# HISTORY 07 May 2016: Updated by: TOUCHUP-v1.18 14 Mar 2016: Updated by: TOUCHUP-v1.12 23 Mar 2016: Updated by: TOUCHUP-v1.15 # molecular_function 20140901: root_PTN000005165 has function ubiquitin-protein transferase activity (GO:0004842) 20140901: Opisthokonta_PTN000799330 has function cysteine-type endopeptidase inhibitor activity (GO:0004869) 20140901: Bilateria_PTN000005232 has function cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027) # cellular_component 20140311: root_PTN000005165 is found in cytoplasm (GO:0005737) 20140901: Opisthokonta_PTN000005168 is found in spindle microtubule (GO:0005876) 20140901: Opisthokonta_PTN000799330 is found in nucleus (GO:0005634) 20140901: Amniota_PTN001295636 is found in IPAF inflammasome complex (GO:0072557) 20140901: Bilateria_PTN000005232 is NOT found in spindle microtubule (GO:0005876) # biological_process 20140901: root_PTN000005165 participates in regulation of signal transduction (GO:0009966) 20140901: Opisthokonta_PTN000005168 participates in mitotic spindle assembly (GO:0090307) 20140901: Opisthokonta_PTN000799330 participates in inhibition of cysteine-type endopeptidase activity involved in apoptotic process (GO:1990001) 20140901: Euteleostomi_PTN000005173 participates in regulation of mitotic cell cycle (GO:0007346) 20140311: Tetrapoda_PTN000005243 participates in positive regulation of canonical Wnt signaling pathway (GO:0090263) 20140901: Tetrapoda_PTN000740861 participates in negative regulation of necroptotic process (GO:0060546) 20140901: Tetrapoda_PTN000740861 participates in regulation of toll-like receptor signaling pathway (GO:0034121) # PRUNED 20140901: Amniota_PTN001295636 participates in innate immune response (GO:0045087) 20140901: Bilateria_PTN000005232 does NOT participate in mitotic spindle assembly (GO:0090307) 07 May 2016: node_PTN001295648 has been pruned from tree 07 May 2016: node_PTN001295607 has been pruned from tree 07 May 2016: Embryophyta_PTN000799418 has been pruned from tree # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES 23 Mar 2016: node_PTN001295607 has been pruned from tree 23 Mar 2016: Embryophyta_PTN000799418 has been pruned from tree 23 Mar 2016: node_PTN001295648 has been pruned from tree 14 Mar 2016: node_PTN001295607 has been pruned from tree 14 Mar 2016: Embryophyta_PTN000799418 has been pruned from tree 14 Mar 2016: node_PTN001295648 has been pruned from tree Difficult to annotate because many processes are found in multiple places on the tree (for example the role in neuron apoptosis and in inflammation). Also, the role in apoptosis and on caspase inhibition is found across the tree, but the tree also contains Dicty and plant sequences, so I was not able to propagate that to the root. Finally, since I was not able to see domains, I had to guess as to which ones had ubiquitin ligase activity (annotated to the root) and which ones inhibited caspases. PG 2014-03-11 I took a quick look at the family in PAINT. I think the family needs to have quite a few the alignment is the BIR domain, but there are quite a few sequences (one vertebrate clade and many of the plant sequences) that don't align well to that region, so they don??t belong in the family. They were probably brought into the family because one of the BIR domain-containing proteins also has a ubiquitin ligase domain, so other ubq-ligases match it. I'd suggest that we prune out these non-BIR-domain-containing sequences, rebuild the tree and then annotate. I went through the tree and pruned out the clades or individual sequences that didn't align we should remove these sequences and rebuild. (NOT YET DONE as of Sept 1, 2014). Paul T 2014-03-11 Annotated despite the tree not being optimal. Pruned several nodes; the tree needs to be reviewed. Propagated cysteine-type endopeptidase inhibitor activity to Opisthokonta_PTN000799330, but limited cysteine-type endopeptidase inhibitor activity involved in apoptotic process to Bilateria_PTN000005232 as other sequences seem to be involved in inflammation rather than apoptosis, and since CASP1 is involved in inflammation, the direct regulation of a caspase does not imply a role in apoptosis. PG 2014-09-01 # 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).