KpKP13 Protein target profile

Xylose isomerase

Accession: KP13_00240

Gene: AHE42152.1 xylA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H006
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Length 444
Pocket druggability (P2Rank · AlphaFold DB model) 0.931
Functional annotation 1 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

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. Moderate predicted binding pocket FPocket selected-pocket score 0.45. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.93. Review the complete evidence below

Risks to review

Microbiome similarity 202 of 4744 screened genomes (4.3%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.93) — 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
4.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
67.431 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.27 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) 0.931
Structure A0A0H3H006
Pocket Pocket 1
Druggability (FPocket) 0.452
Structure A0A0H3H006
Pocket Pocket 14
ColabFold model
P2Rank 0.926 · Pocket 1
FPocket 0.587 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 202 / 4744 genomes with a hit
Prevalence 4.3%

Sequence

Primary amino-acid sequence viewer.

MEFSMQTYFDQLDRVRYEGPKSTNPLAFRHYNPDELVLGKRMEDHLRFAACYWHTFCWNGADMFGVGSFDRPWQQPGDALEMAKRKADVAFEFFHKLNVPYYCFHDVDVSPEGASLKEYSNNFARMVEVLAEKQQQSGVKLLWGTANCFTNPRYGAGAATNPDPEVFSWAATQVVTAMNATHQLGGENYVLWGGREGYETLLNTDLRQEREQIGRFMQLVVEHKHKIGFKGTLLIEPKPQEPTKHQYDYDASTVYGFLKQFGLEKEIKLNIEANHATLAGHSFHHEIATAIALGLFGSVDANRGDPQLGWDTDQFPNSVEENALVMYEILKAGGFTTGGLNFDAKVRRQSTDKYDLFYGHIGAMDTMALSLKVAARMIEDGELDKRVARRYAGWNGELGQQILNGQMTLSDIAQYAAQHQLAPQHRSGQQEQLENLVNHYLFDK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0009045 Catalysis of the reaction: alpha-D-xylose = alpha-D-xylulofuranose.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0042732 The chemical reactions and pathways involving D-xylose, a naturally occurring plant polysaccharide.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
15 441 Hamap MF_00455 Xylose isomerase [xylA].
15 441 InterPro IPR001998 Xylose isomerase
39 441 ProSiteProfiles PS51415 Xylose isomerase family profile.
39 441 InterPro IPR001998 Xylose isomerase
7 444 Gene3D G3DSA:3.20.20.150 -
6 443 FunFam G3DSA:3.20.20.150:FF:000002 Xylose isomerase
8 441 NCBIfam TIGR02630 xylose isomerase
8 441 InterPro IPR013452 Xylose isomerase, bacterial-type
8 442 SUPERFAMILY SSF51658 Xylose isomerase-like
8 442 InterPro IPR036237 Xylose isomerase-like superfamily
116 136 Coils Coil Coil
160 179 PRINTS PR00688 Xylose isomerase signature
160 179 InterPro IPR001998 Xylose isomerase
275 302 PRINTS PR00688 Xylose isomerase signature
275 302 InterPro IPR001998 Xylose isomerase
304 315 PRINTS PR00688 Xylose isomerase signature
304 315 InterPro IPR001998 Xylose isomerase
337 348 PRINTS PR00688 Xylose isomerase signature
337 348 InterPro IPR001998 Xylose isomerase
184 205 PRINTS PR00688 Xylose isomerase signature
184 205 InterPro IPR001998 Xylose isomerase
96 118 PRINTS PR00688 Xylose isomerase signature
96 118 InterPro IPR001998 Xylose isomerase
137 157 PRINTS PR00688 Xylose isomerase signature
137 157 InterPro IPR001998 Xylose isomerase
211 230 PRINTS PR00688 Xylose isomerase signature
211 230 InterPro IPR001998 Xylose isomerase
233 257 PRINTS PR00688 Xylose isomerase signature
233 257 InterPro IPR001998 Xylose isomerase
6 440 PANTHER PTHR48306 XYLOSE ISOMERASE
6 440 InterPro IPR013452 Xylose isomerase, bacterial-type

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
0.931
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Surrounding area
Pocket 2 P2Rank #2
0.154
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Surrounding area
Pocket 3 P2Rank #3
0.058
Likely same site as FPocket 14 0.6 Å 7 shared residues 100% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.052
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Surrounding area
Pocket 5 P2Rank #5
0.008
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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 #14
0.452
Likely same site as P2Rank 3 0.6 Å 7 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #31
0.342 Unusual size
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Surrounding area
Residue sets
UniProt: Active site:101-101
UniProt: Active site:104-104
UniProt: Binding site:232-232
UniProt: Binding site:268-268
UniProt: Binding site:271-271
UniProt: Binding site:296-296
UniProt: Binding site:307-307
UniProt: Binding site:309-309
UniProt: Binding site:339-339
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_A0A0H3H006
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_00240
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3H006