Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease III |
|---|
| MTBC0 PGAP re-annotation | ribonuclease III |
|---|
| Revised (this work) | Ribonuclease III. Pfam: Ribonucleas_3_3 (PF14622.12), Ribonuclease_3 (PF00636.32), dsrm (PF00035.33). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH03
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Ribonuclease 3 |
|---|
| EC (curated) |
EC 3.1.26.3
|
|---|
| Curated function | Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism (By similarity). |
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Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|
| Preferred name | rnc |
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| eggNOG description | Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre- crRNA and tracrRNA of type II CRISPR loci if present in the organism |
|---|
| Orthologous group | COG0571 |
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| EC number |
EC 3.1.26.3
|
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| KEGG orthology |
K03685
|
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| KEGG pathways |
map03008, map05205
|
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| Gene Ontology (40) |
GO:0003674, GO:0003676, GO:0003723, GO:0003725, GO:0003824, GO:0004518, GO:0004519, GO:0004521, GO:0004525, GO:0004540, GO:0005488, GO:0006139 +28 more
|
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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 |
0.36 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
1 synonymous, 1 missense, 0 nonsense, 0 frameshift
|
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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 |
|---|
Ribonucleas_3_3 | PF14622.12 |
9.1e-37 | 18–144 |
Ribonuclease-III-like |
Ribonuclease_3 | PF00636.32 |
1.6e-22 | 41–134 |
Ribonuclease III domain |
dsrm | PF00035.33 |
4.9e-17 | 162–227 |
Double-stranded RNA binding motif |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv2441c rpmA |
50S ribosomal protein L27 |
955 |
951 |
coexpression:405 experimental:918 |
Rv0979A rpmF |
50S ribosomal protein L32 |
947 |
947 |
experimental:917 |
Rv3442c rpsI |
30S ribosomal protein S9 |
957 |
945 |
experimental:916 |
Rv0708 rplP |
50S ribosomal protein L16 |
944 |
941 |
experimental:914 |
Rv2926c hyp |
hypothetical protein |
992 |
939 ctx |
neighborhood:882 coexpression:505 textmining:877 |
Rv2904c rplS |
50S ribosomal protein L19 |
945 |
938 |
experimental:923 |
Rv3443c rplM |
50S ribosomal protein L13 |
952 |
937 |
experimental:919 |
Rv0706 rplV |
50S ribosomal protein L22 |
940 |
936 |
experimental:920 |
Rv2785c rpsO |
30S ribosomal protein S15 |
967 |
934 |
experimental:917 textmining:519 |
Rv3456c rplQ |
50S ribosomal protein L17 |
942 |
934 |
experimental:917 |
Rv0682 rpsL |
30S ribosomal protein S12 |
939 |
931 |
experimental:910 |
Rv2909c rpsP |
30S ribosomal protein S16 |
937 |
930 |
experimental:916 |
Rv0723 rplO |
50S ribosomal protein L15 |
934 |
930 |
experimental:916 |
Rv0702 rplD |
50S ribosomal protein L4 |
936 |
929 |
experimental:910 |
Rv2890c rpsB |
30S ribosomal protein S2 |
933 |
926 |
experimental:911 |
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 III
- MTBC0 PGAP product: ribonuclease III
- Pfam (hmmscan --cut_ga): Ribonucleas_3_3 PF14622.12 (E=9e-37), Ribonuclease_3 PF00636.32 (E=2e-22), dsrm PF00035.33 (E=5e-17)
- (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_217441.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribonucleas_3_3 (PF14622.12), Ribonuclease_3 (PF00636.32), dsrm (PF00035.33)
- 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
COG0571
- Curated reference: UniProt
P9WH03
(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 —
182 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003108|Rv2925c|rnc
MIRSRQPLLDALGVDLPDELLSLALTHRSYAYENGGLPTNERLEFLGDAVLGLTITDALFHRHPDRSEGDLAKLRASVVNTQALADVARRLCAEGLGVHVLLGRGEANTGGADKSSILADGMESLLGAIYLQHGMEKAREVILRLFGPLLDAAPTLGAGLDWKTSLQELTAARGLGAPSYLVTSTGPDHDKEFTAVVVVMDSEYGSGVGRSKKEAEQKAAAAAWKALEVLDNAMPGKTSA
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