Rv1692 Family assigned · medium auto-curated
H37Rv Rv1692 · MTBC0 mtbc0_001800 ·
353 aa · 1928713–1929774 (+) ·
RefSeq NP_216208.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphatase |
|---|---|
| MTBC0 PGAP re-annotation | HAD-IIA family hydrolase |
| Revised (this work) | HAD-IIA family hydrolase. Pfam: Hydrolase (PF00702.33), Hydrolase_6 (PF13344.13), Hydrolase_like (PF13242.13), GNAT_like (PF18407.8). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33194
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | D-glycerol 3-phosphate phosphatase |
| Curated function | Dephosphorylates D-glycerol 3-phosphate (sn-glycerol 1-phosphate). Is the final enzyme involved in the recycling/catabolism of glycerophospholipid polar heads. To a lesser extent, is also able to act on glycerol 2-phosphate and D-ribulose 5-phosphate, but cannot use D-glyceraldehyde 3-phosphate, dihydroxyacetone-phosphate, UMP or GMP as substrates. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | yutF |
| eggNOG description | hydrolase |
| Orthologous group | COG0647 |
| Gene Ontology (43) |
GO:0000121, GO:0000287, GO:0003674, GO:0003824, GO:0005488, GO:0005515, GO:0006629, GO:0006644, GO:0006650, GO:0006793, GO:0006796, GO:0008150 +31 more
|
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 | 0.358 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
Hydrolase | PF00702.33 | 1.3e-10 | 9–222 | haloacid dehalogenase-like hydrolase |
Hydrolase_6 | PF13344.13 | 2.7e-20 | 12–108 | Haloacid dehalogenase-like hydrolase |
Hydrolase_like | PF13242.13 | 2.9e-17 | 183–256 | HAD-hyrolase-like |
GNAT_like | PF18407.8 | 1.5e-17 | 269–340 | GCN5-related N-acetyltransferase like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ppnK (inorganic polyphosphate/ATP-NAD kinase), high confidence from genomic context alone (score 882 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1691 hyp |
hypothetical protein | 996 | 976 ctx | neighborhood:882 fusion:795 textmining:876 |
Rv3696c glpK |
glycerol kinase | 913 | 905 | database:900 |
Rv1551 plsB1 |
acyltransferase PlsB | 900 | 901 | database:900 |
Rv2482c plsB2 |
glycerol-3-phosphate acyltransferase | 900 | 901 | database:900 |
Rv3045 adhC |
NADP-dependent alcohol dehydrogenase | 900 | 900 | database:900 |
Rv1695 ppnK |
inorganic polyphosphate/ATP-NAD kinase | 984 | 882 ctx | neighborhood:882 textmining:870 |
Rv1693 hyp |
hypothetical protein | 984 | 882 ctx | neighborhood:882 textmining:870 |
Rv1694 tlyA |
16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA | 944 | 882 ctx | neighborhood:882 textmining:548 |
Rv1696 recN |
DNA repair protein RecN | 980 | 867 ctx | neighborhood:867 textmining:861 |
Rv1690 lprJ |
lipoprotein LprJ | 741 | 741 ctx | neighborhood:741 |
Rv1697 steA hyp |
hypothetical protein | 606 | 606 ctx | neighborhood:606 |
Rv1698 mctB |
copper transporter MctB | 573 | 574 ctx | neighborhood:574 |
Rv1712 cmk |
cytidylate kinase | 468 | 469 | |
Rv1700 |
NUDIX hydrolase | 485 | 464 ctx | neighborhood:451 |
Rv1699 pyrG |
CTP synthase | 471 | 451 ctx | neighborhood:451 |
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: phosphatase
- MTBC0 PGAP product: HAD-IIA family hydrolase
- Pfam (hmmscan --cut_ga): Hydrolase PF00702.33 (E=1e-10), Hydrolase_6 PF13344.13 (E=3e-20), Hydrolase_like PF13242.13 (E=3e-17), GNAT_like PF18407.8 (E=2e-17)
- (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_216208.1)
- Domains: Pfam-A via hmmscan --cut_ga — Hydrolase (PF00702.33), Hydrolase_6 (PF13344.13), Hydrolase_like (PF13242.13), GNAT_like (PF18407.8)
- 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
COG0647 - Curated reference: UniProt O33194 (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 —
20 functional partner(s); context anchor
ppnK - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001800|Rv1692| MKSIAQEHDCLLIDLDGTVFCGRQPTGGAVQSLSQVRSRKLFVTNNASRSADEVAAHLCELGFTATGEDVVTSAQSAAHLLAGQLAPGARVLIVGTEALANEVAAVGLRPVRRFEDRPDAVVQGLSMTTGWSDLAEAALAIRAGALWVAANVDPTLPTERGLLPGNGSMVAALRTATGMDPRVAGKPAPALMTEAVARGDFRAALVVGDRLDTDIEGANAAGLPSLMVLTGVNSAWDAVYAEPVRRPTYIGHDLRSLHQDSKLLAVAPQPGWQIDVGGGAVTVCANGDVDDLEFIDDGLSIVRAVASAVWEARAADLHQRPLRIEAGDERARAALQRWSLMRSDHPVTSVGTQ