Rv2955c Resolved · high auto-curated
H37Rv Rv2955c · MTBC0 mtbc0_003137 ·
321 aa · 3328755–3329720 (-) ·
RefSeq NP_217471.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | [2-O-methyl-alpha-L-fucopyranosyl-(1->3)-alpha-L-rhamnopyranosyl-(1->3)-2-O-methyl-alpha-L-rhamnopyranosyl] dimycocerosyl phenol-phthiocerol 4'''-O-methyltransferase |
| Revised (this work) | [2-O-methyl-alpha-L-fucopyranosyl-(1->3)-alpha-L-rhamnopyranosyl-(1->3)-2-O-methyl-alpha-L-rhamnopyranosyl] dimycocerosyl phenol-phthiocerol 4'''-O-methyltransferase. Pfam: Methyltransf_21 (PF05050.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95137
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 |
H Coenzyme transport and metabolism
|
|---|---|
| eggNOG description | Methyltransferase FkbM domain |
| Orthologous group | COG2242 |
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 | 0.538 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 1.09% of strains (1588) · 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_21 | PF05050.20 | 2.5e-17 | 133–290 | Methyltransferase FkbM domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2957 (PGL/p-HBAD biosynthesis glycosyltransferase), medium confidence from genomic context alone (score 541 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) |
|---|---|---|---|---|
Rv2956 hyp |
hypothetical protein | 952 | 867 ctx | neighborhood:544 cooccurence:462 database:500 textmining:658 |
Rv2954c hyp |
hypothetical protein | 968 | 780 ctx | neighborhood:460 database:500 textmining:864 |
Rv2957 |
PGL/p-HBAD biosynthesis glycosyltransferase | 728 | 541 ctx | neighborhood:427 textmining:434 |
Rv3727 |
oxidoreductase | 505 | 505 ctx | cooccurence:505 |
Rv0341 iniB |
isoniazid inducible protein IniB | 471 | 472 | |
Rv2305 hyp |
hypothetical protein | 466 | 466 | |
Rv2949c |
chorismate pyruvate-lyase | 433 | 434 ctx | cooccurence:430 |
Rv0240 vapC24 |
ribonuclease VapC24 | 701 | 412 ctx | cooccurence:408 textmining:513 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 408 | 408 ctx | cooccurence:407 |
Rv0754 PE_PGRS11 |
PE-PGRS family protein PE_PGRS11 | 420 | 256 | |
Rv3377c |
type B diterpene cyclase | 553 | 237 | textmining:439 |
Rv2946c pks1 |
polyketide synthase | 418 | 231 | |
Rv2275 |
cyclo(L-tyrosyl-L-tyrosyl) synthase | 684 | 195 | textmining:624 |
Rv1359 |
transcriptional regulator | 472 | 195 | |
Rv3376 |
phosphatase | 590 | 192 | textmining:514 |
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: [2-O-methyl-alpha-L-fucopyranosyl-(1->3)-alpha-L-rhamnopyranosyl-(1->3)-2-O-methyl-alpha-L-rhamnopyranosyl] dimycocerosyl phenol-phthiocerol 4'''-O-methyltransferase
- Pfam (hmmscan --cut_ga): Methyltransf_21 PF05050.20 (E=2e-17)
- (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_217471.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_21 (PF05050.20)
- 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
COG2242 - Curated reference: UniProt P95137 (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 —
26 functional partner(s); context anchor
Rv2957 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003137|Rv2955c| MQFQDVRLMRVVVCRRLGPAKGQRRWRPLDLGTTGCFENLGAQRPTYRMRAIRMLECAMPNRLVRSLQRWRPFGLPPHRWRLAPWYWRGLQVTLEPGSAIAWIVRLTGGFEETEIDIAAALYSALYPDRCILDVGANVGIHSLAWARLAPVVALEPAPGTHSRLEANVAANGLQDRIRTLRTAAGDAVGEVDFFVAADSAFSSLNDTGRIRIRERTRVPCTTLDALAAELPLPVGLLKIDVEGLERAVIAGAAELLRRDRPVLLVEIYGGAASNPDPERTIADIRAYGYEPFVYADDAGLQPYQRHRDDRYCYFFIPSRKG