lysS Resolved · high auto-curated
H37Rv Rv3598c · MTBC0 mtbc0_003817 ·
505 aa · 4065127–4066644 (-) ·
RefSeq NP_218115.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lysine--tRNA ligase |
|---|---|
| MTBC0 PGAP re-annotation | lysine--tRNA ligase |
| Revised (this work) | Lysine--tRNA ligase. Pfam: tRNA_anti-codon (PF01336.32), tRNA-synt_2 (PF00152.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFU9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Lysine--tRNA ligase 1 |
| EC (curated) |
EC 6.1.1.6
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | lysS |
| eggNOG description | Belongs to the class-II aminoacyl-tRNA synthetase family |
| Orthologous group | COG1190 |
| EC number |
EC 6.1.1.6
|
| KEGG orthology |
K04567
|
| KEGG pathways |
map00970
|
| KEGG modules |
M00359, M00360
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.336 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 6 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_anti-codon | PF01336.32 | 1.9e-12 | 64–140 | OB-fold nucleic acid binding domain |
tRNA-synt_2 | PF00152.26 | 5.8e-80 | 156–499 | tRNA synthetases class II (D, K and N) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: coaX (type III pantothenate kinase), high confidence from genomic context alone (score 800 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1640c lysX |
bifunctional lysine--tRNA ligase/phosphatidylglycerol lysyltransferase | 924 | 911 | database:900 |
Rv2992c gltS |
glutamate--tRNA ligase | 930 | 903 | coexpression:653 experimental:488 |
Rv1536 ileS |
isoleucine--tRNA ligase | 937 | 848 | coexpression:579 experimental:448 textmining:603 |
Rv3396c guaA |
GMP synthase | 901 | 838 | coexpression:818 textmining:418 |
Rv1292 argS |
arginine--tRNA ligase | 887 | 835 | coexpression:452 experimental:462 |
Rv1007c metS |
methionine--tRNA ligase | 874 | 825 | experimental:610 |
Rv2845c proS |
proline--tRNA ligase | 889 | 803 | coexpression:416 experimental:473 textmining:462 |
Rv3600c coaX |
type III pantothenate kinase | 958 | 800 ctx | neighborhood:773 textmining:803 |
Rv3603c hyp |
hypothetical protein | 957 | 791 ctx | neighborhood:773 textmining:803 |
Rv0041 leuS |
leucine--tRNA ligase | 915 | 790 | coexpression:401 experimental:469 textmining:616 |
Rv3602c panC |
pantothenate synthetase | 881 | 787 ctx | neighborhood:773 textmining:465 |
Rv3601c panD |
aspartate 1-decarboxylase | 824 | 774 ctx | neighborhood:773 |
Rv1307 atpH |
ATP synthase subunit b/delta | 744 | 745 | coexpression:741 |
Rv3105c prfB |
peptide chain release factor PrfB | 890 | 739 | coexpression:688 textmining:595 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 766 | 737 | coexpression:650 |
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: lysine--tRNA ligase
- MTBC0 PGAP product: lysine--tRNA ligase
- Pfam (hmmscan --cut_ga): tRNA_anti-codon PF01336.32 (E=2e-12), tRNA-synt_2 PF00152.26 (E=6e-80)
- (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_218115.1)
- Domains: Pfam-A via hmmscan --cut_ga — tRNA_anti-codon (PF01336.32), tRNA-synt_2 (PF00152.26)
- 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
COG1190 - Curated reference: UniProt P9WFU9 (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 —
150 functional partner(s); context anchor
coaX - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003817|Rv3598c|lysS MSAADTAEDLPEQFRIRRDKRARLLAQGRDPYPVAVPRTHTLAEVRAAHPDLPIDTATEDIVGVAGRVIFARNSGKLCFATLQDGDGTQLQVMISLDKVGQAALDAWKADVDLGDIVYVHGAVISSRRGELSVLADCWRIAAKSLRPLPVAHKEMSEESRVRQRYVDLIVRPEARAVARLRIAVVRAIRTALQRRGFLEVETPVLQTLAGGAAARPFATHSNALDIDLYLRIAPELFLKRCIVGGFDKVFELNRVFRNEGADSTHSPEFSMLETYQTYGTYDDSAVVTRELIQEVADEAIGTRQLPLPDGSVYDIDGEWATIQMYPSLSVALGEEITPQTTVDRLRGIADSLGLEKDPAIHDNRGFGHGKLIEELWERTVGKSLSAPTFVKDFPVQTTPLTRQHRSIPGVTEKWDLYLRGIELATGYSELSDPVVQRERFADQARAAAAGDDEAMVLDEDFLAALEYGMPPCTGTGMGIDRLLMSLTGLSIRETVLFPIVRPHSN