KpATCC43816 Protein target profile

putative L,D-transpeptidase YbiS

Accession: VK055_1678

Gene: AIK80298.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 4 reactions UniProt A0A0H3GQM2
Export view
Length 271
Pocket druggability (P2Rank · AlphaFold DB model) 0.81
Metabolic reactions 4
Chokepoint No
Functional annotation 0 EC 8 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. Moderate predicted binding pocket FPocket selected-pocket score 0.64. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.81. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 137 of 4744 screened genomes (2.9%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.81) — 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
2.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
41.155 Higher values support similarity to known essential genes.
DEG E-value
2.24e-62 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
95.62 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) 0.81
Structure A0A0H3GQM2
Pocket Pocket 1
Druggability (FPocket) 0.638
Structure A0A0H3GQM2
Pocket Pocket 8
ColabFold model
P2Rank 0.839 · Pocket 1
FPocket 0.763 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 137 / 4744 genomes with a hit
Prevalence 2.9%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reactions

4 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MVGQNQVITIPDDNKQPLEYFAAKYQMGLSNMLEANPGVDTYLPKGGSVLNIPQQLILPDTVHEGIIINSAEMRLYYYPKGTNTVIVLPIGIGQLGKDTPINWTTKVERKKAGPTWTPTAKMHAEYAAAGNPLPAVVPAGPDNPMGLYALYIGRLYAIHGTNANFGIGLRVSHGCVRLRNDDIKFLFENVPVGTRVQFIDEPVKATTEPDGSRYIEVHNPLSTTEAQFQGGEIVPITLTQPVQAVTSQSDVDQNVVEQAIQNRSGMPVRLN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Subcellular localization

Localization
Unknown

Gene Ontology (GO)

8
  • GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
  • GO:0005576 The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
  • GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
  • GO:0016757 Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
  • GO:0071972 Catalysis of the reaction: 2 a peptidoglycan dimer (tetrapeptide) + 3 H2O = a peptidoglycan tetramer with L,D cross-links (L-Lys-D-Asn-L-Lys) + di-trans,poly-cis-undecaprenyl diphosphate + 4 D-alanine.
  • GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
  • GO:0018104 The process of covalently linking peptidoglycan (murein) to proteins.
  • GO:0008360 Any process that modulates the surface configuration of a cell.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
12 208 PANTHER PTHR30582 L,D-TRANSPEPTIDASE
66 196 CDD cd16913 YkuD_like
66 196 InterPro IPR005490 L,D-transpeptidase catalytic domain
202 269 Pfam PF17969 L,D-transpeptidase C-terminal domain
202 269 InterPro IPR041597 L,D-transpeptidase C-terminal domain
64 198 SUPERFAMILY SSF141523 L,D-transpeptidase catalytic domain-like
64 198 InterPro IPR038063 L,D-transpeptidase catalytic domain-like
56 198 Gene3D G3DSA:2.40.440.10 -
56 198 InterPro IPR038063 L,D-transpeptidase catalytic domain-like
60 199 FunFam G3DSA:2.40.440.10:FF:000001 L,D-transpeptidase YbiS
66 196 Pfam PF03734 L,D-transpeptidase catalytic 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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.81
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.3
Likely same site as FPocket 8 2.3 Å 13 shared residues 93% of smaller site
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #8
0.638
Likely same site as P2Rank 2 2.3 Å 13 shared residues 93% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #5
0.212
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_A0A0H3GQM2
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_1678
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GQM2

Pathways

BioCyc RXN-16665[CCO-PERI-BAC]-A-DONOR-PG-WITH-MESODAP-TETRAPEPTIDE/GLY//CPD-17969/D-ALANINE.76. BioCyc RXN-16665[CCO-CYTOSOL]-A-DONOR-PG-WITH-MESODAP-TETRAPEPTIDE/GLY//CPD-17969/D-ALANINE.75. BioCyc RXN0-7489[CCO-CYTOSOL]-A-DONOR-PG-WITH-MESODAP-TETRAPEPTIDE/AN-ACCEPTOR-PG-WITH-MESODAP-TETRAPEPTIDE//CPD-17947/D-ALANINE.112. BioCyc RXN0-7489[CCO-PERI-BAC]-A-DONOR-PG-WITH-MESODAP-TETRAPEPTIDE/AN-ACCEPTOR-PG-WITH-MESODAP-TETRAPEPTIDE//CPD-17947/D-ALANINE.113.