metS Resolved · high auto-curated
H37Rv Rv1007c · MTBC0 mtbc0_001082 ·
519 aa · 1132780–1134339 (-) ·
RefSeq NP_215523.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | methionine--tRNA ligase |
|---|---|
| MTBC0 PGAP re-annotation | methionine--tRNA ligase |
| Revised (this work) | Methionine--tRNA ligase. Pfam: tRNA-synt_1g (PF09334.18), tRNA-synt_1 (PF00133.29), Anticodon_3 (PF19303.6). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFU5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Methionine--tRNA ligase |
| EC (curated) |
EC 6.1.1.10
|
| Curated function | Catalyzes the attachment of L-methionine to tRNA(Met). Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | metG |
| eggNOG description | Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation |
| Orthologous group | COG0143 |
| EC number |
EC 6.1.1.10
|
| KEGG orthology |
K01874
|
| KEGG pathways |
map00450, map00970
|
| KEGG modules |
M00359, M00360
|
| Gene Ontology (61) |
GO:0003674, GO:0003824, GO:0004812, GO:0004825, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005886, GO:0006082, GO:0006139, GO:0006399 +49 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 | 0.27 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 4 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (162) · clonal |
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_1g | PF09334.18 | 6.3e-64 | 149–362 | tRNA synthetases class I (M) |
tRNA-synt_1 | PF00133.29 | 1.2e-13 | 222–335 | tRNA synthetases class I (I, L, M and V) |
Anticodon_3 | PF19303.6 | 8.0e-10 | 374–508 | Anticodon binding domain of methionyl tRNA ligase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tatD (deoxyribonuclease TatD), high confidence from genomic context alone (score 970 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2992c gltS |
glutamate--tRNA ligase | 992 | 972 | experimental:896 database:518 textmining:754 |
Rv0041 leuS |
leucine--tRNA ligase | 996 | 970 | coexpression:667 experimental:792 database:571 textmining:875 |
Rv1008 tatD |
deoxyribonuclease TatD | 969 | 970 ctx | neighborhood:783 fusion:723 |
Rv1292 argS |
arginine--tRNA ligase | 962 | 947 | experimental:814 database:571 |
Rv1536 ileS |
isoleucine--tRNA ligase | 980 | 933 | experimental:784 database:571 textmining:717 |
Rv2124c metH |
methionine synthase | 921 | 914 | database:900 |
Rv2845c proS |
proline--tRNA ligase | 990 | 907 | coexpression:425 experimental:629 database:571 textmining:900 |
Rv1133c metE |
5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase | 905 | 901 | database:900 |
Rv1406 fmt |
methionyl-tRNA formyltransferase | 912 | 900 | database:900 |
Rv1640c lysX |
bifunctional lysine--tRNA ligase/phosphatidylglycerol lysyltransferase | 880 | 839 | experimental:610 |
Rv3598c lysS |
lysine--tRNA ligase | 874 | 825 | experimental:610 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 894 | 772 | coexpression:739 textmining:554 |
Rv1009 rpfB |
resuscitation-promoting factor RpfB | 621 | 621 ctx | neighborhood:619 |
Rv2555c alaS |
alanine--tRNA ligase | 670 | 569 | coexpression:470 |
Rv2614c thrS |
threonine--tRNA ligase | 931 | 566 | experimental:428 textmining:849 |
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: methionine--tRNA ligase
- MTBC0 PGAP product: methionine--tRNA ligase
- Pfam (hmmscan --cut_ga): tRNA-synt_1g PF09334.18 (E=6e-64), tRNA-synt_1 PF00133.29 (E=1e-13), Anticodon_3 PF19303.6 (E=8e-10)
- (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_215523.1)
- Domains: Pfam-A via hmmscan --cut_ga — tRNA-synt_1g (PF09334.18), tRNA-synt_1 (PF00133.29), Anticodon_3 (PF19303.6)
- 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
COG0143 - Curated reference: UniProt P9WFU5 (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 —
71 functional partner(s); context anchor
tatD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001082|Rv1007c|metS MKPYYVTTAIAYPNAAPHVGHAYEYIATDAIARFKRLDGYDVRFLTGTDEHGLKVAQAAAAAGVPTAALARRNSDVFQRMQEALNISFDRFIRTTDADHHEASKELWRRMSAAGDIYLDNYSGWYSVRDERFFVESETQLVDGTRLTVETGTPVTWTEEQTYFFRLSAYTDKLLAHYHANPDFIAPETRRNEVISFVSGGLDDLSISRTSFDWGVQVPEHPDHVMYVWVDALTNYLTGAGFPDTDSELFRRYWPADLHMIGKDIIRFHAVYWPAFLMSAGIELPRRIFAHGFLHNRGEKMSKSVGNIVDPVALAEALGVDQVRYFLLREVPFGQDGSYSDEAIVTRINTDLANELGNLAQRSLSMVAKNLDGRVPNPGEFADADAALLATADGLLERVRGHFDAQAMHLALEAIWLMLGDANKYFSVQQPWVLRKSESEADQARFRTTLYVTCEVVRIAALLIQPVMPESAGKILDLLGQAPNQRSFAAVGVRLTPGTALPPPTGVFPRYQPPQPPEGK