purN Resolved · high auto-curated
H37Rv Rv0956 · MTBC0 mtbc0_001020 ·
215 aa · 1074776–1075423 (+) ·
RefSeq NP_215471.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphoribosylglycinamide formyltransferase PurN |
|---|---|
| MTBC0 PGAP re-annotation | phosphoribosylglycinamide formyltransferase |
| Revised (this work) | Phosphoribosylglycinamide formyltransferase. Pfam: Formyl_trans_N (PF00551.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHM5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphoribosylglycinamide formyltransferase |
| EC (curated) |
EC 2.1.2.2
|
| Curated function | Catalyzes the transfer of a formyl group from 10-formyltetrahydrofolate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR) and tetrahydrofolate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | purN |
| eggNOG description | Catalyzes the transfer of a formyl group from 10- formyltetrahydrofolate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR) and tetrahydrofolate |
| Orthologous group | COG0299 |
| EC number |
EC 2.1.2.2
|
| KEGG orthology |
K11175
|
| KEGG pathways |
map00230, map00670, map01100, map01110, map01130
|
| KEGG modules |
M00048
|
| Gene Ontology (28) |
GO:0000287, GO:0003674, GO:0005488, GO:0006082, GO:0006575, GO:0006725, GO:0006732, GO:0006760, GO:0006807, GO:0008150, GO:0008152, GO:0009987 +16 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 | 0.789 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 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 |
|---|---|---|---|---|
Formyl_trans_N | PF00551.25 | 7.8e-42 | 14–191 | Formyl transferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: purD (phosphoribosylamine--glycine ligase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0772 purD |
phosphoribosylamine--glycine ligase | 999 | 1000 ctx | fusion:900 cooccurence:753 coexpression:858 database:900 textmining:529 |
Rv0957 purH |
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosinemonophosphate cyclohydrolase | 999 | 1000 ctx | neighborhood:882 fusion:899 cooccurence:631 coexpression:860 database:900 textmining:956 |
Rv0809 purM |
phosphoribosylformylglycinamidine cyclo-ligase PurM | 998 | 997 ctx | fusion:900 cooccurence:755 coexpression:857 textmining:606 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 995 | 992 ctx | cooccurence:451 coexpression:857 database:900 textmining:432 |
Rv0803 purL |
phosphoribosylformylglycinamidine synthase 2 | 995 | 992 ctx | cooccurence:443 coexpression:857 database:900 textmining:441 |
Rv0787A purS hyp |
hypothetical protein | 993 | 986 | coexpression:843 database:900 textmining:576 |
Rv0808 purF |
amidophosphoribosyltransferase | 975 | 968 ctx | cooccurence:719 coexpression:857 |
Rv3356c folD |
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase | 995 | 962 | coexpression:425 database:900 textmining:895 |
Rv0389 purT |
phosphoribosylglycinamide formyltransferase PurT | 968 | 959 | coexpression:610 database:900 |
Rv0070c glyA2 |
serine hydroxymethyltransferase | 966 | 953 | coexpression:458 database:900 |
Rv1093 glyA1 |
serine hydroxymethyltransferase | 966 | 952 | coexpression:453 database:900 |
Rv3275c purE |
5-(carboxyamino)imidazole ribonucleotide mutase | 961 | 949 ctx | cooccurence:608 coexpression:859 |
Rv0780 purC |
phosphoribosylaminoimidazole-succinocarboxamide synthase | 957 | 932 | coexpression:861 textmining:407 |
Rv0992c |
5-formyltetrahydrofolate cyclo-ligase | 929 | 922 | database:900 |
Rv2754c thyX |
thymidylate synthase ThyX | 943 | 918 | 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 PurN
- MTBC0 PGAP product: phosphoribosylglycinamide formyltransferase
- Pfam (hmmscan --cut_ga): Formyl_trans_N PF00551.25 (E=8e-42)
- (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_215471.1)
- Domains: Pfam-A via hmmscan --cut_ga — Formyl_trans_N (PF00551.25)
- 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
COG0299 - Curated reference: UniProt P9WHM5 (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 —
71 functional partner(s); context anchor
purD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001020|Rv0956|purN MQEPLRVPPSAPARLVVLASGTGSLLRSLLDAAVGDYPARVVAVGVDRECRAAEIAAEASVPVFTVRLADHPSRDAWDVAITAATAAHEPDLVVSAGFMRILGPQFLSRFYGRTLNTHPALLPAFPGTHGVADALAYGVKVTGATVHLVDAGTDTGPILAQQPVPVLDGDDEETLHERIKVTERRLLVAAVAALATHGVTVVGRTATMGRKVTIG