trpC Resolved · high auto-curated
H37Rv Rv1611 · MTBC0 mtbc0_001717 ·
272 aa · 1822204–1823022 (+) ·
RefSeq NP_216127.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | indole-3-glycerol phosphate synthase |
|---|---|
| MTBC0 PGAP re-annotation | indole-3-glycerol phosphate synthase TrpC |
| Revised (this work) | Indole-3-glycerol phosphate synthase TrpC. Pfam: IGPS (PF00218.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFX7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Indole-3-glycerol phosphate synthase |
| EC (curated) |
EC 4.1.1.48
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | trpC |
| eggNOG description | Belongs to the TrpC family |
| Orthologous group | COG0134 |
| EC number |
EC 4.1.1.48
|
| KEGG orthology |
K01609
|
| KEGG pathways |
map00400, map01100, map01110, map01130, map01230
|
| KEGG modules |
M00023
|
| Gene Ontology (70) |
GO:0000162, GO:0000287, GO:0003674, GO:0003824, GO:0004425, GO:0005488, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006082, GO:0006520 +58 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 | 0.363 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 3 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 |
|---|---|---|---|---|
IGPS | PF00218.28 | 1.0e-76 | 7–258 | Indole-3-glycerol phosphate synthase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trpA (tryptophan synthase subunit alpha), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1613 trpA |
tryptophan synthase subunit alpha | 999 | 1000 ctx | neighborhood:793 cooccurence:774 coexpression:925 database:900 textmining:754 |
Rv1612 trpB |
tryptophan synthase subunit beta | 999 | 1000 ctx | neighborhood:793 fusion:856 cooccurence:774 coexpression:794 database:900 textmining:569 |
Rv1609 trpE |
anthranilate synthase component I | 998 | 997 ctx | neighborhood:778 fusion:737 cooccurence:769 coexpression:653 experimental:461 textmining:656 |
Rv0013 trpG |
anthranilate synthase component II | 997 | 994 ctx | fusion:900 cooccurence:761 coexpression:733 textmining:602 |
Rv2192c trpD |
anthranilate phosphoribosyltransferase | 997 | 982 ctx | fusion:674 cooccurence:774 coexpression:734 textmining:871 |
Rv2386c mbtI |
salicylate synthase | 973 | 957 ctx | cooccurence:766 coexpression:646 experimental:461 textmining:416 |
Rv1005c pabB |
para-aminobenzoate synthase component I | 952 | 949 ctx | cooccurence:744 coexpression:647 experimental:461 |
Rv1614 lgt |
prolipoprotein diacylglyceryl transferase | 935 | 935 ctx | neighborhood:793 coexpression:700 |
Rv1603 hisA |
1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase | 979 | 928 | database:900 textmining:725 |
Rv1887 hyp |
hypothetical protein | 783 | 783 | coexpression:783 |
Rv1610 |
membrane protein | 781 | 781 ctx | neighborhood:778 |
Rv0544c |
transmembrane protein | 761 | 761 | coexpression:761 |
Rv0701 rplC |
50S ribosomal protein L3 | 732 | 733 | coexpression:733 |
Rv3215 entC |
isochorismate synthase | 803 | 730 ctx | cooccurence:706 |
Rv2238c ahpE |
peroxiredoxin | 724 | 725 | coexpression:716 |
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: indole-3-glycerol phosphate synthase
- MTBC0 PGAP product: indole-3-glycerol phosphate synthase TrpC
- Pfam (hmmscan --cut_ga): IGPS PF00218.28 (E=1e-76)
- (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_216127.1)
- Domains: Pfam-A via hmmscan --cut_ga — IGPS (PF00218.28)
- 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
COG0134 - Curated reference: UniProt P9WFX7 (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 —
47 functional partner(s); context anchor
trpA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001717|Rv1611|trpC MSPATVLDSILEGVRADVAAREASVSLSEIKAAAAAAPPPLDVMAALREPGIGVIAEVKRASPSAGALATIADPAKLAQAYQDGGARIVSVVTEQRRFQGSLDDLDAVRASVSIPVLRKDFVVQPYQIHEARAHGADMLLLIVAALEQSVLVSMLDRTESLGMTALVEVHTEQEADRALKAGAKVIGVNARDLMTLDVDRDCFARIAPGLPSSVIRIAESGVRGTADLLAYAGAGADAVLVGEGLVTSGDPRAAVADLVTAGTHPSCPKPAR