rsgA Family assigned · medium auto-curated
H37Rv Rv3228 · MTBC0 mtbc0_003437 ·
330 aa · 3626868–3627860 (+) ·
RefSeq NP_217745.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | ribosome small subunit-dependent GTPase A |
| Revised (this work) | Ribosome small subunit-dependent GTPase A. Pfam: RsgA_GTPase (PF03193.23), MMR_HSR1 (PF01926.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05873
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribosome small subunit-dependent GTPase A |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | rsgA |
| eggNOG description | One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Helps release RbfA from mature subunits. May play a role in the assembly of ribosomal proteins into the subunit. Circularly permuted GTPase that catalyzes slow GTP hydrolysis, GTPase activity is stimulated by the 30S ribosomal subunit |
| Orthologous group | COG1162 |
| EC number |
EC 3.1.3.100
|
| KEGG orthology |
K06949
|
| KEGG pathways |
map00730, map01100
|
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 | 0.395 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
RsgA_GTPase | PF03193.23 | 3.1e-43 | 96–267 | RsgA GTPase |
MMR_HSR1 | PF01926.30 | 1.8e-04 | 201–263 | 50S ribosome-binding GTPase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aroA (3-phosphoshikimate 1-carboxyvinyltransferase), high confidence from genomic context alone (score 904 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3227 aroA |
3-phosphoshikimate 1-carboxyvinyltransferase | 948 | 904 ctx | neighborhood:882 textmining:485 |
Rv2977c thiL |
thiamine-monophosphate kinase | 913 | 901 | database:900 |
Rv0414c thiE |
thiamine-phosphate synthase | 913 | 901 | database:900 |
Rv0733 adk |
adenylate kinase | 900 | 900 | database:900 |
Rv0682 rpsL |
30S ribosomal protein S12 | 860 | 860 | experimental:849 |
Rv3442c rpsI |
30S ribosomal protein S9 | 846 | 846 | experimental:845 |
Rv2785c rpsO |
30S ribosomal protein S15 | 834 | 834 | experimental:784 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 824 | 824 | experimental:784 |
Rv2412 rpsT |
30S ribosomal protein S20 | 822 | 822 | experimental:784 |
Rv0718 rpsH |
30S ribosomal protein S8 | 821 | 821 | experimental:784 |
Rv3458c rpsD |
30S ribosomal protein S4 | 810 | 810 | experimental:784 |
Rv0683 rpsG |
30S ribosomal protein S7 | 802 | 803 | experimental:786 |
Rv2909c rpsP |
30S ribosomal protein S16 | 791 | 791 | experimental:788 |
Rv2890c rpsB |
30S ribosomal protein S2 | 790 | 791 | experimental:786 |
Rv0707 rpsC |
30S ribosomal protein S3 | 790 | 790 | 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: hypothetical protein
- MTBC0 PGAP product: ribosome small subunit-dependent GTPase A
- Pfam (hmmscan --cut_ga): RsgA_GTPase PF03193.23 (E=3e-43), MMR_HSR1 PF01926.30 (E=2e-04)
- (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_217745.1)
- Domains: Pfam-A via hmmscan --cut_ga — RsgA_GTPase (PF03193.23), MMR_HSR1 (PF01926.30)
- 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
COG1162 - Curated reference: UniProt O05873 (TrEMBL, unreviewed; 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 —
40 functional partner(s); context anchor
aroA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003437|Rv3228|rsgA MRPGDYDESDVKVRSGRSSRPRTKTRPEHADAEAAMVVSVDRGRWGCVLGGRPDRRITAMRARELGRTPIVVGDDVDVVGDLSGRPDTLARIVRRAPRRTVLRRTADDTDPTERVVVANADQLLIVVALADPPPRTGLVDRALIAAYAGGLTPILCLTKTDLAPAEPFGKQFADLELTVTAAGVDDPLLAVADLLAGKITVLLGHSGVGKSTLVNRLVPEADRAVGEVTEIGRGRHTSTRSVALPLGDTLSGSGWVIDTPGIRSFGLAHIQPDNVLLAFSDLAEATRECPRGCGHMGPPADPECALDTLSGPAARRAAAARRLLAVLSQT