Rv2570 Family assigned · medium auto-curated
H37Rv Rv2570 · MTBC0 mtbc0_002737 ·
129 aa · 2918056–2918445 (+) ·
RefSeq NP_217086.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | MmcQ/YjbR family DNA-binding protein |
| Revised (this work) | MmcQ/YjbR family DNA-binding protein. Pfam: YjbR (PF04237.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL91
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv2570 |
UniProt still lists this protein as Uncharacterized protein Rv2570; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Catalyzes the transfer of a formyl group from 10- formyltetrahydrofolate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR) and tetrahydrofolate |
| Orthologous group | COG3801 |
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) pseudogene candidate
| pN/pS | 0.435 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 3.30% of strains (4790) · clonal |
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 |
|---|---|---|---|---|
YjbR | PF04237.19 | 7.4e-08 | 14–113 | YjbR |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0541c (integral membrane protein), medium confidence from genomic context alone (score 440 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) |
|---|---|---|---|---|
Rv2569c hyp |
hypothetical protein | 656 | 656 ctx | neighborhood:655 |
Rv2568c hyp |
hypothetical protein | 655 | 655 ctx | neighborhood:655 |
Rv2036 hyp |
hypothetical protein | 561 | 562 ctx | cooccurence:559 |
Rv2828A hyp |
hypothetical protein | 478 | 478 ctx | cooccurence:478 |
Rv1868 hyp |
hypothetical protein | 451 | 452 ctx | cooccurence:444 |
Rv0541c |
integral membrane protein | 440 | 440 ctx | cooccurence:440 |
Rv1006 hyp |
hypothetical protein | 413 | 413 ctx | cooccurence:413 |
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: MmcQ/YjbR family DNA-binding protein
- Pfam (hmmscan --cut_ga): YjbR PF04237.19 (E=7e-08)
- (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_217086.1)
- Domains: Pfam-A via hmmscan --cut_ga — YjbR (PF04237.19)
- 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
COG3801 - Curated reference: UniProt P9WL91 (SwissProt, reviewed; Predicted)
- 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 —
7 functional partner(s); context anchor
Rv0541c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002737|Rv2570| MATWDDVARIVGGLPLTAEQAPHDWRVGRKLLAWERPLRKSDREALTRAGSEPPSGDIVGVRVSDEGVKFALIADEPGVYFTTPHFDGYPAVLVRLAEIEVRDLEELITEAWLMQAPKQLVQAFLANSG