Rv1728c Resolved · high auto-curated
H37Rv Rv1728c · MTBC0 mtbc0_001840 ·
256 aa · 1965879–1966649 (-) ·
RefSeq NP_216244.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | glycoside hydrolase |
| Revised (this work) | Glycoside hydrolase. Pfam: VldE (PF26571.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71986
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ARB-07466-like C-terminal domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | lytic transglycosylase activity |
| Orthologous group | COG0741 |
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 | 0.323 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 3 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 |
|---|---|---|---|---|
VldE | PF26571.1 | 1.2e-22 | 123–226 | VldE, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1729c (S-adenosylmethionine-dependent methyltransferase), high confidence from genomic context alone (score 846 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) |
|---|---|---|---|---|
Rv1729c |
S-adenosylmethionine-dependent methyltransferase | 846 | 846 ctx | neighborhood:799 |
Rv3658c |
transmembrane protein | 656 | 656 ctx | cooccurence:656 |
Rv0538 |
membrane protein | 625 | 625 ctx | cooccurence:624 |
Rv2862c hyp |
hypothetical protein | 584 | 584 ctx | cooccurence:584 |
Rv1730c |
penicillin-binding protein | 535 | 535 ctx | neighborhood:528 |
Rv2721c hyp |
hypothetical protein | 529 | 530 ctx | cooccurence:525 |
Rv0048c |
membrane protein | 518 | 518 ctx | cooccurence:513 |
Rv1024 |
membrane protein | 489 | 490 ctx | cooccurence:482 |
Rv3909 hyp |
hypothetical protein | 488 | 489 ctx | cooccurence:481 |
Rv0227c |
membrane protein | 469 | 469 ctx | cooccurence:464 |
Rv3732 hyp |
hypothetical protein | 459 | 460 ctx | cooccurence:458 |
Rv2015c hyp |
hypothetical protein | 457 | 457 ctx | cooccurence:457 |
Rv2164c hyp |
hypothetical protein | 455 | 456 ctx | cooccurence:449 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 448 | 448 ctx | cooccurence:446 |
Rv3776 hyp |
hypothetical protein | 447 | 447 ctx | cooccurence:447 |
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: glycoside hydrolase
- Pfam (hmmscan --cut_ga): VldE PF26571.1 (E=1e-22)
- (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_216244.1)
- Domains: Pfam-A via hmmscan --cut_ga — VldE (PF26571.1)
- 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
COG0741 - Curated reference: UniProt P71986 (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 —
36 functional partner(s); context anchor
Rv1729c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001840|Rv1728c| MSVNGLPGAHNAGLQPIDSKGCHTRRTRHTKVLFVSKGVLANGRGRWLAIAASLVVSAAILYAQGAEHTCCRETPAAIPTGPDSAPANAPRIASPTEADLLAASAPVAAQQFQFALPAGVASEEGLQVKTIWVARAVSVLFPQITNIFGYRQDPLKWHPNGLAIDVMIPNHHSDEGIQLGNQVAGLALANAKRWGVLHVIWRQGYYPGIGAPSWTADYGSETLNHYDHVHIATDGGGYPTGRETYYVGSMSPTPPE