Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oligoribonuclease |
|---|
| MTBC0 PGAP re-annotation | oligoribonuclease |
|---|
| Revised (this work) | Oligoribonuclease. Pfam: RNase_T (PF00929.32). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIU1
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Oligoribonuclease |
|---|
| EC (curated) |
EC 3.1.15.-
|
|---|
| Curated function | 3'-to-5' exoribonuclease specific for small oligoribonucleotides. |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
A RNA processing and modification
|
|---|
| Preferred name | orn |
|---|
| eggNOG description | 3'-to-5' exoribonuclease specific for small oligoribonucleotides |
|---|
| Orthologous group | COG1949 |
|---|
| KEGG orthology |
K13288
|
|---|
| KEGG pathways |
map03008
|
|---|
| Gene Ontology (32) |
GO:0000175, GO:0003674, GO:0003824, GO:0004518, GO:0004527, GO:0004532, GO:0004540, GO:0006139, GO:0006725, GO:0006807, GO:0008150, GO:0008152 +20 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 |
0.33 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
2 synonymous, 2 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_T | PF00929.32 |
4.5e-35 | 6–169 |
Exonuclease |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv2510c hyp |
hypothetical protein |
633 |
633 ctx |
neighborhood:632 |
Rv2478c hyp |
hypothetical protein |
505 |
481 |
|
Rv0054 ssb |
single-strand DNA-binding protein |
453 |
426 |
|
Rv2444c rne |
ribonuclease E |
588 |
267 |
textmining:462 |
Rv2191 hyp |
hypothetical protein |
422 |
264 |
|
Rv3907c pcnA |
poly(A) polymerase PcnA |
736 |
248 |
textmining:664 |
Rv1340 rphA |
ribonuclease PH |
735 |
227 |
textmining:672 |
Rv2783c gpsI |
bifunctional guanosine pentaphosphate synthetase/polyribonucleotide nucleotidyltransferase |
637 |
169 |
textmining:582 |
Rv1930c hyp |
hypothetical protein |
481 |
153 |
textmining:413 |
Rv2837c nrnA |
bifunctional oligoribonuclease/PAP phosphatase NrnA |
932 |
71 |
textmining:930 |
Rv2131c cysQ |
3'(2'),5'-bisphosphate nucleotidase CysQ |
895 |
41 |
textmining:895 |
Rv2752c rnj |
ribonuclease J |
617 |
41 |
textmining:617 |
Rv2555c alaS |
alanine--tRNA ligase |
544 |
41 |
textmining:545 |
Rv1641 infC |
initiation factor IF-3 |
516 |
41 |
textmining:516 |
Rv2407 rnz |
ribonuclease Z |
410 |
41 |
textmining:411 |
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: oligoribonuclease
- MTBC0 PGAP product: oligoribonuclease
- Pfam (hmmscan --cut_ga): RNase_T PF00929.32 (E=5e-35)
- (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_217027.1)
- Domains: Pfam-A via hmmscan --cut_ga — RNase_T (PF00929.32)
- 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
COG1949
- Curated reference: UniProt
P9WIU1
(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 —
15 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002673|Rv2511|orn
MQDELVWIDCEMTGLDLGSDKLIEIAALVTDADLNILGDGVDVVMHADDAALSGMIDVVAEMHSRSGLIDEVKASTVDLATAEAMVLDYINEHVKQPKTAPLAGNSIATDRAFIARDMPTLDSFLHYRMIDVSSIKELCRRWYPRIYFGQPPKGLTHRALADIHESIRELRFYRRTAFVPQPGPSTSEIAAVVAELSDGAGAQEETDSAEAPQSG
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