ileS Resolved · high auto-curated
H37Rv Rv1536 · MTBC0 mtbc0_001643 ·
1041 aa · 1746328–1749453 (+) ·
RefSeq NP_216052.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | isoleucine--tRNA ligase |
|---|---|
| MTBC0 PGAP re-annotation | isoleucine--tRNA ligase |
| Revised (this work) | Isoleucine--tRNA ligase. Pfam: tRNA-synt_1 (PF00133.29), tRNA-synt_1g (PF09334.18), Anticodon_1 (PF08264.20), DUF5915 (PF19302.5). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFV3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Isoleucine--tRNA ligase |
| EC (curated) |
EC 6.1.1.5
|
| Curated function | Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile) (By similarity)..; FUNCTION: Confers high-level resistance to the antibiotic mupirocin (pseudomonic acid A), an Ile-analog that competitively in. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | ileS |
| eggNOG description | amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile) |
| Orthologous group | COG0060 |
| EC number |
EC 6.1.1.5
|
| KEGG orthology |
K01870
|
| KEGG pathways |
map00970
|
| KEGG modules |
M00359, M00360
|
| Gene Ontology (62) |
GO:0003674, GO:0003824, GO:0004812, GO:0004822, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005886, GO:0006082, GO:0006139 +50 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 | 0.351 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 14 synonymous, 15 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-synt_1 | PF00133.29 | 1.0e-124 | 23–653 | tRNA synthetases class I (I, L, M and V) |
tRNA-synt_1g | PF09334.18 | 3.7e-06 | 53–116 | tRNA synthetases class I (M) |
Anticodon_1 | PF08264.20 | 4.1e-25 | 701–841 | Anticodon-binding domain of tRNA ligase |
DUF5915 | PF19302.5 | 3.4e-23 | 857–1026 | Domain of unknown function (DUF5915) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gltB (glutamate synthase large subunit), medium confidence from genomic context alone (score 660 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2845c proS |
proline--tRNA ligase | 993 | 987 | coexpression:763 experimental:875 database:597 textmining:513 |
Rv2992c gltS |
glutamate--tRNA ligase | 991 | 973 | coexpression:432 experimental:898 database:546 textmining:700 |
Rv0041 leuS |
leucine--tRNA ligase | 997 | 960 | coexpression:661 experimental:598 database:597 textmining:930 |
Rv1292 argS |
arginine--tRNA ligase | 993 | 958 | coexpression:513 experimental:788 database:597 textmining:851 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 980 | 958 | coexpression:916 textmining:554 |
Rv1007c metS |
methionine--tRNA ligase | 980 | 933 | experimental:784 database:571 textmining:717 |
Rv1640c lysX |
bifunctional lysine--tRNA ligase/phosphatidylglycerol lysyltransferase | 962 | 849 | coexpression:581 experimental:448 textmining:763 |
Rv3598c lysS |
lysine--tRNA ligase | 937 | 848 | coexpression:579 experimental:448 textmining:603 |
Rv2448c valS |
valine--tRNA ligase | 908 | 828 | coexpression:775 textmining:492 |
Rv2555c alaS |
alanine--tRNA ligase | 821 | 767 | coexpression:646 |
Rv2357c glyS |
glycine--tRNA ligase | 890 | 698 | textmining:653 |
Rv3859c gltB |
glutamate synthase large subunit | 661 | 660 ctx | neighborhood:544 |
Rv2572c aspS |
aspartate--tRNA ligase | 908 | 649 | coexpression:648 textmining:751 |
Rv1689 tyrS |
tyrosine--tRNA ligase | 934 | 634 | coexpression:544 textmining:829 |
Rv2614c thrS |
threonine--tRNA ligase | 939 | 600 | textmining:856 |
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: isoleucine--tRNA ligase
- MTBC0 PGAP product: isoleucine--tRNA ligase
- Pfam (hmmscan --cut_ga): tRNA-synt_1 PF00133.29 (E=1e-124), tRNA-synt_1g PF09334.18 (E=4e-06), Anticodon_1 PF08264.20 (E=4e-25), DUF5915 PF19302.5 (E=3e-23)
- (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_216052.1)
- Domains: Pfam-A via hmmscan --cut_ga — tRNA-synt_1 (PF00133.29), tRNA-synt_1g (PF09334.18), Anticodon_1 (PF08264.20), DUF5915 (PF19302.5)
- 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
COG0060 - Curated reference: UniProt P9WFV3 (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 —
102 functional partner(s); context anchor
gltB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001643|Rv1536|ileS MTDNAYPKLAGGAPDLPALELEVLDYWSRDDTFRASIARRDGAPEYVFYDGPPFANGLPHYGHLLTGYVKDIVPRYRTMRGYKVERRFGWDTHGLPAELEVERQLGITDKSQIEAMGIAAFNDACRASVLRYTDEWQAYVTRQARWVDFDNDYKTLDLAYMESVIWAFKQLWDKGLAYEGYRVLPYCWRDETPLSNHELRMDDDVYQSRQDPAVTVGFKVVGGQPDNGLDGAYLLVWTTTPWTLPSNLAVAVSPDITYVQVQAGDRRFVLAEARLAAYARELGEEPVVLGTYRGAELLGTRYLPPFAYFMDWPNAFQVLAGDFVTTDDGTGIVHMAPAYGEDDMVVAEAVGIAPVTPVDSKGRFDVTVADYQGQHVFDANAQIVRDLKTQSGPAAVNGPVLIRHETYEHPYPHCWRCRNPLIYRSVSSWFVRVTDFRDRMVELNQQITWYPEHVKDGQFGKWLQGARDWSISRNRYWGTPIPVWKSDDPAYPRIDVYGSLDELERDFGVRPANLHRPYIDELTRPNPDDPTGRSTMRRIPDVLDVWFDSGSMPYAQVHYPFENLDWFQGHYPGDFIVEYIGQTRGWFYTLHVLATALFDRPAFKTCVAHGIVLGFDGQKMSKSLRNYPDVTEVFDRDGSDAMRWFLMASPILRGGNLIVTEQGIRDGVRQVLLPLWNTYSFLALYAPKVGTWRVDSVHVLDRYILAKLAVLRDDLSESMEVYDIPGACEHLRQFTEALTNWYVRRSRSRFWAEDADAIDTLHTVLEVTTRLAAPLLPLITEIIWRGLTRERSVHLTDWPAPDLLPSDADLVAAMDQVRDVCSAASSLRKAKKLRVRLPLPKLIVAVENPQLLRPFVDLIGDELNVKQVELTDAIDTYGRFELTVNARVAGPRLGKDVQAAIKAVKAGDGVINPDGTLLAGPAVLTPDEYNSRLVAADPESTAALPDGAGLVVLDGTVTAELEAEGWAKDRIRELQELRKSTGLDVSDRIRVVMSVPAEREDWARTHRDLIAGEILATDFEFADLADGVAIGDGVRVSIEKT