MTBC Gene Atlas

raiA Resolved · high auto-curated

H37Rv Rv3241c · MTBC0 mtbc0_003449 · 214 aa · 3642753–3643397 (-) · RefSeq NP_217758.3

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hypothetical protein
MTBC0 PGAP re-annotationribosome-associated translation inhibitor RaiA
Revised (this work)Ribosome-associated translation inhibitor RaiA. Pfam: Ribosomal_S30AE (PF02482.26), Ribosom_S30AE_C (PF16321.11).

Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.

Curated reference (UniProt)

UniProt O05886 SwissProt · reviewed · Evidence at protein level
UniProt nameRibosome hibernation promotion factor
Curated functionRequired for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase; 100S ribosomes are translationally inactive and sometimes present during exponential growth.

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category J Translation, ribosomal structure and biogenesis
Preferred namehpf
eggNOG descriptionRequired for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase
Orthologous groupCOG1544
KEGG orthology K05808
Gene Ontology (64) GO:0003674, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005840, GO:0006417, GO:0006448, GO:0008150, GO:0009889 +52 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 0.484 · purifying
Polymorphic sites (≥ 0.1% of strains) 2 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)

PfamAccessioni-EvalueResiduesDescription
Ribosomal_S30AEPF02482.26 1.0e-1916–112 Sigma 54 modulation protein / S30EA ribosomal protein
Ribosom_S30AE_CPF16321.11 1.8e-26155–210 Sigma 54 modulation/S30EA ribosomal protein C terminus

Functional interaction network (STRING v12, guilt-by-association)

PartnerProductScoreNo text-miningChannels (≥400)
Rv0053 rpsF 30S ribosomal protein S6 999 999 experimental:999
Rv3442c rpsI 30S ribosomal protein S9 998 999 experimental:997 database:540
Rv0707 rpsC 30S ribosomal protein S3 998 999 experimental:997 database:540
Rv2785c rpsO 30S ribosomal protein S15 943 941 experimental:870 database:540
Rv0721 rpsE 30S ribosomal protein S5 943 939 experimental:870 database:540
Rv0705 rpsS 30S ribosomal protein S19 940 938 experimental:870 database:540
Rv0710 rpsQ 30S ribosomal protein S17 940 938 experimental:870 database:540
Rv0683 rpsG 30S ribosomal protein S7 939 938 experimental:870 database:540
Rv3459c rpsK 30S ribosomal protein S11 938 938 experimental:870 database:540
Rv0055 rpsR1 30S ribosomal protein S18 937 938 experimental:870 database:540
Rv0718 rpsH 30S ribosomal protein S8 937 938 experimental:870 database:540
Rv2890c rpsB 30S ribosomal protein S2 937 938 experimental:870 database:540
Rv2055c rpsR2 30S ribosomal protein S18 937 938 experimental:870 database:540
Rv0709 rpmC 50S ribosomal protein L29 925 918 experimental:870
Rv1630 rpsA 30S ribosomal protein S1 914 911 experimental:806 database:540

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-associated translation inhibitor RaiA
  • Pfam (hmmscan --cut_ga): Ribosomal_S30AE PF02482.26 (E=1e-19), Ribosom_S30AE_C PF16321.11 (E=2e-26)
  • (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_217758.3)
  • Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_S30AE (PF02482.26), Ribosom_S30AE_C (PF16321.11)
  • 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 COG1544
  • Curated reference: UniProt O05886 (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 — 106 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_003449|Rv3241c|raiA
MDSGQVLAEPKSNAEIVFKGRNVEIPDHFRIYVSQKLARLERFDRTIYLFDVELDHERNRRQRKSCQRVEITARGRGPVVRGEACADSFYAALESAVVKLESRLRRGKDRRKVHYGDKTPVSLAEATAVVPAPENGFNTRPAEAHDHDGAVVEREPGRIVRTKEHPAKPMSVDDALYQMELVGHDFFLFYDKDTERPSVVYRRHAYDYGLIRLA