Rv2704 Family assigned · medium auto-curated
H37Rv Rv2704 · MTBC0 mtbc0_002878 ·
142 aa · 3041873–3042301 (+) ·
RefSeq NP_217220.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | RidA family protein |
| Revised (this work) | RidA family protein. Pfam: Ribonuc_L-PSP (PF01042.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YA21
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| eggNOG description | Endoribonuclease L-psp |
| Orthologous group | COG0251 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
Ribonuc_L-PSP | PF01042.27 | 2.7e-28 | 12–121 | Endoribonuclease L-PSP |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sigA (RNA polymerase sigma factor SigA), high confidence from genomic context alone (score 819 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2703 sigA |
RNA polymerase sigma factor SigA | 900 | 819 ctx | neighborhood:815 textmining:469 |
Rv0684 fusA1 |
elongation factor G | 693 | 682 | database:629 |
Rv0120c fusA2 |
elongation factor G | 691 | 680 | database:629 |
Rv1340 rphA |
ribonuclease PH | 572 | 553 | experimental:434 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 616 | 485 | coexpression:415 |
Rv2702 ppgK |
polyphosphate glucokinase | 491 | 468 ctx | neighborhood:468 |
Rv0021c hyp |
hypothetical protein | 414 | 414 ctx | fusion:414 |
Rv3005c hyp |
hypothetical protein | 454 | 223 | |
Rv3916c hyp |
hypothetical protein | 581 | 180 | textmining:511 |
Rv3722c hyp |
hypothetical protein | 454 | 165 | |
Rv3192 hyp |
hypothetical protein | 652 | 102 | textmining:629 |
Rv0024 |
NLP/P60 family protein | 463 | 100 | textmining:429 |
Rv3256c hyp |
hypothetical protein | 574 | 99 | textmining:547 |
Rv3630 |
integral membrane protein | 451 | 74 | textmining:432 |
Rv0052 hyp |
hypothetical protein | 527 | 61 | textmining:517 |
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: hypothetical protein
- MTBC0 PGAP product: RidA family protein
- Pfam (hmmscan --cut_ga): Ribonuc_L-PSP PF01042.27 (E=3e-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_217220.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribonuc_L-PSP (PF01042.27)
- 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
COG0251 - Curated reference: UniProt I6YA21 (TrEMBL, unreviewed; 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 —
19 functional partner(s); context anchor
sigA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002878|Rv2704| MSASRTMVSSGSEFESAVGYSRAVRIGPLVVVAGTTGSGDDIAAQTRDALRRIEIALGQAGATLADVVRTRIYVTDISRWREVGEVHAQAFGKIRPVTSMVEVTALIAPGLLVEIEADAYVGSAVADRNSGAGPKDPSPAGG