Rv2037c Family assigned · medium auto-curated
H37Rv Rv2037c · MTBC0 mtbc0_002170 ·
324 aa · 2311360–2312334 (-) ·
RefSeq NP_216553.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | patatin-like phospholipase family protein |
| Revised (this work) | Patatin-like phospholipase family protein. Pfam: Patatin (PF01734.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
L0TB61
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Phospholipase |
| Orthologous group | COG1752 |
| KEGG orthology |
K07001
|
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 | 0.895 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 10 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 |
|---|---|---|---|---|
Patatin | PF01734.28 | 1.1e-33 | 11–209 | Patatin-like phospholipase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2041c (sugar ABC transporter substrate-binding lipoprotein), high confidence from genomic context alone (score 827 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2041c |
sugar ABC transporter substrate-binding lipoprotein | 827 | 827 ctx | neighborhood:774 |
Rv2039c |
sugar ABC transporter permease | 812 | 812 ctx | neighborhood:807 |
Rv2038c ugpC |
sugar ABC transporter ATP-binding protein | 807 | 806 ctx | neighborhood:801 |
Rv2040c |
sugar ABC transporter permease | 785 | 786 ctx | neighborhood:781 |
Rv2043c pncA |
pyrazinamidase/nicotinamidase PncA | 674 | 675 ctx | neighborhood:664 |
Rv2042c hyp |
hypothetical protein | 670 | 670 ctx | neighborhood:656 |
Rv2044c hyp |
hypothetical protein | 555 | 555 ctx | neighborhood:550 |
Rv0629c recD |
exonuclease V subunit alpha RecD | 514 | 514 ctx | neighborhood:511 |
Rv0631c recC |
exonuclease V subunit gamma RecC | 513 | 514 ctx | neighborhood:511 |
Rv0630c recB |
exonuclease V subunit beta RecB | 513 | 513 ctx | neighborhood:511 |
Rv1063c |
NTE family protein | 426 | 427 ctx | cooccurence:425 |
Rv2045c lipT |
carboxylesterase LipT | 414 | 413 ctx | neighborhood:406 |
Rv3600c coaX |
type III pantothenate kinase | 874 | 74 | textmining:870 |
Rv2225 panB |
3-methyl-2-oxobutanoate hydroxymethyltransferase | 662 | 72 | textmining:651 |
Rv2003c hyp |
hypothetical protein | 805 | 55 | textmining:803 |
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: transmembrane protein
- MTBC0 PGAP product: patatin-like phospholipase family protein
- Pfam (hmmscan --cut_ga): Patatin PF01734.28 (E=1e-33)
- (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_216553.1)
- Domains: Pfam-A via hmmscan --cut_ga — Patatin (PF01734.28)
- 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
COG1752 - Curated reference: UniProt L0TB61 (TrEMBL, unreviewed; 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 —
19 functional partner(s); context anchor
Rv2041c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002170|Rv2037c| MALVSTARVDLVCEGGGVRGIGLVGAVDALADAGYRFPRVAGSSAGAIVASLVAALQTAGEPVTRLAEMMRSIDYPKFLDRNLIGHVPLIGGGLSLLLSDGVYRGAYLEQLLGGLLADLGVHTFGDLRTGEAPEQFAWSLVVTASDLSRRRLVRIPWDLDSYGIHPDDFSVARAVHASSAIPFVFEPVRVRGATWVDGGLLSNFPVALFDRTDAEPRWPTFGIRLSARPGIPPTRPVQGPVSLGIAAIETLVSNQDNAYIDDPCTVRRTIFVPAHDVSPIDFDITAEQREALYQRGFQAGQKFLANWNYADYLADCGGPFTPSL