Rv1998c Family assigned · medium auto-curated
H37Rv Rv1998c · MTBC0 mtbc0_002125 ·
258 aa · 2266558–2267334 (-) ·
RefSeq NP_216514.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | isocitrate lyase/phosphoenolpyruvate mutase family protein |
| Revised (this work) | Isocitrate lyase/phosphoenolpyruvate mutase family protein. Pfam: PEP_mutase (PF13714.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLN9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1998c |
UniProt still lists this protein as Uncharacterized protein Rv1998c; 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 | Phosphoenolpyruvate phosphomutase |
| Orthologous group | COG2513 |
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 | 0.135 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 |
|---|---|---|---|---|
PEP_mutase | PF13714.13 | 8.9e-69 | 3–229 | Phosphoenolpyruvate phosphomutase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1999c (transporter), medium confidence from genomic context alone (score 637 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) |
|---|---|---|---|---|
Rv3195 hyp |
hypothetical protein | 767 | 768 | coexpression:768 |
Rv0819 mshD |
mycothiol acetyltransferase | 767 | 768 | coexpression:768 |
Rv1130 prpD |
2-methylcitrate dehydratase | 804 | 744 | coexpression:723 |
Rv3470c ilvB2 |
acetolactate synthase large subunit | 741 | 725 | coexpression:716 |
Rv0896 gltA2 |
citrate synthase 1 | 750 | 724 | coexpression:674 |
Rv1131 prpC |
methylcitrate synthase PrpC | 749 | 723 | coexpression:673 |
Rv0889c citA |
citrate synthase 2 | 749 | 723 | coexpression:673 |
Rv1999c |
transporter | 636 | 637 ctx | neighborhood:583 |
Rv1317c alkA |
bifunctional regulatory protein/DNA repair enzyme AlkA | 546 | 546 ctx | cooccurence:404 |
Rv1837c glcB |
malate synthase | 623 | 509 | coexpression:508 |
Rv3667 acs |
acetyl-CoAsynthetase | 622 | 508 | coexpression:467 |
Rv1240 mdh |
malate dehydrogenase | 595 | 472 | |
Rv0250c hyp |
hypothetical protein | 464 | 464 ctx | neighborhood:461 |
Rv2781c |
oxidoreductase | 447 | 447 | |
Rv1234 |
transmembrane protein | 443 | 444 | coexpression:444 |
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: isocitrate lyase/phosphoenolpyruvate mutase family protein
- Pfam (hmmscan --cut_ga): PEP_mutase PF13714.13 (E=9e-69)
- (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_216514.1)
- Domains: Pfam-A via hmmscan --cut_ga — PEP_mutase (PF13714.13)
- 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
COG2513 - Curated reference: UniProt P9WLN9 (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 —
26 functional partner(s); context anchor
Rv1999c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002125|Rv1998c| MSFHDLHHQGVPFVLPNAWDVPSALAYLAEGFTAIGTTSFGVSSSGGHPDGHRATRGANIALAAALAPLQCYVSVDIEDGYSDEPDAIADYVAQLSTAGINIEDSSAEKLIDPALAAAKIVAIKQRNPEVFVNARVDTYWLRQHADTTSTIQRALRYVDAGADGVFVPLANDPDELAELTRNIPCPVNTLPVPGLTIADLGELGVARVSTGSVPYSAGLYAAAHAARAVRDGEQLPRSVPYAELQARLVDYENRTSTT