Protein target profile

VK055_5087

trbL/VirB6 plasmid conjugal transfer family protein

Genome: KpATCC43816 Gene: AIK83613.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A4GZG2
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Length 359
Pocket druggability 0.999
Functional annotation 0 EC 2 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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. Second pocket predictor agrees P2Rank predicted binding-site probability 0.71. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 1 of 4744 screened genomes (0.0%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 1.00) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant. Best pocket may be a modeling artifact FPocket selected-pocket score 1.00, 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
76.51 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 0.999
Structure A4GZG2
Pocket Pocket 25
P2Rank 0.711
Structure A4GZG2
Pocket Pocket 1
ColabFold model
FPocket 0.981 · Pocket 14
P2Rank 0.388 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 1 / 4744 genomes with a hit
Prevalence 0.0%

Cross-references

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

Sequence

UniProt A4GZG2

Sequence

Primary amino-acid sequence viewer.

MAELGTFEFIDKQLIGGITQSTSGLMMEHSSMVMGLAAVSATIYIMWRGYQTLAGKLSTPMEDTMWDIMRMAIILSFVANVSGYLDGVIDAINGLKEGFSGGDNIWQILDTLWDKAKVLGKTLHDMDNSTYVKDEGMTAQFYVWLGIFILMALTAFVSMVAEIMILLLSITAPIFIFCLMYGFLRPMFNNWLQNIFAAILTVLFSALSLRVVINFMTKILAQSQAGAAQSNIVELGAQVCLAGICAAILVYISAKVAAALAGASATVSMQGLAAVGIGAAFGAGKLAGGGLKETKRSALDNIQGWKDANAGKPGKPGGELGYNASKARKYAIEQMIARNEARRLAQRRESAVKKFNSQV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2
  • GO:0030255 The process in which proteins are transferred into the extracellular milieu or directly into host cells, via the type IV protein secretion system.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
31 50 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
136 158 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
41 251 Pfam PF04610 TrbL/VirB6 plasmid conjugal transfer protein
41 251 InterPro IPR007688 Plasmid conjugal transfer TrbL/VirB6
258 283 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
68 85 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
269 291 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 28 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
284 359 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
165 187 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
141 158 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
232 254 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
165 184 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
190 212 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
86 140 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
191 213 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
159 164 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
253 257 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
232 252 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
48 67 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
185 189 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
29 47 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
213 231 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
71 93 TMHMM TMhelix 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 · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #25
0.999
Likely same site as P2Rank 1 1.5 Å 19 shared residues 100% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #2
0.435
Likely same site as P2Rank 3 4.6 Å 9 shared residues 100% of smaller site
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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
0.711
Likely same site as FPocket 25 1.5 Å 19 shared residues 100% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.195
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Surrounding area
Site 3 P2Rank #3
0.053
Likely same site as FPocket 2 4.6 Å 9 shared residues 100% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.049
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Surrounding area
Site 5 P2Rank #5
0.024
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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_A4GZG2
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_5087
ColabFold — — full sequence — Loaded