KpATCC43816 Protein target profile

branched-chain amino acid transport system / permease component family protein

Accession: VK055_3652

Gene: AIK82207.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3H460
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Length 425
Pocket druggability (P2Rank · AlphaFold DB model) 0.806
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.

Main supporting evidence

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.81, FPocket 0.89). 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 129 of 4744 screened genomes (2.7%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.81) — check the ligand evidence before deprioritizing on off-target risk alone.

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
2.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
82.4 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) 0.806
Structure A0A0H3H460
Pocket Pocket 1
Druggability (FPocket) 0.891
Structure A0A0H3H460
Pocket Pocket 19
ColabFold model
P2Rank 0.65 · Pocket 1
FPocket 0.938 · Pocket 27
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 129 / 4744 genomes with a hit
Prevalence 2.7%

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.

MKPMQIAMALLSAVMFFILAGVFMGVQLELNGTKLVVDTAAYIRWQWIFIGTAVVFFFQLLRPLFQKAVKNVSGPKFIMPAIDGSTVKQKLFLIALLVIAVAWPFMVSRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAIGAYTFALLNHYYGLGFWTCLPLAGLVSAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRILLLNNTEITGGPNGISQIPKPTFFGLEFSRSAREGGWDTFSNFFGVKYDPSDRVIFLYLVALLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPTRIKLTAFTISAAFAGFAGTLFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFNEYSMLMLGGLMVLMMIWRPQGLLPMTRVQLKLKNGQAKGEQA

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:0015658 Enables the transfer of branched-chain amino acids from one side of a membrane to the other. Branched-chain amino acids are amino acids with a branched carbon skeleton without rings.
  • 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.

43 records
Show feature table
Start End DB Term Name
133 136 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
47 66 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
120 142 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
9 20 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
374 384 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
80 423 PANTHER PTHR30482 HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT SYSTEM PERMEASE
80 423 InterPro IPR043428 High-affinity branched-chain amino acid transport system permease protein LivM-like
185 190 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
261 283 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
313 336 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
352 374 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
385 403 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
348 373 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
162 184 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
284 312 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
112 398 Pfam PF02653 Branched-chain amino acid transport system / permease component
112 398 InterPro IPR001851 ABC transporter, permease
26 40 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
41 61 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 8 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
157 161 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
62 90 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
109 113 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
91 108 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 25 Phobius SIGNAL_PEPTIDE Signal peptide region
381 400 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
4 26 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
193 210 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
7 103 Pfam PF11862 Domain of unknown function (DUF3382)
7 103 InterPro IPR021807 High-affinity branched-chain amino acid transport system permease, LivHM, N-terminal
404 425 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
262 283 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
114 132 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
119 407 CDD cd06581 TM_PBP1_LivM_like
119 407 InterPro IPR043428 High-affinity branched-chain amino acid transport system permease protein LivM-like
210 261 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
162 184 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
315 337 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
191 209 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
137 156 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
91 108 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
337 347 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
21 25 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.

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
0.806
Likely same site as FPocket 19 3.7 Å 12 shared residues 92% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.185
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Surrounding area
Pocket 3 P2Rank #3
0.086
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Surrounding area
Pocket 4 P2Rank #4
0.074
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Surrounding area
Pocket 5 P2Rank #5
0.065
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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 #19
0.891
Likely same site as P2Rank 1 3.7 Å 12 shared residues 92% of smaller site
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Surrounding area
Pocket 2 FPocket #7
0.301
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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_A0A0H3H460
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_3652
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3H460