KpKP13 Protein target profile

Raffinose permease

Accession: KP13_00600

Gene: AHE47075.1 rafB 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GPM5
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Length 435
Pocket druggability (P2Rank · AlphaFold DB model) 0.956
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 0.96, FPocket 0.71). 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 0.71. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Microbiome similarity 57 of 4744 screened genomes (1.2%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.96) — 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
1.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
58.734 Higher values support similarity to known essential genes.
DEG E-value
3.3e-170 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
83.68 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) 0.956
Structure A0A0H3GPM5
Pocket Pocket 1
Druggability (FPocket) 0.709
Structure A0A0H3GPM5
Pocket Pocket 1
ColabFold model
P2Rank 0.935 · Pocket 1
FPocket 0.311 · Pocket 26
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 57 / 4744 genomes with a hit
Prevalence 1.2%

Sequence

Primary amino-acid sequence viewer.

MVSGRAAALLEENIMNPTVCTHKNNPNFWIFGLFFFLYFFIMATCFPFLPIWLSDVIGLNKTETGLVFSSLSLFAICFQPILGVISDKLGLKKHLMWIVTVLLVLIAPFFLYVFAPLLKTNIWLGALSGGAYIGFVFSAGAGAMEAYIERVSRNSGFEYGKARTFGCLGWALCATTAGMLFSINPEWVFWMGSAAALLLVVLVAIAKPQASQSAQVMDSLGANRPAIDLKTAVRMFRQRKMWMFILYVIGVACVYDVFDQQFATFFKSFFATPEAGTRAFGFATTAGEICNAIIMFSSPWIINRIGAKNTLLIAGMVMAARMIGSSFATTAAEVVALKMLHALEVPFLLVGAFKYITGVFDVRLSATIYLVGFQFAKQVAAIFLSAFAGNMYDRIGFQETYMILGGIALTVTLISAFTLAGKTKTEPLRDNAMTV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

4
  • GO:0008643 The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0005351 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: carbohydrate(out) + H+(out) = carbohydrate(in) + H+(in).
  • 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

71 records
Show feature table
Start End DB Term Name
299 313 ProSitePatterns PS00897 LacY family proton/sugar symporters signature 2.
299 313 InterPro IPR018457 LacY/RafB permease family, conserved site
278 298 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
122 144 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
28 419 CDD cd06172 MFS_LacY
421 435 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
367 389 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
23 424 SUPERFAMILY SSF103473 MFS general substrate transporter
23 424 InterPro IPR036259 MFS transporter superfamily
399 421 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
23 424 Pfam PF01306 LacY proton/sugar symporter
23 424 InterPro IPR000576 LacY/RafB permease family
144 163 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
65 85 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
28 53 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
27 423 ProSiteProfiles PS50850 Major facilitator superfamily (MFS) profile.
27 423 InterPro IPR020846 Major facilitator superfamily domain
259 277 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
309 331 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
24 429 PANTHER PTHR23522 BLL5896 PROTEIN
225 435 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains
225 435 InterPro IPR036259 MFS transporter superfamily
95 117 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
330 334 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
187 206 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 27 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
357 367 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
23 224 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains
23 224 InterPro IPR036259 MFS transporter superfamily
116 120 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
241 258 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
207 240 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
164 181 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
25 419 NCBIfam TIGR00882 oligosaccharide MFS transporter
25 419 InterPro IPR000576 LacY/RafB permease family
54 64 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
299 309 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
97 115 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
83 97 ProSitePatterns PS00896 LacY family proton/sugar symporters signature 1.
83 97 InterPro IPR018457 LacY/RafB permease family, conserved site
164 182 PRINTS PR00174 LacY proton/sugar symporter family signature
164 182 InterPro IPR000576 LacY/RafB permease family
233 261 PRINTS PR00174 LacY proton/sugar symporter family signature
233 261 InterPro IPR000576 LacY/RafB permease family
334 353 PRINTS PR00174 LacY proton/sugar symporter family signature
334 353 InterPro IPR000576 LacY/RafB permease family
303 329 PRINTS PR00174 LacY proton/sugar symporter family signature
303 329 InterPro IPR000576 LacY/RafB permease family
87 116 PRINTS PR00174 LacY proton/sugar symporter family signature
87 116 InterPro IPR000576 LacY/RafB permease family
122 144 PRINTS PR00174 LacY proton/sugar symporter family signature
122 144 InterPro IPR000576 LacY/RafB permease family
365 385 PRINTS PR00174 LacY proton/sugar symporter family signature
365 385 InterPro IPR000576 LacY/RafB permease family
279 300 PRINTS PR00174 LacY proton/sugar symporter family signature
279 300 InterPro IPR000576 LacY/RafB permease family
389 399 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
182 186 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
310 329 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
27 49 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
164 183 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
341 360 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
280 302 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
335 356 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
187 206 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
86 96 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
368 388 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
400 420 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
64 86 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
243 265 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
121 143 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
0.956
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Surrounding area
Pocket 2 P2Rank #2
0.054
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Surrounding area
Pocket 3 P2Rank #3
0.041
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Surrounding area
Pocket 4 P2Rank #4
0.039
Likely same site as FPocket 1 1.2 Å 10 shared residues 100% of smaller site
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Surrounding area
Pocket 5 P2Rank #5
0.006
Likely same site as FPocket 5 1.7 Å 7 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
0.709
Likely same site as P2Rank 4 1.2 Å 10 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #5
0.701
Likely same site as P2Rank 5 1.7 Å 7 shared residues 100% of smaller site
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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_A0A0H3GPM5
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_00600
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GPM5