# 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 20150508: node_PTN000107810 has function phosphoglycerate dehydrogenase activity (GO:0004617) 20150501: Eukaryota_PTN000107673 has function formate dehydrogenase (NAD+) activity (GO:0008863) 20150508: node_PTN000107947 has function glyoxylate reductase (NADP) activity (GO:0030267) 20150508: node_PTN000107947 has function hydroxypyruvate reductase activity (GO:0016618) 20150501: Eukaryota_PTN000107684 has function transcription corepressor activity (GO:0003714) 20150501: Eukaryota_PTN000107684 has function protein homodimerization activity (GO:0042803) 20150508: node_PTN000108045 has function phosphoglycerate dehydrogenase activity (GO:0004617) 20150508: Bacteria _PTN001335230 has function 4-phosphoerythronate dehydrogenase activity (GO:0033711) 20150501: Bacteria _PTN000108096 has function D-lactate dehydrogenase activity (GO:0008720) 20150508: Embryophyta_PTN000864064 has LOST/MODIFIED function glyoxylate reductase (NADP) activity (GO:0030267) 20150508: Embryophyta_PTN000864064 has LOST/MODIFIED function hydroxypyruvate reductase activity (GO:0016618) 20150508: Eukaryota_PTN000107673 has LOST/MODIFIED function phosphoglycerate dehydrogenase activity (GO:0004617) 20150508: Bacteria _PTN001335230 has LOST/MODIFIED function phosphoglycerate dehydrogenase activity (GO:0004617) # cellular_component 20150501: Dikarya_PTN000863804 is found in cytosol (GO:0005829) 20150501: Embryophyta_PTN000863833 is found in mitochondrion (GO:0005739) 20150508: node_PTN000107947 is found in cytosol (GO:0005829) 20150501: Eukaryota_PTN000107684 is found in nucleus (GO:0005634) 20150501: Embryophyta_PTN000863790 is NOT found in nucleus (GO:0005634) # biological_process 20150508: node_PTN000107810 participates in serine family amino acid biosynthetic process (GO:0009070) 20150507: Eukaryota_PTN000107673 participates in formate catabolic process (GO:0042183) 20150501: Eukaryota_PTN000107685 participates in negative regulation of transcription from RNA polymerase II promoter (GO:0000122) 20150508: node_PTN000108045 participates in serine family amino acid biosynthetic process (GO:0009070) 20150508: Eukaryota_PTN000107673 does NOT participate in serine family amino acid biosynthetic process (GO:0009070) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES This family includes D2-hydroxy-acid dehydrogenases that use NAD/H to reduce a beta keto group (formate dehydrogenases - despite the lack of beta hydroxyl group, belong to this family, see pmid:) Based on a summary in this paper (and references): pmid:12419229 and coordinates in Hs CTBP1, the catalytically important, highly conserved residues are: R266, E(D)295, H315. For NAD binding the GXGXXG motif at G181, G183, G186 is important. PTN000107684 clade is a group of eukaryotic CTBPs (C-terminal binding protein) - that are transcriptional co-repressors with enzymatic activity with unclear substrate (pmid:17336131 and 12419229). Within this clade PTN000107755 and - PTN000863790 are missing key residues, so they don't have the enzymatic activity. In plants this gene seems to be active in the mitochondria (PTN000863790). R266 is missing in PTN000863790 and celegans ctbp-1. PTN000863790 is missing H315 and also the GXGXXG motif. So these 2 clades don't have catalytic activity. PTN000107673 clade is a plant-fungal formate dehydrogenase group. A good summary is pmid:15627379 and references therein. PTN000108045 is a phosphoglycerate dehydrogenase clade. Only PTN001335230 (a bacterial clade with its own activity) and PTN000107673 (with formate dehydrogenase activity) are excluded from the propagations. PTN000107947 is a glyoxylate reductase/hydroxypyruvate reductase clade; within this clade, PTN000864064 lacks the GXGXXG nucleotide binding motif, so the function propagations were not extended to this clade. # 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).