Genome KpKP13

Protein target profile

Endo-type membrane-bound lytic murein transglycosylase A

Accession: KP13_01546

Gene: emtA AHE43925.1 3D evidence: AlphaFold DB model + ColabFold model UniProt W1DGZ0
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Length 167
Pocket druggability (P2Rank · AlphaFold DB model) 0.025
Functional annotation 1 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

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 0.82. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 109 of 4744 screened genomes (2.3%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.82) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.03.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. 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
2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
97.2 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) 0.025
Structure W1DGZ0
Pocket Pocket 1
Druggability (FPocket) 0.82
Structure W1DGZ0
Pocket Pocket 3
ColabFold model
P2Rank 0.073 · Pocket 1
FPocket 0.184 · Pocket 8
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 109 / 4744 genomes with a hit
Prevalence 2.3%

Cross-references

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

Sequence

UniProt W1DGZ0

Sequence

Primary amino-acid sequence viewer.

MQWMPISEKAGAAWGVDPQLITAIIAIESGGNPAVVSKSGAVGLMQLKPSTSGRDVYRRMGWRGEPSVSELKNPERNISMGAAYLSILENGPLAGIKDPQVMRYAVVVSYANGAGALLRTFSSNRQDAIEEINDLDADEFFEHVVKKHPAPQAPRYIWKLQKALDAM

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Unknown

Enzyme Commission (EC)

1

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:0000270 The chemical reactions and pathways involving peptidoglycans, any of a class of glycoconjugates found only in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
  • GO:0008933 Catalysis of the cleavage of a peptidoglycan chain into a peptidoglycan chain with N-acetyl-1,6-anhydromuramyl-[peptide] at the reducing end + a peptidoglycan chain with N-acetylglucosamine at the non-reducing end. Includes endolytic transglycosylase activity that fragments the glycan chain internally and exolytic transgylcosylase activity that cleaves a terminal disaccharide from the end of the glycan strand.
  • GO:0016798 Catalysis of the hydrolysis of any glycosyl bond.
  • 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

9 records
Show feature table
Start End DB Term Name
1 162 SUPERFAMILY SSF53955 Lysozyme-like
1 162 InterPro IPR023346 Lysozyme-like domain superfamily
5 163 CDD cd16893 LT_MltC_MltE
1 167 Gene3D G3DSA:1.10.530.10 -
7 132 Pfam PF01464 Transglycosylase SLT domain
7 132 InterPro IPR008258 Transglycosylase SLT domain 1
6 160 PANTHER PTHR37423 SOLUBLE LYTIC MUREIN TRANSGLYCOSYLASE-RELATED
24 52 ProSitePatterns PS00922 Prokaryotic transglycosylases signature.
24 52 InterPro IPR000189 Prokaryotic transglycosylase, active site

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
0.025
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.008
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #3
0.82 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_W1DGZ0
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_01546
ColabFold — — full sequence — Loaded