gid Resolved · high auto-curated
H37Rv Rv3919c · MTBC0 mtbc0_004153 ·
224 aa · 4431779–4432453 (-) ·
RefSeq NP_218436.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG |
|---|---|
| MTBC0 PGAP re-annotation | 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG |
| Revised (this work) | 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG. Pfam: GidB (PF02527.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGW9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribosomal RNA small subunit methyltransferase G |
| EC (curated) |
EC 2.1.1.-
|
| Curated function | Specifically methylates the N7 position of guanine in position 518 of 16S rRNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rsmG |
| eggNOG description | Specifically methylates the N7 position of a guanine in 16S rRNA |
| Orthologous group | COG0357 |
| EC number |
EC 2.1.1.170
|
| KEGG orthology |
K03501
|
| Gene Ontology (60) |
GO:0000154, GO:0001510, GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006139, GO:0006364 +48 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 | 1.499 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 23 missense, 1 nonsense, 6 frameshift |
| Disruption | 7 distinct premature-stop/frameshift site(s); most common in 0.99% of strains (1438) · convergent |
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 |
|---|---|---|---|---|
GidB | PF02527.22 | 3.1e-56 | 19–194 | rRNA small subunit methyltransferase G |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: parB (chromosome partitioning protein ParB), high confidence from genomic context alone (score 981 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3917c parB |
chromosome partitioning protein ParB | 983 | 981 ctx | neighborhood:881 coexpression:850 |
Rv3918c parA |
chromosome partitioning protein ParA | 982 | 976 ctx | neighborhood:881 coexpression:803 |
Rv3920c hyp |
hypothetical protein | 947 | 938 ctx | neighborhood:727 coexpression:783 |
Rv3921c yidC |
membrane protein insertase YidC | 820 | 742 ctx | neighborhood:501 coexpression:505 |
Rv3923c rnpA |
ribonuclease P protein component | 857 | 663 ctx | neighborhood:501 textmining:595 |
Rv1713 engA |
GTPase Der | 615 | 615 ctx | cooccurence:572 |
Rv3922c yidD |
membrane protein insertion efficiency factor | 605 | 606 ctx | neighborhood:501 |
Rv1644 tsnR |
23S rRNA methyltransferase TsnR | 584 | 552 ctx | cooccurence:406 |
Rv2364c era |
GTPase Era | 538 | 539 ctx | cooccurence:530 |
Rv3916c hyp |
hypothetical protein | 531 | 531 ctx | neighborhood:524 |
Rv3924c rpmH |
50S ribosomal protein L34 | 656 | 516 ctx | neighborhood:501 |
Rv2647 hyp |
hypothetical protein | 553 | 503 | coexpression:474 |
Rv2921c ftsY |
signal recognition particle receptor FtsY | 613 | 495 ctx | cooccurence:417 |
Rv3579c rlmB |
23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB | 519 | 481 ctx | cooccurence:459 |
Rv2883c pyrH |
uridylate kinase | 471 | 472 ctx | cooccurence:451 |
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: 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG
- MTBC0 PGAP product: 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG
- Pfam (hmmscan --cut_ga): GidB PF02527.22 (E=3e-56)
- (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_218436.2)
- Domains: Pfam-A via hmmscan --cut_ga — GidB (PF02527.22)
- 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
COG0357 - Curated reference: UniProt P9WGW9 (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 —
70 functional partner(s); context anchor
parB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004153|Rv3919c|gid MSPIEPAASAIFGPRLGLARRYAEALAGPGVERGLVGPREVGRLWDRHLLNCAVIGELLERGDRVVDIGSGAGLPGVPLAIARPDLQVVLLEPLLRRTEFLREMVTDLGVAVEIVRGRAEESWVQDQLGGSDAAVSRAVAALDKLTKWSMPLIRPNGRMLAIKGERAHDEVREHRRVMIASGAVDVRVVTCGANYLRPPATVVFARRGKQIARGSARMASGGTA