KpATCC43816 Protein target profile

tRNAMet cytidine acetyltransferase

Accession: VK055_4703

Gene: AIK83237.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A422ZQ75
Export view
Length 672
Pocket druggability (P2Rank · AlphaFold DB model) 0.8
Metabolic reactions 1
Chokepoint No
Functional annotation 1 EC 10 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 isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. Second pocket predictor agrees P2Rank predicted binding-site probability 0.80. Structure available AlphaFold DB model + ColabFold model

Risks to review

Low human similarity A human hit was flagged, but identity is only 23.399% - a weak match, lower risk than a close homolog. This target also has a predicted binding pocket (P2Rank 0.80) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 87 of 4744 screened genomes (1.8%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.80) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant. Weak predicted binding pocket FPocket selected-pocket score 0.24.

Evidence gaps

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
Hit
Human identity (%)
23.399 Lower values reduce human off-target concern.
Human E-value
2.04e-17
Gut microbiome similarity
1.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
90.45 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) 0.8
Structure A0A422ZQ75
Pocket Pocket 1
Druggability (FPocket) 0.245
Structure A0A422ZQ75
Pocket Pocket 4
ColabFold model
P2Rank 0.869 · Pocket 1
FPocket 0.531 · Pocket 48
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 87 / 4744 genomes with a hit
Prevalence 1.8%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network
Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MDALLNLTAQMAREGIRRLLVLSGDESWTLQQAQALRERLGGDGLWVGPEPVSAPCVAPGALKTLLGREVMHAFFDARRGFDVAAMAALSGTLRAGSWLVLLTPPFADWPTRADEDSLRWSDTPDPIVTPNFVHRCCWQFIADPEVLLWRQSDRPRFPLAAPRPDWHPADGRPQAEQAAILEQLIRLPPGIAAVTAERGRGKSALAGMLLRQLGGEAIVTAPTRSAVEVLASFAGETLRFMAPDALLASKEKAAWLIVDEAAAIPAPLLRQLVSRFPRTLLTTTVQGYEGTGRGFLLKFCASLPHLQSFTLSAPIRWAAGCPLESAISQLLIFNDEAFRDAPMGEIALEAVNQSCWQTQPALPEAMYQLLSGAHYRTSPLDLRRMMDAPGQAFRCARAGGAVAGALWLVAEGGLSRELSRAVWAGFRRPRGNLVAQSLAAHGGSPLAATLRGLRVSRIAVHPTRQREGLGRKMIADIAADAAGYDYLSVSFGYTAELWRFWQRCGFTLVRLGTHREASSGCYTAMALYPLTAAGRQLAQREAQRLQRDEYWLRPWREESAPLPAVADAMLSDEDWLEAASFAFAHRPLAAALGCLNRLLMQADMPLPALRGRLQGKEEAALCAVLQLTGRKALQARWRREAADALRFLDAARADALRQQVAHLQFFLTNSFS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • GO:0051392 Catalysis of the reaction: a cytidine in tRNA + acetyl-CoA + ATP + H2O = ADP + an N4-acetylcytidine in tRNA + CoA + H+ + phosphate.
  • GO:0002101 The process in which a cytosine at position 34 of a tRNA is post-transcriptionally modified. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon.
  • GO:0016747 Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
  • GO:0008080 Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.
  • GO:0051391 The modification of tRNA structure by addition of an acetyl group to tRNA. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
  • GO:0000049 Binding to a transfer RNA.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:1990883 Catalysis of the reaction: a cytidine in 18S rRNA + acetyl-CoA + ATP + H2O = an N(4)-acetylcytidine in 18S rRNA + ADP + phosphate + CoA + H+.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:1904812 Any rRNA acetylation that is involved in maturation of SSU-rRNA.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
366 477 Pfam PF13718 GNAT acetyltransferase 2
366 477 InterPro IPR000182 GNAT domain
483 530 Pfam PF13718 GNAT acetyltransferase 2
483 530 InterPro IPR000182 GNAT domain
483 554 PANTHER PTHR10925 N-ACETYLTRANSFERASE 10
483 554 InterPro IPR032672 TmcA/NAT10/Kre33
12 647 Hamap MF_01886 tRNA(Met) cytidine acetyltransferase TmcA [tmcA].
12 647 InterPro IPR024914 tRNA(Met) cytidine acetyltransferase TmcA
325 528 Gene3D G3DSA:3.40.630.30 -
1 188 Gene3D G3DSA:3.40.50.11040 -
325 528 FunFam G3DSA:3.40.630.30:FF:000054 tRNA(Met) cytidine acetyltransferase TmcA
189 324 Gene3D G3DSA:3.40.50.300 -
189 324 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
368 510 SUPERFAMILY SSF55729 Acyl-CoA N-acyltransferases (Nat)
368 510 InterPro IPR016181 Acyl-CoA N-acyltransferase
529 667 Gene3D G3DSA:1.20.120.890 tRNA(Met) cytidine acetyltransferase, tail domain
529 667 InterPro IPR038321 TmcA, C-terminal domain superfamily
194 334 Pfam PF05127 Helicase
194 334 InterPro IPR007807 Helicase domain
1 188 FunFam G3DSA:3.40.50.11040:FF:000003 tRNA(Met) cytidine acetyltransferase TmcA
534 650 Pfam PF17176 tRNA-binding domain
534 650 InterPro IPR033442 tRNA(Met) cytidine acetyltransferase TmcA, tRNA-binding domain
189 324 FunFam G3DSA:3.40.50.300:FF:001011 tRNA(Met) cytidine acetyltransferase TmcA
170 280 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
170 280 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.8
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.729
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.365
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.254
Likely same site as FPocket 4 0.6 Å 15 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.212
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #4
0.245
Likely same site as P2Rank 4 0.6 Å 15 shared residues 100% of smaller site
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_A0A422ZQ75
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4703
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A422ZQ75

Pathways

BioCyc RXN0-5418