KpATCC43816 Protein target profile

inner-membrane protein insertion factor

Accession: VK055_3358

Gene: AIK81915.1 oxaA 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3H4V7
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Length 531
Pocket druggability (P2Rank · AlphaFold DB model) 0.937
Functional annotation 0 EC 5 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

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.94. Structure available AlphaFold DB model + ColabFold model

Risks to review

Low human similarity A human hit was flagged, but identity is only 27.536% - a weak match, lower risk than a close homolog. This target also has a predicted binding pocket (P2Rank 0.94) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 155 of 4744 screened genomes (3.3%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.94) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.91, 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 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
Hit
Human identity (%)
27.536 Lower values reduce human off-target concern.
Human E-value
1.89e-12
Gut microbiome similarity
3.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
87.28 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) 0.937
Structure A0A0H3H4V7
Pocket Pocket 1
Druggability (FPocket) 0.913
Structure A0A0H3H4V7
Pocket Pocket 11
ColabFold model
P2Rank 0.854 · Pocket 1
FPocket 0.961 · Pocket 4
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 155 / 4744 genomes with a hit
Prevalence 3.3%

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.

MIWQAWEQDKNPQPQQQTTQTTTTAAGSAADQGVPASGQGKLITVKTDVLELTINTNGGDIEQALLLAYPKTLKSTEPFQLLETTPQFVYQAQSGLTGRDGPDNPANGPRPLYNVDKEAFVLADGQDELVIPLTYTDKAGNVFTKTFTLKRGGYAVNVGYSVQNASEKPLEVSTFGQLKQTAALPTSRDTQTGGLSTMHTFRGAAFSTADSKYEKYKFDTILDNENLNVSTKNGWVAMLQQYFTTAWVPRNNGTNNFYTANLGNGVVAIGYKSQPVLVQPGQTDKLQSTLWVGPAIQDKMAAVAPHLDLTVDYGWLWFISQPLFKLLKFIHSFLGNWGFSIIVITFIVRGIMYPLTKAQYTSMAKMRMLQPKIQAMRERLGDDKQRQSQEMMALYKAEKVNPLGGCFPLIIQMPIFLALYYMLSASVELRHAPFILWIHDLSAQDPYYILPIIMGATMFFIQKMSPTTVTDPMQQKIMTFMPVIFTVFFLWFPSGLVVYYIVSNLVTIIQQQLIYRGLEKRGLHSREKKKS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

5
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0032977 Binds transmembrane domain-containing proteins and mediates their integration into a membrane.
  • 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:0051205 The process that results in the incorporation of a protein into a biological membrane. Incorporation in this context means having some part or covalently attached group that is inserted into the the hydrophobic region of one or both bilayers.
  • GO:0015031 The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

55 records
Show feature table
Start End DB Term Name
333 355 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
38 318 Gene3D G3DSA:2.70.98.90 -
38 318 InterPro IPR038221 YidC, periplasmic domain superfamily
140 160 PRINTS PR00701 60kDa inner membrane protein signature
140 160 InterPro IPR001708 Membrane insertase YidC/ALB3/OXA1/COX18
307 327 PRINTS PR00701 60kDa inner membrane protein signature
307 327 InterPro IPR001708 Membrane insertase YidC/ALB3/OXA1/COX18
445 467 PRINTS PR00701 60kDa inner membrane protein signature
445 467 InterPro IPR001708 Membrane insertase YidC/ALB3/OXA1/COX18
482 505 PRINTS PR00701 60kDa inner membrane protein signature
482 505 InterPro IPR001708 Membrane insertase YidC/ALB3/OXA1/COX18
200 218 PRINTS PR00701 60kDa inner membrane protein signature
200 218 InterPro IPR001708 Membrane insertase YidC/ALB3/OXA1/COX18
234 249 PRINTS PR00701 60kDa inner membrane protein signature
234 249 InterPro IPR001708 Membrane insertase YidC/ALB3/OXA1/COX18
398 421 PRINTS PR00701 60kDa inner membrane protein signature
398 421 InterPro IPR001708 Membrane insertase YidC/ALB3/OXA1/COX18
48 69 PRINTS PR00701 60kDa inner membrane protein signature
48 69 InterPro IPR001708 Membrane insertase YidC/ALB3/OXA1/COX18
1 33 MobiDBLite mobidb-lite consensus disorder prediction
1 335 NCBIfam TIGR03593 membrane protein insertase, YidC/Oxa1 family, N-terminal domain
1 335 InterPro IPR028053 Membrane insertase YidC, N-terminal
1 336 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
357 399 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
38 318 FunFam G3DSA:2.70.98.90:FF:000001 Membrane protein insertase YidC
336 516 NCBIfam TIGR03592 membrane protein insertase YidC
336 516 InterPro IPR028055 Membrane insertase YidC/Oxa/ALB, C-terminal
337 516 Pfam PF02096 60Kd inner membrane protein
337 516 InterPro IPR028055 Membrane insertase YidC/Oxa/ALB, C-terminal
480 502 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
477 502 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
400 422 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
400 423 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
447 465 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
466 476 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
8 30 MobiDBLite mobidb-lite consensus disorder prediction
41 313 CDD cd19961 EcYidC-like_peri
41 313 InterPro IPR028053 Membrane insertase YidC, N-terminal
471 495 PRINTS PR01900 YidC translocation/secretion protein signature
471 495 InterPro IPR001708 Membrane insertase YidC/ALB3/OXA1/COX18
322 338 PRINTS PR01900 YidC translocation/secretion protein signature
322 338 InterPro IPR001708 Membrane insertase YidC/ALB3/OXA1/COX18
451 466 PRINTS PR01900 YidC translocation/secretion protein signature
451 466 InterPro IPR001708 Membrane insertase YidC/ALB3/OXA1/COX18
15 518 Hamap MF_01810 Membrane protein insertase YidC [yidC].
15 518 InterPro IPR019998 Membrane insertase YidC
295 521 PANTHER PTHR12428 OXA1
295 521 InterPro IPR001708 Membrane insertase YidC/ALB3/OXA1/COX18
43 326 Pfam PF14849 YidC periplasmic domain
43 326 InterPro IPR028053 Membrane insertase YidC, N-terminal
424 446 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
338 516 CDD cd20070 5TM_YidC_Alb3
338 516 InterPro IPR047196 Membrane insertase YidC/ALB, C-terminal
503 531 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
337 356 Phobius TRANSMEMBRANE 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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.937
Likely same site as FPocket 11 2.5 Å 31 shared residues 82% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.262
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Surrounding area
Pocket 3 P2Rank #3
0.242
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Surrounding area
Pocket 4 P2Rank #4
0.13
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Surrounding area
Pocket 5 P2Rank #5
0.02
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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 #11
0.913 Unusual size
Likely same site as P2Rank 1 2.5 Å 31 shared residues 82% 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_A0A0H3H4V7
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_3358
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3H4V7