rnhB Resolved · high auto-curated
H37Rv Rv2902c · MTBC0 mtbc0_003084 ·
264 aa · 3232991–3233785 (-) ·
RefSeq NP_217418.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease HII |
|---|---|
| MTBC0 PGAP re-annotation | ribonuclease HII |
| Revised (this work) | Ribonuclease HII. Pfam: RNase_HII (PF01351.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH01
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease HII |
| EC (curated) |
EC 3.1.26.4
|
| Curated function | Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | rnhB |
| eggNOG description | Endonuclease that specifically degrades the RNA of RNA- DNA hybrids |
| Orthologous group | COG0164 |
| EC number |
EC 3.1.26.4
|
| KEGG orthology |
K03470
|
| KEGG pathways |
map03030
|
| Gene Ontology (69) |
GO:0003674, GO:0003824, GO:0004518, GO:0004519, GO:0004521, GO:0004523, GO:0004540, GO:0005575, GO:0005622, GO:0005623, GO:0006139, GO:0006259 +57 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 | 0.483 · 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 |
|---|---|---|---|---|
RNase_HII | PF01351.26 | 1.4e-50 | 36–215 | Ribonuclease HII |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lepB (signal peptidase), high confidence from genomic context alone (score 975 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2903c lepB |
signal peptidase | 975 | 975 ctx | neighborhood:872 coexpression:813 |
Rv2904c rplS |
50S ribosomal protein L19 | 868 | 860 ctx | neighborhood:798 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 861 | 843 | coexpression:423 experimental:738 |
Rv2116 lppK |
lipoprotein LppK | 860 | 842 | coexpression:419 experimental:738 |
Rv2901c hyp |
hypothetical protein | 821 | 821 ctx | neighborhood:809 |
Rv1631 coaE |
dephospho-CoA kinase CoaE | 786 | 787 | coexpression:772 |
Rv2228c |
multifunctional RNASE H/alpha-ribazole phosphatase/acid phosphatase | 954 | 767 | experimental:741 textmining:813 |
Rv0514 |
transmembrane protein | 731 | 731 | coexpression:731 |
Rv2764c thyA |
thymidylate synthase ThyA | 755 | 708 | coexpression:652 |
Rv2492 hyp |
hypothetical protein | 717 | 705 | coexpression:649 |
Rv1644 tsnR |
23S rRNA methyltransferase TsnR | 678 | 662 | coexpression:594 |
Rv1481 |
membrane protein | 604 | 605 | coexpression:553 |
Rv3151 nuoG |
NADH-quinone oxidoreductase subunit G | 602 | 603 | experimental:474 |
Rv1629 polA |
DNA polymerase I | 913 | 588 | textmining:799 |
Rv1480 hyp |
hypothetical protein | 586 | 587 | coexpression:580 |
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 HII
- MTBC0 PGAP product: ribonuclease HII
- Pfam (hmmscan --cut_ga): RNase_HII PF01351.26 (E=1e-50)
- (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_217418.1)
- Domains: Pfam-A via hmmscan --cut_ga — RNase_HII (PF01351.26)
- 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
COG0164 - Curated reference: UniProt P9WH01 (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 —
103 functional partner(s); context anchor
lepB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003084|Rv2902c|rnhB MTKTWPPRTVIRKSGGLRGMRTLESALHRGGLGPVAGVDEVGRGACAGPLVVAACVLGPGRIASLAALDDSKKLSEQAREKLFPLICRYAVAYHVVFIPSAEVDRRGVHVANIEGMRRAVAGLAVRPGYVLSDGFRVPGLPMPSLPVIGGDAAAACIAAASVLAKVSRDRVMVALDADHPGYGFAEHKGYSTPAHSRALARLGPCPQHRYSFINVRRVASGSNTAEVADGQPDPRDGTAQTGEGRWSKSSHPATMRATGRAQGT