aspS Resolved · high auto-curated
H37Rv Rv2572c · MTBC0 mtbc0_002739 ·
596 aa · 2919557–2921347 (-) ·
RefSeq NP_217088.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | aspartate--tRNA ligase |
|---|---|
| MTBC0 PGAP re-annotation | aspartate--tRNA ligase |
| Revised (this work) | Aspartate--tRNA ligase. Pfam: tRNA_anti-codon (PF01336.32), tRNA-synt_2 (PF00152.26), GAD (PF02938.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFW3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Aspartate--tRNA(Asp/Asn) ligase |
| EC (curated) |
EC 6.1.1.23
|
| Curated function | Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | aspS |
| eggNOG description | Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp Asn) |
| Orthologous group | COG0173 |
| EC number |
EC 6.1.1.12
|
| KEGG orthology |
K01876
|
| KEGG pathways |
map00970
|
| KEGG modules |
M00359, M00360
|
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, 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) pseudogene candidate
| pN/pS | 0.401 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 10.19% of strains (14793) · 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_anti-codon | PF01336.32 | 9.9e-17 | 21–106 | OB-fold nucleic acid binding domain |
tRNA-synt_2 | PF00152.26 | 3.8e-115 | 122–562 | tRNA synthetases class II (D, K and N) |
GAD | PF02938.20 | 6.1e-12 | 315–395 | GAD domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gatB (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B), high confidence from genomic context alone (score 989 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3009c gatB |
aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B | 993 | 989 ctx | fusion:850 coexpression:644 experimental:790 textmining:478 |
Rv3012c gatC |
glutamyl-tRNA(GLN) amidotransferase subunit C | 985 | 871 | experimental:836 textmining:895 |
Rv2571c |
transmembrane protein | 847 | 848 ctx | neighborhood:811 |
Rv2580c hisS |
histidine--tRNA ligase | 877 | 836 | coexpression:808 |
Rv2555c alaS |
alanine--tRNA ligase | 829 | 792 | coexpression:684 |
Rv3396c guaA |
GMP synthase | 847 | 754 | coexpression:707 textmining:405 |
Rv2448c valS |
valine--tRNA ligase | 810 | 752 | coexpression:732 |
Rv2573 |
2-dehydropantoate 2-reductase | 745 | 746 ctx | neighborhood:745 |
Rv1536 ileS |
isoleucine--tRNA ligase | 908 | 649 | coexpression:648 textmining:751 |
Rv2363 amiA2 |
amidase | 664 | 643 | coexpression:405 experimental:405 |
Rv2845c proS |
proline--tRNA ligase | 825 | 641 | coexpression:612 textmining:533 |
Rv3011c gatA |
glutamyl-tRNA(GLN) amidotransferase subunit A | 771 | 639 | experimental:405 |
Rv2888c amiC |
amidase AmiC | 656 | 634 | experimental:405 |
Rv2239c hyp |
hypothetical protein | 634 | 634 ctx | cooccurence:632 |
Rv3375 amiD |
amidase | 727 | 633 | experimental:405 |
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: aspartate--tRNA ligase
- MTBC0 PGAP product: aspartate--tRNA ligase
- Pfam (hmmscan --cut_ga): tRNA_anti-codon PF01336.32 (E=1e-16), tRNA-synt_2 PF00152.26 (E=4e-115), GAD PF02938.20 (E=6e-12)
- (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_217088.1)
- Domains: Pfam-A via hmmscan --cut_ga — tRNA_anti-codon (PF01336.32), tRNA-synt_2 (PF00152.26), GAD (PF02938.20)
- 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
COG0173 - Curated reference: UniProt P9WFW3 (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 —
112 functional partner(s); context anchor
gatB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002739|Rv2572c|aspS MFVLRSHAAGLLREGDAGQQVTLAGWVARRRDHGGVIFIDLRDASGIAQVVFRDPQDTEVLAQAHRLRAEFCVSVAGVVEIRPEGNANPEIATGEIEVNATSLTVLGECAPLPFQLDEPAGEELRLKYRYLDLRRDDPAAAIRLRSRVNAAARAVLARHDFVEIETPTITRSTPEGARDFLVPARLHPGSFYALPQSPQLFKQLLMVAGMERYYQIARCYRDEDFRADRQPEFTQLDMEMSFVDAEDIIAISEEVLTELWALIGYRIPTPIPRIGYAEAMRRFGTDKPDLRFGLELVECTDFFSDTTFRVFQAPYVGAVVMPGGASQPRRTLDGWQDWAKQRGHRGLAYVLVAEDGTLGGPVAKNLTEAERTGLADHVGAKPGDCIFFSAGPVKSSRALLGAARVEIANRLGLIDPDAWAFVWVVDPPLFEPADEATAAGEVAVGSGAWTAVHHAFTAPKPEWEDRIESDTGSVLADAYDIVCNGHEIGGGSVRIHRRDIQERVFAVMGLDKAEAEEKFGFLLEAFMFGAPPHGGIAFGWDRTTALLAGMDSIREVIAFPKTGGGVDPLTDAPAPITAQQRKESGIDAQPKRVQQA