KpATCC43816 Protein target profile

amino acid permease family protein

Accession: VK055_2933

Gene: AIK81519.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GH59
Length 416
Pocket druggability (P2Rank · AlphaFold DB model) 0.753
Direct ligand evidence 0 54 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
Hit
Human identity (%)
26.316 Lower values reduce human off-target concern.
Human E-value
6.78e-08
Gut microbiome similarity
1.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
86.92 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) 0.753
Structure A0A0H3GH59
Pocket Pocket 1
Druggability (FPocket) 0.761
Structure A0A0H3GH59
Pocket Pocket 1
ColabFold model
P2Rank 0.86 · Pocket 1
FPocket 0.83 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 81 / 4744 genomes with a hit
Prevalence 1.7%

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.

MGGLKQELGLGQGVGLLSTSLLGTGVFAVPALAALVAGDNSLWAWPLLILLVFPIAIVFALLGRHFPSAGGVAHFVDMAFGPRLASVTGWLFLSVIPVGLPAALHIATGFGQALFGWHDAQLLLAELGTLAIVWWVGSRGASSSANLQTLVAVLIVALIVVVWWRGGISPAQIPFPAPAEIDRGQLFSALSVMFWCFVGLEAFAHLASEFKHPERDFPRALMIGLLLAGSVYWACTVLVLHFHAFGEEMAAAASLPNIVVRLFGVEALWVACVIGYLACFASLNIYIQSFARLVWSQAQHKPHSYLARLSPRQIPRNALNAVLGSCVVSTLGIYLLDINLDALIVYANGIFIMIYLLCMLAGCRLLRGRYRLLAVVGSILCLLLLAMVGWKSLYALVMLAGLWLFLPRRKLATGSV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

4
  • GO:0022857 Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.
  • 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.

39 records
Show feature table
Start End DB Term Name
318 336 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
220 242 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
337 341 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
209 219 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
43 63 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
344 366 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
184 206 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
13 35 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
138 148 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 13 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
373 406 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
223 245 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 414 PIRSF PIRSF006060 AA_transporter
64 83 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
150 169 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
243 261 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
109 119 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
288 317 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
120 137 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
362 372 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
262 287 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
4 412 Gene3D G3DSA:1.20.1740.10 Amino acid/polyamine transporter I
84 106 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
265 287 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
121 138 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
84 108 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 404 PANTHER PTHR42770 AMINO ACID TRANSPORTER-RELATED
149 166 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
373 406 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
41 63 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
342 361 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
186 208 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
407 416 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
14 37 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
167 185 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
38 42 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
318 340 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
13 388 Pfam PF13520 Amino acid permease
13 388 InterPro IPR002293 Amino acid/polyamine transporter I

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

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.753
Likely same site as FPocket 1 0.3 Å 19 shared residues 100% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.556
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Surrounding area
Pocket 3 P2Rank #3
0.487
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Surrounding area
Pocket 4 P2Rank #4
0.422
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Surrounding area
Pocket 5 P2Rank #5
0.227
Likely same site as FPocket 21 1.2 Å 12 shared residues 100% of smaller site
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.761
Likely same site as P2Rank 1 0.3 Å 19 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #18
0.514
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Surrounding area
Pocket 3 FPocket #21
0.508
Likely same site as P2Rank 5 1.2 Å 12 shared residues 100% of smaller site
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Surrounding area
Pocket 4 FPocket #12
0.271
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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_A0A0H3GH59
AlphaFold DB full sequence Viewing
ColabFold VK055_2933
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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AG2 PDB via homolog 130.2 Da · LogP -0.79 · TPSA 87.9 Open detail RCSB PDB
BNG PDB via homolog Detail RCSB PDB
D10 PDB via homolog Detail RCSB PDB
HEX PDB via homolog Detail RCSB PDB
ZINC100034925 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
AG2 RCSB PDB P60061 130.2 Da LogP -0.79 TPSA 87.9 ✓ Ro5 ✓ Clean C(CCNC(=N)N)CN
BNG RCSB PDB P60061 306.4 Da LogP 0.55 TPSA 99.4 ✓ Ro5 ✓ Clean CCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO…
D10 RCSB PDB P60061 142.3 Da LogP 4.15 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCCCCCC
HEX RCSB PDB P60061 86.2 Da LogP 2.59 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCC

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.

Cross-references

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