thrS Resolved · high auto-curated
H37Rv Rv2614c · MTBC0 mtbc0_002782 ·
692 aa · 2964742–2966820 (-) ·
RefSeq NP_217130.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | threonine--tRNA ligase |
|---|---|
| MTBC0 PGAP re-annotation | threonine--tRNA ligase |
| Revised (this work) | Threonine--tRNA ligase. Pfam: tRNA_SAD (PF07973.20), 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 |
P9WFT5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Threonine--tRNA ligase |
| EC (curated) |
EC 6.1.1.3
|
| Curated function | Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | thrS |
| eggNOG description | Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr) |
| Orthologous group | COG0441 |
| EC number |
EC 6.1.1.3
|
| KEGG orthology |
K01868
|
| KEGG pathways |
map00970
|
| KEGG modules |
M00359, M00360
|
| Gene Ontology (61) |
GO:0003674, GO:0003824, GO:0004812, GO:0004829, 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 | 0.184 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 4 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_SAD | PF07973.20 | 1.4e-11 | 204–245 | Threonyl and Alanyl tRNA synthetase second additional domain |
tRNA-synt_2b | PF00587.31 | 5.1e-45 | 364–570 | tRNA synthetase class II core domain (G, H, P, S and T) |
HGTP_anticodon | PF03129.26 | 1.2e-17 | 582–671 | Anticodon binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2613c (AP-4-A phosphorylase), high confidence from genomic context alone (score 900 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2839c infB |
translation initiation factor IF-2 | 957 | 944 | experimental:879 |
Rv0723 rplO |
50S ribosomal protein L15 | 941 | 933 | experimental:908 |
Rv2785c rpsO |
30S ribosomal protein S15 | 930 | 909 | experimental:899 |
Rv2613c |
AP-4-A phosphorylase | 955 | 900 ctx | neighborhood:881 textmining:569 |
Rv0979A rpmF |
50S ribosomal protein L32 | 899 | 899 | experimental:868 |
Rv0701 rplC |
50S ribosomal protein L3 | 921 | 898 | experimental:863 |
Rv0640 rplK |
50S ribosomal protein L11 | 916 | 890 | experimental:880 |
Rv2612c pgsA1 |
CDP-diacylglycerol--inositol 3-phosphatidyltransferase | 929 | 888 ctx | neighborhood:881 textmining:400 |
Rv0706 rplV |
50S ribosomal protein L22 | 914 | 888 | experimental:860 |
Rv0708 rplP |
50S ribosomal protein L16 | 893 | 887 | experimental:792 |
Rv2611c |
phosphatidylinositol mannoside acyltransferase | 920 | 881 ctx | neighborhood:881 |
Rv2610c pimA |
alpha-(1-2)-phosphatidylinositol mannosyltransferase | 887 | 881 ctx | neighborhood:879 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 956 | 877 ctx | neighborhood:544 coexpression:710 textmining:658 |
Rv0721 rpsE |
30S ribosomal protein S5 | 889 | 877 | experimental:810 |
Rv3442c rpsI |
30S ribosomal protein S9 | 890 | 874 | experimental:791 |
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: threonine--tRNA ligase
- MTBC0 PGAP product: threonine--tRNA ligase
- Pfam (hmmscan --cut_ga): tRNA_SAD PF07973.20 (E=1e-11), tRNA-synt_2b PF00587.31 (E=5e-45), HGTP_anticodon PF03129.26 (E=1e-17)
- (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_217130.1)
- Domains: Pfam-A via hmmscan --cut_ga — tRNA_SAD (PF07973.20), 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 P9WFT5 (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 —
164 functional partner(s); context anchor
Rv2613c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002782|Rv2614c|thrS MSAPAQPAPGVDGGDPSQARIRVPAGTTAATAVGEAGLPRRGTPDAIVVVRDADGNLRDLSWVPDVDTDITPVAANTDDGRSVIRHSTAHVLAQAVQELFPQAKLGIGPPITDGFYYDFDVPEPFTPEDLAALEKRMRQIVKEGQLFDRRVYESTEQARAELANEPYKLELVDDKSGDAEIMEVGGDELTAYDNLNPRTRERVWGDLCRGPHIPTTKHIPAFKLTRSSAAYWRGDQKNASLQRIYGTAWESQEALDRHLEFIEEAQRRDHRKLGVELDLFSFPDEIGSGLAVFHPKGGIVRRELEDYSRRKHTEAGYQFVNSPHITKAQLFHTSGHLDWYADGMFPPMHIDAEYNADGSLRKPGQDYYLKPMNCPMHCLIFRARGRSYRELPLRLFEFGTVYRYEKSGVVHGLTRVRGLTMDDAHIFCTRDQMRDELRSLLRFVLDLLADYGLTDFYLELSTKDPEKFVGAEEVWEEATTVLAEVGAESGLELVPDPGGAAFYGPKISVQVKDALGRTWQMSTIQLDFNFPERFGLEYTAADGTRHRPVMIHRALFGSIERFFGILTEHYAGAFPAWLAPVQVVGIPVADEHVAYLEEVATQLKSHGVRAEVDASDDRMAKKIVHHTNHKVPFMVLAGDRDVAAGAVSFRFGDRTQINGVARDDAVAAIVAWIADRENAVPTAELVKVAGRE