trpD Resolved · high auto-curated
H37Rv Rv2192c · MTBC0 mtbc0_002328 ·
370 aa · 2481638–2482750 (-) ·
RefSeq NP_216708.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | anthranilate phosphoribosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | anthranilate phosphoribosyltransferase |
| Revised (this work) | Anthranilate phosphoribosyltransferase. Pfam: Glycos_trans_3N (PF02885.23), Glycos_transf_3 (PF00591.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFX5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Anthranilate phosphoribosyltransferase |
| EC (curated) |
EC 2.4.2.18
|
| Curated function | Catalyzes the transfer of the phosphoribosyl group of 5-phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | trpD |
| eggNOG description | Catalyzes the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA) |
| Orthologous group | COG0547 |
| EC number |
EC 2.4.2.18
|
| KEGG orthology |
K00766
|
| KEGG pathways |
map00400, map01100, map01110, map01130, map01230
|
| KEGG modules |
M00023
|
| Gene Ontology (58) |
GO:0000162, GO:0003674, GO:0003824, GO:0004048, GO:0005575, GO:0005576, GO:0005623, GO:0005886, GO:0006082, GO:0006520, GO:0006568, GO:0006576 +46 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 | 1.119 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Glycos_trans_3N | PF02885.23 | 2.2e-18 | 29–90 | Glycosyl transferase family, helical bundle domain |
Glycos_transf_3 | PF00591.28 | 5.7e-90 | 101–356 | Glycosyl transferase family, a/b domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trpG (anthranilate synthase component II), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0013 trpG |
anthranilate synthase component II | 999 | 998 ctx | fusion:900 cooccurence:757 coexpression:857 database:500 textmining:605 |
Rv1609 trpE |
anthranilate synthase component I | 999 | 998 ctx | cooccurence:768 coexpression:697 experimental:778 database:900 textmining:904 |
Rv2386c mbtI |
salicylate synthase | 991 | 984 ctx | cooccurence:762 coexpression:694 experimental:778 textmining:506 |
Rv1611 trpC |
indole-3-glycerol phosphate synthase | 997 | 982 ctx | fusion:674 cooccurence:774 coexpression:734 textmining:871 |
Rv1005c pabB |
para-aminobenzoate synthase component I | 982 | 980 ctx | cooccurence:725 coexpression:695 experimental:778 |
Rv1613 trpA |
tryptophan synthase subunit alpha | 994 | 973 ctx | cooccurence:774 coexpression:857 textmining:790 |
Rv1612 trpB |
tryptophan synthase subunit beta | 991 | 973 ctx | cooccurence:772 coexpression:858 textmining:696 |
Rv1603 hisA |
1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase | 961 | 909 | database:900 textmining:599 |
Rv2193 ctaE |
cytochrome C oxidase subunit III | 859 | 772 ctx | neighborhood:770 textmining:408 |
Rv1435c hyp |
hypothetical protein | 781 | 751 | coexpression:737 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 748 | 748 ctx | neighborhood:733 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 736 | 737 ctx | neighborhood:733 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 736 | 736 ctx | neighborhood:731 |
Rv3215 entC |
isochorismate synthase | 749 | 669 ctx | cooccurence:662 |
Rv2976c ung |
uracil-DNA glycosylase | 592 | 592 ctx | fusion:555 |
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: anthranilate phosphoribosyltransferase
- MTBC0 PGAP product: anthranilate phosphoribosyltransferase
- Pfam (hmmscan --cut_ga): Glycos_trans_3N PF02885.23 (E=2e-18), Glycos_transf_3 PF00591.28 (E=6e-90)
- (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_216708.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glycos_trans_3N (PF02885.23), Glycos_transf_3 (PF00591.28)
- 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
COG0547 - Curated reference: UniProt P9WFX5 (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 —
76 functional partner(s); context anchor
trpG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002328|Rv2192c|trpD MALSAEGSSGGSRGGSPKAEAASVPSWPQILGRLTDNRDLARGQAAWAMDQIMTGNARPAQIAAFAVAMTMKAPTADEVGELAGVMLSHAHPLPADTVPDDAVDVVGTGGDGVNTVNLSTMAAIVVAAAGVPVVKHGNRAASSLSGGADTLEALGVRIDLGPDLVARSLAEVGIGFCFAPRFHPSYRHAAAVRREIGVPTVFNLLGPLTNPARPRAGLIGCAFADLAEVMAGVFAARRSSVLVVHGDDGLDELTTTTTSTIWRVAAGSVDKLTFDPAGFGFARAQLDQLAGGDAQANAAAVRAVLGGARGPVRDAVVLNAAGAIVAHAGLSSRAEWLPAWEEGLRRASAAIDTGAAEQLLARWVRFGRQI