Rv2990c Resolved · medium auto-curated
H37Rv Rv2990c · MTBC0 mtbc0_003175 ·
286 aa · 3368168–3369028 (-) ·
RefSeq NP_217506.1
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. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YEW1
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Class I SAM-dependent methyltransferase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 28I17 |
|---|
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 | 0.642 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 8 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0280 PPE3 |
PPE family protein PPE3 | 971 | 860 | coexpression:860 textmining:803 |
Rv2058c rpmB2 |
50S ribosomal protein L28 | 765 | 765 | coexpression:765 |
Rv0106 hyp |
hypothetical protein | 950 | 757 | coexpression:757 textmining:803 |
Rv2056c rpsN2 |
30S ribosomal protein S14 | 738 | 738 | coexpression:738 |
Rv2059 hyp |
hypothetical protein | 615 | 615 | coexpression:615 |
Rv0282 eccA3 |
ESX-3 secretion system protein EccA | 580 | 580 | coexpression:580 |
Rv2991 hyp |
hypothetical protein | 476 | 476 ctx | neighborhood:472 |
Rv3134c |
universal stress protein | 548 | 47 | textmining:546 |
Rv2711 ideR |
iron-dependent repressor and activator IdeR | 401 | 44 | textmining:400 |
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
- (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_217506.1)
- 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
28I17 - Curated reference: UniProt I6YEW1 (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 — 9 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003175|Rv2990c| MCVTWAEMPKIAALIRHIEDLHARHGRSYILRAGISSLFRYIEGVHGERPWGTVLDAGTGVKSLQWIQTLPTERWTAVTAARSLADKTRAALGSAMRPQDRLLVGNWVDDSLLAGETFDTILVDYLVGAIEGFAPYWQDRVFERLRPHLADHGRLYLVGLEPYVQFEPETESGKIIWEIGRVRDACLLLAGERPYREFPLDWMLGRLGLAGFRILEARRFPIRYRARYVNGQLNMCLARIERFSSNGLGMAMRAYVEELRARALQLNERQDGLWHGNDYVIAVEPM