KpKP13 Protein target profile

N-acetylmuramoyl-L-alanine amidase amiB

Accession: KP13_00527

Gene: amiB AHE46740.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GH87
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Length 447
Pocket druggability (P2Rank · AlphaFold DB model) 0.782
Functional annotation 1 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

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.78, FPocket 0.77). Use the 3D pocket comparison to verify whether they identify the same site. 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. Strong predicted binding pocket FPocket selected-pocket score 0.77. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Microbiome similarity 107 of 4744 screened genomes (2.3%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.78) — check the ligand evidence before deprioritizing on off-target risk alone.

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)
Y
DEG identity (%)
55.319 Higher values support similarity to known essential genes.
DEG E-value
5.07e-154 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
76.57 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) 0.782
Structure A0A0H3GH87
Pocket Pocket 1
Druggability (FPocket) 0.77
Structure A0A0H3GH87
Pocket Pocket 4
ColabFold model
P2Rank 0.957 · Pocket 1
FPocket 0.093 · Pocket 20
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 107 / 4744 genomes with a hit
Prevalence 2.3%

Sequence

Primary amino-acid sequence viewer.

MKYRITTWLAAALMLSSLHATAASLSDIQVSNGDQQARITLSFVGEPEYSFTPQGKRLVALDIKQTGVLQGLPLQFSGSNLVKSIRAGTPQDTQTLRLLVDLTEDGKTRAVKQQNGANYTVVFTINAEAPPPPVVVKRADPPPVMPSRTTTPGRNPFSSSGHERQTVMTSSQPAMTNNQTVTRPAARTVSADDKVIIAIDAGHGGQDPGAIGPNGTKEKNVTIAIARKLRALLNADPQFKPVLTRDGDYFISVMGRSEVARKQNANFLVSIHADAAPNRDATGASVWVLSNRRANSEMAGWLEQHEKQSELLGGAGDVLANSQADPYLSQAVLDLQFGHSQRVGYDVATNVLSQLQRIGNLHKRRPEHASLGVLRSPDIPSILVETGFISNNGEERLLGSDDYQEQIAEAIYNGLRNYFMQHPLQSAPRGEAAQTASAAAPGGMLIN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
Unknown

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0009253 The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found 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:0008745 Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
  • GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
  • 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.

21 records
Show feature table
Start End DB Term Name
257 416 SMART SM00646 ami_3
257 416 InterPro IPR002508 N-acetylmuramoyl-L-alanine amidase, catalytic domain
1 23 SignalP_EUK SignalP-noTM SignalP-noTM
19 22 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
16 127 Gene3D G3DSA:2.60.40.3500 -
10 420 PANTHER PTHR30404 N-ACETYLMURAMOYL-L-ALANINE AMIDASE
184 423 FunFam G3DSA:3.40.630.40:FF:000003 N-acetylmuramoyl-L-alanine amidase AmiB
23 447 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 22 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
196 415 CDD cd02696 MurNAc-LAA
196 415 InterPro IPR002508 N-acetylmuramoyl-L-alanine amidase, catalytic domain
184 423 Gene3D G3DSA:3.40.630.40 -
195 419 SUPERFAMILY SSF53187 Zn-dependent exopeptidases
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
7 18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 22 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
197 416 Pfam PF01520 N-acetylmuramoyl-L-alanine amidase
197 416 InterPro IPR002508 N-acetylmuramoyl-L-alanine amidase, catalytic domain
144 185 MobiDBLite mobidb-lite consensus disorder prediction
150 185 MobiDBLite mobidb-lite consensus disorder prediction
1 22 Phobius SIGNAL_PEPTIDE Signal peptide region

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
0.782
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Surrounding area
Pocket 2 P2Rank #2
0.55
Likely same site as FPocket 4 2.1 Å 15 shared residues 94% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.147
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Surrounding area
Pocket 4 P2Rank #4
0.021
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Surrounding area
Pocket 5 P2Rank #5
0.015
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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 #4
0.77 Unusual size
Likely same site as P2Rank 2 2.1 Å 15 shared residues 94% 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_A0A0H3GH87
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_00527
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GH87