# HISTORY
08 Jun 2016: Saved by krc using Paint 2.0-beta19

# molecular_function
20160608: Eukaryota_PTN000602176 has function cyclin-dependent protein serine/threonine kinase activator activity (GO:0061575) 
20160608: Eukaryota_PTN000602176 has function ubiquitin binding (GO:0043130) 
20160608: Eukaryota_PTN000602176 has function protein kinase binding (GO:0019901) 
20160608: Eukaryota_PTN000602176 has function histone binding (GO:0042393) 

# cellular_component
20160608: Eukaryota_PTN000602176 is found in cyclin-dependent protein kinase holoenzyme complex (GO:0000307) 
20160608: Eukaryota_PTN000602176 is found in SCF ubiquitin ligase complex (GO:0019005) 
20160608: Eukaryota_PTN000602113 is found in preribosome, large subunit precursor (GO:0030687) 
20160608: Eukaryota_PTN000602113 is found in nucleolus (GO:0005730) 

# biological_process
20160608: Eukaryota_PTN000602176 participates in positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737) 
20160608: Eukaryota_PTN000602176 participates in positive regulation of transcription, DNA-templated (GO:0045893) 
20160608: Eukaryota_PTN000602176 participates in regulation of mitotic cell cycle (GO:0007346) 
20160608: Eukaryota_PTN000602113 participates in ribosomal large subunit biogenesis (GO:0042273) 
20160608: Eukaryota_PTN000602113 participates in ribosomal large subunit biogenesis (GO:0042273) 

# WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED

# NOTES
9ZZZZ:PTN000602112 (root; duplication node)
- 9EUKA:PTN000602176 - ScCKS1, vert CKS2 & CKS1B
- 9EUKA:PTN000602113 - ScNIP7, vert NIP7
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Looking at the full view of the MSA, it looks like the duplication node at the root of this tree is false. The MSA for each of the two clades under it, CKS1 or NIP7, look really conserved within each other, but significantly different from each other.
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In addition, CKS1 is well characterized in several species. NIP7 is well characterized in S. cerevisiae. They do not share similar roles biologically.

# 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).