Protein profile

VK055_1321

tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase

Genome: KpATCC43816

Gene: trmU AIK79944.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GRM1
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Amino acids 368
Annotations 3
Features 21
PDB binders 0
Druggability 0.22

Overview

Basic information about this protein and its source genome.

Accession
VK055_1321
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
trmU AIK79944.1
Status
annotated
Amino acids
368
Structure source
AlphaFold + ColabFold
GO
GO:0016783 Catalysis of the transfer of sulfur atoms from one compound (donor) to another (acceptor). GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group. 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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
54.639
Human E-value
1.05e-31
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
93.443
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
92.94

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 0.22
Structure A0A0H3GRM1
Pocket Pocket 5
P2Rank 0.969
Structure A0A0H3GRM1
Pocket Pocket 1
ColabFold model
FPocket 0.429 · Pocket 16
P2Rank 0.962 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 912 / 4744 genomes with a hit
Normalized 0.192

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0016783 Catalysis of the transfer of sulfur atoms from one compound (donor) to another (acceptor).
  • GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
7 360 CDD cd01998 tRNA_Me_trans
7 360 InterPro IPR004506 tRNA-specific 2-thiouridylase
4 362 PANTHER PTHR11933 TRNA 5-METHYLAMINOMETHYL-2-THIOURIDYLATE -METHYLTRANSFERASE
4 295 SUPERFAMILY SSF52402 Adenine nucleotide alpha hydrolases-like
282 368 Gene3D G3DSA:2.40.30.10 Translation factors
6 361 Hamap MF_00144 tRNA-specific 2-thiouridylase MnmA [mnmA].
6 361 InterPro IPR004506 tRNA-specific 2-thiouridylase
1 211 Gene3D G3DSA:3.40.50.620 HUPs
1 211 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
6 203 Pfam PF03054 tRNA methyl transferase HUP domain
213 281 Gene3D G3DSA:2.30.30.280 -
213 281 InterPro IPR023382 tRNA-specific 2-thiouridylase MnmA-like, central domain superfamily
282 367 FunFam G3DSA:2.40.30.10:FF:000023 tRNA-specific 2-thiouridylase MnmA
286 360 Pfam PF20258 Aminomethyltransferase beta-barrel domain
286 360 InterPro IPR046885 tRNA-specific 2-thiouridylase MnmA-like, C-terminal domain
1 212 FunFam G3DSA:3.40.50.620:FF:000004 tRNA-specific 2-thiouridylase MnmA
6 360 NCBIfam TIGR00420 tRNA 2-thiouridine(34) synthase MnmA
6 360 InterPro IPR004506 tRNA-specific 2-thiouridylase
213 280 FunFam G3DSA:2.30.30.280:FF:000001 tRNA-specific 2-thiouridylase MnmA
207 275 Pfam PF20259 tRNA methyl transferase PRC-barrel domain
207 275 InterPro IPR046884 tRNA-specific 2-thiouridylase MnmA-like, central domain

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_A0A0H3GRM1
AlphaFold — — full sequence — Viewing
ColabFold VK055_1321
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
5 0.22

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 31.81 0.94
2 2.27 0.057
3 1.95 0.041