mshC Resolved · high auto-curated
H37Rv Rv2130c · MTBC0 mtbc0_002263 ·
414 aa · 2418478–2419722 (-) ·
RefSeq NP_216646.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cysteine:1D-myo-inosityl 2-amino-2-deoxy--D-glucopyranoside ligase |
|---|---|
| MTBC0 PGAP re-annotation | cysteine--1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase |
| Revised (this work) | Cysteine--1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase. Pfam: tRNA-synt_1e (PF01406.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJM9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | L-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligase |
| EC (curated) |
EC 6.3.1.13
|
| Curated function | Catalyzes the ATP-dependent condensation of GlcN-Ins and L-cysteine to form L-Cys-GlcN-Ins. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | mshC |
| eggNOG description | Catalyzes the ATP-dependent condensation of GlcN-Ins and L-cysteine to form L-Cys-GlcN-Ins |
| Orthologous group | COG0215 |
| EC number |
EC 6.1.1.16, EC 6.3.1.13
|
| KEGG orthology |
K01883, K15526
|
| KEGG pathways |
map00970
|
| KEGG modules |
M00359, M00360
|
| Gene Ontology (95) |
GO:0000166, GO:0003674, GO:0003824, GO:0004812, GO:0004817, GO:0005488, GO:0005524, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829 +83 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 | 0.555 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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 | 5.0e-83 | 36–338 | tRNA synthetases class I (C) catalytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cysQ (3'(2'),5'-bisphosphate nucleotidase CysQ), high confidence from genomic context alone (score 814 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2131c cysQ |
3'(2'),5'-bisphosphate nucleotidase CysQ | 823 | 814 ctx | neighborhood:805 |
Rv2335 cysE |
serine acetyltransferase | 816 | 792 | coexpression:720 |
Rv0819 mshD |
mycothiol acetyltransferase | 989 | 777 ctx | cooccurence:549 database:500 textmining:955 |
Rv2133c hyp |
hypothetical protein | 748 | 738 ctx | neighborhood:544 cooccurence:416 |
Rv2134c hyp |
hypothetical protein | 723 | 723 ctx | neighborhood:544 |
Rv2129c |
oxidoreductase | 721 | 721 ctx | neighborhood:707 |
Rv1170 mshB |
1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase | 986 | 704 | database:500 textmining:955 |
Rv1976c hyp |
hypothetical protein | 706 | 700 | coexpression:683 |
Rv2614c thrS |
threonine--tRNA ligase | 726 | 690 ctx | cooccurence:594 |
Rv2466c hyp |
hypothetical protein | 694 | 683 ctx | cooccurence:666 |
Rv2135c hyp |
hypothetical protein | 675 | 676 ctx | neighborhood:544 |
Rv2555c alaS |
alanine--tRNA ligase | 707 | 668 | coexpression:417 |
Rv3834c serS |
serine--tRNA ligase | 653 | 606 ctx | cooccurence:471 |
Rv1082 mca |
mycothiol S-conjugate amidase | 941 | 594 ctx | cooccurence:563 textmining:862 |
Rv0041 leuS |
leucine--tRNA ligase | 634 | 585 | coexpression:415 |
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: cysteine:1D-myo-inosityl 2-amino-2-deoxy--D-glucopyranoside ligase
- MTBC0 PGAP product: cysteine--1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase
- Pfam (hmmscan --cut_ga): tRNA-synt_1e PF01406.26 (E=5e-83)
- (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_216646.1)
- Domains: Pfam-A via hmmscan --cut_ga — tRNA-synt_1e (PF01406.26)
- 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
COG0215 - Curated reference: UniProt P9WJM9 (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 —
82 functional partner(s); context anchor
cysQ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002263|Rv2130c|mshC MQSWYCPPVPVLPGRGPQLRLYDSADRQVRPVAPGSKATMYVCGITPYDATHLGHAATYVTFDLIHRLWLDLGHELHYVQNITDIDDPLFERADRDGVDWRDLAQAEVALFCEDMAALRVLPPQDYVGATEAIAEMVELIEKMLACGAAYVIDREMGEYQDIYFRADATLQFGYESGYDRDTMLRLCEERGGDPRRPGKSDELDALLWRAARPGEPSWPSPFGPGRPGWHVECAAIALSRIGSGLDIQGGGSDLIFPHHEFTAAHAECVSGERRFARHYVHAGMIGWDGHKMSKSRGNLVLVSALRAQDVEPSAVRLGLLAGHYRADRFWSQQVLDEATARLHRWRTATALPAGPAAVDVVARVRRYLADDLDTPKAIAALDGWVTDAVEYGGHDAGAPKLVATAIDALLGVDL