Rv3688c Family assigned · medium auto-curated
H37Rv Rv3688c · MTBC0 mtbc0_003909 ·
154 aa · 4153841–4154305 (-) ·
RefSeq NP_218205.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | GatB/YqeY domain-containing protein |
| Revised (this work) | GatB/YqeY domain-containing protein. Pfam: YqeY (PF09424.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X831
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | yqeY |
| eggNOG description | Yqey-like protein |
| Orthologous group | COG1610 |
| KEGG orthology |
K09117
|
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 | 0.495 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
YqeY | PF09424.16 | 1.5e-44 | 5–154 | Yqey-like protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3690 (membrane protein), high confidence from genomic context alone (score 769 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) |
|---|---|---|---|---|
Rv3690 |
membrane protein | 770 | 769 ctx | neighborhood:766 |
Rv3691 hyp |
hypothetical protein | 693 | 693 ctx | neighborhood:690 |
Rv3692 moxR2 |
methanol dehydrogenase transcriptional regulator MoxR | 691 | 691 ctx | neighborhood:690 |
Rv3693 |
membrane protein | 646 | 646 ctx | neighborhood:645 |
Rv2785c rpsO |
30S ribosomal protein S15 | 617 | 617 | coexpression:610 |
Rv3689 |
transmembrane protein | 598 | 599 ctx | neighborhood:596 |
Rv3687c rsfB |
anti-anti-sigma factor RsfB | 480 | 480 ctx | neighborhood:474 |
Rv1298 rpmE |
50S ribosomal protein L31 | 463 | 463 | coexpression:463 |
Rv0979A rpmF |
50S ribosomal protein L32 | 433 | 434 | coexpression:421 |
Rv2442c rplU |
50S ribosomal protein L21 | 432 | 433 | coexpression:414 |
Rv2904c rplS |
50S ribosomal protein L19 | 419 | 420 | coexpression:418 |
Rv1292 argS |
arginine--tRNA ligase | 413 | 414 | coexpression:404 |
Rv2534c efp |
elongation factor P | 405 | 405 | coexpression:402 |
Rv2441c rpmA |
50S ribosomal protein L27 | 403 | 404 | coexpression:404 |
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: GatB/YqeY domain-containing protein
- Pfam (hmmscan --cut_ga): YqeY PF09424.16 (E=2e-44)
- (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_218205.1)
- Domains: Pfam-A via hmmscan --cut_ga — YqeY (PF09424.16)
- 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
COG1610 - Curated reference: UniProt I6X831 (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 —
14 functional partner(s); context anchor
Rv3690 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003909|Rv3688c| MAELKSQLRSDLTQAMKTQDKLRTATIRMLLAAIQTEEVSGKQARELSDDEVIKVLARESRKRGEAAEIYTQNGRGELAATEHAEARIIDEYLPTPLTEGELADVADTAIAEVAEELGHRPSMKQMGLVMKAATVIAAGKADGARLSAAVKERL