Protein target profile

KP13_01527

High-affinity branched-chain amino acid transport system permease protein braE

Genome: KpKP13 Gene: braE AHE43944.1 3D evidence: AlphaFold DB model + ColabFold model UniProt W9BPM1
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Length 428
Pocket druggability 0.998
Functional annotation 0 EC 5 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: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 1.00, P2Rank 0.82). 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 1.00. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Microbiome similarity 149 of 4744 screened genomes (3.1%) 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.

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
3.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
81.75 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 0.998
Structure W9BPM1
Pocket Pocket 32
P2Rank 0.816
Structure W9BPM1
Pocket Pocket 1
ColabFold model
FPocket 0.987 · Pocket 2
P2Rank 0.819 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 149 / 4744 genomes with a hit
Prevalence 3.1%

Cross-references

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

Sequence

UniProt W9BPM1

Sequence

Primary amino-acid sequence viewer.

MGEITRQPARAIQNALIDSVLAGLCALIVFGPIVGVVLKGYGFTLAPARVAILVAVVMAGRLALSLLLQSHRGKAFIARFEGADDGVYVRPPGYRSRLRWIIPLLVGLAIVFPFLATKYLLTVAILGLIYVLLGLGLNIVVGLAGLLDLGYVAFYAIGAYGLALGYQYLGLGFWAMLPLGAVMAALAGALLGFPVLRMHGDYLAIVTLGFGEIIRLVLNNWVSFTGGPNGVPVPSPTLFGLEFTRRAKDGGIPIHEFFHVSYNPNLKFIFLYAVLCLVVMLVLLVKHRLTRMPIGRAWEALREDEIACRAMGLNHVLVKLSAFMLGASTAGIAGVFFASYQGFVNPTSFTFFESALILAIVVLGGMGSTLGVVLAAFVLTVTPELLRGFDEYRVLLFGVLMVMMMIWRPRGLVRTSRSGVALRKGVAP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • 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: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: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: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.

42 records
Show feature table
Start End DB Term Name
98 116 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
202 224 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
50 68 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 19 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.
117 121 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
173 195 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
15 112 Pfam PF11862 Domain of unknown function (DUF3382)
15 112 InterPro IPR021807 High-affinity branched-chain amino acid transport system permease, LivHM, N-terminal
355 380 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
39 49 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
410 428 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
120 405 Pfam PF02653 Branched-chain amino acid transport system / permease component
120 405 InterPro IPR001851 ABC transporter, permease
128 413 CDD cd06581 TM_PBP1_LivM_like
128 413 InterPro IPR043428 High-affinity branched-chain amino acid transport system permease protein LivM-like
392 409 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
170 174 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
357 379 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
93 424 PANTHER PTHR30482 HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT SYSTEM PERMEASE
93 424 InterPro IPR043428 High-affinity branched-chain amino acid transport system permease protein LivM-like
122 144 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
20 38 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
286 319 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
268 285 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
69 97 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
151 169 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
20 42 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
381 391 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
223 267 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
315 337 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
145 150 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
202 222 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
98 117 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
121 143 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
320 343 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
46 68 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
392 409 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
196 201 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
175 195 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
268 285 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
344 354 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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 #32
0.998
Likely same site as P2Rank 1 6.3 Å 20 shared residues 83% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #1
0.358
Likely same site as P2Rank 3 5.2 Å 9 shared residues 75% of smaller site
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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
0.816
Likely same site as FPocket 32 6.3 Å 20 shared residues 83% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.231
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Surrounding area
Site 3 P2Rank #3
0.172
Likely same site as FPocket 1 5.2 Å 9 shared residues 75% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.145
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Surrounding area
Site 5 P2Rank #5
0.037
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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_W9BPM1
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_01527
ColabFold — — full sequence — Loaded