Protein profile

VK055_0325

putative L,D-transpeptidase YcfS

Genome: KpATCC43816

Gene: AIK78951.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GR62
Export view
Amino acids 328
Annotations 8
Features 28
PDB binders 0
Druggability 0.339

Overview

Basic information about this protein and its source genome.

Accession
VK055_0325
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK78951.1
Status
annotated
Amino acids
328
Structure source
AlphaFold + ColabFold
GO
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.

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 (%)
43.023
DEG E-value
2.2700000000000002e-63
Localization
Periplasmic
ColabFold pLDDT
87.37

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 0.339
Structure A0A0H3GR62
Pocket Pocket 6
P2Rank 0.722
Structure A0A0H3GR62
Pocket Pocket 1
ColabFold model
FPocket 0.628 · Pocket 5
P2Rank 0.738 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 110 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

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 Features

Domain/signature hits from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
5 242 PANTHER PTHR30582 L,D-TRANSPEPTIDASE
95 233 SUPERFAMILY SSF141523 L,D-transpeptidase catalytic domain-like
95 233 InterPro IPR038063 L,D-transpeptidase catalytic domain-like
1 23 Phobius SIGNAL_PEPTIDE Signal peptide region
40 85 ProSiteProfiles PS51782 LysM domain profile.
40 85 InterPro IPR018392 LysM domain
95 234 Gene3D G3DSA:2.40.440.10 -
95 234 InterPro IPR038063 L,D-transpeptidase catalytic domain-like
19 23 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
43 86 Pfam PF01476 LysM domain
43 86 InterPro IPR018392 LysM domain
237 303 Pfam PF17969 L,D-transpeptidase C-terminal domain
237 303 InterPro IPR041597 L,D-transpeptidase C-terminal domain
98 233 Pfam PF03734 L,D-transpeptidase catalytic domain
98 233 InterPro IPR005490 L,D-transpeptidase catalytic domain
1 20 SignalP_EUK SignalP-noTM SignalP-noTM
93 234 FunFam G3DSA:2.40.440.10:FF:000001 L,D-transpeptidase YbiS
1 23 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
24 328 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
99 234 CDD cd16913 YkuD_like
99 234 InterPro IPR005490 L,D-transpeptidase catalytic domain
7 18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
37 92 Gene3D G3DSA:3.10.350.10 LysM domain
37 92 InterPro IPR036779 LysM domain superfamily
7 24 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
40 85 CDD cd00118 LysM
1 23 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM

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

Loading 3D structure...

Legend High Medium Low

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_A0A0H3GR62
AlphaFold — — full sequence — Viewing
ColabFold VK055_0325
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
6 0.339
2 0.235
1 0.108
8 0.013

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 17.28 0.722
2 3.12 0.084
3 0.96 0.004