KpKP13 Protein target profile

Ribosomal RNA small subunit methyltransferase H

Accession: KP13_01429

Gene: rsmH AHE47403.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A1J0QYY8
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Length 313
Pocket druggability (P2Rank · AlphaFold DB model) 0.943
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

Moderate predicted binding pocket FPocket selected-pocket score 0.53. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.94. Structure available AlphaFold DB model + ColabFold model

Risks to review

Human similarity Top human hit identity: 37.778%. This target also has a predicted binding pocket (P2Rank 0.94) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 1695 of 4744 screened genomes (35.7%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.94) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. 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 (%)
37.778 Lower values reduce human off-target concern.
Human E-value
4.82e-17
Gut microbiome similarity
35.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
47.923 Higher values support similarity to known essential genes.
DEG E-value
1.6799999999999998e-94 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
95.3 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) 0.943
Structure A0A1J0QYY8
Pocket Pocket 1
Druggability (FPocket) 0.527
Structure A0A1J0QYY8
Pocket Pocket 1
ColabFold model
P2Rank 0.878 · Pocket 1
FPocket 0.901 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 1695 / 4744 genomes with a hit
Prevalence 35.7%

Sequence

Primary amino-acid sequence viewer.

MEFHHLPVLLHECMDGLNIRPDGTYLDCTLGGAGHSSEIFLRLHGGRLIGIDRDADAIEAAGARMAALNGDAEFTAIRGNFHDAPALLSGIGVRRVDGILADLGVSSHQLDVRERGFSYHDDAPLDMRMDASQPLSAREIVNTWSEDEINRVLRDYGEENWSRQIARVICDRRQKRMIETTGDLVSIIDAAIPKKFRSKDGSHPARRTFQALRIAVNDELDPLDKAIEDLVNLLNPAGRICIITFHSLEDRIVKNTFRRLNNPCTCPKEFPVCMCGKKPVIELISRKPITASAQELSENPRARSASLRIAEKI

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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0071424 Catalysis of the reaction: a cytidine in rRNA + S-adenosyl-L-methionine = an N(4)-methylcytidine in rRNA + H+ + S-adenosyl-L-homocysteine.
  • GO:0070475 The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
5 313 Hamap MF_01007 Ribosomal RNA small subunit methyltransferase H [rsmH].
5 313 InterPro IPR002903 Ribosomal RNA small subunit methyltransferase H
4 312 PANTHER PTHR11265 S-ADENOSYL-METHYLTRANSFERASE MRAW
4 312 InterPro IPR002903 Ribosomal RNA small subunit methyltransferase H
113 219 Gene3D G3DSA:1.10.150.170 Putative methyltransferase TM0872, insert domain
113 219 InterPro IPR023397 S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily
5 311 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
5 311 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
114 216 SUPERFAMILY SSF81799 Putative methyltransferase TM0872, insert domain
114 216 InterPro IPR023397 S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily
1 313 PIRSF PIRSF004486 MraW
1 313 InterPro IPR002903 Ribosomal RNA small subunit methyltransferase H
31 114 CDD cd02440 AdoMet_MTases
2 313 Pfam PF01795 MraW methylase family
2 313 InterPro IPR002903 Ribosomal RNA small subunit methyltransferase H
3 312 NCBIfam TIGR00006 16S rRNA (cytosine(1402)-N(4))-methyltransferase RsmH
3 312 InterPro IPR002903 Ribosomal RNA small subunit methyltransferase H
4 313 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
4 313 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase 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.

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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
0.943
Likely same site as FPocket 1 2.9 Å 34 shared residues 87% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.015
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Surrounding area
Pocket 3 P2Rank #3
0.012
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.527 Unusual size
Likely same site as P2Rank 1 2.9 Å 34 shared residues 87% of smaller site
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Surrounding area
Pocket 2 FPocket #6
0.204
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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_A0A1J0QYY8
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_01429
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A1J0QYY8