apt Resolved · high auto-curated
H37Rv Rv2584c · MTBC0 mtbc0_002751 ·
223 aa · 2933773–2934444 (-) ·
RefSeq NP_217100.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | adenine phosphoribosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | adenine phosphoribosyltransferase |
| Revised (this work) | Adenine phosphoribosyltransferase. Pfam: Pribosyltran (PF00156.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQ07
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Adenine phosphoribosyltransferase |
| EC (curated) |
EC 2.4.2.7
|
| Curated function | Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | apt |
| eggNOG description | Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis |
| Orthologous group | COG0503 |
| EC number |
EC 2.4.2.7
|
| KEGG orthology |
K00759
|
| KEGG pathways |
map00230, map01100
|
| Gene Ontology (50) |
GO:0003674, GO:0003824, GO:0003999, GO:0005575, GO:0005623, GO:0005886, GO:0006139, GO:0006144, GO:0006168, GO:0006725, GO:0006807, GO:0008150 +38 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 | 0.698 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
Pribosyltran | PF00156.34 | 5.8e-15 | 87–202 | Phosphoribosyl transferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pnp (5'-methylthioadenosine phosphorylase), high confidence from genomic context alone (score 900 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3396c guaA |
GMP synthase | 996 | 992 | coexpression:872 database:900 textmining:554 |
Rv0777 purB |
adenylosuccinate lyase PurB | 979 | 963 | coexpression:402 database:900 textmining:485 |
Rv0957 purH |
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosinemonophosphate cyclohydrolase | 968 | 959 | coexpression:426 database:900 |
Rv1389 gmk |
guanylate kinase | 975 | 953 | coexpression:535 database:900 textmining:499 |
Rv3307 deoD |
purine nucleoside phosphorylase | 991 | 950 | database:938 textmining:831 |
Rv2202c adoK |
adenosine kinase | 963 | 948 | database:900 |
Rv0733 adk |
adenylate kinase | 961 | 940 | database:900 |
Rv3624c hpt |
hypoxanthine-guanine phosphoribosyltransferase | 993 | 917 | database:900 textmining:922 |
Rv0805 cpdA |
3',5'-cyclic adenosine monophosphate phosphodiesterase CpdA | 912 | 906 | database:900 |
Rv3393 iunH |
nucleoside hydrolase | 982 | 903 | database:900 textmining:832 |
Rv0535 pnp |
5'-methylthioadenosine phosphorylase | 913 | 900 ctx | fusion:766 database:408 |
Rv2894c xerC |
tyrosine recombinase XerC | 853 | 853 | coexpression:853 |
Rv2587c secD |
protein translocase subunit SecD | 839 | 839 ctx | neighborhood:771 |
Rv1605 hisF |
imidazole glycerol phosphate synthase subunit HisF | 840 | 823 | database:800 |
Rv1602 hisH |
imidazole glycerol phosphate synthase subunit HisH | 811 | 812 | database:800 |
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: adenine phosphoribosyltransferase
- MTBC0 PGAP product: adenine phosphoribosyltransferase
- Pfam (hmmscan --cut_ga): Pribosyltran PF00156.34 (E=6e-15)
- (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_217100.1)
- Domains: Pfam-A via hmmscan --cut_ga — 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
COG0503 - Curated reference: UniProt P9WQ07 (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 —
92 functional partner(s); context anchor
pnp - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002751|Rv2584c|apt MCHGGTWAGDYVLNVIATGLSLKARGKRRRQRWVDDGRVLALGESRRSSAISVADVVASLTRDVADFPVPGVEFKDLTPLFADRRGLAAVTEALADRASGADLVAGVDARGFLVAAAVATRLEVGVLAVRKGGKLPRPVLSEEYYREYGAATLEILAEGIEVAGRRVVIIDDVLATGGTIGATRRLLERGGANVAGAAVVVELAGLSGRAALAPLPVHSLSRL