Rv1678 Family assigned · low
H37Rv Rv1678 · MTBC0 mtbc0_001786 ·
300 aa · 1914412–1915314 (+) ·
RefSeq NP_216194.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Polytopic integral membrane protein with a GT-C-like / membrane-enzyme-chaperone fold; weakly linked to M.tb Emb arabinosyltransferases (cell-wall GT-C family); specific function undetermined RefSeq leaves this locus uncharacterised. |
Curated reference (UniProt)
| UniProt |
O53925
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2EA1Q |
|---|
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 | 0.284 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 4 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.85% of strains (1236) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE16 (acyl-CoA dehydrogenase FadE16), high confidence from genomic context alone (score 982 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1679 fadE16 |
acyl-CoA dehydrogenase FadE16 | 982 | 982 ctx | neighborhood:881 coexpression:855 |
Rv1681 moeX |
molybdopterin biosynthesis protein MoeX | 977 | 978 ctx | neighborhood:879 coexpression:826 |
Rv1680 hyp |
hypothetical protein | 976 | 977 ctx | neighborhood:879 coexpression:815 |
Rv1676 hyp |
hypothetical protein | 564 | 563 ctx | neighborhood:540 |
Rv1677 dsbF |
lipoprotein DsbF | 556 | 555 ctx | neighborhood:532 |
Rv1682 hyp |
hypothetical protein | 505 | 506 ctx | neighborhood:483 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 424 | 423 |
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
- HHpred: top hit 9H9E membrane-protein chaperone Prob 98.5%, E 2e-6, 98 cols; vitamin-K gamma-carboxylase (GT-C-like) 95.9%; weak EmbC/EmbA arabinosyltransferases (M.tb cell wall) 42/27%
- HHpred web (MPI Bioinformatics Toolkit, profile-profile remote homology), interpreted in project 'Still unknown gene function', 2026-06-10. A fold/family-level assignment, not a demonstrated function.
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_216194.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2EA1Q - Curated reference: UniProt O53925 (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 —
7 functional partner(s); context anchor
fadE16 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001786|Rv1678| MARVRRGTELLLSPQSPPATGGLIVLTGLRLLAGLIWLYNVVWKVPPDFGERGRRDLYHFTHLAVEHPVFTPFSWVIEHAVLPYFTAFGWGVLFAESALAVLLLTGTAVRLAALIGIGQSVAIGLSVAESPGEWPWAYAMLLGIHVVLLFTCSTRYAAVDAVRAAATGSAARTAAQRLLAGWGIVLGLIGLVAVWRGLGDDRPAYVGIRALEFSLGEYNLRGALALIAIALAMLAAAKRGWRTVALVAAVVAVAAAAAIYLQVGRTAVWLGGTNTTAAVFVCAAVVSLATEFRIGRVEGA