Rv3038c Family assigned · medium auto-curated
H37Rv Rv3038c · MTBC0 mtbc0_003230 ·
327 aa · 3419735–3420718 (-) ·
RefSeq NP_217554.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | methyltransferase domain-containing protein |
| Revised (this work) | Methyltransferase domain-containing protein. Pfam: Ubie_methyltran (PF01209.25), Methyltransf_31 (PF13847.13), Methyltransf_23 (PF13489.13), Methyltransf_11 (PF08241.19), Methyltransf_25 (PF13649.13), Methyltransf_12 (PF08242.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YAZ1
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)
| pN/pS | 0.113 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 2 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 |
|---|---|---|---|---|
Ubie_methyltran | PF01209.25 | 9.8e-12 | 74–178 | ubiE/COQ5 methyltransferase family |
Methyltransf_31 | PF13847.13 | 6.1e-18 | 80–180 | Methyltransferase domain |
Methyltransf_23 | PF13489.13 | 5.8e-11 | 80–181 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 1.6e-23 | 82–179 | Methyltransferase domain |
Methyltransf_25 | PF13649.13 | 2.2e-20 | 82–175 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 3.0e-14 | 82–177 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: echA17 (enoyl-CoA hydratase EchA17), high confidence from genomic context alone (score 880 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) |
|---|---|---|---|---|
Rv3039c echA17 |
enoyl-CoA hydratase EchA17 | 879 | 880 ctx | neighborhood:879 |
Rv3041c |
ABC transporter ATP-binding protein | 879 | 880 ctx | neighborhood:879 |
Rv3042c serB2 |
phosphoserine phosphatase SerB | 879 | 879 ctx | neighborhood:861 |
Rv3040c hyp |
hypothetical protein | 878 | 879 ctx | neighborhood:879 |
Rv3034c |
acetyltransferase | 799 | 799 ctx | cooccurence:764 |
Rv2186c hyp |
hypothetical protein | 771 | 771 ctx | cooccurence:771 |
Rv3030 |
S-adenosylmethionine-dependent methyltransferase | 744 | 742 ctx | cooccurence:706 |
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 732 | 722 ctx | neighborhood:720 |
Rv3036c TB22.2 hyp |
hypothetical protein | 702 | 703 ctx | neighborhood:698 |
Rv3031 |
1,4-alpha-glucan-branching protein | 688 | 688 ctx | cooccurence:676 |
Rv2418c octT hyp |
hypothetical protein | 673 | 673 ctx | cooccurence:672 |
Rv3032 |
glycogen synthase | 649 | 649 ctx | cooccurence:646 |
Rv2695 hyp |
hypothetical protein | 559 | 560 ctx | cooccurence:558 |
Rv1632c hyp |
hypothetical protein | 552 | 552 ctx | cooccurence:549 |
Rv3037c |
S-adenosylmethionine-dependent methyltransferase | 646 | 504 ctx | neighborhood:493 |
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: methyltransferase domain-containing protein
- Pfam (hmmscan --cut_ga): Ubie_methyltran PF01209.25 (E=1e-11), Methyltransf_31 PF13847.13 (E=6e-18), Methyltransf_23 PF13489.13 (E=6e-11), Methyltransf_11 PF08241.19 (E=2e-23), Methyltransf_25 PF13649.13 (E=2e-20), Methyltransf_12 PF08242.19 (E=3e-14)
- (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_217554.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ubie_methyltran (PF01209.25), Methyltransf_31 (PF13847.13), Methyltransf_23 (PF13489.13), Methyltransf_11 (PF08241.19), Methyltransf_25 (PF13649.13), Methyltransf_12 (PF08242.19)
- 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 I6YAZ1 (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 —
20 functional partner(s); context anchor
echA17 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003230|Rv3038c| MTRSSNIPADATPNPHATAEQVAAARHDSKLAQVLYHDWEAENYDEKWSISYDQRCVDYARGRFDAIVPDEVIAQLPYDRALELGCGTGFFLLNLIQAGVARRGSVTDLSPGMVKVATRNGQALGLDIDGRVADAEGIPYDDDAFDLVVGHAVLHHIPDVELSLREVVRVLKPGGRFVFAGEPTTVGDGYARTLSTLTWRVVTNATKLPGLRGWRRPQGELDESSRAAALEALVDLHTFTPQDLQRIAHNAGAVEVQTATEEFTAAMLGWPLRTFECTVPPGRLGWGWARFAFTSWKTLGWVDANVWRHVVPKGWFYNVMITGVKPS