Protein target profile

VK055_5021

putative serotype K2 polymerase

Genome: KpATCC43816 Gene: AIK83547.1 3D evidence: AlphaFold DB model + ColabFold model UniProt Q48456
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Length 414
Pocket druggability 0.983
Functional annotation 0 EC 1 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. No similar gut-microbiome protein detected The current microbiome screen did not find a significant match in the screened reference genomes. Second pocket predictor agrees P2Rank predicted binding-site probability 0.97. Structure available AlphaFold DB model + ColabFold model

Risks to review

Mixed conservation Core/accessory calls are not fully concordant. Best pocket may be a modeling artifact FPocket selected-pocket score 0.98, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity.

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
0.0% 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
84.34 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 0.983
Structure Q48456
Pocket Pocket 34
P2Rank 0.97
Structure Q48456
Pocket Pocket 1
ColabFold model
FPocket 0.996 · Pocket 30
P2Rank 0.953 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 0 / 4744 genomes with a hit
Prevalence 0.0%

Cross-references

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

Sequence

UniProt Q48456

Sequence

Primary amino-acid sequence viewer.

MHNIIRLLFRNPFFFLFCLFIPFDNTSLQSIGGIMTASPSALILLPGLFVSILSKGLKVNKNILLCFFGVLLISFLYYFYWVFYFPELDPIFILDRGSRYFLLYVFYFLALYYSLRQNIKDIRAGAALIIIVVIFSVLLNYLDPAIINNKSIIQYNDFISPERLRGFSLEASVFGYQIVCSILLLAVLLNWSTFFLVTVTIVIAILTTSKGAALSFLICICFYFSLKGKLMFRVLLSLCSIVISYIIFKYYFLDALASDIDTYSSVATRGTMFIVGLKIFLFNPLGVGFFGYLPSIYDFTSGVIDFIKSHFPFLNFDEVYTYTIPGEYKTVGTKSLILDLLIIYGVFFLIPFIYFIKKILKEFDAQSERNSYFLLLFIIFSNMFFISHLGSYFTPFCIAFLIILSKNRAENDIN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

1
  • 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.

36 records
Show feature table
Start End DB Term Name
97 115 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
116 126 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
29 50 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
370 392 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
198 353 Pfam PF04932 O-Antigen ligase
198 353 InterPro IPR007016 O-antigen ligase-related
62 85 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
173 195 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
231 252 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
372 404 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
167 188 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
226 230 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
335 357 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
127 147 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
274 296 TMHMM TMhelix 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.
7 24 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
63 85 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
405 414 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
28 50 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
189 194 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
51 61 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
24 28 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
253 272 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
273 293 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
128 147 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
294 335 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
195 225 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
234 253 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
148 166 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
336 356 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
7 23 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
86 96 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
357 371 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
100 115 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.

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 #34
0.983
Likely same site as P2Rank 1 1.2 Å 28 shared residues 97% of smaller site
Unusual size
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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
0.97
Likely same site as FPocket 34 1.2 Å 28 shared residues 97% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.501
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Surrounding area
Site 3 P2Rank #3
0.243
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Surrounding area
Site 4 P2Rank #4
0.224
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Surrounding area
Site 5 P2Rank #5
0.148
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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_Q48456
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_5021
ColabFold — — full sequence — Loaded