Protein target profile

VK055_0023

positive DNA-binding transcriptional regulator of capsular polysaccharide synthesis, activates its own expression

Genome: KpATCC43816 Gene: AIK78654.1 rcsA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQD4
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Length 204
Pocket druggability 0.263
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. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 74 of 4744 screened genomes (1.6%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.26. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.02.

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
1.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
67.157 Higher values support similarity to known essential genes.
DEG E-value
2.93e-99 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Unknown

Structure confidence

ColabFold pLDDT
91.77 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 0.263
Structure A0A0H3GQD4
Pocket Pocket 4
P2Rank 0.016
Structure A0A0H3GQD4
Pocket Pocket 1
ColabFold model
FPocket 0.545 · Pocket 5
P2Rank 0.326 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 74 / 4744 genomes with a hit
Prevalence 1.6%

Cross-references

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

Sequence

UniProt A0A0H3GQD4

Sequence

Primary amino-acid sequence viewer.

MIMDLCSYTRLGLTGYLTSRGIKKQEIVEVNSAADLQKHCTSCCPAVVFLNEDCFVHDDESNGIIRQIITQNPATLFVIFMSLANIHFDRYLRVRKNLLISSKSITPKDLDVILVNYLKYKNTSVGQLTLPTLSLSKTESNMLQMWMAGHGTSQISTQMNIKAKTVSSHKGNIKKKIQTHNKQVIYHIVRLTENITSGIQVNMR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
119 185 SUPERFAMILY SSF46894 C-terminal effector domain of the bipartite response regulators
119 185 InterPro IPR016032 Signal transduction response regulator, C-terminal effector
98 193 Gene3D G3DSA:1.10.10.10 -
98 193 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
149 176 ProSitePatterns PS00622 LuxR-type HTH domain signature.
149 176 InterPro IPR000792 Transcription regulator LuxR, C-terminal
128 193 ProSiteProfiles PS50043 LuxR-type HTH domain profile.
128 193 InterPro IPR000792 Transcription regulator LuxR, C-terminal
134 188 Pfam PF00196 Bacterial regulatory proteins, luxR family
134 188 InterPro IPR000792 Transcription regulator LuxR, C-terminal
135 191 CDD cd06170 LuxR_C_like
135 191 InterPro IPR000792 Transcription regulator LuxR, C-terminal
149 165 PRINTS PR00038 LuxR bacterial regulatory protein HTH signature
149 165 InterPro IPR000792 Transcription regulator LuxR, C-terminal
135 149 PRINTS PR00038 LuxR bacterial regulatory protein HTH signature
135 149 InterPro IPR000792 Transcription regulator LuxR, C-terminal
165 177 PRINTS PR00038 LuxR bacterial regulatory protein HTH signature
165 177 InterPro IPR000792 Transcription regulator LuxR, C-terminal
1 204 Hamap MF_00982 Transcriptional regulatory protein RcsA [rcsA].
1 204 InterPro IPR030866 Transcriptional regulatory protein RcsA
132 189 SMART SM00421 luxrmega5
132 189 InterPro IPR000792 Transcription regulator LuxR, C-terminal

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 #4
0.263
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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
0.016
Show in viewer
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_A0A0H3GQD4
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_0023
ColabFold — — full sequence — Loaded