adk Resolved · high auto-curated
H37Rv Rv0733 · MTBC0 mtbc0_000775 ·
181 aa · 830315–830860 (+) ·
RefSeq NP_215247.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | adenylate kinase |
|---|---|
| MTBC0 PGAP re-annotation | adenylate kinase |
| Revised (this work) | Adenylate kinase. Pfam: AAA_33 (PF13671.13), AAA_18 (PF13238.13), ADK (PF00406.30), AAA_17 (PF13207.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKF5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Adenylate kinase |
| EC (curated) |
EC 2.7.4.3
|
| Curated function | Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Has a broad specificity for nucleoside triphosphates, being highly active with ATP or dATP as phosphate donors, and less active with GTP or UTP. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | adk |
| eggNOG description | Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism |
| Orthologous group | COG0563 |
| EC number |
EC 2.7.4.3
|
| KEGG orthology |
K00939
|
| KEGG pathways |
map00230, map00730, map01100, map01110, map01130
|
| KEGG modules |
M00049
|
| Gene Ontology (108) |
GO:0000166, GO:0003674, GO:0003824, GO:0004017, GO:0004550, GO:0005488, GO:0005524, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737 +96 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 0 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 |
|---|---|---|---|---|
AAA_33 | PF13671.13 | 7.8e-10 | 3–145 | AAA domain |
AAA_18 | PF13238.13 | 8.3e-07 | 3–132 | AAA domain |
ADK | PF00406.30 | 4.1e-53 | 5–158 | Adenylate kinase |
AAA_17 | PF13207.13 | 1.9e-31 | 6–137 | AAA domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: secY (preprotein translocase SecY), high confidence from genomic context alone (score 989 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0732 secY |
preprotein translocase SecY | 994 | 989 ctx | neighborhood:881 coexpression:912 textmining:507 |
Rv0734 mapA |
methionine aminopeptidase | 985 | 984 ctx | neighborhood:882 cooccurence:434 coexpression:750 |
Rv3459c rpsK |
30S ribosomal protein S11 | 955 | 948 ctx | cooccurence:507 coexpression:861 |
Rv1307 atpH |
ATP synthase subunit b/delta | 959 | 944 | coexpression:943 |
Rv0777 purB |
adenylosuccinate lyase PurB | 971 | 943 | database:900 textmining:517 |
Rv2584c apt |
adenine phosphoribosyltransferase | 961 | 940 | database:900 |
Rv0716 rplE |
50S ribosomal protein L5 | 947 | 936 | coexpression:885 |
Rv1617 pykA |
pyruvate kinase | 940 | 930 | database:900 |
Rv2445c ndkA |
nucleoside diphosphate kinase | 943 | 926 | database:900 |
Rv2202c adoK |
adenosine kinase | 974 | 920 | database:900 textmining:691 |
Rv0714 rplN |
50S ribosomal protein L14 | 930 | 917 | coexpression:865 |
Rv3624c hpt |
hypoxanthine-guanine phosphoribosyltransferase | 940 | 916 ctx | fusion:887 |
Rv0721 rpsE |
30S ribosomal protein S5 | 925 | 915 | coexpression:865 |
Rv0704 rplB |
50S ribosomal protein L2 | 932 | 911 | coexpression:871 |
Rv0701 rplC |
50S ribosomal protein L3 | 925 | 911 | coexpression:845 |
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: adenylate kinase
- MTBC0 PGAP product: adenylate kinase
- Pfam (hmmscan --cut_ga): AAA_33 PF13671.13 (E=8e-10), AAA_18 PF13238.13 (E=8e-07), ADK PF00406.30 (E=4e-53), AAA_17 PF13207.13 (E=2e-31)
- (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_215247.1)
- Domains: Pfam-A via hmmscan --cut_ga — AAA_33 (PF13671.13), AAA_18 (PF13238.13), ADK (PF00406.30), AAA_17 (PF13207.13)
- 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
COG0563 - Curated reference: UniProt P9WKF5 (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 —
185 functional partner(s); context anchor
secY - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000775|Rv0733|adk MRVLLLGPPGAGKGTQAVKLAEKLGIPQISTGELFRRNIEEGTKLGVEAKRYLDAGDLVPSDLTNELVDDRLNNPDAANGFILDGYPRSVEQAKALHEMLERRGTDIDAVLEFRVSEEVLLERLKGRGRADDTDDVILNRMKVYRDETAPLLEYYRDQLKTVDAVGTMDEVFARALRALGK