Rv0948c Resolved · high auto-curated
H37Rv Rv0948c · MTBC0 mtbc0_001012 ·
105 aa · 1064861–1065178 (-) ·
RefSeq NP_215463.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | chorismate mutase |
|---|---|
| MTBC0 PGAP re-annotation | chorismate mutase |
| Revised (this work) | Chorismate mutase. Pfam: CM_2 (PF01817.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIC1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Intracellular chorismate mutase |
| EC (curated) |
EC 5.4.99.5
|
| Curated function | Catalyzes the Claisen rearrangement of chorismate to prephenate. Probably involved in the aromatic amino acid biosynthesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | csm |
| eggNOG description | chorismate mutase |
| Orthologous group | COG1605 |
| EC number |
EC 5.4.99.5
|
| KEGG orthology |
K04093
|
| KEGG pathways |
map00400, map01100, map01110, map01130, map01230
|
| KEGG modules |
M00024, M00025
|
| Gene Ontology (41) |
GO:0003674, GO:0003824, GO:0004106, GO:0005575, GO:0005623, GO:0005886, GO:0006082, GO:0006520, GO:0006725, GO:0006807, GO:0008150, GO:0008152 +29 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 | 0.331 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
CM_2 | PF01817.27 | 2.6e-12 | 32–88 | Chorismate mutase type II |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2179c (3'-5' exoribonuclease), high confidence from genomic context alone (score 774 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2178c aroG |
phospho-2-dehydro-3-deoxyheptonate aldolase AroG | 999 | 999 | experimental:999 textmining:823 |
Rv2540c aroF |
chorismate synthase | 975 | 965 | coexpression:644 database:900 |
Rv3754 tyrA |
prephenate dehydrogenase TyrA | 962 | 947 | database:900 |
Rv3838c pheA |
prephenate dehydratase | 940 | 909 | database:900 |
Rv1609 trpE |
anthranilate synthase component I | 981 | 906 | database:900 textmining:815 |
Rv1885c |
chorismate mutase | 979 | 901 | database:900 textmining:803 |
Rv3215 entC |
isochorismate synthase | 887 | 870 | database:800 |
Rv0013 trpG |
anthranilate synthase component II | 928 | 814 | database:800 textmining:629 |
Rv2386c mbtI |
salicylate synthase | 836 | 811 | database:800 |
Rv1005c pabB |
para-aminobenzoate synthase component I | 822 | 811 | database:800 |
Rv2949c |
chorismate pyruvate-lyase | 821 | 810 | database:800 |
Rv2179c |
3'-5' exoribonuclease | 773 | 774 ctx | cooccurence:773 |
Rv2744c 35kd_ag hyp |
hypothetical protein | 770 | 770 ctx | cooccurence:768 |
Rv3311 hyp |
hypothetical protein | 742 | 742 ctx | cooccurence:738 |
Rv1209 hyp |
hypothetical protein | 730 | 730 ctx | cooccurence:729 |
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: chorismate mutase
- MTBC0 PGAP product: chorismate mutase
- Pfam (hmmscan --cut_ga): CM_2 PF01817.27 (E=3e-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_215463.1)
- Domains: Pfam-A via hmmscan --cut_ga — CM_2 (PF01817.27)
- 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
COG1605 - Curated reference: UniProt P9WIC1 (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 —
111 functional partner(s); context anchor
Rv2179c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001012|Rv0948c| MRPEPPHHENAELAAMNLEMLESQPVPEIDTLREEIDRLDAEILALVKRRAEVSKAIGKARMASGGTRLVHSREMKVIERYSELGPDGKDLAILLLRLGRGRLGH