serS Resolved · high auto-curated
H37Rv Rv3834c · MTBC0 mtbc0_004063 ·
419 aa · 4331765–4333024 (-) ·
RefSeq NP_218351.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | serine--tRNA ligase |
|---|---|
| MTBC0 PGAP re-annotation | serine--tRNA ligase |
| Revised (this work) | Serine--tRNA ligase. Pfam: Seryl_tRNA_N (PF02403.28), tRNA-synt_2b (PF00587.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFT7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Serine--tRNA ligase |
| EC (curated) |
EC 6.1.1.11
|
| Curated function | Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | serS |
| eggNOG description | Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec) |
| Orthologous group | COG0172 |
| EC number |
EC 6.1.1.11
|
| KEGG orthology |
K01875
|
| KEGG pathways |
map00970
|
| KEGG modules |
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 | 0.144 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 2 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 |
|---|---|---|---|---|
Seryl_tRNA_N | PF02403.28 | 7.1e-26 | 1–105 | Seryl-tRNA synthetase N-terminal domain |
tRNA-synt_2b | PF00587.31 | 3.9e-30 | 217–393 | tRNA synthetase class II core domain (G, H, P, S and T) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cysS1 (cysteine--tRNA ligase), high confidence from genomic context alone (score 789 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3580c cysS1 |
cysteine--tRNA ligase | 851 | 789 ctx | cooccurence:716 |
Rv3835 hyp |
hypothetical protein | 775 | 776 ctx | neighborhood:775 |
Rv2133c hyp |
hypothetical protein | 771 | 771 | experimental:771 |
Rv3836 hyp |
hypothetical protein | 752 | 753 ctx | neighborhood:751 |
Rv2448c valS |
valine--tRNA ligase | 835 | 730 | coexpression:651 textmining:416 |
Rv3922c yidD |
membrane protein insertion efficiency factor | 728 | 728 | coexpression:719 |
Rv2357c glyS |
glycine--tRNA ligase | 779 | 711 | coexpression:671 |
Rv2614c thrS |
threonine--tRNA ligase | 851 | 703 ctx | cooccurence:520 textmining:519 |
Rv1307 atpH |
ATP synthase subunit b/delta | 664 | 664 | coexpression:645 |
Rv3598c lysS |
lysine--tRNA ligase | 935 | 642 | coexpression:427 textmining:826 |
Rv1527c pks5 |
polyketide synthase | 660 | 620 | experimental:591 |
Rv2048c pks12 |
polyketide synthase | 659 | 619 | experimental:591 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 659 | 619 | experimental:591 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 658 | 618 | experimental:591 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 658 | 618 | experimental:591 |
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: serine--tRNA ligase
- MTBC0 PGAP product: serine--tRNA ligase
- Pfam (hmmscan --cut_ga): Seryl_tRNA_N PF02403.28 (E=7e-26), tRNA-synt_2b PF00587.31 (E=4e-30)
- (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_218351.1)
- Domains: Pfam-A via hmmscan --cut_ga — Seryl_tRNA_N (PF02403.28), tRNA-synt_2b (PF00587.31)
- 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
COG0172 - Curated reference: UniProt P9WFT7 (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 —
107 functional partner(s); context anchor
cysS1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004063|Rv3834c|serS MIDLKLLRENPDAVRRSQLSRGEDPALVDALLTADAARRAVISTADSLRAEQKAASKSVGGASPEERPPLLRRAKELAEQVKAAEADEVEAEAAFTAAHLAISNVIVDGVPAGGEDDYAVLDVVGEPSYLENPKDHLELGESLGLIDMQRGAKVSGSRFYFLTGRGALLQLGLLQLALKLAVDNGFVPTIPPVLVRPEVMVGTGFLGAHAEEVYRVEGDGLYLVGTSEVPLAGYHSGEILDLSRGPLRYAGWSSCFRREAGSHGKDTRGIIRVHQFDKVEGFVYCTPADAEHEHERLLGWQRQMLARIEVPYRVIDVAAGDLGSSAARKFDCEAWIPTQGAYRELTSTSNCTTFQARRLATRYRDASGKPQIAATLNGTLATTRWLVAILENHQRPDGSVRVPDALVPFVGVEVLEPVA