KpKP13 Protein target profile

Inner membrane transport permease

Accession: KP13_01773

Gene: AHE46544.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GLZ6
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Length 372
Pocket druggability (P2Rank · AlphaFold DB model) 0.116
Functional annotation 0 EC 2 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

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 0.76. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 77 of 4744 screened genomes (1.6%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.76) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.12.

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
1.6% 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.

Structure confidence

ColabFold pLDDT
86.91 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) 0.116
Structure A0A0H3GLZ6
Pocket Pocket 1
Druggability (FPocket) 0.763
Structure A0A0H3GLZ6
Pocket Pocket 1
ColabFold model
P2Rank 0.295 · Pocket 1
FPocket 0.871 · Pocket 5
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 77 / 4744 genomes with a hit
Prevalence 1.6%

Sequence

Primary amino-acid sequence viewer.

MMRGLRNIYNLGVKELRSLLGDKAMLALIVFAFTVSVYSSATVMPGSLHLAPIAVADMDKSQLSSRIINAFYRPWFLEPELITADEMDAGLDAGRYTFAINIPPNFQRDVLAGRQPEIQVNVDATRMSQAFTGNGYIQNIITGEVNSFIARYRDNSVLPVELAVRMRFNPNLEQERFGAVMAIINNITMLAIVLTGSALIREREHGTIEHLLVMPVTPFEIMLAKIWSMGLVVSGLSLILMVQGILQVPIEGSITLFMLGVALSLFATTSIGIFMGTLARSMPQLGLLMILVLLPLQMLSGGSTPRESMPQLVQDIMLTMPTTHFVSLAQAILYRGASFAIVWPQFLTLLAIGGVFFTIALLRFRKTIGEMA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

2
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0140359 Primary active transporter characterized by two nucleotide-binding domains and two transmembrane domains. Uses the energy generated from ATP hydrolysis to drive the transport of a substance across a membrane.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
254 279 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
178 200 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
134 367 ProSiteProfiles PS51012 ABC transporter integral membrane type-2 domain profile.
134 367 InterPro IPR047817 ABC-2 type transporter, transmembrane domain, bacterial-type
340 362 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
316 334 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
26 48 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
221 242 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
285 302 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
280 284 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
335 339 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
363 372 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
177 201 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
202 220 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
45 176 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
27 361 Pfam PF12698 ABC-2 family transporter protein
27 361 InterPro IPR013525 ABC-2 type transporter, transmembrane domain
47 176 Gene3D G3DSA:3.40.1710.10 -
7 366 PANTHER PTHR30294 MEMBRANE COMPONENT OF ABC TRANSPORTER YHHJ-RELATED
24 44 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
285 304 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
224 246 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
243 253 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
256 278 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
305 315 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
340 362 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 23 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.

Download VMD script Full viewer

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Drag to rotate — click the view, then scroll to zoom.

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
0.116
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Surrounding area
Pocket 2 P2Rank #2
0.108
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Surrounding area
Pocket 3 P2Rank #3
0.057
Likely same site as FPocket 1 2.5 Å 6 shared residues 86% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.04
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Surrounding area
Pocket 5 P2Rank #5
0.022
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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
0.763
Likely same site as P2Rank 3 2.5 Å 6 shared residues 86% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #3
0.258
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_A0A0H3GLZ6
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_01773
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GLZ6