Rv2079 Family assigned · medium auto-curated
H37Rv Rv2079 · MTBC0 mtbc0_002213 ·
656 aa · 2363968–2365938 (+) ·
RefSeq NP_216595.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | alpha/beta hydrolase |
| Revised (this work) | Alpha/beta hydrolase. Pfam: Hydro_N_hd (PF22905.3), Abhydrolase_8 (PF06259.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLK7
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv2079 |
UniProt still lists this protein as Uncharacterized protein Rv2079; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Alpha/beta hydrolase |
| Orthologous group | COG1511 |
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 | 0.43 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 12 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 26.31% of strains (38200) · 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 |
|---|---|---|---|---|
Hydro_N_hd | PF22905.3 | 2.7e-83 | 1–195 | Hydrolase N-terminal helical domain |
Abhydrolase_8 | PF06259.19 | 1.9e-30 | 348–520 | Alpha/beta hydrolase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lppJ (lipoprotein LppJ), high confidence from genomic context alone (score 813 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) |
|---|---|---|---|---|
Rv2078 hyp |
hypothetical protein | 969 | 969 ctx | neighborhood:833 coexpression:822 |
Rv2080 lppJ |
lipoprotein LppJ | 814 | 813 ctx | neighborhood:801 |
Rv1359 |
transcriptional regulator | 793 | 793 ctx | cooccurence:656 coexpression:423 |
Rv2423 hyp |
hypothetical protein | 764 | 764 ctx | cooccurence:763 |
Rv1904 hyp |
hypothetical protein | 739 | 740 ctx | cooccurence:736 |
Rv0048c |
membrane protein | 739 | 739 ctx | cooccurence:739 |
Rv3899c hyp |
hypothetical protein | 738 | 739 ctx | cooccurence:728 |
Rv1635c |
mannosyltransferase | 729 | 730 ctx | cooccurence:729 |
Rv3166c hyp |
hypothetical protein | 712 | 712 ctx | cooccurence:712 |
Rv0875c hyp |
hypothetical protein | 705 | 706 ctx | cooccurence:705 |
Rv2067c hyp |
hypothetical protein | 678 | 678 ctx | cooccurence:676 |
Rv3435c |
transmembrane protein | 677 | 677 ctx | cooccurence:674 |
Rv3779 |
transmembrane protein | 661 | 661 ctx | cooccurence:660 |
Rv2638 hyp |
hypothetical protein | 651 | 651 ctx | cooccurence:646 |
Rv3830c |
TetR family transcriptional regulator | 627 | 627 ctx | cooccurence:535 |
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: alpha/beta hydrolase
- Pfam (hmmscan --cut_ga): Hydro_N_hd PF22905.3 (E=3e-83), Abhydrolase_8 PF06259.19 (E=2e-30)
- (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_216595.1)
- Domains: Pfam-A via hmmscan --cut_ga — Hydro_N_hd (PF22905.3), Abhydrolase_8 (PF06259.19)
- 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
COG1511 - Curated reference: UniProt P9WLK7 (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 —
68 functional partner(s); context anchor
lppJ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002213|Rv2079| MQLRHINIRALIAEAGGDPWAIEHSLHAGRPAQIAELAEAFHAAGRCTAEANAAFEEARRRFEASWNRENGEHPINDSAEVQRVTAALGVQSLQLPKIGVDLENIAADLAEAQRAAAGRIATLESQLQRIDDQLDQALELEHDPRLAAAERSELDALITCLEQDAIDDTASALGQLQSIRAGYSDHLQQSLAMLRADGYDGAGLQGLDAPQSPVKPEEPIQIPPPGTGAPEVHRWWTSLTSEERQRLIAEHPEQIGNLNGVPVSARSDANIAVMTRDLNRVRDIATRYRTSVDDVLGDPAKYGLSAGDITRYRNADETKKGLDHNARNDPRNPSPVYLFAYDPMAFGGKGRAAIAIGNPDTAKHTAVIVPGTSSSVKGGWLHDNHDDALNLFNQAKAADPNNPTAVIAWMGYDAPNDFTDPRIATPMLARIGGAALAEDVNGLWVTHLGVGQNVTVLGHSYGSTTVADAFALGGMHANDAVLLGCPGTDLAHSAASFHLDGGRVYVGAASTDPISMLGQLDSLSQYVNRGNLAGQLQGLAVGLGTDPAGDGFGSVRFRAEVPNSDGINPHDHSYYYHRGSEALRSMADIASGHGDALASDGMLAQPRHQPGVEIDIPGLGSVEIDIPGTPASIDPEWSRPPGSITDDHVFDAPLHR