Protein profile

VK055_2897

N-acetylmuramoyl-L-alanine amidase 2

Genome: KpATCC43816

Gene: AIK81486.1 amiB Structure source: AlphaFold + ColabFold UniProt A0A0H3GH87
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Amino acids 451
Annotations 5
Features 21
PDB binders 0
Druggability 0.77

Overview

Basic information about this protein and its source genome.

Accession
VK055_2897
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK81486.1 amiB
Status
annotated
Amino acids
451
Structure source
AlphaFold + ColabFold
EC
3.5.1.28
GO
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: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: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.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
60.811
DEG E-value
1.3000000000000001e-89
Localization
Unknown
ColabFold pLDDT
76.7

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.77
Structure A0A0H3GH87
Pocket Pocket 4
P2Rank 0.782
Structure A0A0H3GH87
Pocket Pocket 1
ColabFold model
FPocket 0.373 · Pocket 11
P2Rank 0.944 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 106 / 4744 genomes with a hit
Normalized 0.022

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • 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: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: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 Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
1 22 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
200 419 CDD cd02696 MurNAc-LAA
200 419 InterPro IPR002508 N-acetylmuramoyl-L-alanine amidase, catalytic domain
16 126 Gene3D G3DSA:2.60.40.3500 -
1 22 Phobius SIGNAL_PEPTIDE Signal peptide region
1 23 SignalP_EUK SignalP-noTM SignalP-noTM
188 427 FunFam G3DSA:3.40.630.40:FF:000003 N-acetylmuramoyl-L-alanine amidase AmiB
1 22 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
188 427 Gene3D G3DSA:3.40.630.40 -
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
149 189 MobiDBLite mobidb-lite consensus disorder prediction
201 420 Pfam PF01520 N-acetylmuramoyl-L-alanine amidase
201 420 InterPro IPR002508 N-acetylmuramoyl-L-alanine amidase, catalytic domain
199 423 SUPERFAMILY SSF53187 Zn-dependent exopeptidases
19 22 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
23 451 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
10 424 PANTHER PTHR30404 N-ACETYLMURAMOYL-L-ALANINE AMIDASE
7 18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
261 420 SMART SM00646 ami_3
261 420 InterPro IPR002508 N-acetylmuramoyl-L-alanine amidase, catalytic domain
144 189 MobiDBLite mobidb-lite consensus disorder prediction

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GH87
AlphaFold — — full sequence — Viewing
ColabFold VK055_2897
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
4 0.77

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 11.23 0.602
2 10.62 0.57
3 2.64 0.077
4 0.82 0.003