KpATCC43816 Protein target profile

bamD

Accession: VK055_4582

Gene: AIK83120.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GWW7
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Length 245
Pocket druggability (P2Rank · AlphaFold DB model) 0.178
Functional annotation 0 EC 4 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

Risks to review

Microbiome similarity 120 of 4744 screened genomes (2.5%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.37. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.18.

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
2.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
93.878 Higher values support similarity to known essential genes.
DEG E-value
1.64e-173 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
91.17 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) 0.178
Structure A0A0H3GWW7
Pocket Pocket 1
Druggability (FPocket) 0.367
Structure A0A0H3GWW7
Pocket Pocket 1
ColabFold model
P2Rank 0.127 · Pocket 1
FPocket 0.408 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 120 / 4744 genomes with a hit
Prevalence 2.5%

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.

MTRMKYLVAAATLSLALVGCSGSKEEVPDNPPNEIYATAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFMRLNPTHPNIDYVIYMRGLTNMALDDSALQGFFGVDRSDRDPQHARDAFNDFSKLVRGYPNSQYATDAYKRMVFLKDRLAKYELSVVDYYTDRGAWVAVVNRVEGMMRNYPDTQATRDALPKMENAYRQMQMNAQADKVAKIIAANSKNT

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
OuterMembrane

Gene Ontology (GO)

4
  • GO:0005515 Binding to a protein.
  • GO:1990063 Protein complex which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. In E. coli it is composed of BamABCDE, of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE. BamA interacts directly with BamB and the BamCDE subcomplex.
  • 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.

23 records
Show feature table
Start End DB Term Name
1 22 SignalP_EUK SignalP-noTM SignalP-noTM
29 245 FunFam G3DSA:1.25.40.10:FF:000015 Outer membrane protein assembly factor BamD
1 23 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
1 22 Phobius SIGNAL_PEPTIDE Signal peptide region
1 20 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile.
1 242 PANTHER PTHR37423 SOLUBLE LYTIC MUREIN TRANSGLYCOSYLASE-RELATED
29 245 Gene3D G3DSA:1.25.40.10 Tetratricopeptide repeat domain
29 245 InterPro IPR011990 Tetratricopeptide-like helical domain superfamily
27 121 SUPERFAMILY SSF48452 TPR-like
27 121 InterPro IPR011990 Tetratricopeptide-like helical domain superfamily
23 245 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
28 236 Pfam PF13525 Outer membrane lipoprotein
28 236 InterPro IPR039565 Outer membrane lipoprotein BamD-like
1 25 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
4 242 Hamap MF_00922 Outer membrane protein assembly factor BamD [bamD].
4 242 InterPro IPR017689 Outer membrane protein assembly factor BamD
19 22 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
7 18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
31 241 CDD cd15830 BamD
31 241 InterPro IPR017689 Outer membrane protein assembly factor BamD
5 244 NCBIfam TIGR03302 outer membrane protein assembly factor BamD
5 244 InterPro IPR017689 Outer membrane protein assembly factor BamD

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
0.178
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.003
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
0.367 Unusual size
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_A0A0H3GWW7
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4582
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GWW7