Rv1301 Resolved · high auto-curated
H37Rv Rv1301 · MTBC0 mtbc0_001393 ·
217 aa · 1466597–1467250 (+) ·
RefSeq NP_215817.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | threonylcarbamoyl-AMP synthase |
|---|---|
| MTBC0 PGAP re-annotation | L-threonylcarbamoyladenylate synthase |
| Revised (this work) | L-threonylcarbamoyladenylate synthase. Pfam: Sua5_yciO_yrdC (PF01300.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGC9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative threonylcarbamoyl-AMP synthase |
| EC (curated) |
EC 2.7.7.87
|
| Curated function | Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Catalyzes the conversion of L-threonine, HCO(3)(-)/CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of diphosphate. |
UniProt still lists this protein as Putative threonylcarbamoyl-AMP synthase; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | ywlC |
| eggNOG description | Belongs to the SUA5 family |
| Orthologous group | COG0009 |
| EC number |
EC 2.7.7.87
|
| KEGG orthology |
K07566
|
| Gene Ontology (47) |
GO:0000049, GO:0002949, GO:0003674, GO:0003676, GO:0003723, GO:0003824, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0006139 +35 more
|
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 | 0.361 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
Sua5_yciO_yrdC | PF01300.25 | 8.3e-48 | 23–197 | Telomere recombination |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hemK (release factor glutamine methyltransferase), high confidence from genomic context alone (score 980 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1300 hemK |
release factor glutamine methyltransferase | 982 | 980 ctx | neighborhood:863 fusion:758 coexpression:440 |
Rv1299 prfA |
peptide chain release factor PrfA | 874 | 867 ctx | neighborhood:863 |
Rv1302 rfe |
decaprenyl-phosphate N-acetylglucosaminephosphotransferase | 816 | 788 ctx | neighborhood:782 |
Rv1298 rpmE |
50S ribosomal protein L31 | 785 | 773 ctx | neighborhood:767 |
Rv1297 rho |
transcription termination factor Rho | 719 | 707 ctx | neighborhood:502 coexpression:436 |
Rv1304 atpB |
ATP synthase subunit A | 713 | 679 ctx | neighborhood:676 |
Rv1303 hyp |
hypothetical protein | 678 | 678 ctx | neighborhood:676 |
Rv1305 atpE |
ATP synthase subunit C | 690 | 673 ctx | neighborhood:655 |
Rv1307 atpH |
ATP synthase subunit b/delta | 697 | 652 ctx | neighborhood:644 |
Rv1010 ksgA |
rRNA small subunit methyltransferase A | 599 | 584 | coexpression:413 |
Rv1311 atpC |
ATP synthase subunit epsilon | 575 | 552 ctx | neighborhood:531 |
Rv3422c tsaE |
tRNA threonylcarbamoyladenosine biosynthesis protein | 650 | 543 | database:500 |
Rv3859c gltB |
glutamate synthase large subunit | 517 | 518 ctx | neighborhood:511 |
Rv1278 hyp |
hypothetical protein | 517 | 518 | coexpression:454 |
Rv1988 erm(37) |
23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(37) | 518 | 500 |
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: threonylcarbamoyl-AMP synthase
- MTBC0 PGAP product: L-threonylcarbamoyladenylate synthase
- Pfam (hmmscan --cut_ga): Sua5_yciO_yrdC PF01300.25 (E=8e-48)
- (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_215817.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sua5_yciO_yrdC (PF01300.25)
- 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
COG0009 - Curated reference: UniProt P9WGC9 (SwissProt, reviewed; 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 —
42 functional partner(s); context anchor
hemK - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001393|Rv1301| MTETFDCADPEQRSRGIVSAVGAIKAGQLVVMPTDTVYGIGADAFDSSAVAALLSAKGRGRDMPVGVLVGSWHTIEGLVYSMPDGARELIRAFWPGALSLVVVQAPSLQWDLGDAHGTVMLRMPLHPVAIELLREVGPMAVSSANISGHPPPVDAEQARSQLGDHVAVYLDAGPSEQQAGSTIVDLTGATPRVLRQGPVSTERIAEVLGVDAASLFG