KpATCC43816 Protein target profile

23S rRNA m5C1962 methyltransferase monomer

Accession: VK055_1491

Gene: AIK80111.1 rlmI 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GQU0
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Length 367
Pocket druggability (P2Rank · AlphaFold DB model) 0.775
Functional annotation 1 EC 4 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 similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.78. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 113 of 4744 screened genomes (2.4%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.78) — check the ligand evidence before deprioritizing on off-target risk alone. Weak predicted binding pocket FPocket selected-pocket score 0.37.

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
No hit
Gut microbiome similarity
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
96.64 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) 0.775
Structure A0A0H3GQU0
Pocket Pocket 1
Druggability (FPocket) 0.372
Structure A0A0H3GQU0
Pocket Pocket 4
ColabFold model
P2Rank 0.666 · Pocket 1
FPocket 0.752 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 113 / 4744 genomes with a hit
Prevalence 2.4%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MEGKARSGETIDIVDHQGKWLARGAYSPSSQIRARVWTFDRNEAIDSAFFERRLQQAQTWRAWLAERDGLDSYRLIAGESDGLPGVTIDRFGNFFVLQLLSAGAEYQRAAIISALQNLFPDCAIYDRSDVAVRKKEGLELAQGPVVGELPPALLPITEHGMKLLVDIQGGHKTGYYLDQRDSRLATRRYVADKRVLNCFSYTGGFAVSALMGGCRQVTSVDTSQEALDVARQNVEINGLDLSKAEFVRDDVFKLLRKYRDQGEKFDVIVMDPPKFVENKSQLMGACRGYKDINMLAIQLLNPGGVLLTFSCSGLMTTDLFQKIIADAAIDAGRDVQFIEQFRQAADHPVIATYPEGLYLKGFACRVM

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0016434 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methylcytosine.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
1 42 Gene3D G3DSA:2.30.130.10 PUA domain
1 42 InterPro IPR036974 PUA domain superfamily
44 152 Gene3D G3DSA:3.30.750.80 RNA methyltransferase domain (HRMD) like
1 51 ProSiteProfiles PS50890 PUA domain profile.
3 367 PANTHER PTHR42873 RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE
153 367 FunFam G3DSA:3.40.50.150:FF:000044 Ribosomal RNA large subunit methyltransferase I
48 147 CDD cd11572 RlmI_M_like
50 363 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
50 363 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
194 308 CDD cd02440 AdoMet_MTases
4 39 Pfam PF17785 PUA-like domain
4 39 InterPro IPR041532 RlmI-like, PUA domain
153 367 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
153 367 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
1 43 CDD cd21153 PUA_RlmI
1 43 InterPro IPR041532 RlmI-like, PUA domain
153 342 Pfam PF10672 S-adenosylmethionine-dependent methyltransferase
153 342 InterPro IPR019614 S-adenosylmethionine-dependent methyltransferase
2 43 SUPERFAMILY SSF88697 PUA domain-like
2 43 InterPro IPR015947 PUA-like superfamily

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

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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
0.775
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Surrounding area
Pocket 2 P2Rank #2
0.202
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Surrounding area
Pocket 3 P2Rank #3
0.108
Likely same site as FPocket 4 1.3 Å 10 shared residues 100% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.065
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Surrounding area
Pocket 5 P2Rank #5
0.023
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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 #4
0.372
Likely same site as P2Rank 3 1.3 Å 10 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_A0A0H3GQU0
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_1491
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GQU0