purK Resolved · high auto-curated
H37Rv Rv3276c · MTBC0 mtbc0_003484 ·
429 aa · 3680778–3682067 (-) ·
RefSeq NP_217793.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 5-(carboxyamino)imidazole ribonucleotide synthase |
|---|---|
| MTBC0 PGAP re-annotation | 5-(carboxyamino)imidazole ribonucleotide synthase |
| Revised (this work) | 5-(carboxyamino)imidazole ribonucleotide synthase. Pfam: RS_preATP-grasp-like (PF22660.3), CPSase_L_D2 (PF02786.23), ATP-grasp (PF02222.28), PurK_C (PF17769.8). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHL9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | N5-carboxyaminoimidazole ribonucleotide synthase |
| EC (curated) |
EC 6.3.4.18
|
| Curated function | Catalyzes the ATP-dependent conversion of 5-aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5-carboxyaminoimidazole ribonucleotide (N5-CAIR). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | purK |
| eggNOG description | Catalyzes the ATP-dependent conversion of 5- aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5- carboxyaminoimidazole ribonucleotide (N5-CAIR) |
| Orthologous group | COG0026 |
| EC number |
EC 6.3.4.18
|
| KEGG orthology |
K01589
|
| KEGG pathways |
map00230, map01100, map01110, map01130
|
| KEGG modules |
M00048
|
| Gene Ontology (11) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0044424, GO:0044444, GO:0044464, GO:0071944
|
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 | 0.089 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
RS_preATP-grasp-like | PF22660.3 | 8.2e-21 | 20–115 | Ribonucleotide synthetase preATP-grasp domain |
CPSase_L_D2 | PF02786.23 | 1.4e-07 | 116–279 | Carbamoyl-phosphate synthase L chain, ATP binding domain |
ATP-grasp | PF02222.28 | 1.2e-61 | 123–302 | ATP-grasp domain |
PurK_C | PF17769.8 | 8.0e-16 | 324–384 | Phosphoribosylaminoimidazole carboxylase C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: purE (5-(carboxyamino)imidazole ribonucleotide mutase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3275c purE |
5-(carboxyamino)imidazole ribonucleotide mutase | 999 | 1000 ctx | neighborhood:881 fusion:900 cooccurence:738 coexpression:891 database:900 textmining:954 |
Rv0809 purM |
phosphoribosylformylglycinamidine cyclo-ligase PurM | 995 | 992 ctx | cooccurence:420 coexpression:857 database:900 textmining:449 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 946 | 929 ctx | cooccurence:479 coexpression:858 |
Rv0803 purL |
phosphoribosylformylglycinamidine synthase 2 | 959 | 928 ctx | cooccurence:473 coexpression:859 textmining:462 |
Rv0772 purD |
phosphoribosylamine--glycine ligase | 953 | 924 ctx | cooccurence:452 coexpression:856 textmining:416 |
Rv0957 purH |
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosinemonophosphate cyclohydrolase | 991 | 915 | coexpression:859 textmining:904 |
Rv0808 purF |
amidophosphoribosyltransferase | 992 | 901 | coexpression:857 textmining:928 |
Rv0956 purN |
phosphoribosylglycinamide formyltransferase PurN | 942 | 900 | coexpression:859 textmining:455 |
Rv0787A purS hyp |
hypothetical protein | 911 | 879 | coexpression:840 |
Rv0777 purB |
adenylosuccinate lyase PurB | 978 | 870 | coexpression:859 textmining:845 |
Rv0780 purC |
phosphoribosylaminoimidazole-succinocarboxamide synthase | 952 | 869 | coexpression:858 textmining:656 |
Rv3274c fadE25 |
acyl-CoA dehydrogenase | 855 | 855 ctx | neighborhood:849 |
Rv0423c thiC |
phosphomethylpyrimidine synthase | 801 | 802 | database:800 |
Rv0389 purT |
phosphoribosylglycinamide formyltransferase PurT | 786 | 761 | coexpression:642 |
Rv0357c purA |
adenylosuccinate synthetase | 743 | 665 | coexpression:653 |
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: 5-(carboxyamino)imidazole ribonucleotide synthase
- MTBC0 PGAP product: 5-(carboxyamino)imidazole ribonucleotide synthase
- Pfam (hmmscan --cut_ga): RS_preATP-grasp-like PF22660.3 (E=8e-21), CPSase_L_D2 PF02786.23 (E=1e-07), ATP-grasp PF02222.28 (E=1e-61), PurK_C PF17769.8 (E=8e-16)
- (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_217793.1)
- Domains: Pfam-A via hmmscan --cut_ga — RS_preATP-grasp-like (PF22660.3), CPSase_L_D2 (PF02786.23), ATP-grasp (PF02222.28), PurK_C (PF17769.8)
- 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
COG0026 - Curated reference: UniProt P9WHL9 (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 —
47 functional partner(s); context anchor
purE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003484|Rv3276c|purK MMAVASSRTPAVTSFIAPLVAMVGGGQLARMTHQAAIALGQNLRVLVTSADDPAAQVTPNVVIGSHTDLAALRRVAAGADVLTFDHEHVPNELLEKLVADGVNVAPSPQALVHAQDKLVMRQRLAAAGVAVPRYAGIKDPDEIDVFAARVDAPIVVKAVRGGYDGRGVRMARDVADARDFARECLADGVAVLVEERVDLRRELSALVARSPFGQGAAWPVVQTVQRDGTCVLVIAPAPALPDDLATAAQRLALQLADELGVVGVLAVELFETTDGALLVNELAMRPHNSGHWTIDGARTSQFEQHLRAVLDYPLGDSDAVVPVTVMANVLGAAQPPAMSVDERLHHLFARMPDARVHLYGKAERPGRKVGHINFLGSDVAQLCERAELAAHWLSHGRWTDGWDPHRASDDAVGVPPACGGRSDEEERRL