rbfA Resolved · high auto-curated
H37Rv Rv2838c · MTBC0 mtbc0_003017 ·
183 aa · 3165286–3165837 (-) ·
RefSeq NP_217354.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribosome-binding factor RbfA |
|---|---|
| MTBC0 PGAP re-annotation | 30S ribosome-binding factor RbfA |
| Revised (this work) | 30S ribosome-binding factor RbfA. Pfam: RBFA (PF02033.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHJ7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribosome-binding factor A |
| Curated function | One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rbfA |
| eggNOG description | One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA |
| Orthologous group | COG0858 |
| KEGG orthology |
K02834
|
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 | 0.275 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
RBFA | PF02033.24 | 2.3e-25 | 6–113 | Ribosome-binding factor A |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: infB (translation initiation factor IF-2), high confidence from genomic context alone (score 997 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2839c infB |
translation initiation factor IF-2 | 998 | 997 ctx | neighborhood:882 coexpression:969 textmining:611 |
Rv2837c nrnA |
bifunctional oligoribonuclease/PAP phosphatase NrnA | 983 | 982 ctx | neighborhood:882 coexpression:853 |
Rv2836c dinF |
DNA-damage-inducible protein DinF | 895 | 882 ctx | neighborhood:881 |
Rv2793c truB |
tRNA pseudouridine synthase B | 967 | 876 | coexpression:853 textmining:745 |
Rv2840c hyp |
hypothetical protein | 870 | 870 ctx | neighborhood:782 coexpression:429 |
Rv3459c rpsK |
30S ribosomal protein S11 | 871 | 864 | experimental:790 |
Rv0683 rpsG |
30S ribosomal protein S7 | 891 | 859 | experimental:790 |
Rv2842c rimP |
ribosome maturation factor RimP | 892 | 830 ctx | neighborhood:492 coexpression:416 experimental:474 |
Rv3458c rpsD |
30S ribosomal protein S4 | 846 | 813 | coexpression:648 experimental:474 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 898 | 812 | coexpression:658 experimental:474 textmining:481 |
Rv0721 rpsE |
30S ribosomal protein S5 | 848 | 812 | coexpression:657 experimental:474 |
Rv2785c rpsO |
30S ribosomal protein S15 | 949 | 810 | coexpression:596 experimental:474 textmining:745 |
Rv2055c rpsR2 |
30S ribosomal protein S18 | 805 | 796 | experimental:652 |
Rv2835c ugpA |
sn-glycerol-3-phosphate ABC transporter permease UgpA | 783 | 784 ctx | neighborhood:782 |
Rv2834c ugpE |
sn-glycerol-3-phosphate ABC transporter permease UgpE | 782 | 783 ctx | neighborhood:782 |
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: ribosome-binding factor RbfA
- MTBC0 PGAP product: 30S ribosome-binding factor RbfA
- Pfam (hmmscan --cut_ga): RBFA PF02033.24 (E=2e-25)
- (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_217354.1)
- Domains: Pfam-A via hmmscan --cut_ga — RBFA (PF02033.24)
- 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
COG0858 - Curated reference: UniProt P9WHJ7 (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 —
99 functional partner(s); context anchor
infB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003017|Rv2838c|rbfA MADAARARRLAKRIAAIVASAIEYEIKDPGLAGVTITDAKVTADLHDATVYYTVMGRTLHDEPNCAGAAAALERAKGVLRTKVGAGTGVRFTPTLTFTLDTISDSVHRMDELLARARAADADLARVRVGAKPAGEADPYRDNGSVAQSPAPGGLGIRTSDGPEAVEAPLTCGGDTGDDDRPKE