# HISTORY
07 May 2016: Updated by: TOUCHUP-v1.18
24 Mar 2016: Updated by: TOUCHUP-v1.15
14 Mar 2016: Updated by: TOUCHUP-v1.14
07 May 2016: Updated by: TOUCHUP-v1.18

# molecular_function
20140519: Eukaryota_PTN000155295 has function alpha-galactosidase activity (GO:0004557) 

# cellular_component
20140519: Eukaryota_PTN000155295 is found in cytoplasm (GO:0005737) 
20140521: Embryophyta_PTN000894237 is found in plant-type cell wall (GO:0009505) 

# biological_process
20140519: Eukaryota_PTN000155295 participates in glycoside catabolic process (GO:0016139) 

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

# NOTES
Fast-pass curation of PTHR11452 (alpha-galactosidase/alpha-N-acetylgalactosaminidase family)
Phylogeny
This family tree appears pretty straightforward: 1 major clade spanning bacteria to humans, with a duplication in the vertebrates.  Descriptions of "alpha galactosidase" activity span the entire family, but one of the vertebrate clades (AN35) appears to have switched to alpha-N-acetylgalactosaminidase.  There are no experimental annotations among the eukaryotes.
MF
-Propagate GO:0004557 "alpha-galactosidase activity" to AN0.  Since the sequences of the NAGA clade (AN35) appear to be the same as the other proteins in the MSA (at first glance), allow this term to propagate through to the NAGA clade.
-Propagate GO:0008456 "alpha-N-acetylgalactosaminidase activity" to the NAGA clade.
CC
-There are no CC annotations to the NAGA clade, so just allow everything to propagate into it.
-There are annotations to GO:0005737 "cytoplasm" throughout the family.  Propagate to AN0, but expect possible more specific terms to follow.
-Do not propagate vacuolar or lysosomal annotations as they may just be due to overexpression artifacts.
-Ignore the pombe ER annotation (HTP).
-Propagate GO:0009505 "plant-type cell wall" to the plant clade based on 1 LTP and several HTP annotations to this term and the parental term "cell wall."
BP
-Propagate GO:0009311 "oligosaccharide metabolic process" to AN0 in agreement with the MF 4557 activity.
-There are 5 annotations to GO:0046477 "glycosylceramide catabolic process" on mouse Gla and an annotation to the parent term GO:0019377 "glycolipid catabolic process" on human NAGA.  However, the abstract of the NAGA paper (PMID 9741689) identifies the substrate, blood group A glycolipid A-6-2, as having a ceramide group.  Therefore, the more specific term is appropriate.  Propagate 46477 to AN0.
-Also propagate GO:0016139 "glycoside catabolic process" to AN0 to reflect that these are carbohydrate enzymes.  (GO:0016052 "carbohydrate catabolic process" is a parental term.)
-Ignore leaf and flower development terms as too far downstream.
=Questions for ontology curators=
==Cellular Component==
* The definition of GO:0005773 "vacuole" specifies that it is eukaryotic only, but the taxon constraint limits it to "cellular_organisms," not eukaryotes. (SF# 3220821)
**'''Curator answer: '''vacuole ; GO:0005773 inherits the 'cellular organism' taxon restraint from the parent term 'cell ; GO:0005623'. We'll give it a more specific restriction.
MSL, 4 Jan 20111
MSL, 26 Aug 2011: Added answer to question
HM updated on May 19, 2014

# 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).