# HISTORY 07 May 2016: Updated by: TOUCHUP-v1.18 14 Mar 2016: Updated by: TOUCHUP-v1.14 24 Mar 2016: Updated by: TOUCHUP-v1.15 # molecular_function 20140731: root_PTN000192421 has function aldehyde dehydrogenase (NAD) activity (GO:0004029) 20140801: Euteleostomi_PTN000192774 has function retinal dehydrogenase activity (GO:0001758) 20140801: Euteleostomi_PTN000192774 has function 3-chloroallyl aldehyde dehydrogenase activity (GO:0004028) 20140801: Tetrapoda_PTN000192776 has function benzaldehyde dehydrogenase (NAD+) activity (GO:0018479) 20140801: Eukaryota_PTN000916659 has function aminobutyraldehyde dehydrogenase activity (GO:0019145) 20140801: Eukaryota_PTN000916659 has function 4-trimethylammoniobutyraldehyde dehydrogenase activity (GO:0047105) 20140801: Gammaproteobacteria_PTN000193442 has function betaine-aldehyde dehydrogenase activity (GO:0008802) 20140801: Eumetazoa_PTN000916306 has function formyltetrahydrofolate dehydrogenase activity (GO:0016155) 20140801: Bacteria _PTN000193466 has function 1-pyrroline dehydrogenase activity (GO:0033737) 20140801: Bacteria _PTN000193466 has function aminobutyraldehyde dehydrogenase activity (GO:0019145) 20140801: Gammaproteobacteria_PTN000193020 has function phenylacetaldehyde dehydrogenase activity (GO:0008957) 20140801: node_PTN000192580 has function succinate-semialdehyde dehydrogenase [NAD(P)+] activity (GO:0009013) 20140801: node_PTN000192580 has function succinate-semialdehyde dehydrogenase (NAD+) activity (GO:0004777) 20140801: Archaea_PTN000916156 has function glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity (GO:0008886) 20140801: node_PTN000193023 has function 1-pyrroline-5-carboxylate dehydrogenase activity (GO:0003842) 20140801: Proteobacteria_PTN000192500 has function proline dehydrogenase activity (GO:0004657) 20140801: node_PTN000192513 has function methylmalonate-semialdehyde dehydrogenase (acylating) activity (GO:0004491) 20140801: node_PTN000192513 has function malonate-semialdehyde dehydrogenase (acetylating) activity (GO:0018478) 20140801: node_PTN000193476 has function succinate-semialdehyde dehydrogenase (NAD+) activity (GO:0004777) 20140801: node_PTN000193476 has function succinate-semialdehyde dehydrogenase [NAD(P)+] activity (GO:0009013) 20140801: Euteleostomi_PTN000193361 has function retinal dehydrogenase activity (GO:0001758) 20140731: Bacteria _PTN000193002 has function enoyl-CoA hydratase activity (GO:0004300) 20140801: node_PTN000193237 has function lactaldehyde dehydrogenase activity (GO:0008911) 20140801: node_PTN000193080 has function 3-chloroallyl aldehyde dehydrogenase activity (GO:0004028) 20140801: Eukaryota_PTN001364699 has function 1-pyrroline-5-carboxylate dehydrogenase activity (GO:0003842) # cellular_component # biological_process # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES All clades with EXP evidence have aldehyde dehydrogenase activity, so clearly ancestral; in general each clade appears to have conserved specificity - putA clade: E. coli gene has three functions: based on the MSA, the C-terminal P5C dehydrogenase domain is shared across the entire clade; the Pro dehydrogenase domain is found only in proteobacteria, and the N-terminal DNA binding domain appears to be unique - ALDH1L1/2: formyltetrahydrofolate dehyd activity requires both the C-terminal dehyd domain as well as an N-terminal hydrolase domain (PMID:17302434), so propagate activity to ancestor of genes with this additional N-terminal domain - retinal dehydrogenases do not appear to be monophyletic, as it would include a large number of uncharacterized genes; also I can't find evidence that retinal occurs in non-vertebrates (as its most prominent function is in the eye) so propagate only to base of vertebrates - do not propagate acetaldehyd dehyd activity of fly Aldh, as it is a detoxification function and not clear how widely distributed - propagate aminoadipate-semialdehyde dehyd to root of clade even though only one human EXP, as it is in lysine biosynthesis and thus likely to be broadly distributed # REFERENCE Annotation inferences using phylogenetic trees The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes. To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool).