Protein target profile

VK055_0556

binding-protein-dependent transport system innermembrane component family protein

Genome: KpATCC43816 Gene: AIK79179.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQI9
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Length 268
Pocket druggability 0.999
Functional annotation 0 EC 3 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 70 of 4744 screened genomes (1.5%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 1.00) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 1.00, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.16.

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
1.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
89.313 Higher values support similarity to known essential genes.
DEG E-value
2.32e-149 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
89.72 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 0.999
Structure A0A0H3GQI9
Pocket Pocket 1
P2Rank 0.162
Structure A0A0H3GQI9
Pocket Pocket 1
ColabFold model
FPocket 0.836 · Pocket 9
P2Rank 0.194 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 70 / 4744 genomes with a hit
Prevalence 1.5%

Cross-references

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

Sequence

UniProt A0A0H3GQI9

Sequence

Primary amino-acid sequence viewer.

MHSERAPWYLRLATWGGVIFLHFPLLIIAIYAFNTEDAAFSFPPQGLTLRWFSEAAGRSDILQAVTLSLKIAALSTAIALVLGTLAAGALWRSAFFGKNAVSLLLLLPIALPGIITGLALLTAFKAVGLEPGLLTIVVGHATFCVVVVFNNVIARFRRTSWSMVEASMDLGATGWQTFRYVVLPNLGSALLAGGMLAFALSFDEIIVTTFTAGHERTLPLWLLNQLGRPRDVPVTNVVALLVMLVTTIPILGAWWLTRDGDNDAGNGK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • 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.
  • 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.

31 records
Show feature table
Start End DB Term Name
92 102 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
133 153 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
232 256 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
213 231 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
17 258 Gene3D G3DSA:1.10.3720.10 -
17 258 InterPro IPR035906 MetI-like superfamily
71 91 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
234 256 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
5 260 SUPERFAMILY SSF161098 MetI-like
5 260 InterPro IPR035906 MetI-like superfamily
71 93 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
100 122 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
132 154 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
103 127 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 259 PANTHER PTHR43848 PUTRESCINE TRANSPORT SYSTEM PERMEASE PROTEIN POTI
12 34 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
68 251 CDD cd06261 TM_PBP2
68 251 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
189 212 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
128 132 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
80 247 Pfam PF00528 Binding-protein-dependent transport system inner membrane component
80 247 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
180 202 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
65 253 ProSiteProfiles PS50928 ABC transporter integral membrane type-1 domain profile.
65 253 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
12 33 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
257 268 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
7 261 FunFam G3DSA:1.10.3720.10:FF:000039 Inner membrane ABC transporter permease ydcV
154 188 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
34 70 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.

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
0.999
Unusual size
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Surrounding area
Site 2 FPocket #10
0.815
Likely same site as P2Rank 3 0.9 Å 12 shared residues 100% of smaller site
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Surrounding area
Site 3 FPocket #12
0.274
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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
0.162
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Surrounding area
Site 2 P2Rank #2
0.139
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Surrounding area
Site 3 P2Rank #3
0.111
Likely same site as FPocket 10 0.9 Å 12 shared residues 100% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.029
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Surrounding area
Site 5 P2Rank #5
0.01
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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_A0A0H3GQI9
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_0556
ColabFold — — full sequence — Loaded