Protein target profile

KP13_05438

Peptide transport system permease protein sapC

Genome: KpKP13 Gene: sapC AHE44971.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GRQ6
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Length 296
Pocket druggability 0.891
Functional annotation 0 EC 2 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

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.89, P2Rank 0.61). Use the 3D pocket comparison to verify whether they identify the same site. 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. Strong predicted binding pocket FPocket selected-pocket score 0.89. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Microbiome similarity 118 of 4744 screened genomes (2.5%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.89) — check the ligand evidence before deprioritizing on off-target risk alone.

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
2.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
90.541 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
92.28 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 0.891
Structure A0A0H3GRQ6
Pocket Pocket 1
P2Rank 0.615
Structure A0A0H3GRQ6
Pocket Pocket 1
ColabFold model
FPocket 0.894 · Pocket 2
P2Rank 0.487 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 118 / 4744 genomes with a hit
Prevalence 2.5%

Cross-references

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

Sequence

UniProt A0A0H3GRQ6

Sequence

Primary amino-acid sequence viewer.

MPYDSVYLEKRPPGALRTVWRKFYGDTTAMIGLYGCAGLLLLCVFGGWFAPYGIDQQFLGYQLLPPSWSRYGEVSFFLGTDDLGRDVLSRLLSGAAPTVGGAFVVTLGATLFGLVLGVIAGSTHGLRSAVMNHILDTLLSIPSLLLAIIVVAFAGPHLSHAMFAVWLALLPRMVRSVYSMVHDELEKEYIIAARLDGASTLNILLFAILPNIASGLVTEITRALSMAILDIAALGFLDLGAQLPSPEWGAMLGDALELIYVAPWTVMLPGAAIMLSVLLVNLLGDGIRRAIIAGVE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

33 records
Show feature table
Start End DB Term Name
99 284 ProSiteProfiles PS50928 ABC transporter integral membrane type-1 domain profile.
99 284 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
261 283 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
198 217 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
258 280 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
85 292 Gene3D G3DSA:1.10.3720.10 -
85 292 InterPro IPR035906 MetI-like superfamily
224 243 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
16 66 Pfam PF12911 N-terminal TM domain of oligopeptide transport permease C
16 66 InterPro IPR025966 Oligopeptide transport permease C-like, N-terminal domain
284 296 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
242 260 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
170 188 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
98 268 CDD cd06261 TM_PBP2
98 268 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
210 220 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
31 54 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
55 98 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
134 156 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
99 123 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
124 143 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
85 292 FunFam G3DSA:1.10.3720.10:FF:000019 Antimicrobial peptide ABC transporter permease SapC
90 276 SUPERFAMILY SSF161098 MetI-like
90 276 InterPro IPR035906 MetI-like superfamily
30 52 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
144 169 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
113 292 Pfam PF00528 Binding-protein-dependent transport system inner membrane component
113 292 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
1 30 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
17 291 PANTHER PTHR43386 OLIGOPEPTIDE TRANSPORT SYSTEM PERMEASE PROTEIN APPC
99 121 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
189 209 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
221 241 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.

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: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1
0.891
Likely same site as P2Rank 1 2.8 Å 11 shared residues 85% of smaller site
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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.615
Likely same site as FPocket 1 2.8 Å 11 shared residues 85% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.181
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Surrounding area
Site 3 P2Rank #3
0.043
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Surrounding area
Site 4 P2Rank #4
0.016
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Surrounding area
Site 5 P2Rank #5
0.012
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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_A0A0H3GRQ6
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_05438
ColabFold — — full sequence — Loaded