rphA Resolved · high auto-curated
H37Rv Rv1340 · MTBC0 mtbc0_001437 ·
259 aa · 1517457–1518236 (+) ·
RefSeq NP_215856.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease PH |
|---|---|
| MTBC0 PGAP re-annotation | ribonuclease PH |
| Revised (this work) | Ribonuclease PH. Pfam: RNase_PH (PF01138.28), RNase_PH_C (PF03725.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGZ7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease PH |
| EC (curated) |
EC 2.7.7.56
|
| Curated function | Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rph |
| eggNOG description | Phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates |
| Orthologous group | COG2123 |
| EC number |
EC 2.7.7.56
|
| KEGG orthology |
K00989
|
| Gene Ontology (37) |
GO:0005575, GO:0005623, GO:0005886, GO:0006139, GO:0006401, GO:0006725, GO:0006807, GO:0008150, GO:0008152, GO:0009056, GO:0009057, GO:0009987 +25 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 | 1.089 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
RNase_PH | PF01138.28 | 2.2e-30 | 12–142 | 3' exoribonuclease family, domain 1 |
RNase_PH_C | PF03725.21 | 8.4e-11 | 161–225 | 3' exoribonuclease family, domain 2 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rdgB (non-canonical purine NTP pyrophosphatase), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1341 rdgB |
non-canonical purine NTP pyrophosphatase | 993 | 994 ctx | neighborhood:825 fusion:900 coexpression:678 |
Rv2681 hyp |
hypothetical protein | 991 | 988 | experimental:921 database:844 |
Rv1630 rpsA |
30S ribosomal protein S1 | 904 | 903 | experimental:434 database:806 |
Rv1339 hyp |
hypothetical protein | 906 | 896 ctx | neighborhood:861 |
Rv3458c rpsD |
30S ribosomal protein S4 | 898 | 896 | database:783 |
Rv3459c rpsK |
30S ribosomal protein S11 | 856 | 849 | database:746 |
Rv1336 cysM |
O-phosphoserine sulfhydrylase | 835 | 835 ctx | neighborhood:825 |
Rv2343c dnaG |
DNA primase | 852 | 824 | experimental:821 |
Rv1335 cysO |
sulfur carrier protein CysO | 824 | 824 ctx | neighborhood:821 |
Rv0721 rpsE |
30S ribosomal protein S5 | 816 | 814 | database:802 |
Rv1334 mec |
[CysO | 816 | 809 ctx | neighborhood:797 |
Rv1333 |
hydrolase | 803 | 803 ctx | neighborhood:797 |
Rv1332 |
transcriptional regulator | 789 | 790 ctx | neighborhood:783 |
Rv1331 clpS |
ATP-dependent Clp protease adapter protein ClpS | 784 | 784 ctx | neighborhood:783 |
Rv1338 murI |
glutamate racemase | 743 | 743 ctx | neighborhood:714 |
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: ribonuclease PH
- MTBC0 PGAP product: ribonuclease PH
- Pfam (hmmscan --cut_ga): RNase_PH PF01138.28 (E=2e-30), RNase_PH_C PF03725.21 (E=8e-11)
- (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_215856.1)
- Domains: Pfam-A via hmmscan --cut_ga — RNase_PH (PF01138.28), RNase_PH_C (PF03725.21)
- 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
COG2123 - Curated reference: UniProt P9WGZ7 (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 —
61 functional partner(s); context anchor
rdgB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001437|Rv1340|rphA MSKREDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTAEYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVVDGRIRVDLPYEEDSRAEVDMNVVATDTGTLVEIQGTGEGATFARSTLDKLLDMALGACDTLFAAQRDALALPYPGVLPQGPPPPKAFGT