Rv1571 Family assigned · medium auto-curated
H37Rv Rv1571 · MTBC0 mtbc0_001679 ·
169 aa · 1790503–1791012 (+) ·
RefSeq NP_216087.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | 2'-5' RNA ligase family protein |
| Revised (this work) | 2'-5' RNA ligase family protein. Pfam: 2_5_RNA_ligase2 (PF13563.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06619
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 | 2'-5' RNA ligase superfamily |
| Orthologous group | COG1514 |
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 | 0.52 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
2_5_RNA_ligase2 | PF13563.13 | 2.8e-10 | 12–134 | 2'-5' RNA ligase superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: bioD (ATP-dependent dethiobiotin synthetase BioD), high confidence from genomic context alone (score 953 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) |
|---|---|---|---|---|
Rv1570 bioD |
ATP-dependent dethiobiotin synthetase BioD | 990 | 953 ctx | neighborhood:882 coexpression:615 textmining:806 |
Rv1569 bioF1 |
8-amino-7-oxononanoate synthase | 985 | 895 ctx | neighborhood:882 textmining:870 |
Rv1568 bioA |
adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA | 975 | 882 ctx | neighborhood:881 textmining:803 |
Rv1567c |
membrane protein | 741 | 741 ctx | neighborhood:741 |
Rv1563c treY |
maltooligosyl trehalose synthase | 686 | 686 ctx | neighborhood:623 |
Rv3300c hyp |
hypothetical protein | 463 | 464 | |
Rv0519c |
membrane protein | 498 | 459 | coexpression:414 |
Rv1776c |
transcriptional regulator | 453 | 454 ctx | cooccurence:453 |
Rv1972 |
Mce associated membrane protein | 441 | 442 ctx | cooccurence:436 |
Rv1125 hyp |
hypothetical protein | 428 | 428 ctx | cooccurence:409 |
Rv1140 |
integral membrane protein | 427 | 428 | |
Rv1026 ppx2 hyp |
hypothetical protein | 422 | 423 | coexpression:423 |
Rv3584 lpqE |
lipoprotein LpqE | 419 | 419 | |
Rv1274 lprB |
lipoprotein LprB | 412 | 412 ctx | cooccurence:412 |
Rv1901 cinA |
competence damage-inducible protein CinA | 672 | 392 | textmining:484 |
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: 2'-5' RNA ligase family protein
- Pfam (hmmscan --cut_ga): 2_5_RNA_ligase2 PF13563.13 (E=3e-10)
- (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_216087.1)
- Domains: Pfam-A via hmmscan --cut_ga — 2_5_RNA_ligase2 (PF13563.13)
- 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
COG1514 - Curated reference: UniProt O06619 (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 —
16 functional partner(s); context anchor
bioD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001679|Rv1571| MVHSIELVFDSDTEAAIRRIWAGLAAAGIPSQAPASRPHVSLAVAERIAPEVDEPLGAVARRLPLDCVIGAPVLFGRANVVFTRLVVPTSELLALHAEVHRLCGPHLAPAPMANSLPGQWTAHVTLARRVGGHQLGRALRIAGRPSRIDGRFAGLRRWDGNTRAEYLLG