argS Resolved · high auto-curated
H37Rv Rv1292 · MTBC0 mtbc0_001384 ·
550 aa · 1455418–1457070 (+) ·
RefSeq NP_215808.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | arginine--tRNA ligase |
|---|---|
| MTBC0 PGAP re-annotation | arginine--tRNA ligase |
| Revised (this work) | Arginine--tRNA ligase. Pfam: Arg_tRNA_synt_N (PF03485.22), tRNA-synt_1d (PF00750.26), tRNA-synt_1 (PF00133.29), DALR_1 (PF05746.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFW5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Arginine--tRNA ligase |
| EC (curated) |
EC 6.1.1.19
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | argS |
| eggNOG description | Arginyl-tRNA synthetase |
| Orthologous group | COG0018 |
| EC number |
EC 6.1.1.19
|
| KEGG orthology |
K01887
|
| KEGG pathways |
map00970
|
| KEGG modules |
M00359, M00360
|
| Gene Ontology (63) |
GO:0003674, GO:0003824, GO:0004812, GO:0004814, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006082, GO:0006139 +51 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 | 0.448 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 8 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 |
|---|---|---|---|---|
Arg_tRNA_synt_N | PF03485.22 | 7.0e-23 | 13–93 | Arginyl tRNA synthetase N terminal domain |
tRNA-synt_1d | PF00750.26 | 1.0e-16 | 120–390 | tRNA synthetases class I (R), catalytic domain |
tRNA-synt_1 | PF00133.29 | 4.5e-05 | 327–412 | tRNA synthetases class I (I, L, M and V) |
DALR_1 | PF05746.22 | 1.5e-35 | 429–550 | DALR anticodon binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lysA (diaminopimelate decarboxylase), high confidence from genomic context alone (score 903 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3396c guaA |
GMP synthase | 988 | 980 | coexpression:979 textmining:432 |
Rv2992c gltS |
glutamate--tRNA ligase | 995 | 967 | coexpression:432 experimental:844 database:546 textmining:881 |
Rv1536 ileS |
isoleucine--tRNA ligase | 993 | 958 | coexpression:513 experimental:788 database:597 textmining:851 |
Rv1007c metS |
methionine--tRNA ligase | 962 | 947 | experimental:814 database:571 |
Rv2845c proS |
proline--tRNA ligase | 957 | 940 | coexpression:704 experimental:512 database:597 |
Rv0041 leuS |
leucine--tRNA ligase | 994 | 919 | coexpression:411 experimental:675 database:597 textmining:940 |
Rv1293 lysA |
diaminopimelate decarboxylase | 912 | 903 ctx | neighborhood:882 |
Rv1295 thrC |
threonine synthase | 906 | 903 ctx | neighborhood:882 |
Rv1294 thrA |
homoserine dehydrogenase | 896 | 891 ctx | neighborhood:881 |
Rv3598c lysS |
lysine--tRNA ligase | 887 | 835 | coexpression:452 experimental:462 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 920 | 815 | coexpression:708 textmining:588 |
Rv1640c lysX |
bifunctional lysine--tRNA ligase/phosphatidylglycerol lysyltransferase | 859 | 811 | coexpression:450 experimental:462 |
Rv1699 pyrG |
CTP synthase | 813 | 800 | coexpression:783 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 778 | 769 | coexpression:702 |
Rv1296 thrB |
homoserine kinase | 746 | 745 ctx | neighborhood:731 |
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: arginine--tRNA ligase
- MTBC0 PGAP product: arginine--tRNA ligase
- Pfam (hmmscan --cut_ga): Arg_tRNA_synt_N PF03485.22 (E=7e-23), tRNA-synt_1d PF00750.26 (E=1e-16), tRNA-synt_1 PF00133.29 (E=5e-05), DALR_1 PF05746.22 (E=1e-35)
- (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_215808.1)
- Domains: Pfam-A via hmmscan --cut_ga — Arg_tRNA_synt_N (PF03485.22), tRNA-synt_1d (PF00750.26), tRNA-synt_1 (PF00133.29), DALR_1 (PF05746.22)
- 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
COG0018 - Curated reference: UniProt P9WFW5 (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 —
118 functional partner(s); context anchor
lysA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001384|Rv1292|argS MTPADLAELLKATAAAVLAERGLDASALPQMVTVERPRIPEHGDYASNLAMQLAKKVGTNPRELAGWLAEALTKVDGIASAEVAGPGFINMRLETAAQAKVVTSVIDAGHSYGHSLLLAGRKVNLEFVSANPTGPIHIGGTRWAAVGDALGRLLTTQGADVVREYYFNDHGAQIDRFANSLIAAAKGEPTPQDGYAGSYITNIAEQVLQKAPDALSLPDAELRETFRAIGVDLMFDHIKQSLHEFGTDFDVYTHEDSMHTGGRVENAIARLRETGNIYEKDGATWLRTSAFGDDKDRVVIKSDGKPAYIAGDLAYYLDKRQRGFDLCIYMLGADHHGYIARLKAAAAAFGDDPATVEVLIGQMVNLVRDGQPVRMSKRAGTVLTLDDLVEAIGVDAARYSLIRSSVDTAIDIDLALWSSASNENPVYYVQYAHARLSALARNAAELALIPDTNHLELLNHDKEGTLLRTLGEFPRVLETAASLREPHRVCRYLEDLAGDYHRFYDSCRVLPQGDEQPTDLHTARLALCQATRQVIANGLAIIGVTAPERM