KpATCC43816 Protein target profile

tRNA (guanine-N(7)-)-methyltransferase

Accession: VK055_4083

Gene: trmB AIK82629.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GT61
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Length 239
Pocket druggability (P2Rank · AlphaFold DB model) 0.717
Metabolic reactions 1
Chokepoint No
Functional annotation 1 EC 3 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 0.72, FPocket 0.76). Use the 3D pocket comparison to verify whether they identify the same site. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.76. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Low human similarity A human hit was flagged, but identity is only 27.119% - a weak match, lower risk than a close homolog. This target also has a predicted binding pocket (P2Rank 0.72) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 197 of 4744 screened genomes (4.2%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.72) — check the ligand evidence before deprioritizing on off-target risk alone.

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 (%)
27.119 Lower values reduce human off-target concern.
Human E-value
6.87e-06
Gut microbiome similarity
4.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
67.932 Higher values support similarity to known essential genes.
DEG E-value
2.4e-121 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
94.44 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) 0.717
Structure A0A0H3GT61
Pocket Pocket 1
Druggability (FPocket) 0.757
Structure A0A0H3GT61
Pocket Pocket 14
ColabFold model
P2Rank 0.677 · Pocket 1
FPocket 0.568 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 197 / 4744 genomes with a hit
Prevalence 4.2%

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.

MKNDVISPEFDENGRPLRRIRSFVRRQGRLTKGQQHALDNIWPVMGVEFNDAPLDFAALFGRDAPVTLEIGFGMGASLVAMAKAKPEQNFLGIEVHSPGVGACLASAEEEGVQNLRVMCHDAVEVLHTMIPDNSLNMVQLFFPDPWHKARHNKRRIVQPPFAELVKSKLKLGGVFHMATDWEAYAVHMLEVMSSLEGYRNQSASNDYVPRPESRPVTKFEQRGHRLGHGVWDLMFERVK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • GO:0006400 The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
  • GO:0008176 Catalysis of the reaction: guanosine46 in tRNA + S-adenosyl-L-methionine = N7-methylguanosine46 in tRNA + S-adenosyl-L-homocysteine.
  • GO:0043527 A multimeric protein complex involved in the methylation of specific nucleotides in tRNA.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
24 238 Hamap MF_01057 tRNA (guanine-N(7)-)-methyltransferase [trmB].
24 238 InterPro IPR003358 tRNA (guanine-N-7) methyltransferase, Trmb type
64 233 Pfam PF02390 Putative methyltransferase
64 233 InterPro IPR003358 tRNA (guanine-N-7) methyltransferase, Trmb type
50 238 NCBIfam TIGR00091 tRNA (guanosine(46)-N7)-methyltransferase TrmB
50 238 InterPro IPR003358 tRNA (guanine-N-7) methyltransferase, Trmb type
18 237 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
18 237 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
21 237 ProSiteProfiles PS51625 SAM-dependent methyltransferase TRMB-type domain profile.
21 237 InterPro IPR003358 tRNA (guanine-N-7) methyltransferase, Trmb type
21 237 PANTHER PTHR23417 3-DEOXY-D-MANNO-OCTULOSONIC-ACID TRANSFERASE/TRNA GUANINE-N 7 - -METHYLTRANSFERASE
30 239 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
30 239 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
30 239 FunFam G3DSA:3.40.50.150:FF:000024 tRNA (guanine-N(7)-)-methyltransferase

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
0.717
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Surrounding area
Pocket 2 P2Rank #2
0.253
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Surrounding area
Pocket 3 P2Rank #3
0.148
Likely same site as FPocket 14 1.3 Å 12 shared residues 92% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.034
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Surrounding area
Pocket 5 P2Rank #5
0.022
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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 #14
0.757
Likely same site as P2Rank 3 1.3 Å 12 shared residues 92% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:121-121
UniProt: Binding site:144-144
UniProt: Binding site:148-148
UniProt: Binding site:180-180
UniProt: Binding site:217-220
UniProt: Binding site:69-69
UniProt: Binding site:94-94
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_A0A0H3GT61
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4083
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GT61

Pathways

KEGG R00600 BioCyc TRNA-GUANINE-N7--METHYLTRANSFERASE-RXN