Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphoribosylglycinamide formyltransferase PurT |
|---|
| MTBC0 PGAP re-annotation | phosphoribosylglycinamide formyltransferase 2 |
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| Revised (this work) | Phosphoribosylglycinamide formyltransferase 2. Pfam: ATP-grasp (PF02222.28). |
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Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95197
TrEMBL · unreviewed
· Evidence at protein level
|
|---|
| UniProt name | Phosphoribosylglycinamide formyltransferase 2 |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
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| Preferred name | purT |
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| eggNOG description | Involved in the de novo purine biosynthesis. Catalyzes the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR). Formate is provided by PurU via hydrolysis of 10-formyl-tetrahydrofolate |
|---|
| Orthologous group | COG0027 |
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| EC number |
EC 2.1.2.2
|
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| KEGG orthology |
K08289
|
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| KEGG pathways |
map00230, map00670, map01100, map01110, map01130
|
|---|
| KEGG modules |
M00048
|
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| Gene Ontology (22) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006793, GO:0006796, GO:0008150, GO:0008152, GO:0008776 +10 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 |
0.511 · relaxed/neutral
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
5 synonymous, 6 missense, 1 nonsense, 1 frameshift
|
|---|
| Disruption |
2 distinct premature-stop/frameshift site(s); most common in
0.48% of strains
(690) · clonal
|
|---|
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 |
|---|
ATP-grasp | PF02222.28 |
1.7e-23 | 137–325 |
ATP-grasp domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase |
980 |
974 |
coexpression:731 database:900 |
Rv0803 purL |
phosphoribosylformylglycinamidine synthase 2 |
980 |
974 |
coexpression:731 database:900 |
Rv0957 purH |
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosinemonophosphate cyclohydrolase |
979 |
973 |
coexpression:742 database:900 |
Rv0772 purD |
phosphoribosylamine--glycine ligase |
973 |
966 |
coexpression:646 database:900 |
Rv0956 purN |
phosphoribosylglycinamide formyltransferase PurN |
968 |
959 |
coexpression:610 database:900 |
Rv1093 glyA1 |
serine hydroxymethyltransferase |
916 |
914 |
database:900 |
Rv0070c glyA2 |
serine hydroxymethyltransferase |
916 |
913 |
database:900 |
Rv2211c gcvT |
aminomethyltransferase |
913 |
913 |
database:900 |
Rv0787A purS hyp |
hypothetical protein |
929 |
908 |
database:900 |
Rv2964 purU |
formyltetrahydrofolate deformylase |
920 |
904 |
database:900 |
Rv0992c |
5-formyltetrahydrofolate cyclo-ligase |
908 |
904 |
database:900 |
Rv1406 fmt |
methionyl-tRNA formyltransferase |
900 |
901 |
database:900 |
Rv2124c metH |
methionine synthase |
900 |
901 |
database:900 |
Rv3356c folD |
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
906 |
900 |
database:900 |
Rv2763c dfrA |
dihydrofolate reductase |
900 |
900 |
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: phosphoribosylglycinamide formyltransferase PurT
- MTBC0 PGAP product: phosphoribosylglycinamide formyltransferase 2
- Pfam (hmmscan --cut_ga): ATP-grasp PF02222.28 (E=2e-23)
- (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_214903.1)
- Domains: Pfam-A via hmmscan --cut_ga — ATP-grasp (PF02222.28)
- 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
COG0027
- Curated reference: UniProt
P95197
(TrEMBL, unreviewed; 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 —
39 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000408|Rv0389|purT
MIDGWTEGQHEPTVRHERPAAPQDVRRVMLLGSAEPSRELAIALQGLGAEVIAVDGYVGAPAHRIADQSVVVTMTDAEELTAVIRRLQPDFLVTVTAAVSVDALDAVEQADGECTELVPNARAVRCTADREGLRRLAADQLGLPTAPFWFVGSLGELQAVAVHAGFPLLVSPVAGVAGQGSSVVAGPNEVEPAWQRAAGHQVQPQTGGVSPRVCAESVVEIEFLVTMIVVCSQGPNGPLIEFCAPIGHRDADAGELESWQPQKLSTAALDAAKSIAARIVKALGGRGVFGVELMINGDEVYFADVTVCPAGSAWVTVRSQRLSVFELQARAILGLAVDTLMISPGAARVINPDHTAGRAAVGAAPPADALTGALGVPESDVVIFGRGLGVALATAPEVAIARERAREVASRLNVPDSRE
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