Rv2556c Resolved · high auto-curated
H37Rv Rv2556c · MTBC0 mtbc0_002724 ·
129 aa · 2900121–2900510 (-) ·
RefSeq NP_217072.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | secondary thiamine-phosphate synthase enzyme YjbQ |
| Revised (this work) | Secondary thiamine-phosphate synthase enzyme YjbQ. Pfam: YjbQ (PF01894.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFP9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | UPF0047 protein Rv2556c |
UniProt still lists this protein as UPF0047 protein Rv2556c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Uncharacterised protein family UPF0047 |
| Orthologous group | COG0432 |
| Gene Ontology (6) |
GO:0005575, 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 | 0.36 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
YjbQ | PF01894.23 | 5.1e-27 | 13–124 | UPF0047 protein YjbQ-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: alaS (alanine--tRNA ligase), high confidence from genomic context alone (score 789 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) |
|---|---|---|---|---|
Rv2555c alaS |
alanine--tRNA ligase | 789 | 789 ctx | neighborhood:779 |
Rv2554c ruvX |
Holliday junction resolvase | 788 | 789 ctx | neighborhood:779 |
Rv2553c mltG |
membrane protein | 782 | 782 ctx | neighborhood:779 |
Rv2552c aroE |
shikimate 5-dehydrogenase | 782 | 782 ctx | neighborhood:779 |
Rv2551c hyp |
hypothetical protein | 746 | 746 ctx | neighborhood:735 |
Rv2557 hyp |
hypothetical protein | 596 | 596 ctx | neighborhood:594 |
Rv2558 hyp |
hypothetical protein | 469 | 469 ctx | neighborhood:466 |
Rv2540c aroF |
chorismate synthase | 402 | 403 |
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: secondary thiamine-phosphate synthase enzyme YjbQ
- Pfam (hmmscan --cut_ga): YjbQ PF01894.23 (E=5e-27)
- (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_217072.1)
- Domains: Pfam-A via hmmscan --cut_ga — YjbQ (PF01894.23)
- 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
COG0432 - Curated reference: UniProt P9WFP9 (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 —
8 functional partner(s); context anchor
alaS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002724|Rv2556c| MLDVDTARRRIVDLTDAVRAFCTAHDDGLCNVFVPHATAGVAIIETGAGSDEDLVDTLVRLLPRDDRYRHAHGSYGHGADHLLPAFVAPSVTVPVSGGQPLLGTWQSIVLVDLNQDNPRRSVRLSFVEG