Protein target profile

KP13_01836

General secretion pathway protein C

Genome: KpKP13 Gene: AHE46276.1 3D evidence: Experimental + AlphaFold DB model + ColabFold model UniProt A0A0H3GMS7
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Length 275
Pocket druggability 0.059
Functional annotation 0 EC 4 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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

Main supporting evidence

Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. 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. Second pocket predictor agrees P2Rank predicted binding-site probability 0.88. Review the complete evidence below

Risks to review

Microbiome similarity 8 of 4744 screened genomes (0.2%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.06.

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
0.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
74.01 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.059
Structure A0A0H3GMS7
Pocket Pocket 4
P2Rank 0.883
Structure A0A0H3GMS7
Pocket Pocket 1
ColabFold model
FPocket 0.915 · Pocket 10
P2Rank 0.866 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 8 / 4744 genomes with a hit
Prevalence 0.2%

Cross-references

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

Sequence

UniProt A0A0H3GMS7

Structure

PDB 6HCG

Sequence

Primary amino-acid sequence viewer.

MRLTNINKGIIKLLPQIVTLIILITAIPQLAKLTWRVVFPVSPEDISALPLTMPPAADPELKNVRPAFTLFGLAVKNSPTPTDAASLNQVPVSSLKLRLAGLLASSNPARSIAIIEKGNQQVSLSTGDPLPGYDARIAAILPDRIIVNYQGRKEAILLFNDSRAPSPPPTAAGNPPLVKRLREQPQNILTYLSISPVLSGDKLLGYRLNPGKDASLFRQSGLQANDLAIALNGIDLRDQEQAQQALQNLADMTEITLTVEREGQRHDIAFALGDE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • 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:0005515 Binding to a protein.
  • 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.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
173 275 Gene3D G3DSA:2.30.42.10 -
173 275 InterPro IPR036034 PDZ superfamily
210 236 ProSitePatterns PS01141 Bacterial type II secretion system protein C signature.
210 236 InterPro IPR001639 Type II secretion system protein GspC
32 275 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
18 157 Pfam PF11356 Type II secretion system protein C
18 157 InterPro IPR024961 Type II secretion system protein GspC, N-terminal
9 31 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
175 270 SUPERFAMILY SSF50156 PDZ domain-like
175 270 InterPro IPR036034 PDZ superfamily
12 31 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
92 159 Gene3D G3DSA:2.30.30.830 -
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
17 270 NCBIfam TIGR01713 type II secretion system protein GspC
17 270 InterPro IPR001639 Type II secretion system protein GspC

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

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #4
0.733
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Surrounding area
Site 2 P2Rank #8
0.702
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Surrounding area
Site 3 P2Rank #24
0.514
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Surrounding area
Site 4 P2Rank #28
0.504
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Surrounding area
Site 5 P2Rank #32
0.49
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Surrounding area
All structural evidence 1 experimental · 2 predicted

Structural evidence

1 + 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
PDB 6HCG
X-ray — A —
PDBe RCSB PDBj File
Viewing
AlphaFold DB AF_A0A0H3GMS7
AlphaFold DB — — full sequence — Loaded
ColabFold KP13_01836
ColabFold — — full sequence — Loaded