Rv1639c Family assigned · medium auto-curated
H37Rv Rv1639c · MTBC0 mtbc0_001748 ·
489 aa · 1859010–1860479 (-) ·
RefSeq NP_216155.1
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: 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 |
P94973
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Conserved hypothetical membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | esterase |
| 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 | 0.584 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.69% of strains (1000) · 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 |
|---|---|---|---|---|
Esterase | PF00756.27 | 2.5e-10 | 200–371 | Putative esterase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lysX (bifunctional lysine--tRNA ligase/phosphatidylglycerol lysyltransferase), medium confidence from genomic context alone (score 645 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) |
|---|---|---|---|---|
Rv1638A hyp |
hypothetical protein | 946 | 947 ctx | neighborhood:741 coexpression:802 |
Rv0696 mftF |
mycofactocin biosynthesis glycosyltransferase MftF | 760 | 752 | coexpression:746 |
Rv2160A |
Rv2160A, len: 211 aa. Conserved hypothetical protein, possibly a TetR-family transcriptional regulator,similar to N-terminal half of AL51266 | 731 | 731 | coexpression:731 |
Rv0695 mftE |
mycofactocin system creatinine amidohydrolase family protein MftE | 731 | 731 | coexpression:731 |
Rv1640c lysX |
bifunctional lysine--tRNA ligase/phosphatidylglycerol lysyltransferase | 830 | 645 ctx | neighborhood:640 textmining:541 |
Rv3479 |
transmembrane protein | 553 | 553 | coexpression:553 |
Rv0412c glnX |
membrane protein | 561 | 544 | coexpression:407 |
Rv3086 adhD |
alcohol dehydrogenase D | 551 | 531 | coexpression:448 |
Rv2259 mscR |
S-nitrosomycothiol reductase MscR | 547 | 527 | coexpression:444 |
Rv0761c adhB |
alcohol dehydrogenase B | 547 | 527 | coexpression:444 |
Rv0162c adhE1 |
zinc-type alcohol dehydrogenase subunit E | 545 | 525 | coexpression:441 |
Rv2905 lppW |
lipoprotein LppW | 521 | 519 ctx | cooccurence:504 |
Rv0784 hyp |
hypothetical protein | 484 | 485 ctx | cooccurence:480 |
Rv0383c ttfA hyp |
hypothetical protein | 478 | 478 ctx | cooccurence:478 |
Rv3587c |
membrane protein | 558 | 469 ctx | cooccurence:466 |
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): Esterase PF00756.27 (E=3e-10)
- (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_216155.1)
- Domains: Pfam-A via hmmscan --cut_ga — 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 P94973 (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 —
34 functional partner(s); context anchor
lysX - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001748|Rv1639c| MAQNELVTASTPPAATQPLAVGHTSLMHGWVPLAVQVVTAVVLVLAAGWRSRHWQRRWLPTAAAIGATLAWGTRWYVTGNGLANERPPSTLWIWVALTGAAATVLILGWRSARWWRRGASLLAVPLCLLSATLTLNLWVGYFPTVQTAWNQLTSGPLPDQADQAAVAALAHSGVRPSHGTLLPVVIPSDASHFKHRGELVYLPPAWFDREHRSENPPPPQLPTVMMIGGQFNTPADWARAGNAVKTLDDFAAAHSGNAPVVVFVDSGGAFNNDTECVNGRRGNAADHLTKDVVPYMVSKFGVSPEQTSWGIVGWSMGGTCAVDLTVMHPTLFSAFVDIAGDFYPNAGNKTQTIVRLFGGNEDAWSAFDPTTVITRHGSYTGLSGWFAISSPGPPSPDNAVADTTTMRLAGRDAAANPGNQAAAANALCALGRANGIYCAVVPQPGKHDWPFADRVFAAALPWLAGQLATPGVPKIPLPGTTQQIAGTGR