purM Resolved · high auto-curated
H37Rv Rv0809 · MTBC0 mtbc0_000858 ·
364 aa · 906792–907886 (+) ·
RefSeq NP_215324.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphoribosylformylglycinamidine cyclo-ligase PurM |
|---|---|
| MTBC0 PGAP re-annotation | phosphoribosylformylglycinamidine cyclo-ligase |
| Revised (this work) | Phosphoribosylformylglycinamidine cyclo-ligase. Pfam: AIRS (PF00586.30), AIRS_C (PF02769.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y4V6
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphoribosylformylglycinamidine cyclo-ligase |
| EC (curated) |
EC 6.3.3.1
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | purM |
| eggNOG description | Phosphoribosylformylglycinamidine cyclo-ligase |
| Orthologous group | COG0150 |
| EC number |
EC 6.3.3.1
|
| KEGG orthology |
K01933
|
| KEGG pathways |
map00230, map01100, map01110, map01130
|
| KEGG modules |
M00048
|
| Gene Ontology (14) |
GO:0003674, GO:0003824, GO:0004641, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0016874, GO:0016879, GO:0016882, GO:0044424 +2 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 | 0.059 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 1 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 |
|---|---|---|---|---|
AIRS | PF00586.30 | 7.5e-24 | 69–174 | AIR synthase related protein, N-terminal domain |
AIRS_C | PF02769.28 | 5.2e-35 | 186–352 | AIR synthase related protein, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: purF (amidophosphoribosyltransferase), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0808 purF |
amidophosphoribosyltransferase | 998 | 998 ctx | neighborhood:830 fusion:680 cooccurence:773 coexpression:859 textmining:409 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 998 | 998 ctx | fusion:552 cooccurence:646 coexpression:857 database:900 |
Rv0956 purN |
phosphoribosylglycinamide formyltransferase PurN | 998 | 997 ctx | fusion:900 cooccurence:755 coexpression:857 textmining:606 |
Rv0772 purD |
phosphoribosylamine--glycine ligase | 998 | 997 ctx | fusion:900 cooccurence:774 coexpression:857 textmining:593 |
Rv0803 purL |
phosphoribosylformylglycinamidine synthase 2 | 996 | 993 ctx | cooccurence:496 coexpression:857 database:900 textmining:519 |
Rv3276c purK |
5-(carboxyamino)imidazole ribonucleotide synthase | 995 | 992 ctx | cooccurence:420 coexpression:857 database:900 textmining:449 |
Rv0787A purS hyp |
hypothetical protein | 991 | 989 | coexpression:857 database:900 |
Rv3275c purE |
5-(carboxyamino)imidazole ribonucleotide mutase | 976 | 970 ctx | cooccurence:768 coexpression:858 |
Rv0957 purH |
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosinemonophosphate cyclohydrolase | 976 | 962 ctx | cooccurence:705 coexpression:858 textmining:413 |
Rv1296 thrB |
homoserine kinase | 909 | 899 ctx | fusion:898 |
Rv0780 purC |
phosphoribosylaminoimidazole-succinocarboxamide synthase | 936 | 892 | coexpression:857 textmining:431 |
Rv0777 purB |
adenylosuccinate lyase PurB | 903 | 868 | coexpression:830 |
Rv0423c thiC |
phosphomethylpyrimidine synthase | 814 | 803 | database:800 |
Rv0389 purT |
phosphoribosylglycinamide formyltransferase PurT | 909 | 750 | coexpression:729 textmining:655 |
Rv1383 carA |
carbamoyl-phosphate synthase small subunit | 702 | 674 | coexpression:663 |
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: phosphoribosylformylglycinamidine cyclo-ligase PurM
- MTBC0 PGAP product: phosphoribosylformylglycinamidine cyclo-ligase
- Pfam (hmmscan --cut_ga): AIRS PF00586.30 (E=8e-24), AIRS_C PF02769.28 (E=5e-35)
- (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_215324.1)
- Domains: Pfam-A via hmmscan --cut_ga — AIRS (PF00586.30), AIRS_C (PF02769.28)
- 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
COG0150 - Curated reference: UniProt I6Y4V6 (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 —
58 functional partner(s); context anchor
purF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000858|Rv0809|purM MTDLAKGPGKDPGSRGITYASAGVDIEAGDRAIDLFKPLASKATRPEVRGGLGGFAGLFTLRGDYREPVLAASSDGVGTKLAIAQAMDKHDTVGLDLVAMVVDDLVVCGAEPLFLLDYIAVGRIVPERLSAIVAGIADGCMRAGCALLGGETAEHPGLIEPDHYDISATGVGVVEADNVLGPDRVKPGDVIIAMGSSGLHSNGYSLVRKVLLEIDRMNLAGHVEEFGRTLGEELLEPTRIYAKDCLALAAETRVRTFCHVTGGGLAGNLQRVIPHGLIAEVDRGTWTPAPVFTMIAQRGRVRRTEMEKTFNMGVGMIAVVAPEDTTRALAVLTARHLDCWVLGTVCKGGKQGPRAKLVGQHPRF