Rv2630 Resolved · high auto-curated
H37Rv Rv2630 · MTBC0 mtbc0_002799 ·
179 aa · 2980455–2980994 (+) ·
RefSeq NP_217146.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | archease |
| Revised (this work) | Archease. Pfam: Archease (PF01951.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQ03
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable protein archease |
| Curated function | Activates the tRNA-splicing ligase complex by facilitating the enzymatic turnover of catalytic subunit RtcB. Acts by promoting the guanylylation of RtcB, a key intermediate step in tRNA ligation. Can also alter the NTP specificity of RtcB such that ATP, dGTP or ITP is used efficiently (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Archease protein family (MTH1598/TM1083) |
| Orthologous group | COG1371 |
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 | 0.743 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
Archease | PF01951.22 | 5.3e-21 | 49–179 | Archease protein family (MTH1598/TM1083) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rtcB (RNA-splicing ligase RtcB), high confidence from genomic context alone (score 984 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) |
|---|---|---|---|---|
Rv2631 rtcB |
RNA-splicing ligase RtcB | 987 | 984 ctx | neighborhood:754 coexpression:834 database:597 |
Rv2629 hyp |
hypothetical protein | 968 | 969 ctx | neighborhood:785 coexpression:860 |
Rv0571c hyp |
hypothetical protein | 795 | 796 | coexpression:780 |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 791 | 791 | coexpression:791 |
Rv2004c hyp |
hypothetical protein | 788 | 788 | coexpression:788 |
Rv3132c devS |
two component sensor histidine kinase DevS | 733 | 733 | coexpression:733 |
Rv2628 hyp |
hypothetical protein | 534 | 534 | |
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 474 | 450 | database:447 |
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 471 | 447 | database:447 |
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: archease
- Pfam (hmmscan --cut_ga): Archease PF01951.22 (E=5e-21)
- (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_217146.1)
- Domains: Pfam-A via hmmscan --cut_ga — Archease (PF01951.22)
- 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
COG1371 - Curated reference: UniProt P9WQ03 (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 —
9 functional partner(s); context anchor
rtcB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002799|Rv2630| MLHRDDHINPPRPRGLDVPCARLRATNPLRALARCVQAGKPGTSSGHRSVPHTADLRIEAWAPTRDGCIRQAVLGTVESFLDLESAHAVHTRLRRLTADRDDDLLVAVLEEVIYLLDTVGETPVDLRLRDVDGGVDVTFATTDASTLVQVGAVPKAVSLNELRFSQGRHGWRCAVTLDV