Rv1377c Resolved · high auto-curated
H37Rv Rv1377c · MTBC0 mtbc0_001478 ·
212 aa · 1559923–1560561 (-) ·
RefSeq NP_215893.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transferase |
|---|---|
| MTBC0 PGAP re-annotation | class I SAM-dependent methyltransferase |
| Revised (this work) | Class I SAM-dependent methyltransferase. Pfam: MTS (PF05175.21), Methyltransf_23 (PF13489.13), TehB (PF03848.21), Methyltransf_31 (PF13847.13), Ubie_methyltran (PF01209.25), Methyltransf_25 (PF13649.13), CMAS (PF02353.27), Methyltransf_11 (PF08241.19), Methyltransf_12 (PF08242.19), TPMT (PF05724.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71805
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transferase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Tellurite resistance protein TehB |
| 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 | 1.156 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 7 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 |
|---|---|---|---|---|
MTS | PF05175.21 | 5.7e-07 | 46–120 | Methyltransferase small domain |
Methyltransf_23 | PF13489.13 | 3.3e-09 | 47–154 | Methyltransferase domain |
TehB | PF03848.21 | 4.5e-07 | 47–149 | Tellurite resistance protein TehB |
Methyltransf_31 | PF13847.13 | 1.1e-15 | 48–151 | Methyltransferase domain |
Ubie_methyltran | PF01209.25 | 2.4e-07 | 48–152 | ubiE/COQ5 methyltransferase family |
Methyltransf_25 | PF13649.13 | 3.2e-22 | 49–142 | Methyltransferase domain |
CMAS | PF02353.27 | 7.0e-08 | 49–152 | Mycolic acid cyclopropane synthetase |
Methyltransf_11 | PF08241.19 | 4.9e-18 | 50–146 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 2.6e-15 | 50–145 | Methyltransferase domain |
TPMT | PF05724.18 | 1.5e-08 | 52–189 | Thiopurine S-methyltransferase (TPMT) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pyrR (bifunctional pyrimidine operon regulatory protein/uracil phosphoribosyltransferase), medium confidence from genomic context alone (score 621 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1378c hyp |
hypothetical protein | 819 | 819 ctx | neighborhood:776 |
Rv1379 pyrR |
bifunctional pyrimidine operon regulatory protein/uracil phosphoribosyltransferase | 621 | 621 ctx | neighborhood:617 |
Rv1380 pyrB |
aspartate carbamoyltransferase | 620 | 620 ctx | neighborhood:617 |
Rv1385 pyrF |
orotidine 5'-phosphate decarboxylase | 619 | 619 ctx | neighborhood:614 |
Rv1381 pyrC |
dihydroorotase | 618 | 618 ctx | neighborhood:617 |
Rv1382 hyp |
hypothetical protein | 617 | 617 ctx | neighborhood:617 |
Rv1383 carA |
carbamoyl-phosphate synthase small subunit | 617 | 617 ctx | neighborhood:617 |
Rv1384 carB |
carbamoyl-phosphate synthase large subunit | 614 | 614 ctx | neighborhood:614 |
Rv1367c hyp |
hypothetical protein | 602 | 603 ctx | neighborhood:544 |
Rv2678c hemE |
uroporphyrinogen decarboxylase | 543 | 517 ctx | neighborhood:453 |
Rv2676c hemQ hyp |
hypothetical protein | 467 | 468 ctx | neighborhood:453 |
Rv2677c hemY |
protoporphyrinogen oxidase | 490 | 461 ctx | neighborhood:453 |
Rv0520 |
Possible methyltransferase/methylase (fragment); Rv0520, (MTCY20G10.10), len: 116 aa. Possible fragment of methyltransferase (possibly first | 439 | 434 ctx | cooccurence:419 |
Rv3092c |
integral membrane protein | 870 | 47 | textmining:870 |
Rv0783c emrB |
multidrug resistance protein EmrB | 870 | 42 | textmining:870 |
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: transferase
- MTBC0 PGAP product: class I SAM-dependent methyltransferase
- Pfam (hmmscan --cut_ga): MTS PF05175.21 (E=6e-07), Methyltransf_23 PF13489.13 (E=3e-09), TehB PF03848.21 (E=4e-07), Methyltransf_31 PF13847.13 (E=1e-15), Ubie_methyltran PF01209.25 (E=2e-07), Methyltransf_25 PF13649.13 (E=3e-22), CMAS PF02353.27 (E=7e-08), Methyltransf_11 PF08241.19 (E=5e-18), Methyltransf_12 PF08242.19 (E=3e-15), TPMT PF05724.18 (E=1e-08)
- (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_215893.1)
- Domains: Pfam-A via hmmscan --cut_ga — MTS (PF05175.21), Methyltransf_23 (PF13489.13), TehB (PF03848.21), Methyltransf_31 (PF13847.13), Ubie_methyltran (PF01209.25), Methyltransf_25 (PF13649.13), CMAS (PF02353.27), Methyltransf_11 (PF08241.19), Methyltransf_12 (PF08242.19), TPMT (PF05724.18)
- 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 P71805 (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 —
15 functional partner(s); context anchor
pyrR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001478|Rv1377c| MPGIDFDALYRGESPGEGLPPITTPPWDTKAPKDNVIGWHTGGWVHGDVLDIGCGLGDNAIYLARNGYQVTGLDISPTALTTAKRRASDAGVDVKFAVGDATKLTGYTGAFDTVIDCGMFHCLDDDGKRSYAASVHRATRPGATLLLSCFSNAMPPDEEWPRSTVSEQTLRDVLGGAGWDIESLEPATVRRELDGTEVEMAFWNVRAQRRGS