trpA Family assigned · medium auto-curated
H37Rv Rv1613 · MTBC0 mtbc0_001719 ·
270 aa · 1824323–1825135 (+) ·
RefSeq NP_216129.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tryptophan synthase subunit alpha |
|---|---|
| MTBC0 PGAP re-annotation | tryptophan synthase subunit alpha |
| Revised (this work) | Tryptophan synthase subunit alpha. Pfam: Trp_syntA (PF00290.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFY1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Tryptophan synthase alpha chain |
| EC (curated) |
EC 4.2.1.20
|
| Curated function | The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | trpA |
| eggNOG description | The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3- phosphate |
| Orthologous group | COG0159 |
| EC number |
EC 4.2.1.20
|
| KEGG orthology |
K01695
|
| KEGG pathways |
map00260, map00400, map01100, map01110, map01130, map01230
|
| KEGG modules |
M00023
|
| Gene Ontology (8) |
GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040007, GO:0044464, GO:0071944
|
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 | 0.228 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 |
|---|---|---|---|---|
Trp_syntA | PF00290.27 | 7.6e-68 | 16–249 | Tryptophan synthase alpha chain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trpC (indole-3-glycerol phosphate synthase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1611 trpC |
indole-3-glycerol phosphate synthase | 999 | 1000 ctx | neighborhood:793 cooccurence:774 coexpression:925 database:900 textmining:754 |
Rv1612 trpB |
tryptophan synthase subunit beta | 999 | 1000 ctx | neighborhood:882 fusion:900 cooccurence:774 coexpression:979 experimental:999 database:900 textmining:843 |
Rv1614 lgt |
prolipoprotein diacylglyceryl transferase | 995 | 996 ctx | neighborhood:882 coexpression:964 |
Rv1609 trpE |
anthranilate synthase component I | 995 | 975 ctx | neighborhood:721 cooccurence:767 coexpression:651 textmining:818 |
Rv2192c trpD |
anthranilate phosphoribosyltransferase | 994 | 973 ctx | cooccurence:774 coexpression:857 textmining:790 |
Rv0013 trpG |
anthranilate synthase component II | 974 | 964 ctx | cooccurence:760 coexpression:819 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 941 | 941 | coexpression:941 |
Rv1559 ilvA |
threonine dehydratase IlvA | 934 | 924 | database:900 |
Rv2386c mbtI |
salicylate synthase | 958 | 922 ctx | cooccurence:761 coexpression:648 textmining:487 |
Rv1093 glyA1 |
serine hydroxymethyltransferase | 922 | 912 | database:900 |
Rv0070c glyA2 |
serine hydroxymethyltransferase | 921 | 911 | database:900 |
Rv3042c serB2 |
phosphoserine phosphatase SerB | 910 | 908 | database:900 |
Rv1077 cbs |
cystathionine beta-synthase | 915 | 906 | database:900 |
Rv0069c sdaA |
L-serine dehydratase | 908 | 905 | database:900 |
Rv0436c pssA |
CDP-diacylglycerol--serine O-phosphatidyltransferase | 900 | 901 | database:900 |
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: tryptophan synthase subunit alpha
- MTBC0 PGAP product: tryptophan synthase subunit alpha
- Pfam (hmmscan --cut_ga): Trp_syntA PF00290.27 (E=8e-68)
- (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_216129.1)
- Domains: Pfam-A via hmmscan --cut_ga — Trp_syntA (PF00290.27)
- 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
COG0159 - Curated reference: UniProt P9WFY1 (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 —
108 functional partner(s); context anchor
trpC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001719|Rv1613|trpA MVAVEQSEASRLGPVFDSCRANNRAALIGYLPTGYPDVPASVAAMTALVESGCDIIEVGVPYSDPGMDGPTIARATEAALRGGVRVRDTLAAVEAISIAGGRAVVMTYWNPVLRYGVDAFARDLAAAGGLGLITPDLIPDEAQQWLAASEEHRLDRIFLVAPSSTPERLAATVEASRGFVYAASTMGVTGARDAVSQAAPELVGRVKAVSDIPVGVGLGVRSRAQAAQIAQYADGVIVGSALVTALTEGLPRLRALTGELAAGVRLGMSA