KpATCC43816 Protein target profile

rcsB

Accession: VK055_4883

Gene: rcsB AIK83410.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GVM1
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Length 216
Pocket druggability (P2Rank · AlphaFold DB model) 0.21
Direct ligand evidence 0 52 total records
Functional annotation 0 EC 3 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 0.41. This supports review but is not experimental validation. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Microbiome similarity 109 of 4744 screened genomes (2.3%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.21) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.21.

Evidence coverage

Core evidence streams are available for this target.
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
2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
97.685 Higher values support similarity to known essential genes.
DEG E-value
2.41e-153 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
88.18 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) 0.21
Structure A0A0H3GVM1
Pocket Pocket 1
Druggability (FPocket) 0.409
Structure A0A0H3GVM1
Pocket Pocket 1
ColabFold model
P2Rank 0.2 · Pocket 1
FPocket 0.54 · Pocket 14
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 109 / 4744 genomes with a hit
Prevalence 2.3%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MNTMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHFPDLSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKISASGYGDKRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVSLSATDKE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

3
  • GO:0000160 A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
  • 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.

35 records
Show feature table
Start End DB Term Name
1 208 PANTHER PTHR45566 HTH-TYPE TRANSCRIPTIONAL REGULATOR YHJB-RELATED
1 214 Hamap MF_00981 Transcriptional regulatory protein RcsB [rcsB].
1 214 InterPro IPR030864 Transcriptional regulatory protein RcsB
148 207 Gene3D G3DSA:1.10.10.10 -
148 207 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
148 205 SMART SM00421 luxrmega5
148 205 InterPro IPR000792 Transcription regulator LuxR, C-terminal
1 147 Gene3D G3DSA:3.40.50.2300 -
165 192 ProSitePatterns PS00622 LuxR-type HTH domain signature.
165 192 InterPro IPR000792 Transcription regulator LuxR, C-terminal
4 120 SMART SM00448 REC_2
4 120 InterPro IPR001789 Signal transduction response regulator, receiver domain
151 201 Pfam PF00196 Bacterial regulatory proteins, luxR family
151 201 InterPro IPR000792 Transcription regulator LuxR, C-terminal
6 122 CDD cd17535 REC_NarL-like
1 147 FunFam G3DSA:3.40.50.2300:FF:000023 Transcriptional regulatory protein RcsB
148 207 FunFam G3DSA:1.10.10.10:FF:000072 Transcriptional regulatory protein RcsB
142 207 SUPERFAMILY SSF46894 C-terminal effector domain of the bipartite response regulators
142 207 InterPro IPR016032 Signal transduction response regulator, C-terminal effector
151 165 PRINTS PR00038 LuxR bacterial regulatory protein HTH signature
151 165 InterPro IPR000792 Transcription regulator LuxR, C-terminal
165 181 PRINTS PR00038 LuxR bacterial regulatory protein HTH signature
165 181 InterPro IPR000792 Transcription regulator LuxR, C-terminal
181 193 PRINTS PR00038 LuxR bacterial regulatory protein HTH signature
181 193 InterPro IPR000792 Transcription regulator LuxR, C-terminal
6 120 Pfam PF00072 Response regulator receiver domain
6 120 InterPro IPR001789 Signal transduction response regulator, receiver domain
3 135 SUPERFAMILY SSF52172 CheY-like
3 135 InterPro IPR011006 CheY-like superfamily
144 209 ProSiteProfiles PS50043 LuxR-type HTH domain profile.
144 209 InterPro IPR000792 Transcription regulator LuxR, C-terminal
151 204 CDD cd06170 LuxR_C_like
151 204 InterPro IPR000792 Transcription regulator LuxR, C-terminal
5 124 ProSiteProfiles PS50110 Response regulatory domain profile.
5 124 InterPro IPR001789 Signal transduction response regulator, receiver domain

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
0.21
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Surrounding area
Pocket 2 P2Rank #2
0.014
Likely same site as FPocket 1 6.2 Å 10 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.009
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.409
Likely same site as P2Rank 2 6.2 Å 10 shared residues 100% of smaller site
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_A0A0H3GVM1
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4883
ColabFold — — full sequence — Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
BEF PDB via homolog 66.0 Da · LogP 0.88 · TPSA 0.0 Open detail RCSB PDB
PE4 PDB via homolog Detail RCSB PDB
ZINC5650743 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC6403917 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC12501520 ZINC proposed compound · Tanimoto 0.688 Detail ZINC

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
BEF RCSB PDB
5O8Z
P58663 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
PE4 RCSB PDB
5O8Y
P58663 354.4 Da LogP 0.11 TPSA 84.8 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCO

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.

Cross-references

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

Sequence

UniProt A0A0H3GVM1