ksgA Resolved · high auto-curated
H37Rv Rv1010 · MTBC0 mtbc0_001085 ·
317 aa · 1136488–1137441 (+) ·
RefSeq NP_215526.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | rRNA small subunit methyltransferase A |
|---|---|
| MTBC0 PGAP re-annotation | 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA |
| Revised (this work) | 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA. Pfam: RrnaAD (PF00398.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH07
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribosomal RNA small subunit methyltransferase A |
| EC (curated) |
EC 2.1.1.182
|
| Curated function | Specifically dimethylates two adjacent adenosines (A1511 and A1512) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | ksgA |
| eggNOG description | Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits |
| Orthologous group | COG0030 |
| EC number |
EC 2.1.1.182
|
| KEGG orthology |
K02528
|
| Gene Ontology (52) |
GO:0000154, GO:0000179, GO:0001510, GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0006139, GO:0006364, GO:0006396 +40 more
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.379 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 3 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
RrnaAD | PF00398.27 | 1.6e-41 | 29–287 | Ribosomal RNA adenine dimethylase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpfB (resuscitation-promoting factor RpfB), high confidence from genomic context alone (score 975 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1009 rpfB |
resuscitation-promoting factor RpfB | 995 | 975 ctx | neighborhood:881 coexpression:797 textmining:830 |
Rv1011 ispE |
4-diphosphocytidyl-2C-methyl-D-erythritol kinase | 990 | 932 ctx | neighborhood:633 fusion:813 textmining:870 |
Rv3458c rpsD |
30S ribosomal protein S4 | 888 | 873 | experimental:800 |
Rv0721 rpsE |
30S ribosomal protein S5 | 866 | 849 | experimental:811 |
Rv3442c rpsI |
30S ribosomal protein S9 | 856 | 837 | experimental:784 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 849 | 829 | experimental:811 |
Rv0683 rpsG |
30S ribosomal protein S7 | 849 | 829 | experimental:807 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 842 | 821 | experimental:805 |
Rv2890c rpsB |
30S ribosomal protein S2 | 840 | 819 | experimental:808 |
Rv2785c rpsO |
30S ribosomal protein S15 | 839 | 819 | experimental:811 |
Rv3459c rpsK |
30S ribosomal protein S11 | 839 | 818 | experimental:806 |
Rv0718 rpsH |
30S ribosomal protein S8 | 836 | 815 | experimental:802 |
Rv0682 rpsL |
30S ribosomal protein S12 | 860 | 814 | experimental:805 |
Rv0707 rpsC |
30S ribosomal protein S3 | 828 | 805 | experimental:786 |
Rv0705 rpsS |
30S ribosomal protein S19 | 821 | 797 | experimental:788 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: rRNA small subunit methyltransferase A
- MTBC0 PGAP product: 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA
- Pfam (hmmscan --cut_ga): RrnaAD PF00398.27 (E=2e-41)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215526.1)
- Domains: Pfam-A via hmmscan --cut_ga — RrnaAD (PF00398.27)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG0030 - Curated reference: UniProt P9WH07 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
98 functional partner(s); context anchor
rpfB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001085|Rv1010|ksgA MCCTSGCALTIRLLGRTEIRRLAKELDFRPRKSLGQNFVHDANTVRRVVAASGVSRSDLVLEVGPGLGSLTLALLDRGATVTAVEIDPLLASRLQQTVAEHSHSEVHRLTVVNRDVLALRREDLAAAPTAVVANLPYNVAVPALLHLLVEFPSIRVVTVMVQAEVAERLAAEPGSKEYGVPSVKLRFFGRVRRCGMVSPTVFWPIPRVYSGLVRIDRYETSPWPTDDAFRRRVFELVDIAFAQRRKTSRNAFVQWAGSGSESANRLLAASIDPARRGETLSIDDFVRLLRRSGGSDEATSTGRDARAPDISGHASAS