purD Resolved · high auto-curated
H37Rv Rv0772 · MTBC0 mtbc0_000821 ·
422 aa · 869010–870278 (+) ·
RefSeq NP_215286.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphoribosylamine--glycine ligase |
|---|---|
| MTBC0 PGAP re-annotation | phosphoribosylamine--glycine ligase |
| Revised (this work) | Phosphoribosylamine--glycine ligase. Pfam: GARS_N (PF02844.22), GARS_A (PF01071.25), GARS_C (PF02843.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHM9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphoribosylamine--glycine ligase |
| EC (curated) |
EC 6.3.4.13
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | purD |
| eggNOG description | Belongs to the GarS family |
| Orthologous group | COG0151 |
| EC number |
EC 6.3.3.1, EC 6.3.4.13
|
| KEGG orthology |
K01945, K11788
|
| KEGG pathways |
map00230, map01100, map01110, map01130
|
| KEGG modules |
M00048
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.503 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
GARS_N | PF02844.22 | 2.2e-33 | 1–100 | Phosphoribosylglycinamide synthetase, N domain |
GARS_A | PF01071.25 | 5.5e-62 | 101–292 | Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain |
GARS_C | PF02843.23 | 1.3e-24 | 328–414 | Phosphoribosylglycinamide synthetase, C domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: purN (phosphoribosylglycinamide formyltransferase PurN), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0956 purN |
phosphoribosylglycinamide formyltransferase PurN | 999 | 1000 ctx | fusion:900 cooccurence:753 coexpression:858 database:900 textmining:529 |
Rv0809 purM |
phosphoribosylformylglycinamidine cyclo-ligase PurM | 998 | 997 ctx | fusion:900 cooccurence:774 coexpression:857 textmining:593 |
Rv0808 purF |
amidophosphoribosyltransferase | 997 | 997 ctx | cooccurence:770 coexpression:857 database:900 |
Rv3275c purE |
5-(carboxyamino)imidazole ribonucleotide mutase | 997 | 997 ctx | fusion:900 cooccurence:772 coexpression:848 |
Rv0780 purC |
phosphoribosylaminoimidazole-succinocarboxamide synthase | 998 | 994 ctx | fusion:898 coexpression:857 textmining:732 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 992 | 991 ctx | fusion:823 cooccurence:606 coexpression:857 |
Rv0957 purH |
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosinemonophosphate cyclohydrolase | 984 | 969 ctx | cooccurence:732 coexpression:858 textmining:510 |
Rv0389 purT |
phosphoribosylglycinamide formyltransferase PurT | 973 | 966 | coexpression:646 database:900 |
Rv1832 gcvB |
glycine dehydrogenase | 975 | 955 | coexpression:954 textmining:478 |
Rv0803 purL |
phosphoribosylformylglycinamidine synthase 2 | 966 | 951 ctx | cooccurence:467 coexpression:859 |
Rv3276c purK |
5-(carboxyamino)imidazole ribonucleotide synthase | 953 | 924 ctx | cooccurence:452 coexpression:856 textmining:416 |
Rv0777 purB |
adenylosuccinate lyase PurB | 986 | 909 | coexpression:851 textmining:854 |
Rv0787A purS hyp |
hypothetical protein | 913 | 886 | coexpression:850 |
Rv0771 |
4-carboxymuconolactone decarboxylase | 872 | 873 ctx | neighborhood:872 |
Rv3396c guaA |
GMP synthase | 937 | 865 | coexpression:729 textmining:554 |
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: phosphoribosylamine--glycine ligase
- MTBC0 PGAP product: phosphoribosylamine--glycine ligase
- Pfam (hmmscan --cut_ga): GARS_N PF02844.22 (E=2e-33), GARS_A PF01071.25 (E=6e-62), GARS_C PF02843.23 (E=1e-24)
- (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_215286.1)
- Domains: Pfam-A via hmmscan --cut_ga — GARS_N (PF02844.22), GARS_A (PF01071.25), GARS_C (PF02843.23)
- 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
COG0151 - Curated reference: UniProt P9WHM9 (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 —
78 functional partner(s); context anchor
purN - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000821|Rv0772|purD MRVLVIGSGAREHALLLALGKDPQVSGLIVAPGNAGTARIAEQHDVDITSAEAVVALAREVGADMVVIGPEVPLVLGVADAVRAAGIVCFGPGKDAARIEGSKAFAKDVMAAAGVRTANSEIVDSPAHLDAALDRFGPPAGDPAWVVKDDRLAAGKGVVVTADRDVARAHGAALLEAGHPVLLESYLDGPEVSLFCVVDRTVVVPLLPAQDFKRVGEDDTGLNTGGMGAYAPLPWLPDNIYREVVSRIVEPVAAELVRRGSSFCGLLYVGLAITARGPAVVEFNCRFGDPETQAVLALLESPLGQLLHAAATGKLADFGELRWRDGVAVTVVLAAENYPGRPRVGDVVVGSEAEGVLHAGTTRRDDGAIVSSGGRVLSVVGTGADLSAARAHAYEILSSIRLPGGHFRSDIGLRAAEGKISV