# HISTORY 24 Mar 2016: Updated by: TOUCHUP-v1.15 14 Mar 2016: Updated by: TOUCHUP-v1.12 # molecular_function 20141129: root_PTN000034104 has function pyridoxal phosphate binding (GO:0030170) 20141129: node_PTN000034394 has function tryptophan synthase activity (GO:0004834) 20141126: node_PTN000034251 has function threonine synthase activity (GO:0004795) 20141129: node_PTN000034721 has function D-serine ammonia-lyase activity (GO:0008721) 20141125: node_PTN000034721 has function serine racemase activity (GO:0030378) 20141124: node_PTN000034721 has function L-serine ammonia-lyase activity (GO:0003941) 20141129: node_PTN000034171 has function L-threonine ammonia-lyase activity (GO:0004794) 20141129: node_PTN000034171 has function L-serine ammonia-lyase activity (GO:0003941) 20141125: node_PTN000034360 has function tryptophan synthase activity (GO:0004834) 20141124: node_PTN000034466 has function cysteine synthase activity (GO:0004124) 20141129: Chordata_PTN001307386 has function heme binding (GO:0020037) 20141125: Bacteria _PTN000034535 has function L-cysteine desulfhydrase activity (GO:0080146) 20141129: node_PTN000034237 has function L-serine hydro-lyase (adding indole, L-tryptophan-forming) activity (GO:0052684) 20141129: node_PTN000741516 has function threonine synthase activity (GO:0004795) 20141129: Eukaryota_PTN000816508 has function L-threonine ammonia-lyase activity (GO:0004794) 20141126: Opisthokonta_PTN000816888 has LOST/MODIFIED function threonine synthase activity (GO:0004795) # cellular_component 20141129: root_PTN000034104 is found in cytoplasm (GO:0005737) 20141129: Boreoeutheria_PTN000034733 is found in neuronal cell body (GO:0043025) 20141125: node_PTN000034360 is found in chloroplast (GO:0009507) 20141125: Euryarchaeota_PTN000816705 is NOT found in chloroplast (GO:0009507) 20141125: Bacteria _PTN000034377 is NOT found in chloroplast (GO:0009507) # biological_process 20141126: node_PTN000034251 participates in threonine biosynthetic process (GO:0009088) 20141125: node_PTN000034721 participates in L-serine metabolic process (GO:0006563) 20141125: node_PTN000034721 participates in D-serine biosynthetic process (GO:0070179) 20141129: Boreoeutheria_PTN000034733 participates in brain development (GO:0007420) 20141129: Bacteria _PTN000034699 participates in D-serine catabolic process (GO:0036088) 20141129: node_PTN000034171 participates in threonine catabolic process (GO:0006567) 20141129: node_PTN000034171 participates in L-serine catabolic process (GO:0006565) 20141125: node_PTN000034360 participates in tryptophan biosynthetic process (GO:0000162) 20141124: node_PTN000034466 participates in cysteine biosynthetic process from serine (GO:0006535) 20141129: node_PTN000034237 participates in tryptophan biosynthetic process (GO:0000162) 20141129: Eukaryota_PTN000816508 participates in isoleucine biosynthetic process (GO:0009097) 20141126: Opisthokonta_PTN000816888 does NOT participate in threonine biosynthetic process (GO:0009088) 20141125: Saccharomyces cerevisiae S288c_S000001701 does NOT participate in L-serine metabolic process (GO:0006563) 20141125: Saccharomyces cerevisiae S288c_S000001701 does NOT participate in D-serine biosynthetic process (GO:0070179) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES . The enzyme THNSL does not have Thr synthase activity; see PMID:17034760 for active site residues. - Propagated 'heme binding' to Chordata_PTN001307386 because these sequence have the T and H required for heme binding, according to UniProt annotation of P35520. Dispute - EMINI_cysB annotation to 'cystathionine beta-synthase activity'. P50867 GO:0004122 IMP ECO:0000315 PMID:19685245 Dispute ID: 1813 -> Wrong protein annotated ? The authors mention cysD having this activity. P50867 GO:0019343 IMP ECO:0000315 PMID:19685245 Dispute ID: 1815 -> Response from AspGD: In fact the GAF file of AspGD does not contain this annotation; there is a discrepancy in the data from AspGD and GOA. # 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).