# HISTORY
26 Mar 2016: Updated by: TOUCHUP-v1.15
16 Mar 2016: Updated by: TOUCHUP-v1.14

# molecular_function
20150120: Eukaryota_PTN000482504 has function phosphatidylinositol-3-phosphate binding (GO:0032266) 

# cellular_component
20150120: Eukaryota_PTN000482504 is found in BBSome (GO:0034464) 
20150120: Eukaryota_PTN000482504 is found in ciliary basal body (GO:0036064) 

# biological_process
20150120: Eukaryota_PTN000482504 participates in intracellular transport (GO:0046907) 
20150120: Eukaryota_PTN000482504 participates in cilium assembly (GO:0042384) 

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

# NOTES
This family contains the BBS5 subunit of the highly conserved seven-member BBSome complex, a membrane coat complex that traffics membrane proteins to the primary cilium (PMID:19575670, PMID:20697559, PMID:20603001). Whether this trafficking occurs by a vesicular mechanism or as a planar patch that moves laterally within the membrane is not yet clear as of August 2014. The BBSome also appears to be an adaptor for some retrograde intraflagellar traffic (IFT) within the cilium (PMID:20697559).
Comments on the tree & sequences
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This tree looks very straightforward. The only duplication node looks like a sequence issue rather than true duplication, and there is an additional incomplete sequence.
- From Strongylocentrotus purpuratus, the H3J8A5_STRPU looks complete and highly conserved, while the H3IV02_STRPU has a gap. However, both sequences are obsolete in UniProt.
- The Schistosoma mansoni (Blood fluke) sequence (G4VFM7_SCHMA) looks like a partial sequence containing only the N-terminus
Comments on annotations and propagations
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- I decided not to propagate the MF annotation of the human BBS5 to the term "RNA polymerse II repressing transcription factor binding (GO:0001103 from PMID:22302990) because this was done by yeast two-hybrid with isolated subunits of the BBSome complex against the RNF2 transcription factor and multiple subunits showed the same effect, suggesting that the interaction might be at the level of the BBSome complex, rather than an individual subunit. In addition, they say that they "have shown recently that depletion of BBS4 results in defective proteasome-mediated protein clearance, leading to the accumulation of β-catenin in BBS4 knockdown cells (Gerdes et al., 2007).", and show similar accumulation of RNF2 protein in BBS knockdown cells. Basically, this seems somewhat preliminary and potentially indirect, so I have not chosen to propagate this annotation.
- I did not propagate a large number of BP annotations based on developmental phenotypes because they are all downstream of the primary defect in trafficking to the cilium and the resulting defect in cilary function.

# 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).