Rv1978 Resolved · high auto-curated
H37Rv Rv1978 · MTBC0 mtbc0_002100 ·
282 aa · 2244521–2245369 (+) ·
RefSeq NP_216494.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | class I SAM-dependent methyltransferase |
| Revised (this work) | Class I SAM-dependent methyltransferase. Pfam: Methyltransf_25 (PF13649.13), Methyltransf_12 (PF08242.19), Methyltransf_11 (PF08241.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53979
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 |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Methyltransferase |
| Orthologous group | COG0500 |
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) pseudogene candidate
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 5.77% of strains (8380) · 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 |
|---|---|---|---|---|
Methyltransf_25 | PF13649.13 | 1.2e-11 | 82–174 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 9.3e-10 | 83–161 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 3.4e-07 | 83–175 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2687c (antibiotic ABC transporter permease), high confidence from genomic context alone (score 773 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) |
|---|---|---|---|---|
Rv2687c |
antibiotic ABC transporter permease | 773 | 773 ctx | cooccurence:772 |
Rv2686c |
antibiotic ABC transporter permease | 772 | 772 ctx | cooccurence:771 |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 760 | 761 ctx | cooccurence:759 |
Rv0210 hyp |
hypothetical protein | 732 | 733 ctx | cooccurence:732 |
Rv1181 pks4 |
polyketide beta-ketoacyl synthase | 743 | 730 ctx | cooccurence:726 |
Rv3604c |
transmembrane protein | 725 | 725 ctx | cooccurence:725 |
Rv2633c hyp |
hypothetical protein | 723 | 724 ctx | cooccurence:722 |
Rv0955 |
integral membrane protein | 718 | 718 ctx | cooccurence:718 |
Rv3896c hyp |
hypothetical protein | 698 | 699 ctx | cooccurence:698 |
Rv0804 hyp |
hypothetical protein | 697 | 697 ctx | cooccurence:688 |
Rv3786c hyp |
hypothetical protein | 677 | 677 ctx | cooccurence:655 |
Rv1733c |
transmembrane protein | 666 | 666 ctx | cooccurence:665 |
Rv0204c |
transmembrane protein | 643 | 643 ctx | cooccurence:631 |
Rv2378c mbtG |
L-lysine N6-monooxygenase | 649 | 636 ctx | cooccurence:635 |
Rv2812 |
transposase | 630 | 630 ctx | cooccurence:630 |
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: class I SAM-dependent methyltransferase
- Pfam (hmmscan --cut_ga): Methyltransf_25 PF13649.13 (E=1e-11), Methyltransf_12 PF08242.19 (E=9e-10), Methyltransf_11 PF08241.19 (E=3e-07)
- (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_216494.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_25 (PF13649.13), Methyltransf_12 (PF08242.19), Methyltransf_11 (PF08241.19)
- 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
COG0500 - Curated reference: UniProt O53979 (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 —
58 functional partner(s); context anchor
Rv2687c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002100|Rv1978| MGEANIREQAIATMPRGGPDASWLDRRFQTDALEYLDRDDVPDEVKQKIIGVLDRVGTLTNLHEKYARIALKLVSDIPNPRILELGAGHGKLSAKILELHPTATVTISDLDPTSVANIAAGELGTHPRARTQVIDATAIDGHDHSYDLAVFALAFHHLPPTVACKAIAEATRVGKRFLIIDLKRQKPLSFTLSSVLLLPLHLLLLPWSSMRSSMHDGFISALRAYSPSALQTLARAADPGMQVEILPAPTRLFPPSLAVVFSRSSSAPTESSECSADRQPGE