Rv2542 Family assigned · medium auto-curated
H37Rv Rv2542 · MTBC0 mtbc0_002708 ·
403 aa · 2888020–2889231 (+) ·
RefSeq NP_217058.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | alpha/beta hydrolase family protein |
| Revised (this work) | Alpha/beta hydrolase family protein. Pfam: 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 |
P95011
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | DUF1023 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| eggNOG description | Alpha/beta hydrolase |
| Orthologous group | COG1506 |
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 | 0.596 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 10 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.70% of strains (1021) · 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 |
|---|---|---|---|---|
Abhydrolase_8 | PF06259.19 | 6.6e-77 | 169–349 | Alpha/beta hydrolase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccD1 (ESX-1 secretion system protein EccD1), high confidence from genomic context alone (score 768 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) |
|---|---|---|---|---|
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 836 | 768 ctx | cooccurence:765 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 790 | 760 ctx | cooccurence:758 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 757 | 757 ctx | cooccurence:757 |
Rv3869 eccB1 |
ESX-1 secretion system protein EccB | 848 | 740 ctx | cooccurence:740 textmining:440 |
Rv3875 esxA |
ESAT-6 protein EsxA | 726 | 727 ctx | cooccurence:723 |
Rv3870 eccCa1 |
ESX-1 secretion system protein EccCa | 804 | 721 ctx | cooccurence:720 |
Rv0341 iniB |
isoniazid inducible protein IniB | 691 | 691 ctx | cooccurence:691 |
Rv3871 eccCb1 |
ESX-1 secretion system protein EccCb | 652 | 652 ctx | cooccurence:650 |
Rv3365c hyp |
hypothetical protein | 638 | 638 ctx | cooccurence:636 |
Rv1157c hyp |
hypothetical protein | 617 | 617 ctx | cooccurence:615 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 588 | 588 ctx | cooccurence:588 |
Rv1004c |
membrane protein | 581 | 582 ctx | cooccurence:576 |
Rv3347c PPE55 |
PPE family protein PPE55 | 573 | 573 ctx | cooccurence:573 |
Rv3350c PPE56 |
PPE family protein PPE56 | 562 | 562 ctx | cooccurence:562 |
Rv2544 lppB |
lipoprotein LppB | 560 | 560 ctx | neighborhood:556 |
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 family protein
- Pfam (hmmscan --cut_ga): Abhydrolase_8 PF06259.19 (E=7e-77)
- (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_217058.1)
- Domains: Pfam-A via hmmscan --cut_ga — 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
COG1506 - Curated reference: UniProt P95011 (TrEMBL, unreviewed; 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
eccD1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002708|Rv2542| MLDAVSDARRDGFAVGEDYTVTDRSTGGSRQQRAARLGQAQGHADFIRHRVGALLATDRDIATRVSAATQGLDELAFEDVPGVDTPAEDGVQAVDFRQAPPPGAPGGMSSGDIDAIDAANRALLQDMLAEYSRLPDGQVKTDRLADIAAIQEALRVPDSHLIYVARPDDPADMIPAVTAVGDPFTADHVSVTVPGVSGTTRQTIATMTQEARGLREEARVIAHSVGESENVATIAWVGYQPPPVLASWNTVDDDLAQAGAPKLEAFLRDLQAGSHNPGHTTALFGHSYGSLLSGIALKDGASSLVDNAVLYGSPGFDATSPAKLGMNDHNFFVMTTPDDPIRYPARLAPLHGWGSDGADTIGTVGRQGTPARVGIRPQRDHRRIPGPLPLHPSADRRGIHSAG