KpKP13 Protein target profile

LexA repressor

Accession: KP13_00380

Gene: lexA AHE46881.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQ57
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Length 202
Pocket druggability (P2Rank · AlphaFold DB model) 0.104
Functional annotation 1 EC 8 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 167 of 4744 screened genomes (3.5%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.24. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.10.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
3.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
94.554 Higher values support similarity to known essential genes.
DEG E-value
6.32e-141 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
90.8 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.104
Structure A0A0H3GQ57
Pocket Pocket 1
Druggability (FPocket) 0.237
Structure A0A0H3GQ57
Pocket Pocket 5
ColabFold model
P2Rank 0.072 · Pocket 1
FPocket 0.466 · Pocket 6
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 167 / 4744 genomes with a hit
Prevalence 3.5%

Sequence

Primary amino-acid sequence viewer.

MKALTTRQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGAIEIVSGASRGIRLLTEEEQGLPLIGRVAAGEPLLAQQHIEGHYQVDPSMFKPNADFLLRVSGMSMKDIGILDGDLLAVHKTQDVRNGQVVVARIDEEVTVKRLKKQGNVVELLPENSEFSPIVVDLRQQSFTIEGLAVGVIRNGEWL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0009432 An error-prone process for repairing damaged microbial DNA.
  • GO:0004252 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
  • GO:0045892 Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
  • GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
1 199 NCBIfam TIGR00498 transcriptional repressor LexA
1 199 InterPro IPR006200 Transcription regulator LexA
77 192 Pfam PF00717 Peptidase S24-like
77 192 InterPro IPR015927 Peptidase S24/S26A/S26B/S26C
1 198 PANTHER PTHR33516 LEXA REPRESSOR
111 180 CDD cd06529 S24_LexA-like
111 180 InterPro IPR039418 LexA-like
3 69 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
3 69 InterPro IPR036390 Winged helix DNA-binding domain superfamily
75 199 FunFam G3DSA:2.10.109.10:FF:000001 LexA repressor
3 199 Hamap MF_00015 LexA repressor [lexA].
3 199 InterPro IPR006200 Transcription regulator LexA
75 202 Gene3D G3DSA:2.10.109.10 Umud Fragment, subunit A
75 198 SUPERFAMILY SSF51306 LexA/Signal peptidase
75 198 InterPro IPR036286 LexA/Signal peptidase-like superfamily
111 121 PRINTS PR00726 Repressor LexA serine protease (S24) family signature
111 121 InterPro IPR006197 Peptidase S24, LexA-like
150 162 PRINTS PR00726 Repressor LexA serine protease (S24) family signature
150 162 InterPro IPR006197 Peptidase S24, LexA-like
122 133 PRINTS PR00726 Repressor LexA serine protease (S24) family signature
122 133 InterPro IPR006197 Peptidase S24, LexA-like
1 69 Gene3D G3DSA:1.10.10.10 -
1 69 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
1 69 FunFam G3DSA:1.10.10.10:FF:000009 LexA repressor
1 65 Pfam PF01726 LexA DNA binding domain
1 65 InterPro IPR006199 LexA repressor, DNA-binding domain

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.104
Likely same site as FPocket 5 4.1 Å 11 shared residues 92% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.031
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Surrounding area
Pocket 3 P2Rank #3
0.01
Likely same site as FPocket 5 7.0 Å 6 shared residues 100% of smaller site
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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #5
0.237 Unusual size
Likely same site as P2Rank 1 4.1 Å 11 shared residues 92% of smaller site
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Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GQ57
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_00380
ColabFold — — full sequence — Loaded

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GQ57