KpATCC43816 Protein target profile

electron transport complex, RnfABCDGE type, C subunit

Accession: VK055_0512

Gene: AIK79135.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A486MZF5
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Length 719
Pocket druggability (P2Rank · AlphaFold DB model) 0.947
Functional annotation 1 EC 6 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

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.95, FPocket 0.81). Use the 3D pocket comparison to verify whether they identify the same site. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Strong predicted binding pocket FPocket selected-pocket score 0.81. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.95. Review the complete evidence below

Risks to review

Microbiome similarity 106 of 4744 screened genomes (2.2%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.95) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant.

Evidence gaps

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
2.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
81.523 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
80.85 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) 0.947
Structure A0A486MZF5
Pocket Pocket 1
Druggability (FPocket) 0.81
Structure A0A486MZF5
Pocket Pocket 35
ColabFold model
P2Rank 0.948 · Pocket 1
FPocket 0.615 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 106 / 4744 genomes with a hit
Prevalence 2.2%

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.

MFKLFSAFRKDKVWDFNGGIHPPEMKTQSNGTPLRQVSLPQRFVIPLKQHIGAEGELCVKVGDRVLRGQPLTRGWGRMLPVHAPTSGTIAAIAPHTTAHPSALAEMSVIIDADGEDRWIERDGWSDYQTRTREALIERIHQFGVAGLGGAGFPTGSKLRGGGDKIKTLIINAAECEPYITADDRLMQDCAAQIVEGIRILAHILQPEEVLIGIEDNKPQAISMLRAVLCDAHGISLRVIPTKYPSGGAKQLTQILTGKQVPHGGRSSDIGVLMQNVGTAYAVKRAVIDGEPLTERVVTLTGEAVTRPGNVWARLGTPVRHLLNDAGFCPSAEPMVIMGGPLMGFTLPWLDVPVVKITNCLLAPSASEMGEPQEEKGCIRCSACADACPADLLPQQLYWFSKGQQHDKATAHNLADCIECGACAWVCPSNIPLVQYFRQEKAEIAAIRQEEQRAAEAKARFEARQARLEREKAARAERHKKAAVQPAAKDQEAISAALARVRDKQRDAAQPIVIQAGAKPDNSEAIAAREARKAEARARKAQQQAAPVEAPAAEPVDPRKAAVEAAIARAKARKAEQQAAPVDAPAAEPVDPRKAAVEAAIARAKARKAEQQAAPVDAPAVEPVDPRKAAVEAAIARAKARKAEQQAAPVDAPAAEPVDPRKAAVEAAIARAKARKAEQQATQQDLASAAANDDPRKAAVAAAIARVQARKATQQAVNEE

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:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • 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: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:0046872 Binding to a metal ion.
  • 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

34 records
Show feature table
Start End DB Term Name
296 344 Pfam PF10531 SLBB domain
296 344 InterPro IPR019554 Soluble ligand binding domain
144 291 Gene3D G3DSA:3.40.50.11540 -
144 291 InterPro IPR037225 NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily
407 436 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
407 436 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
661 681 Coils Coil Coil
1 578 PANTHER PTHR43034 ION-TRANSLOCATING OXIDOREDUCTASE COMPLEX SUBUNIT C
1 578 InterPro IPR010208 Ion-translocating oxidoreductase complex, subunit RnfC/RsxC
559 579 Coils Coil Coil
367 397 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
367 397 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
377 430 Pfam PF12838 4Fe-4S dicluster domain
377 430 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
627 647 Coils Coil Coil
371 446 Gene3D G3DSA:3.30.70.20 -
443 470 Coils Coil Coil
1 719 Hamap MF_00461 Ion-translocating oxidoreductase complex subunit C [rsxC].
1 719 InterPro IPR010208 Ion-translocating oxidoreductase complex, subunit RnfC/RsxC
523 543 Coils Coil Coil
139 283 Pfam PF01512 Respiratory-chain NADH dehydrogenase 51 Kd subunit
139 283 InterPro IPR011538 NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain
673 697 MobiDBLite mobidb-lite consensus disorder prediction
416 427 ProSitePatterns PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.
416 427 InterPro IPR017900 4Fe-4S ferredoxin, iron-sulphur binding, conserved site
336 444 SUPERFAMILY SSF46548 alpha-helical ferredoxin
13 445 NCBIfam TIGR01945 RnfABCDGE type electron transport complex subunit C
13 445 InterPro IPR010208 Ion-translocating oxidoreductase complex, subunit RnfC/RsxC
14 115 Pfam PF13375 RnfC Barrel sandwich hybrid domain
14 115 InterPro IPR026902 RnfC Barrel sandwich hybrid domain
94 303 SUPERFAMILY SSF142019 Nqo1 FMN-binding domain-like
94 303 InterPro IPR037225 NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily
593 613 Coils Coil Coil
532 556 MobiDBLite mobidb-lite consensus disorder prediction

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
0.947
Likely same site as FPocket 8 2.7 Å 30 shared residues 88% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.141
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Surrounding area
Pocket 3 P2Rank #3
0.062
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Surrounding area
Pocket 4 P2Rank #4
0.059
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Surrounding area
Pocket 5 P2Rank #5
0.027
Likely same site as FPocket 1 5.9 Å 4 shared residues 57% of smaller site
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #35
0.81
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Surrounding area
Pocket 2 FPocket #8
0.633 Unusual size
Likely same site as P2Rank 1 2.7 Å 30 shared residues 88% of smaller site
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Surrounding area
Pocket 3 FPocket #1
0.607
Likely same site as P2Rank 5 5.9 Å 4 shared residues 57% of smaller site
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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_A0A486MZF5
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_0512
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A486MZF5