Genome KpATCC43816

Protein target profile

binding-protein-dependent transport system innermembrane component family protein

Accession: VK055_2771

Gene: AIK81360.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GIE8
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Length 295
Pocket druggability (P2Rank) 0.546
Functional annotation 0 EC 3 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: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.55, FPocket 0.97). 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. Strong predicted binding pocket FPocket selected-pocket score 0.97. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.55. Review the complete evidence below

Risks to review

Microbiome similarity 16 of 4744 screened genomes (0.3%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.55) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant.

Evidence gaps

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
0.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
84.89 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) 0.546
Structure A0A0H3GIE8
Pocket Pocket 1
Druggability (FPocket) 0.971
Structure A0A0H3GIE8
Pocket Pocket 2
ColabFold model
P2Rank 0.62 · Pocket 1
FPocket 0.965 · Pocket 14
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 16 / 4744 genomes with a hit
Prevalence 0.3%

Cross-references

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

Sequence

UniProt A0A0H3GIE8

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSAEISPLLVRTPAAARPLWLRLRRSSPFTLTVLMCCLALLWVSPFIWMLATSFSATTFGDDMASLLPRLPLTLDNFRDAWQSADWLSLYANTLIFTFGTFCVQLLTITTAGYVFACHEFRGKQTLFLLFLVQLMIMPVVMMVPNMLTLKTFGLLNTLTGVMMPYFTSAFGVFLMRQAFLAIPKELEEAALMEGCRWWQVLFRVLLPMSWPSVLAFATVSITYHWNEYLWPLMMLNDPDKQVLTVGLVSFAMGAESGGQWGTIGAGTLMVCLPLMLAFILFQKQFLRSFGFSGIK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
CytoplasmicMembrane

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.

30 records
Show feature table
Start End DB Term Name
152 174 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
282 295 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
226 259 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
29 51 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
29 51 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
144 162 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
204 225 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
126 143 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
95 117 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
260 281 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
21 287 Gene3D G3DSA:1.10.3720.10 -
21 287 InterPro IPR035906 MetI-like superfamily
1 28 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
26 295 PANTHER PTHR43744 ABC TRANSPORTER PERMEASE PROTEIN MG189-RELATED-RELATED
110 282 Pfam PF00528 Binding-protein-dependent transport system inner membrane component
110 282 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
201 223 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
90 281 ProSiteProfiles PS50928 ABC transporter integral membrane type-1 domain profile.
90 281 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
184 203 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
89 114 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
52 88 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
115 125 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
92 270 CDD cd06261 TM_PBP2
92 270 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
126 148 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
163 183 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
259 281 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
27 295 SUPERFAMILY SSF161098 MetI-like
27 295 InterPro IPR035906 MetI-like superfamily

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.

Download VMD script Full viewer

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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

Pocket 1 P2Rank #1
0.546
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Surrounding area
Pocket 2 P2Rank #2
0.534
Likely same site as FPocket 2 2.2 Å 11 shared residues 79% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.114
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Surrounding area
Pocket 4 P2Rank #4
0.043
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2
0.971
Likely same site as P2Rank 2 2.2 Å 11 shared residues 79% of smaller site
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_A0A0H3GIE8
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_2771
ColabFold — — full sequence — Loaded