gltS Resolved · high auto-curated
H37Rv Rv2992c · MTBC0 - ·
490 aa · 3348805–3350277 (-) ·
RefSeq YP_177915.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glutamate--tRNA ligase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Glutamate--tRNA ligase. Pfam: tRNA-synt_1c (PF00749.28), Anticodon_2 (PF19269.5). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WFV9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glutamate--tRNA ligase |
| EC (curated) |
EC 6.1.1.17
|
| Curated function | Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | gltX |
| eggNOG description | Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu) |
| Orthologous group | COG0008 |
| EC number |
EC 6.1.1.17
|
| KEGG orthology |
K01885
|
| KEGG pathways |
map00860, map00970, map01100, map01110, map01120
|
| KEGG modules |
M00121, M00359, M00360
|
| Gene Ontology (8) |
GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040007, GO:0044464, GO:0071944
|
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 | 0.554 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 13 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_1c | PF00749.28 | 1.0e-74 | 7–323 | tRNA synthetases class I (E and Q), catalytic domain |
Anticodon_2 | PF19269.5 | 2.5e-28 | 343–483 | Anticodon binding domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0703 rplW |
50S ribosomal protein L23 | 997 | 998 | coexpression:807 experimental:928 database:844 |
Rv0720 rplR |
50S ribosomal protein L18 | 997 | 997 | coexpression:715 experimental:928 database:844 |
Rv0719 rplF |
50S ribosomal protein L6 | 997 | 997 | coexpression:733 experimental:928 database:844 |
Rv0706 rplV |
50S ribosomal protein L22 | 996 | 996 | coexpression:677 experimental:928 database:844 |
Rv3443c rplM |
50S ribosomal protein L13 | 996 | 995 | coexpression:782 experimental:928 database:662 |
Rv0651 rplJ |
50S ribosomal protein L10 | 994 | 993 | coexpression:445 experimental:928 database:844 |
Rv0702 rplD |
50S ribosomal protein L4 | 994 | 993 | coexpression:724 experimental:928 database:650 |
Rv0722 rpmD |
50S ribosomal protein L30 | 994 | 993 | coexpression:445 experimental:928 database:844 |
Rv0714 rplN |
50S ribosomal protein L14 | 994 | 993 | coexpression:785 experimental:928 database:558 |
Rv0701 rplC |
50S ribosomal protein L3 | 994 | 993 | coexpression:435 experimental:928 database:804 |
Rv0715 rplX |
50S ribosomal protein L24 | 994 | 993 | coexpression:691 experimental:928 database:728 |
Rv0723 rplO |
50S ribosomal protein L15 | 993 | 993 | coexpression:715 experimental:928 database:671 |
Rv0704 rplB |
50S ribosomal protein L2 | 992 | 991 | coexpression:690 experimental:928 database:550 |
Rv0709 rpmC |
50S ribosomal protein L29 | 992 | 991 | coexpression:647 experimental:928 database:671 |
Rv0716 rplE |
50S ribosomal protein L5 | 992 | 990 | coexpression:700 experimental:928 database:558 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): glutamate--tRNA ligase
- Pfam (hmmscan --cut_ga): tRNA-synt_1c PF00749.28 (E=1e-74), Anticodon_2 PF19269.5 (E=3e-28)
- (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 YP_177915.1)
- Domains: Pfam-A via hmmscan --cut_ga — tRNA-synt_1c (PF00749.28), Anticodon_2 (PF19269.5)
- 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
COG0008 - Curated reference: UniProt P9WFV9 (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 — 176 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2992c|gltS MTATETVRVRFCPSPTGTPHVGLVRTALFNWAYARHTGGTFVFRIEDTDAQRDSEESYLALLDALRWLGLDWDEGPEVGGPYGPYRQSQRAEIYRDVLARLLAAGEAYHAFSTPEEVEARHVAAGRNPKLGYDNFDRHLTDAQRAAYLAEGRQPVVRLRMPDDDLAWNDLVRGPVTFAAGSVPDFALTRASGDPLYTLVNPCDDALMKITHVLRGEDLLPSTPRQLALHQALIRIGVAERIPKFAHLPTVLGEGTKKLSKRDPQSNLFAHRDRGFIPEGLLNYLALLGWSIADDHDLFGLDEMVAAFDVADVNSSPARFDQKKADALNAEHIRMLDVGDFTVRLRDHLDTHGHHIALDEAAFAAAAELVQTRIVVLGDAWELLKFFNDDQYVIDPKAAAKELGPDGAAVLDAALAALTSVTDWTAPLIEAALKDALIEGLALKPRKAFSPIRVAATGTTVSPPLFESLELLGRDRSMQRLRAARQLVGHA