KpATCC43816 Protein target profile

electron transport complex, RnfABCDGE type, B subunit

Accession: VK055_0513

Gene: AIK79136.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GUG2
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Length 185
Pocket druggability (P2Rank · AlphaFold DB model) 0.225
Direct ligand evidence 0 22 total records
Functional annotation 1 EC 6 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 Ligand evidence via structure/bioactivity 2 structural and 0 bioactivity records.

Risks to review

Microbiome similarity 184 of 4744 screened genomes (3.9%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.23) — check the ligand evidence before deprioritizing on off-target risk alone. Weak predicted binding pocket FPocket selected-pocket score 0.37. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.23.

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
3.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
60.355 Higher values support similarity to known essential genes.
DEG E-value
1.6800000000000001e-72 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
87.03 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) 0.225
Structure A0A0H3GUG2
Pocket Pocket 1
Druggability (FPocket) 0.369
Structure A0A0H3GUG2
Pocket Pocket 4
ColabFold model
P2Rank 0.153 · Pocket 1
FPocket 0.351 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 184 / 4744 genomes with a hit
Prevalence 3.9%

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.

MIAISLLGLIFGLILGYASRRFAVQDDPVVEKIDELLPQSQCGQCGYPGCRPYAEAVGVQGEKINRCAPGGEAVMLKIAALLNVDPQPVDGDAQEAEPARMLAVIDEPNCIGCTKCIQACPVDAIVGATRAMHTVMSDLCTGCNLCVAPCPTQCISLVPVATTPETWKWDLHTIPVRNIPVEQHV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0022900 A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
140 151 ProSitePatterns PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.
140 151 InterPro IPR017900 4Fe-4S ferredoxin, iron-sulphur binding, conserved site
78 174 Gene3D G3DSA:3.30.70.20 -
4 15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
30 77 Gene3D G3DSA:1.10.15.40 -
1 23 Phobius SIGNAL_PEPTIDE Signal peptide region
25 84 ProSiteProfiles PS51656 4Fe-4S domain profile.
25 84 InterPro IPR007202 4Fe-4S domain
1 16 SignalP_EUK SignalP-noTM SignalP-noTM
31 169 SUPERFAMILY SSF54862 4Fe-4S ferredoxins
16 23 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 162 Hamap MF_00463 Ion-translocating oxidoreductase complex subunit B [rsxB].
1 162 InterPro IPR010207 Ion-translocating oxidoreductase complex, RnfB/RsxB
2 183 NCBIfam TIGR01944 RnfABCDGE type electron transport complex subunit B
2 183 InterPro IPR010207 Ion-translocating oxidoreductase complex, RnfB/RsxB
24 185 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
30 81 FunFam G3DSA:1.10.15.40:FF:000001 Ion-translocating oxidoreductase complex subunit B
101 130 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
101 130 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
131 160 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
131 160 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
103 157 Pfam PF14697 4Fe-4S dicluster domain
1 184 PIRSF PIRSF005784 RnfB
1 184 InterPro IPR016463 Electron transport complex, RnfB/RsxB, Proteobacteria
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
25 177 PANTHER PTHR42859 OXIDOREDUCTASE
37 69 Pfam PF04060 Putative Fe-S cluster
37 69 InterPro IPR007202 4Fe-4S 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
0.225
Likely same site as FPocket 4 1.0 Å 7 shared residues 100% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.034
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Surrounding area
Pocket 3 P2Rank #3
0.023
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #4
0.369
Likely same site as P2Rank 1 1.0 Å 7 shared residues 100% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:110-110
UniProt: Binding site:113-113
UniProt: Binding site:116-116
UniProt: Binding site:120-120
UniProt: Binding site:140-140
UniProt: Binding site:143-143
UniProt: Binding site:146-146
UniProt: Binding site:150-150
UniProt: Binding site:42-42
UniProt: Binding site:45-45
UniProt: Binding site:50-50
UniProt: Binding site:67-67
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_A0A0H3GUG2
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_0513
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.

22 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 20 similarity-based ZINC candidates
Best available ligand signal
CMO PDB via homolog 28.0 Da · LogP -0.04 · TPSA 19.9 Open detail RCSB PDB
PDT PDB via homolog Detail RCSB PDB
ZINC33364781 ZINC proposed compound · Tanimoto 0.667 Detail ZINC
ZINC39212759 ZINC proposed compound · Tanimoto 0.667 Detail ZINC
ZINC4362803 ZINC proposed compound · Tanimoto 0.667 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
CMO RCSB PDB
1E08
P07598 28.0 Da LogP -0.04 TPSA 19.9 ✓ Ro5 ✓ Clean [C-]#[O+]
PDT RCSB PDB
1E08
P07598 108.2 Da LogP 1.24 TPSA 0.0 ✓ Ro5 ✓ Clean C(CS)CS

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 A0A0H3GUG2