Rv1288 Resolved · high auto-curated
H37Rv Rv1288 · MTBC0 mtbc0_001378 ·
456 aa · 1450331–1451701 (+) ·
RefSeq NP_215804.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | esterase |
| Revised (this work) | Esterase. Pfam: Phage_tail_X (PF05489.19), LysM (PF01476.27), Esterase (PF00756.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WM39
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Esterase Rv1288 |
| EC (curated) |
EC 3.1.1.-
|
| Curated function | Exhibits lipolytic activity with medium chain length esters as optimum substrates. In vitro, pNP-caprylate (C8) is the optimum substrate followed by pNP-capricate (C10). May modulate the cell wall lipids to favor the survival of bacteria under stress conditions. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | xynZ |
| eggNOG description | Lysin motif |
| Orthologous group | COG0627 |
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 | 1.005 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 9 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 |
|---|---|---|---|---|
Phage_tail_X | PF05489.19 | 9.6e-06 | 7–56 | Phage Tail Protein X |
LysM | PF01476.27 | 2.6e-09 | 107–152 | LysM domain |
Esterase | PF00756.27 | 5.0e-60 | 182–442 | Putative esterase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1287 (HTH-type transcriptional regulator), medium confidence from genomic context alone (score 668 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) |
|---|---|---|---|---|
Rv1287 |
HTH-type transcriptional regulator | 684 | 668 ctx | neighborhood:645 |
Rv1289 hyp |
hypothetical protein | 667 | 667 ctx | neighborhood:665 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 637 | 637 ctx | cooccurence:637 |
Rv3594 hyp |
hypothetical protein | 669 | 627 ctx | cooccurence:622 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 614 | 614 ctx | cooccurence:614 |
Rv0097 |
oxidoreductase | 603 | 603 ctx | cooccurence:601 |
Rv1921c lppF |
lipoprotein LppF | 601 | 602 ctx | cooccurence:533 |
Rv1754c hyp |
hypothetical protein | 568 | 541 | |
Rv1285 cysD |
sulfate adenylyltransferase subunit 2 | 531 | 532 ctx | neighborhood:505 |
Rv0899 arfA |
peptidoglycan-binding protein ArfA | 559 | 531 | |
Rv0412c glnX |
membrane protein | 551 | 529 | coexpression:407 |
Rv0761c adhB |
alcohol dehydrogenase B | 548 | 528 | coexpression:443 |
Rv3086 adhD |
alcohol dehydrogenase D | 548 | 528 | coexpression:443 |
Rv2259 mscR |
S-nitrosomycothiol reductase MscR | 547 | 527 | coexpression:442 |
Rv0162c adhE1 |
zinc-type alcohol dehydrogenase subunit E | 547 | 527 | coexpression:442 |
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: esterase
- Pfam (hmmscan --cut_ga): Phage_tail_X PF05489.19 (E=1e-05), LysM PF01476.27 (E=3e-09), Esterase PF00756.27 (E=5e-60)
- (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_215804.1)
- Domains: Pfam-A via hmmscan --cut_ga — Phage_tail_X (PF05489.19), LysM (PF01476.27), Esterase (PF00756.27)
- 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
COG0627 - Curated reference: UniProt P9WM39 (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 —
59 functional partner(s); context anchor
Rv1287 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001378|Rv1288| MVSTHAVVAGETLSALALRFYGDAELYRLIAAASGIADPDVVNVGQRLIMPDFTRYTVVAGDTLSALALRFYGDAELNWLIAAASGIADPDVVNVGQRLIMPDFTRYTVVAGDTLSALAARFYGDASLYPLIAAVNGIADPGVIDVGQVLVIFIGRSDGFGLRIVDRNENDPRLWYYRFQTSAIGWNPGVNVLLPDDYRTSGRTYPVLYLFHGGGTDQDFRTFDFLGIRDLTAGKPIIIVMPDGGHAGWYSNPVSSFVGPRNWETFHIAQLLPWIEANFRTYAEYDGRAVAGFSMGGFGALKYAAKYYGHFASASSHSGPASLRRDFGLVVHWANLSSAVLDLGGGTVYGAPLWDQARVSADNPVERIDSYRNKRIFLVAGTSPDPANWFDSVNETQVLAGQREFRERLSNAGIPHESHEVPGGHVFRPDMFRLDLDGIVARLRPASIGAAAERAD