glyS Resolved · high auto-curated
H37Rv Rv2357c · MTBC0 mtbc0_002509 ·
463 aa · 2663866–2665257 (-) ·
RefSeq NP_216873.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycine--tRNA ligase |
|---|---|
| MTBC0 PGAP re-annotation | glycine--tRNA ligase |
| Revised (this work) | Glycine--tRNA ligase. Pfam: tRNA-synt_2b (PF00587.31), HGTP_anticodon (PF03129.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFV7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glycine--tRNA ligase |
| EC (curated) |
EC 6.1.1.14
|
| Curated function | Catalyzes the attachment of glycine to tRNA(Gly). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | glyQS |
| eggNOG description | Catalyzes the attachment of glycine to tRNA(Gly) |
| Orthologous group | COG0441 |
| EC number |
EC 6.1.1.14
|
| KEGG orthology |
K01880
|
| KEGG pathways |
map00970
|
| KEGG modules |
M00359, M00360
|
| Gene Ontology (105) |
GO:0000959, GO:0003674, GO:0003824, GO:0004081, GO:0004551, GO:0004812, GO:0004820, GO:0005488, GO:0005515, GO:0005575, GO:0005576, GO:0005615 +93 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 | 0.077 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 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 |
|---|---|---|---|---|
tRNA-synt_2b | PF00587.31 | 1.3e-08 | 160–331 | tRNA synthetase class II core domain (G, H, P, S and T) |
HGTP_anticodon | PF03129.26 | 6.1e-19 | 369–457 | Anticodon binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: zur (zinc uptake regulation protein), high confidence from genomic context alone (score 765 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2299c htpG |
chaperone protein HtpG | 827 | 828 | coexpression:806 |
Rv3628 ppa |
inorganic pyrophosphatase | 836 | 821 | coexpression:811 |
Rv1515c hyp |
hypothetical protein | 793 | 794 | coexpression:793 |
Rv2359 zur |
zinc uptake regulation protein | 764 | 765 ctx | neighborhood:764 |
Rv3834c serS |
serine--tRNA ligase | 779 | 711 | coexpression:671 |
Rv1536 ileS |
isoleucine--tRNA ligase | 890 | 698 | textmining:653 |
Rv1629 polA |
DNA polymerase I | 705 | 677 | coexpression:413 experimental:473 |
Rv0041 leuS |
leucine--tRNA ligase | 737 | 656 | coexpression:555 |
Rv2555c alaS |
alanine--tRNA ligase | 733 | 652 | coexpression:414 experimental:412 |
Rv3315c cdd |
cytidine deaminase | 650 | 651 | coexpression:631 |
Rv2365c hyp |
hypothetical protein | 649 | 649 | coexpression:629 |
Rv1292 argS |
arginine--tRNA ligase | 688 | 591 | coexpression:412 |
Rv3598c lysS |
lysine--tRNA ligase | 689 | 590 | coexpression:575 |
Rv2582 ppiB |
peptidyl-prolyl cis-trans isomerase B | 601 | 585 | experimental:415 |
Rv1689 tyrS |
tyrosine--tRNA ligase | 674 | 575 | coexpression:468 |
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: glycine--tRNA ligase
- MTBC0 PGAP product: glycine--tRNA ligase
- Pfam (hmmscan --cut_ga): tRNA-synt_2b PF00587.31 (E=1e-08), HGTP_anticodon PF03129.26 (E=6e-19)
- (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_216873.1)
- Domains: Pfam-A via hmmscan --cut_ga — tRNA-synt_2b (PF00587.31), HGTP_anticodon (PF03129.26)
- 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
COG0441 - Curated reference: UniProt P9WFV7 (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 —
49 functional partner(s); context anchor
zur - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002509|Rv2357c|glyS MHHPVAPVIDTVVNLAKRRGFVYPSGEIYGGTKSAWDYGPLGVELKENIKRQWWRSVVTGRDDVVGIDSSIILPREVWVASGHVDVFHDPLVESLITHKRYRADHLIEAYEAKHGHPPPNGLADIRDPETGEPGQWTQPREFNMMLKTYLGPIETEEGLHYLRPETAQGIFVNFANVVTTARKKPPFGIGQIGKSFRNEITPGNFIFRTREFEQMEMEFFVEPATAKEWHQYWIDNRLQWYIDLGIRRENLRLWEHPKDKLSHYSDRTVDIEYKFGFMGNPWGELEGVANRTDFDLSTHARHSGVDLSFYDQINDVRYTPYVIEPAAGLTRSFMAFLIDAYTEDEAPNTKGGMDKRTVLRLDPRLAPVKAAVLPLSRHADLSPKARDLGAELRKCWNIDFDDAGAIGRRYRRQDEVGTPFCVTVDFDSLQDNAVTVRERDAMTQDRVAMSSVADYLAVRLKGS