# HISTORY 23 Mar 2016: Updated by: TOUCHUP-v1.15 14 Mar 2016: Updated by: TOUCHUP-v1.12 # molecular_function 20121011: Diptera_PTN000000481 has function dopachrome isomerase activity (GO:0004167) # cellular_component # biological_process 20121011: Eukaryota_PTN000000446 participates in secondary metabolite biosynthetic process (GO:0044550) 20121012: node_PTN000000448 participates in cuticle pigmentation (GO:0048067) 20121011: node_PTN000000448 participates in melanin biosynthetic process (GO:0042438) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES Fast-pass curation of PTHR10009 (Protein yellow) family general information about the protein yellow family: PMID: 11237700 Four sets of the yellow-related genes appear side-by-side in the genome, and numerals were used in the new gene names to signify this. GadFly indicates that genes yellow-d & yellow-d2, yellow-e, yellow-e2 & yellow-e3, yellow-f & yellow-f2, and yellow-g & yellow-g2 are located alongside each other. The gene names are not meant to imply that these genes are the product of tandem duplication events, although evidence indicates this to be the case for all but yellow-e, yellow-e2 & yellow-e3. MF only two MF annotations, (yellow-f and yellow-f2) to dopachrome isomerase activity. propagate to orthologous group (which includes mosquito dce and a few others). the same paper shows that yellow (y), yellow-b and -c do NOT have this activity. however, because y is also involved in melanin biosynthesis, it is likely to work by a similar catalytic mechanism (though perhaps on a different substrate). given the conserved alignment (even the homologs in other organisms) the basic function of isomerase is likely to be conserved, so propagate the more general isomerase to root. Mosquito dce should be annotated to this function using PMID:11779167 and PMID:11520691. CC -Propagate GO:0005576 " extracellular region" to LCA of insect and fungal sequences, since they all have signal peptides (looking at the alignment) PMID:12164780 Recombinant yellow-f was purified from the culture media supernatant PMID: 1465112 the protein was detected in epidermal cells and in the cuticle structures secreted by them that later become pigmented BP - Propagate melanin biosynthetic process to root of insects to cover all sequences; propagate less specific secondary metabolite biosynthetic process to also include Dicty and fungi. A role in cuticle pigmentation is likely for this same group based on the general mechanism for melanin-based pigmentation described in PMID:11934851, so propagate this term as well. PMID:12164780 yellow-f and yellow-f2 Flybase please considering add an annotation of GO:0042438, melanin biosynthetic process Other annotations on y should not be propagated as use of paralogs during different developmental stages (development, adult/mating) is not clear and there are no related annotations to other genes in the family. Indole-containing compound metabolic process for yellow-f1 and -f2 should not be propagated since it's just a nonspecific way of representing the MF that was already captured by a different annotation LN, 5 Jan 2011 PDT 12 Oct 2012 # 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).