# HISTORY 26 Mar 2016: Updated by: TOUCHUP-v1.15 17 Mar 2016: Updated by: TOUCHUP-v1.14 # molecular_function 20151218: root_PTN000566730 has function Ran GTPase binding (GO:0008536) 20151216: Eukaryota_PTN001898901 has function R-SMAD binding (GO:0070412) 20151218: Saccharomycetales_PTN001898941 has function nucleocytoplasmic transporter activity (GO:0005487) 20151218: Eukaryota_PTN000566604 contributes to function GTPase activator activity (GO:0005096) # cellular_component 20151216: Eukaryota_PTN001898901 is found in nucleus (GO:0005634) 20151216: Eukaryota_PTN001898901 is found in cytosol (GO:0005829) 20151218: Eukaryota_PTN001898939 is found in microtubule associated complex (GO:0005875) 20151218: Eukaryota_PTN001898939 is found in nuclear pore (GO:0005643) 20151218: Eukaryota_PTN001898939 is found in mitochondrion (GO:0005739) 20151218: Eukaryota_PTN000319227 is found in nuclear pore (GO:0005643) 20151218: Eukaryota_PTN000566604 is found in cytoplasm (GO:0005737) 20151218: Eukaryota_PTN000566604 is found in centrosome (GO:0005813) 20151218: Eukaryota_PTN000566604 is found in nucleus (GO:0005634) 20151218: Saccharomycetales_PTN001898941 is NOT found in microtubule associated complex (GO:0005875) 20151218: Saccharomycetales_PTN001898941 is NOT found in mitochondrion (GO:0005739) 20151218: Viridiplantae_PTN001139107 is NOT found in centrosome (GO:0005813) 20151218: Fungi_PTN001898974 is NOT found in centrosome (GO:0005813) # biological_process 20151217: Eukaryota_PTN001898901 participates in positive regulation of protein export from nucleus (GO:0046827) 20151218: Eukaryota_PTN001898939 participates in NLS-bearing protein import into nucleus (GO:0006607) 20151218: Eukaryota_PTN001898939 participates in regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526) 20151218: Eukaryota_PTN001898939 participates in protein sumoylation (GO:0016925) 20151218: Eukaryota_PTN001898939 participates in negative regulation of glucokinase activity (GO:0033132) 20151218: Saccharomycetales_PTN001898941 participates in transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000972) 20151218: Saccharomycetales_PTN001898941 participates in protein export from nucleus (GO:0006611) 20151218: Saccharomycetales_PTN001898941 participates in RNA export from nucleus (GO:0006405) 20151218: Eukaryota_PTN000319227 participates in protein import into nucleus (GO:0006606) 20151218: Eukaryota_PTN000566604 participates in ubiquitin-dependent protein catabolic process (GO:0006511) 20151218: Eukaryota_PTN000566604 participates in G1/S transition of mitotic cell cycle (GO:0000082) 20151218: Eukaryota_PTN000566604 participates in spindle organization (GO:0007051) 20151218: Eukaryota_PTN000566604 participates in RNA export from nucleus (GO:0006405) 20151218: Eukaryota_PTN000566604 participates in protein import into nucleus (GO:0006606) 20151218: Eukaryota_PTN000566604 participates in positive regulation of mitotic centrosome separation (GO:0046604) 20151218: Saccharomycetales_PTN001898941 does NOT participate in regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526) 20151218: Saccharomycetales_PTN001898941 does NOT participate in protein sumoylation (GO:0016925) 20151218: Saccharomycetales_PTN001898941 does NOT participate in negative regulation of glucokinase activity (GO:0033132) 20151218: Viridiplantae_PTN001139107 does NOT participate in positive regulation of mitotic centrosome separation (GO:0046604) 20151218: Fungi_PTN001898974 does NOT participate in positive regulation of mitotic centrosome separation (GO:0046604) # PRUNED 26 Mar 2016: Homininae_PTN000566697 has been pruned from tree # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED ## Annotations that have been removed. 20151218: Eukaryota_PTN001898939 to cellular response to stress (GO:0033554) is an excluded term and not to be used for annotation # NOTES 17 Mar 2016: Homininae_PTN000566697 has been pruned from tree Tree with duplication node at root and four clades: - Eukaryota_PTN001898901: mammalian RANBP3 & RANBP3L, aka Sc YRB2 (Sp nup61 misplaced within tree?) - Eukaryota_PTN001898939: mammalian RANBP2, Ce npp-9 (Sc NUP2 misplaced within tree?) - Eukaryota_PTN000319227: mammalian & plant NUP50 (no fungi in this clade!??!) - Eukaryota_PTN000566604: mammalian & plant RANBP1, aka Sc YRB1 Comments on tree structure ---------------------- - Pruned node Homo-Pan_PTN000566697 - Both by the MSA and the branch length, this node is clearly out of place in this tree. - I suspect S.pombe nup61 is misplaced under a duplication node with S.pombe hba1 in the RANBP3 clade and that it belongs in the NUP50 clade. - I think the node Saccharomycetales_PTN001898941 is misplaced in the RANBP2 clade. PMID:21495847 lists S.cerevisiae NUP2 as the homolog of human NUP50. In addition, looking at the MSA, I think that ScNUP2 looks better compared with the NUP50 clade than the RANBP2 clade. RANBP2 has a very long N-terminal extension compared to NUP50 and ScNUP2 does not have this either. There are also other places in the alignment where I think NUP2 looks better with NUP50 than with RANBP2. *** I have blocked some RANBP2 clade annotations from propagating to this node since I think it is misplaced within the tree. I have not pruned it because I think it does belong in this tree and I want it to get annotations propagated to the root node. # 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).