cysS1 Resolved · high auto-curated
H37Rv Rv3580c · MTBC0 - ·
469 aa · 4022394–4023803 (-) ·
RefSeq YP_177992.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cysteine--tRNA ligase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Cysteine--tRNA ligase. Pfam: tRNA-synt_1e (PF01406.26), tRNA-synt_1g (PF09334.18), DALR_2 (PF09190.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WFW1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Cysteine--tRNA ligase |
| EC (curated) |
EC 6.1.1.16
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | cysS |
| eggNOG description | Belongs to the class-I aminoacyl-tRNA synthetase family |
| Orthologous group | COG0215 |
| EC number |
EC 6.1.1.16
|
| KEGG orthology |
K01883
|
| KEGG pathways |
map00970
|
| KEGG modules |
M00359, M00360
|
| Gene Ontology (77) |
GO:0000166, GO:0003674, GO:0003824, GO:0004812, GO:0004817, GO:0005488, GO:0005524, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829 +65 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 | 0.325 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 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_1e | PF01406.26 | 7.8e-132 | 20–314 | tRNA synthetases class I (C) catalytic domain |
tRNA-synt_1g | PF09334.18 | 1.1e-05 | 257–310 | tRNA synthetases class I (M) |
DALR_2 | PF09190.18 | 1.2e-06 | 342–394 | DALR domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rlmB (23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB), high confidence from genomic context alone (score 939 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3579c rlmB |
23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB | 947 | 939 ctx | neighborhood:882 coexpression:443 |
Rv2335 cysE |
serine acetyltransferase | 920 | 855 ctx | fusion:477 coexpression:718 textmining:479 |
Rv3581c ispF |
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 801 | 802 ctx | neighborhood:799 |
Rv3582c ispD |
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | 800 | 800 ctx | neighborhood:799 |
Rv3834c serS |
serine--tRNA ligase | 851 | 789 ctx | cooccurence:716 |
Rv3583c carD |
RNA polymerase-binding transcription factor CarD | 788 | 789 ctx | neighborhood:788 |
Rv2614c thrS |
threonine--tRNA ligase | 904 | 733 ctx | cooccurence:676 textmining:657 |
Rv1976c hyp |
hypothetical protein | 702 | 696 | coexpression:679 |
Rv2334 cysK1 |
O-acetylserine sulfhydrylase | 702 | 639 ctx | fusion:578 |
Rv0073 |
glutamine ABC transporter ATP-binding protein | 652 | 639 ctx | cooccurence:519 |
Rv2564 glnQ |
glutamine ABC transporter ATP-binding protein | 632 | 619 ctx | cooccurence:498 |
Rv1077 cbs |
cystathionine beta-synthase | 650 | 598 ctx | fusion:491 |
Rv2448c valS |
valine--tRNA ligase | 972 | 597 | coexpression:419 textmining:934 |
Rv1086 |
(2Z,6E)-farnesyl diphosphate synthase | 616 | 594 ctx | cooccurence:589 |
Rv2555c alaS |
alanine--tRNA ligase | 640 | 592 | coexpression:409 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): cysteine--tRNA ligase
- Pfam (hmmscan --cut_ga): tRNA-synt_1e PF01406.26 (E=8e-132), tRNA-synt_1g PF09334.18 (E=1e-05), DALR_2 PF09190.18 (E=1e-06)
- (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 YP_177992.1)
- Domains: Pfam-A via hmmscan --cut_ga — tRNA-synt_1e (PF01406.26), tRNA-synt_1g (PF09334.18), DALR_2 (PF09190.18)
- 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
COG0215 - Curated reference: UniProt P9WFW1 (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 —
68 functional partner(s); context anchor
rlmB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3580c|cysS1 MTDRARLRLHDTAAGVVRDFVPLRPGHVSIYLCGATVQGLPHIGHVRSGVAFDILRRWLLARGYDVAFIRNVTDIEDKILAKAAAAGRPWWEWAATHERAFTAAYDALDVLPPSAEPRATGHITQMIEMIERLIQAGHAYTGGGDVYFDVLSYPEYGQLSGHKIDDVHQGEGVAAGKRDQRDFTLWKGEKPGEPSWPTPWGRGRPGWHLECSAMARSYLGPEFDIHCGGMDLVFPHHENEIAQSRAAGDGFARYWLHNGWVTMGGEKMSKSLGNVLSMPAMLQRVRPAELRYYLGSAHYRSMLEFSETAMQDAVKAYVGLEDFLHRVRTRVGAVCPGDPTPRFAEALDDDLSVPIALAEIHHVRAEGNRALDAGDHDGALRSASAIRAMMGILGCDPLDQRWESRDETSAALAAVDVLVQAELQNREKAREQRNWALADEIRGRLKRAGIEVTDTADGPQWSLLGGDTK