Rv0498 Resolved · high auto-curated
H37Rv Rv0498 · MTBC0 mtbc0_000524 ·
280 aa · 591666–592508 (+) ·
RefSeq NP_215012.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | sugar phosphate isomerase/epimerase |
| Revised (this work) | Sugar phosphate isomerase/epimerase. Pfam: AP_endonuc_2 (PF01261.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKU1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0498 |
UniProt still lists this protein as Uncharacterized protein Rv0498; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | TIM barrel |
| Orthologous group | COG1082 |
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 | 0.468 · purifying |
|---|---|
| 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 |
|---|---|---|---|---|
AP_endonuc_2 | PF01261.31 | 4.5e-22 | 23–276 | Xylose isomerase-like TIM barrel |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: proC (pyrroline-5-carboxylate reductase), high confidence from genomic context alone (score 831 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) |
|---|---|---|---|---|
Rv0499 hyp |
hypothetical protein | 964 | 965 ctx | neighborhood:863 coexpression:754 |
Rv1752 hyp |
hypothetical protein | 902 | 873 | coexpression:863 |
Rv0496 ppx1 hyp |
hypothetical protein | 864 | 864 ctx | neighborhood:863 |
Rv0500 proC |
pyrroline-5-carboxylate reductase | 831 | 831 ctx | neighborhood:830 |
Rv0497 |
transmembrane protein | 786 | 786 ctx | neighborhood:783 |
Rv0500A |
DNA-binding protein | 740 | 740 ctx | neighborhood:724 |
Rv0495c hyp |
hypothetical protein | 618 | 619 ctx | neighborhood:617 |
Rv2436 rbsK |
ribokinase RbsK | 614 | 562 | coexpression:537 |
Rv2202c adoK |
adenosine kinase | 612 | 560 | coexpression:535 |
Rv1457c |
antibiotic ABC transporter permease | 552 | 553 ctx | cooccurence:540 |
Rv3015c hyp |
hypothetical protein | 529 | 529 ctx | cooccurence:526 |
Rv3597c lsr2 |
iron-regulated H-NS-like protein | 523 | 523 ctx | cooccurence:520 |
Rv0360c hyp |
hypothetical protein | 516 | 516 ctx | cooccurence:516 |
Rv2867c |
GCN5-like N-acetyltransferase | 513 | 513 ctx | cooccurence:510 |
Rv3197A whiB7 |
transcriptional regulator WhiB7 | 510 | 511 ctx | cooccurence:508 |
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: sugar phosphate isomerase/epimerase
- Pfam (hmmscan --cut_ga): AP_endonuc_2 PF01261.31 (E=4e-22)
- (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_215012.1)
- Domains: Pfam-A via hmmscan --cut_ga — AP_endonuc_2 (PF01261.31)
- 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
COG1082 - Curated reference: UniProt P9WKU1 (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 —
22 functional partner(s); context anchor
proC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000524|Rv0498| MRPAIKVGLSTASVYPLRAEAAFEYADRLGYDGVELMVWGESVSQDIDAVRKLSRRYRVPVLSVHAPCLLISQRVWGANPILKLDRSVRAAEQLGAQTVVVHPPFRWQRRYAEGFSDQVAALEAASTVMVAVENMFPFRADRFFGAGQSRERMRKRGGGPGPAISAFAPSYDPLDGNHAHYTLDLSHTATAGTDSLDMARRMGPGLVHLHLCDGSGLPADEHLVPGRGTQPTAEVCQMLAGSGFVGHVVLEVSTSSARSANERESMLAESLQFARTHLLR