Rv2631 Resolved · high auto-curated
H37Rv Rv2631 · MTBC0 - ·
432 aa · 2957572–2958870 (+) ·
RefSeq NP_217147.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | RNA-splicing ligase RtcB |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | RNA-splicing ligase RtcB. Pfam: RtcB (PF01139.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WGW5
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | RNA-splicing ligase RtcB |
| EC (curated) |
EC 6.5.1.8
|
| Curated function | GTP-dependent RNA ligase that is involved RNA repair. Joins RNA with 2',3'-cyclic-phosphate or 3'-phosphate ends to RNA with 5'-hydroxy ends. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | rtcB |
| eggNOG description | tRNA-splicing ligase RtcB |
| Orthologous group | COG1690 |
| EC number |
EC 6.5.1.3
|
| KEGG orthology |
K14415
|
| Gene Ontology (7) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.355 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
RtcB | PF01139.23 | 3.9e-164 | 2–432 | tRNA-splicing ligase RtcB |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2630 hyp |
hypothetical protein | 987 | 984 ctx | neighborhood:754 coexpression:834 database:597 |
Rv2629 hyp |
hypothetical protein | 903 | 904 ctx | neighborhood:491 coexpression:819 |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 747 | 746 | coexpression:746 |
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 664 | 646 | database:447 |
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 663 | 645 | database:447 |
Rv0571c hyp |
hypothetical protein | 781 | 538 | coexpression:431 textmining:546 |
Rv0579 hyp |
hypothetical protein | 433 | 434 ctx | cooccurence:424 |
Rv2628 hyp |
hypothetical protein | 431 | 431 | |
Rv2003c hyp |
hypothetical protein | 713 | 402 | textmining:540 |
Rv3105c prfB |
peptide chain release factor PrfB | 431 | 346 | |
Rv2624c |
universal stress protein | 469 | 250 | |
Rv2625c rip3 |
zinc metalloprotease Rip3 | 716 | 218 | textmining:652 |
Rv0715 rplX |
50S ribosomal protein L24 | 447 | 214 | |
Rv3129 |
Rv3129, (MTCY164.40), len: 110 aa. Conserved hypothetical protein, with some similarity to various hypothetical proteins from Streptomyces c | 674 | 98 | textmining:654 |
Rv1812c |
dehydrogenase | 446 | 98 | 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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): RNA-splicing ligase RtcB
- Pfam (hmmscan --cut_ga): RtcB PF01139.23 (E=4e-164)
- (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_217147.2)
- Domains: Pfam-A via hmmscan --cut_ga — RtcB (PF01139.23)
- 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
COG1690 - Curated reference: UniProt P9WGW5 (SwissProt, reviewed; Evidence at transcript 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 — 24 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2631| MQVVNVATLPGIVRASYAMPDVHWGYGFPIGGVAATDVDNDGVVSPGGVGFDISCGVRLLVGEGLDREELQPRLPAVMDRLDRAIPRGVGTAGVWRLPDRNTLQEVLTGGARFAVEQGHGVALDLERCEDGGVMTGADAAKISDRALQRGLGQIGSLGSGNHFLEVQAVDRVYDPVAAAPMGLAEGTVCVMIHTGSRGLGHQICTDHVRQMEQAMGRYGIAVPDRQLACVPVHSPDGQAYLAAMAAAANYGRANRQLLTEATRRVFADATGTPLDLLYDVSHNLAKIETHPIDGQLRSVCVHRKGATRSLPPHHHELPAELAAVGQPVLIPGTMGTASYVLAGVTGNPAFFSTAHGAGRVLSRHQAARHTSGEAIRASLAKRGIIVRGTSRRGIAEEKPEAYKDVDEVIEASHQSGLARKVARLVPLGCVKG