purF Resolved · high auto-curated
H37Rv Rv0808 · MTBC0 - ·
527 aa · 902111–903694 (+) ·
RefSeq NP_215323.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | amidophosphoribosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Amidophosphoribosyltransferase. Pfam: GATase_6 (PF13522.12), GATase_7 (PF13537.12), Pribosyltran (PF00156.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WHQ7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Amidophosphoribosyltransferase |
| EC (curated) |
EC 2.4.2.14
|
| Curated function | Catalyzes the formation of phosphoribosylamine from phosphoribosylpyrophosphate (PRPP) and glutamine. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | purF |
| eggNOG description | Catalyzes the formation of phosphoribosylamine from phosphoribosylpyrophosphate (PRPP) and glutamine |
| Orthologous group | COG0034 |
| EC number |
EC 2.4.2.14
|
| KEGG orthology |
K00764
|
| KEGG pathways |
map00230, map00250, 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 | 0.226 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 synonymous, 7 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 |
|---|---|---|---|---|
GATase_6 | PF13522.12 | 9.6e-13 | 92–235 | Glutamine amidotransferase domain |
GATase_7 | PF13537.12 | 1.1e-10 | 107–239 | Glutamine amidotransferase domain |
Pribosyltran | PF00156.34 | 1.5e-06 | 309–410 | Phosphoribosyl transferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: purM (phosphoribosylformylglycinamidine cyclo-ligase PurM), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0809 purM |
phosphoribosylformylglycinamidine cyclo-ligase PurM | 998 | 998 ctx | neighborhood:830 fusion:680 cooccurence:773 coexpression:859 textmining:409 |
Rv0772 purD |
phosphoribosylamine--glycine ligase | 997 | 997 ctx | cooccurence:770 coexpression:857 database:900 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 996 | 996 ctx | cooccurence:690 coexpression:859 database:900 |
Rv0803 purL |
phosphoribosylformylglycinamidine synthase 2 | 989 | 984 ctx | fusion:624 cooccurence:577 coexpression:858 |
Rv1384 carB |
carbamoyl-phosphate synthase large subunit | 981 | 975 | coexpression:665 database:900 |
Rv0957 purH |
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosinemonophosphate cyclohydrolase | 978 | 969 ctx | cooccurence:697 coexpression:857 |
Rv0956 purN |
phosphoribosylglycinamide formyltransferase PurN | 975 | 968 ctx | cooccurence:719 coexpression:857 |
Rv1383 carA |
carbamoyl-phosphate synthase small subunit | 969 | 967 | coexpression:594 database:900 |
Rv3275c purE |
5-(carboxyamino)imidazole ribonucleotide mutase | 997 | 965 ctx | cooccurence:728 coexpression:858 textmining:927 |
Rv3859c gltB |
glutamate synthase large subunit | 965 | 953 ctx | neighborhood:544 database:900 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 959 | 918 | database:900 textmining:519 |
Rv0777 purB |
adenylosuccinate lyase PurB | 945 | 914 | coexpression:857 |
Rv3436c glmS |
glucosamine--fructose-6-phosphate aminotransferase | 918 | 908 | database:900 |
Rv3858c gltD |
glutamate synthase small subunit | 913 | 905 | database:900 |
Rv2222c glnA2 |
glutamine synthetase | 912 | 905 | 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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): amidophosphoribosyltransferase
- Pfam (hmmscan --cut_ga): GATase_6 PF13522.12 (E=1e-12), GATase_7 PF13537.12 (E=1e-10), Pribosyltran PF00156.34 (E=2e-06)
- (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_215323.1)
- Domains: Pfam-A via hmmscan --cut_ga — GATase_6 (PF13522.12), GATase_7 (PF13537.12), Pribosyltran (PF00156.34)
- 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
COG0034 - Curated reference: UniProt P9WHQ7 (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 —
77 functional partner(s); context anchor
purM - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0808|purF MAVDSDYVTDRAAGSRQTVTGQQPEQDLNSPREECGVFGVWAPGEDVAKLTYYGLYALQHRGQEAAGIAVADGSQVLVFKDLGLVSQVFDEQTLAAMQGHVAIGHCRYSTTGDTTWENAQPVFRNTAAGTGVALGHNGNLVNAAALAARARDAGLIATRCPAPATTDSDILGALLAHGAADSTLEQAALDLLPTVRGAFCLTFMDENTLYACRDPYGVRPLSLGRLDRGWVVASETAALDIVGASFVRDIEPGELLAIDADGVRSTRFANPTPKGCVFEYVYLARPDSTIAGRSVHAARVEIGRRLARECPVEADLVIGVPESGTPAAVGYAQESGVPYGQGLMKNAYVGRTFIQPSQTIRQLGIRLKLNPLKEVIRGKRLIVVDDSIVRGNTQRALVRMLREAGAVELHVRIASPPVKWPCFYGIDFPSPAELIANAVENEDEMLEAVRHAIGADTLGYISLRGMVAASEQPTSRLCTACFDGKYPIELPRETALGKNVIEHMLANAARGAALGELAADDEVPVGR