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We surveyed 10 TOR- and AMPK-related targets across 210 eukaryotic species and paired that inventory with sequence- and structure-level measurements of the proteins that remain. Across 2100 species-by-target cells, 1255 were coded present, 683 absent and 162 not assessable, with repertoires differing among lineages. Phylogenetically corrected analyses recovered associations among a subset of component absences, especially within canonical complexes, although correlated non-detection in incomplete proteomes remains an alternative explanation. Sequence features varied substantially. In TOR, N-terminal HEAT-region divergence was associated with absence of several TOR-complex partners in discrete-state analyses. In AMPK, the activation-loop threonine was retained in every species with a readable site, while other features varied strongly: \u03b2 carbohydrate-binding-module conservation covaried with \u03b1 C-terminal length under the primary phylogenetic model, and AMPK\u03b3 showed pronounced lineage-associated length variation. In the focal coccidian-group cohort, \u03b3 sequences had a median length of 909 residues versus 396 in other sampled copies; the median was 924 among the nine sequences with a tree-based orthology determination, while two\n                  <jats:italic>Eimeria<\/jats:italic>\n                  sequences remain provisional candidates. Low primary nucleotide-contact-site identity was shared more broadly across sampled Apicomplexa. Together, these analyses reveal lineage-structured variation in TOR and AMPK at three levels: component repertoires, sequence features of retained proteins, and associations among components. Signaling architecture cannot be inferred from presence and absence alone.\n                <\/jats:p>","DOI":"10.64898\/2026.09.26.754375","type":"posted-content","created":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T19:15:16Z","timestamp":1790622916000},"source":"Crossref","is-referenced-by-count":0,"title":["Beyond presence and absence: a survey of TOR and AMPK across 210 eukaryotes reveals unusually long coccidian AMPK\u03b3"],"prefix":"10.64898","author":[{"given":"Aditya","family":"Patwardhan","sequence":"first","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Euwen","family":"Brennan","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9983-1856","authenticated-orcid":false,"given":"Bruno","family":"Martorelli Di Genova","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026093018252121000_2026.09.26.754375v1.1","first-page":"D898","article-title":"VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center","volume":"50","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026093018252121000_2026.09.26.754375v1.2","doi-asserted-by":"publisher","DOI":"10.1111\/2041-210X.12195"},{"key":"2026093018252121000_2026.09.26.754375v1.3","first-page":"11","article-title":". windex: Analyzing Convergent Evolution Using the Wheatsheaf Index in R","volume":"11","year":"2015","journal-title":"Evol. 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