rho Resolved · high auto-curated
H37Rv Rv1297 · MTBC0 mtbc0_001389 ·
602 aa · 1462243–1464051 (+) ·
RefSeq NP_215813.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcription termination factor Rho |
|---|---|
| MTBC0 PGAP re-annotation | transcription termination factor Rho |
| Revised (this work) | Transcription termination factor Rho. Pfam: Rho_N (PF07498.19), Rho_RNA_bind (PF07497.19), ATP-synt_ab (PF00006.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHF3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transcription termination factor Rho |
| EC (curated) |
EC 3.6.4.-
|
| Curated function | Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template. Shows poor RNA-dependent ATP hydrolysis and inefficient DNA-RNA unwinding activities, but exhibits robust and fast transcription termination, which suggests that the transcription termination function of M.tuberculosis Rho is not correlated with its helicase/translocase activities and that these functions may not be important for its RNA release process. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | rho |
| eggNOG description | Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template |
| Orthologous group | COG1158 |
| KEGG orthology |
K03628
|
| KEGG pathways |
map03018
|
| Gene Ontology (42) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006139, GO:0006351, GO:0006353, GO:0006360, GO:0006363, GO:0006725, GO:0006807, GO:0008150 +30 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 | 0.461 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
Rho_N | PF07498.19 | 4.4e-10 | 37–71 | Rho termination factor, N-terminal domain |
Rho_RNA_bind | PF07497.19 | 4.6e-24 | 226–303 | Rho termination factor, RNA-binding domain |
ATP-synt_ab | PF00006.32 | 1.0e-28 | 334–538 | ATP synthase alpha/beta family, nucleotide-binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpmE (50S ribosomal protein L31), high confidence from genomic context alone (score 935 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 969 | 957 | coexpression:784 experimental:793 |
Rv1298 rpmE |
50S ribosomal protein L31 | 943 | 935 ctx | neighborhood:750 coexpression:750 |
Rv2783c gpsI |
bifunctional guanosine pentaphosphate synthetase/polyribonucleotide nucleotidyltransferase | 967 | 928 | coexpression:916 textmining:568 |
Rv3921c yidC |
membrane protein insertase YidC | 933 | 926 | coexpression:922 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 932 | 912 | coexpression:595 experimental:792 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 926 | 904 | coexpression:472 experimental:790 |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 924 | 903 | coexpression:428 experimental:836 |
Rv0639 nusG |
transcription termination/antitermination protein NusG | 972 | 901 | coexpression:502 experimental:810 textmining:730 |
Rv1630 rpsA |
30S ribosomal protein S1 | 895 | 881 | coexpression:836 |
Rv1299 prfA |
peptide chain release factor PrfA | 896 | 876 ctx | neighborhood:649 coexpression:661 |
Rv3923c rnpA |
ribonuclease P protein component | 902 | 873 | coexpression:869 |
Rv3922c yidD |
membrane protein insertion efficiency factor | 857 | 857 | coexpression:825 |
Rv0701 rplC |
50S ribosomal protein L3 | 842 | 843 | coexpression:838 |
Rv0684 fusA1 |
elongation factor G | 852 | 838 | coexpression:838 |
Rv1870c hyp |
hypothetical protein | 820 | 821 | coexpression:796 |
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: transcription termination factor Rho
- MTBC0 PGAP product: transcription termination factor Rho
- Pfam (hmmscan --cut_ga): Rho_N PF07498.19 (E=4e-10), Rho_RNA_bind PF07497.19 (E=5e-24), ATP-synt_ab PF00006.32 (E=1e-28)
- (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_215813.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rho_N (PF07498.19), Rho_RNA_bind (PF07497.19), ATP-synt_ab (PF00006.32)
- 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
COG1158 - Curated reference: UniProt P9WHF3 (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 —
120 functional partner(s); context anchor
rpmE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001389|Rv1297|rho MTDTDLITAGESTDGKPSDAAATDPPDLNADEPAGSLATMVLPELRALANRAGVKGTSGMRKNELIAAIEEIRRQANGAPAVDRSAQEHDKGDRPPSSEAPATQGEQTPTEQIDSQSQQVRPERRSATREAGPSGSGERAGTAADDTDNRQGGQQDAKTEERGTDAGGDQGGDQQASGGQQARGDEDGEARQGRRGRRFRDRRRRGERSGDGAEAELREDDVVQPVAGILDVLDNYAFVRTSGYLPGPHDVYVSMNMVRKNGMRRGDAVTGAVRVPKEGEQPNQRQKFNPLVRLDSINGGSVEDAKKRPEFGKLTPLYPNQRLRLETSTERLTTRVIDLIMPIGKGQRALIVSPPKAGKTTILQDIANAITRNNPECHLMVVLVDERPEEVTDMQRSVKGEVIASTFDRPPSDHTSVAELAIERAKRLVEQGKDVVVLLDSITRLGRAYNNASPASGRILSGGVDSTALYPPKRFLGAARNIEEGGSLTIIATAMVETGSTGDTVIFEEFKGTGNAELKLDRKIAERRVFPAVDVNPSGTRKDELLLSPDEFAIVHKLRRVLSGLDSHQAIDLLMSQLRKTKNNYEFLVQVSKTTPGSMDSD