KpKP13 Protein target profile

competence protein ComEA-related protein

Accession: KP13_03671

Gene: AHE46011.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSS0
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Length 122
Pocket druggability (FPocket · AlphaFold DB model) 0.22
Functional annotation 0 EC 4 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

Structure available AlphaFold DB model + ColabFold model

Risks to review

Human similarity Top human hit identity: 37.5%. Microbiome similarity 61 of 4744 screened genomes (1.3%) have a significant similarity hit. Mixed conservation Core/accessory calls are not fully concordant. Weak predicted binding pocket FPocket selected-pocket score 0.22.

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
Hit
Human identity (%)
37.5 Lower values reduce human off-target concern.
Human E-value
4.21e-06
Gut microbiome similarity
1.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
60.163 Higher values support similarity to known essential genes.
DEG E-value
1.49e-41 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
73.01 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)
Structure A0A0H3GSS0
Pocket No pockets
Druggability (FPocket) 0.22
Structure A0A0H3GSS0
Pocket Pocket 5
ColabFold model
FPocket 0.217 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 61 / 4744 genomes with a hit
Prevalence 1.3%

Sequence

Primary amino-acid sequence viewer.

MKYGIKALMAAGVLVFALGVQGALAAPASGKAAVNKENVQASSSAKAEAVPGESDIGATKVSINRASAEQLAQALNGVGLKKAQAIVSYREEYGPFKTLDDLKQVPGMGSALVERNLAHLTL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

4
  • 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0015627 A large protein complex, containing 12-15 subunits, that spans the cell envelope of Gram-negative bacteria and mediates the movement of proteins into the extracellular environment. The complex includes a component in the cytoplasm, an inner membrane subcomplex that reaches into the periplasmic compartment and a secretion pore in the outer membrane. Proteins using the Type II pathway are transported across the cytoplasmic membrane by the Sec or Tat complex.
  • GO:0015628 The process in which proteins are secreted across the outer membrane of Gram-negative bacteria by the type II secretion system. Proteins using this pathway are first translocated across the cytoplasmic membrane via the Sec or Tat pathways.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
44 121 PANTHER PTHR21180 ENDONUCLEASE/EXONUCLEASE/PHOSPHATASE FAMILY DOMAIN-CONTAINING PROTEIN 1
1 25 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
19 25 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 25 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
1 25 Phobius SIGNAL_PEPTIDE Signal peptide region
54 122 NCBIfam TIGR00426 competence protein ComEA helix-hairpin-helix repeat region
54 122 InterPro IPR004509 Competence protein ComEA, helix-hairpin-helix domain
26 122 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
54 122 Gene3D G3DSA:1.10.150.280 -
58 121 Pfam PF12836 Helix-hairpin-helix motif
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
7 18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
7 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
70 89 SMART SM00278 HhH1_4
70 89 InterPro IPR003583 Helix-hairpin-helix DNA-binding motif, class 1
100 119 SMART SM00278 HhH1_4
100 119 InterPro IPR003583 Helix-hairpin-helix DNA-binding motif, class 1
37 120 SUPERFAMILY SSF47781 RuvA domain 2-like
37 120 InterPro IPR010994 RuvA domain 2-like
45 122 FunFam G3DSA:1.10.150.280:FF:000001 Competence protein ComEA helix-hairpin-helix repeat region

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 · FPocket

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

Pocket 1 FPocket #5
0.22
Show in viewer
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_A0A0H3GSS0
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_03671
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GSS0