KpATCC43816 Protein target profile

outer membrane assembly lipoprotein YfgL

Accession: VK055_4658

Gene: AIK83192.1 yfgL 3D evidence: Experimental + ColabFold model Metabolism Not in network UniProt A0A0W8AU86
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Length 392
Pocket druggability (P2Rank · Experimental) 0.671
Functional annotation 0 EC 4 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

Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. 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 0.44. This supports review but is not experimental validation. Review the complete evidence below

Risks to review

Microbiome similarity 105 of 4744 screened genomes (2.2%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.67) — check the ligand evidence before deprioritizing on off-target risk alone.

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)
N
DEG identity (%)
39.487 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
91.28 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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) 0.671
Structure 8ORR
Pocket Pocket 1
Druggability (FPocket) 0.438
Structure 8ORR
Pocket Pocket 15
ColabFold model
P2Rank 0.406 · Pocket 1
FPocket 0.841 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 105 / 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.

MQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPSTSWSTSVGDGIGEFYSNLHPAFADGVVYAADRKGTVKALNADDGKEVWSVNLAEKDGWFSRTPALLSGGVTVSGGHVYIGSEKAQLYALNTSDGTVAWQTRVAGEALSRPVVSDGMVLVHTSNGQLQALNETDGAVKWTVNLDMPALSLRGESAPATAYGAAIVGGDNGRVSAVLMQQGQMIWQQRISTATGPTEIDRLNDVDTTPIIVNGVVYALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRLLALTTDGGVTLWTQSDLLHRLLTAPVLYNGNLVVGDSEGYMHWVNPEDGHFVAQQKVDSSGFLTDPVVADGRLLIQAKDGTLYAITR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Unknown

Gene Ontology (GO)

4
  • GO:0005515 Binding to a protein.
  • GO:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
  • GO:0043165 The assembly of an outer membrane of the type formed in Gram-negative bacteria. This membrane is enriched in polysaccharide and protein, and the outer leaflet of the membrane contains specific lipopolysaccharide structures.
  • 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

35 records
Show feature table
Start End DB Term Name
31 392 CDD cd10276 BamB_YfgL
1 5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 25 Phobius SIGNAL_PEPTIDE Signal peptide region
21 391 Gene3D G3DSA:2.130.10.10 -
21 391 InterPro IPR015943 WD40/YVTN repeat-like-containing domain superfamily
2 392 Hamap MF_00923 Outer membrane protein assembly factor BamB [bamB].
2 392 InterPro IPR017687 Outer membrane protein assembly factor BamB
1 22 SignalP_EUK SignalP-noTM SignalP-noTM
1 25 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
1 20 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile.
78 319 Pfam PF13360 PQQ-like domain
78 319 InterPro IPR002372 Pyrrolo-quinoline quinone repeat
8 390 NCBIfam TIGR03300 outer membrane protein assembly factor BamB
8 390 InterPro IPR017687 Outer membrane protein assembly factor BamB
6 17 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
45 388 PANTHER PTHR34512 CELL SURFACE PROTEIN
289 320 SMART SM00564 ire1_9
289 320 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
200 231 SMART SM00564 ire1_9
200 231 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
251 282 SMART SM00564 ire1_9
251 282 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
329 361 SMART SM00564 ire1_9
329 361 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
64 96 SMART SM00564 ire1_9
64 96 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
155 186 SMART SM00564 ire1_9
155 186 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
114 146 SMART SM00564 ire1_9
114 146 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
26 392 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 23 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
25 385 SUPERFAMILY SSF50998 Quinoprotein alcohol dehydrogenase-like
25 385 InterPro IPR011047 Quinoprotein alcohol dehydrogenase-like superfamily
18 25 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.

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
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 8ORR
X-ray 1.68 Å AAA
92.3% 31-392
PDBe RCSB PDBj File
Viewing
ColabFold VK055_4658
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0W8AU86

Structure

PDB 8ORR