Genome KpATCC43816

Protein target profile

binding-protein-dependent transport system innermembrane component family protein

Accession: VK055_4956

Gene: AIK83482.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GSR3
Length 385
Pocket druggability (P2Rank) 0.758
Direct ligand evidence 0 53 total records
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.

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
1.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
93.52 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) 0.758
Structure A0A0H3GSR3
Pocket Pocket 1
Druggability (FPocket) 0.987
Structure A0A0H3GSR3
Pocket Pocket 29
ColabFold model
P2Rank 0.755 · Pocket 1
FPocket 0.803 · Pocket 22
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 92 / 4744 genomes with a hit
Prevalence 1.9%

Cross-references

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

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.

MTIRCTHRVGLLLTGLLLVTLALPFITYAPNRLLSGEGRGLWQVMPWLAGVQLAAALAGMLLCWLPGRIVPLLHLLLAELLFPLLIWGSGQAALELSRHGSPLARTSPGSGLWLSLALCLLLASEAIRHLTVRPLWRWLLNAQVWLLPIILLAIGALDQLSLLKEYANRQEVFDDALRQHLLLLFGTLLPGLLIGLPLGVWLWRRPRWQAPAFTALNVIQTIPSVALFGLLIAPLAGLARYFPTLGELGVSGTGVAPALIALTLYALLPLVRGVVTGLQQVPQDALESATAMGMSAGLRFRQVQLPLAMPVLLRSLRVVSVQTVGMAVVAALIGAGGFGALVFQGLLSSALDLVLLGVVPTIALAVVVDALFALWGAWLKGEAND

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

4
  • 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.
  • GO:0031460 The directed movement of glycine betaine, N-trimethylglycine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

44 records
Show feature table
Start End DB Term Name
40 65 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
162 180 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
181 203 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
20 24 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
72 94 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
253 275 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
109 131 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
215 236 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
216 238 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
66 71 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
9 19 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
9 28 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
110 127 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
174 371 SUPERFAMILY SSF161098 MetI-like
174 371 InterPro IPR035906 MetI-like superfamily
353 379 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
72 90 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
91 109 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 8 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
139 161 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
203 368 CDD cd06261 TM_PBP2
203 368 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
128 138 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
177 372 ProSiteProfiles PS50928 ABC transporter integral membrane type-1 domain profile.
177 372 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
237 247 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
181 203 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
324 346 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
356 378 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
162 382 PANTHER PTHR30177 GLYCINE BETAINE/L-PROLINE TRANSPORT SYSTEM PERMEASE PROTEIN PROW
269 323 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
25 39 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
324 347 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
168 380 Gene3D G3DSA:1.10.3720.10 -
168 380 InterPro IPR035906 MetI-like superfamily
1 24 Phobius SIGNAL_PEPTIDE Signal peptide region
248 268 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
380 385 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
192 373 Pfam PF00528 Binding-protein-dependent transport system inner membrane component
192 373 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
348 352 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
138 157 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
204 214 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
43 65 TMHMM TMhelix 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 · P2Rank

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

Pocket 1 P2Rank #1
0.758
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Surrounding area
Pocket 2 P2Rank #2
0.162
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Surrounding area
Pocket 3 P2Rank #3
0.081
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Surrounding area
Pocket 4 P2Rank #4
0.077
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Surrounding area
Pocket 5 P2Rank #5
0.025
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #29
0.987 Unusual size
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_A0A0H3GSR3
AlphaFold DB full sequence Viewing
ColabFold VK055_4956
ColabFold full sequence Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2BA PDB via homolog 658.4 Da · LogP -1.63 · TPSA 309.7 Open detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
BET PDB via homolog Detail RCSB PDB
ZINC12502230 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC3581269 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
2BA RCSB PDB A0A0V8ETW8 658.4 Da LogP -1.63 TPSA 309.7 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)C…
ANP RCSB PDB A0A0V8ETW8 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BET RCSB PDB A0A0V8ETW8 118.2 Da LogP -0.22 TPSA 37.3 ✓ Ro5 ✓ Clean C[N+](C)(C)CC(=O)O

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.