KpKP13 Protein target profile

Cellobiose permease IIC component

Accession: KP13_02559

Gene: AHE43022.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A060VJM1
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Length 466
Pocket druggability (P2Rank · AlphaFold DB model) 0.729
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 0.73, FPocket 0.78). 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 0.78. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Microbiome similarity 13 of 4744 screened genomes (0.3%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.73) — 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
0.3% 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
88.18 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) 0.729
Structure A0A060VJM1
Pocket Pocket 1
Druggability (FPocket) 0.782
Structure A0A060VJM1
Pocket Pocket 3
ColabFold model
P2Rank 0.72 · Pocket 1
FPocket 0.897 · Pocket 29
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 13 / 4744 genomes with a hit
Prevalence 0.3%

Sequence

Primary amino-acid sequence viewer.

MHYGKRFPFVDLLIVTMITYGRLSLSGVVGDHSGETTIRKGRSMNIQLMNVAVDIIEQRLAPLANVLTRNNHITAMRDSFALAMPFVIVGSLLVPILFPPVSIDGASRFGQVYLLLRPILLPTFQLTIGLVALIVAFGASASLAKQYRLPERLCGLTGCLAFLLFIGFRETAVSNVYLGGMGIFTALISSTYSIEIIRFFYKKGWCIRLPDEVPLMTRNGFQLLIPLLVVMLSISVMNAILLQTTGRIVPELISEAVRPLVLASDTLMAVLISLFICNLLWFIGIHGALIITGIMNPFWMTYLFENQQALAAGSPTLPHIYLQGFWDFYLLIGGIGSTLPLVLMAMRSRSRQLKSVAKIGLLPSLFNINEPILFGFPVIMNPVFLLPFLFVPLINACIAWYLTQLGILDRAVAMLPWSMPSPLGAAWSANGSWKNLCMSLFAMFNAWMLYRPFFKVYERQLAETER

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:0009401 The uptake and phosphorylation of specific carbohydrates from the extracellular environment; uptake and phosphorylation are coupled, making the PTS a link between the uptake and metabolism of sugars; phosphoenolpyruvate is the original phosphate donor; phosphoenolpyruvate passes the phosphate via a signal transduction pathway, to enzyme 1 (E1), which in turn passes it on to the histidine protein, HPr; the next step in the system involves sugar-specific membrane-bound complex, enzyme 2 (EII), which transports the sugar into the cell; it includes the sugar permease, which catalyzes the transport reactions; EII is usually divided into three different domains, EIIA, EIIB, and EIIC.
  • GO:0008982 Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + sugar(out) = protein histidine + sugar phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport.
  • 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.

41 records
Show feature table
Start End DB Term Name
178 200 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
282 287 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
383 405 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 78 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
49 466 PIRSF PIRSF006351 PTS_EIIC-Cellobiose
49 466 InterPro IPR004796 Phosphotransferase system, cellobiose-type IIC component
288 304 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
49 465 PANTHER PTHR33989 -
156 173 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
383 402 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
77 392 Pfam PF02378 Phosphotransferase system, EIIC
77 392 InterPro IPR003352 Phosphotransferase system, EIIC
403 431 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
220 242 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
56 453 ProSiteProfiles PS51105 PTS_EIIC type-3 domain profile.
56 453 InterPro IPR004501 Phosphotransferase system, EIIC component, type 3
79 101 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
242 260 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
451 466 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
324 345 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
323 345 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
202 220 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
432 450 Phobius TRANSMEMBRANE 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.
176 201 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
346 382 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
100 118 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
257 279 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
60 465 NCBIfam TIGR00410 PTS system, lactose/cellobiose family IIC component
60 465 InterPro IPR004501 Phosphotransferase system, EIIC component, type 3
119 141 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
281 303 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 23 SignalP_EUK SignalP-noTM SignalP-noTM
425 447 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
79 99 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
171 175 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
305 323 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
142 152 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
221 241 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
153 170 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
261 281 Phobius TRANSMEMBRANE 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

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

Pocket 1 P2Rank #1
0.729
Likely same site as FPocket 3 1.6 Å 18 shared residues 100% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.208
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Surrounding area
Pocket 3 P2Rank #3
0.052
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Surrounding area
Pocket 4 P2Rank #4
0.047
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Surrounding area
Pocket 5 P2Rank #5
0.021
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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 #3
0.782
Likely same site as P2Rank 1 1.6 Å 18 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #11
0.213
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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_A0A060VJM1
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_02559
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A060VJM1