rbpA Family assigned · medium auto-curated
H37Rv Rv2050 · MTBC0 mtbc0_002183 ·
111 aa · 2336434–2336769 (+) ·
RefSeq NP_216566.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | RNA polymerase-binding protein RbpA |
|---|---|
| MTBC0 PGAP re-annotation | RNA polymerase-binding protein RbpA |
| Revised (this work) | RNA polymerase-binding protein RbpA. Pfam: RbpA (PF13397.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHJ5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | RNA polymerase-binding protein RbpA |
| Curated function | Binds to RNA polymerase (RNAP), stimulating and stabilizing the formation of stable RNAP promoter complexes up to 2-fold from principal sigma factor SigA-dependent but not alternative sigma factor SigF-dependent promoters. Increases the affinity of core RNAP for SigA, increasing the transcriptional activity of RNAP. Stimulates transcription driven by SigB more than that driven by SigA. Unlike the case in M.smegmatis or S.coelicolor, has no effect on rifampicin inhibition of transcription. Has no effect on E.coli RNAP. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | rbpA |
| eggNOG description | Binds to RNA polymerase (RNAP), stimulating transcription from principal, but not alternative sigma factor promoters |
| Orthologous group | 2CNY9 |
| Gene Ontology (51) |
GO:0001000, GO:0001098, GO:0001108, GO:0003674, GO:0005488, GO:0005515, GO:0006355, GO:0008150, GO:0008270, GO:0009889, GO:0009891, GO:0009893 +39 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.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
RbpA | PF13397.13 | 3.7e-42 | 4–106 | RNA polymerase-binding protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpoZ (DNA-directed RNA polymerase subunit omega), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 999 | 999 | experimental:999 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 998 | 999 ctx | cooccurence:729 experimental:995 |
Rv2703 sigA |
RNA polymerase sigma factor SigA | 995 | 995 | experimental:995 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 990 | 982 | experimental:982 textmining:504 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 991 | 975 | experimental:974 textmining:669 |
Rv2710 sigB |
RNA polymerase sigma factor SigB | 974 | 964 | experimental:961 |
Rv3197A whiB7 |
transcriptional regulator WhiB7 | 902 | 899 | experimental:898 |
Rv3583c carD |
RNA polymerase-binding transcription factor CarD | 992 | 897 | experimental:895 textmining:930 |
Rv2095c pafC |
proteasome accessory factor C | 928 | 897 | experimental:870 |
Rv2096c pafB |
proteasome accessory factor B | 892 | 820 | experimental:780 textmining:430 |
Rv2699c hyp |
hypothetical protein | 783 | 784 ctx | cooccurence:773 |
Rv1830 |
HTH-type transcriptional regulator | 776 | 776 ctx | cooccurence:766 |
Rv2708c hyp |
hypothetical protein | 769 | 769 ctx | cooccurence:767 |
Rv2413c hyp |
hypothetical protein | 769 | 769 ctx | cooccurence:769 |
Rv2731 hyp |
hypothetical protein | 752 | 753 ctx | cooccurence:750 |
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: RNA polymerase-binding protein RbpA
- MTBC0 PGAP product: RNA polymerase-binding protein RbpA
- Pfam (hmmscan --cut_ga): RbpA PF13397.13 (E=4e-42)
- (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_216566.1)
- Domains: Pfam-A via hmmscan --cut_ga — RbpA (PF13397.13)
- 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
2CNY9 - Curated reference: UniProt P9WHJ5 (SwissProt, reviewed; Evidence at protein level)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
73 functional partner(s); context anchor
rpoZ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002183|Rv2050|rbpA MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPRTHWDMLLERRSIEELEELLKERLELIRSRRRG