5 others:
NZ_CP025957.1 Lanthipeptides: C1A50_RS25095_lanthipeptide NZ_CP040829.1 Lanthipeptides: FGY93_RS09600_lanthipeptide NZ_FNYX01000002.1 Lanthipeptides: BMY87_RS25035_lanthipeptide NZ_JAOYTP010000003.1 Lanthipeptides: OIU26_RS12075_lanthipeptide NZ_POVT01000004.1 Lanthipeptides: C1T20_RS24975_lanthipeptide
Lanthipeptides: AOU00_RS26245_lanthipeptide
1
VLSIVACSSGCGSGKTAASCVETCGNRCFTNVGSLC
36
VLSIVACSSGCGSGKTAASCVETCGNRCFTNVGSLC
1
VLSIVACSSGCGSGKTAASCVETCGNRCFTNVGSLC
36
94.4%
NZ_CP013203.1:
Lanthipeptides: ASL14_RS13885_lanthipeptide
1
VLSIVACSSGCGSGKTAASCVETCGNRCFTNVGSLC
36
VLSIVACSSGCGSGKTAASCV TCGN+CFTNVGSLC
1
VLSIVACSSGCGSGKTAASCVATCGNKCFTNVGSLC
36
61.1%
NZ_CP075175.1:
Lanthipeptides: KIK04_RS00230_lanthipeptide
1
VLSIVACSSGCGSGKTAASCVETCGNRCFTNVGSLC
36
V S+ CS GCG+G TA +CVETCG +CF+N+G+LC
1
VTSVWNCSRGCGNGNTANTCVETCG-KCFSNIGALC
35
with 22 more sequence matches
Only the first 10 are displayed here.
59.5%
NZ_CP041405.1:
Lanthipeptides: FLT43_RS29660_lanthipeptide
1
VLSIVACSSGC-GSGKTAASCVETCGNRCFTNVGSLC
36
VLS+ CS GC G+T+A+CV T G CFTN+GSLC
1
VLSVWRCSGGCSDDGRTSATCVATAGKSCFTNIGSLC
37
58.3%
NZ_CP071875.1:
Lanthipeptides: J4I02_RS23985_lanthipeptide
1
VLSIVACSSGCGSGKTAASCVETCGNRCFTNVGSLC
36
+ SI CSSGCG G T+ +CVETC + CF+N+G+LC
1
IRSIWNCSSGCGGGNTSQTCVETC-SPCFSNIGTLC
35
58.3%
NZ_CP075175.1:
Lanthipeptides: KIK04_RS00235_lanthipeptide
1
VLSIVACSSGCGSGKTAASCVETCGNRCFTNVGSLC
36
+S+ CS GCG+G TA +CVETCG +CF+N+G+LC
1
FISVWNCSGGCGNGNTAGTCVETCG-KCFSNIGALC
35
58.3%
NZ_CP092831.1 and 1 other:
NZ_JAFJXZ010000017.1 Lanthipeptides: JYU28_RS12600_lanthipeptide
Lanthipeptides: MLD56_RS24395_lanthipeptide
1
VLSIVACSSGCGSGKTAASCVETCGNRCFTNVGSLC
36
+ SI CSSGCG G T+ +CVETC + CF+N+G+LC
1
IRSIWNCSSGCGGGNTSQTCVETC-SPCFSNLGTLC
35
55.6%
NZ_JAKVDC010000003.1:
Lanthipeptides: MKN04_RS09455_lanthipeptide
1
VLSIVACSSGCGSGKTAASCVETCGNRCFTNVGSLC
36
+ SI CS GCG G T+ +CVETC + CF+N+G+LC
1
IWSIWNCSIGCGGGNTSKTCVETC-SPCFSNLGTLC
35
48.6%
NZ_CP006872.1:
Lanthipeptides: allorf_5538288_5538485_lanthipeptide
1
VLSIVACSSGCGSGKTA-ASCVETCGNRCFTNVGSLC
36
+ S+ CS GCG KT CV TCG C+TN+G+ C
1
LTSVARCSGGCGDDKTDNTKCVATCGKNCYTNIGAFC
37
48.6%
NZ_CP062165.1 and 1 other:
NZ_LXQN01000019.1 Lanthipeptides: gpAD87_RS32325_lanthipeptide
Lanthipeptides: JNUCC31_RS12820_lanthipeptide
2
LSIVACSSGCGSG-KTAASCVETCGNRCFTNVGSLC
36
LSI C+ GCG +TA +C T G +CF+N+G+LC
2
LSIWNCTGGCGEQTRTANTCAPTAGVKCFSNIGALC
37
40.5%
NZ_VEHS01000008.1:
Lanthipeptides: FS811_RS28905_lanthipeptide
1
VLSIVACSSGCGSG-KTAASCVETCGNRCFTNVGSLC
36
+ S+ C+ GCG +TA +C T G C +N+G+LC
1
LTSVWNCTGGCGPQTRTANTCAPTAGKGCISNIGALC
37
38.9%
NZ_JANAVN010000006.1:
Lanthipeptides: NLX78_RS10700_lanthipeptide
1
VLSIVACSS-GCGS------GKTAASCVETCGNRC
28
+ SI ACS+ CG GKT +CV G+ C
2
LTSIAACSAVACGGQRTENCGKTYGNCVSNIGDWC
36
36.1%
NZ_CP092831.1 and 2 others:
NZ_JAFJXZ010000017.1 Lanthipeptides: JYU28_RS12580_lanthipeptide NZ_JAKVDC010000003.1 Lanthipeptides: MKN04_RS09435_lanthipeptide
Lanthipeptides: MLD56_RS24415_lanthipeptide
14
GKTAASCVETCGNRCFTNVGSLC
36
G TA +C ET G +CF+N+G+LC
13
GGTANTCAETAGVKCFSNIGALC
35

#### MIBiG 4.0 matches for C1A50_RS25095

35.1%
BGC0001229.4 (SBI_06989):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
1
VLSIVACSSGCGSGKTAASCVET-CGNRC
28
+L IVA +G G +AA C T C +RC
9
ILGIVAIQAGVAVGVSAAFCPTTKCTSRC
37
11.1%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
2
LSIVACS
8
LS+V C+
15
LSVVLCT
21

#### 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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 24.28 out of 27.55
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.57 out of 26.33
Confidence: medium
Additional weak hits (4):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.70 out of 31.73
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.69 out of 27.55
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 22.66 out of 26.12
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 26.05 out of 33.14
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

C1A50_RS25095 - Class I
  Cleavage pHMM score: 11.80
  RODEO score: 25
  Monoisotopic mass: 3321.5 Da
  Molecular weight: 3323.8 Da
  Number of bridges: 6
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3341.8 Da N = 1
    3359.8 Da N = 2
    3377.9 Da N = 3

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (5420804...5447095)
C1A50_RS23570
  RRE type: Lanthipeptide_LanB_RRE
  Location: 110 - 204
  Score: 46.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
GnfM | Regulator of nitrogen-fixation genes
ToxT | Regulator of MSHA biosynthesis