# HISTORY 07 May 2016: Updated by: TOUCHUP-v1.18 14 Mar 2016: Updated by: TOUCHUP-v1.12 23 Mar 2016: Updated by: TOUCHUP-v1.15 # molecular_function 20100412: node_PTN000005477 has function ATP-dependent peptidase activity (GO:0004176) 20100412: Eukaryota_PTN000005479 has function mitochondrial light strand promoter anti-sense binding (GO:0070361) 20100412: Eukaryota_PTN000005479 has function single-stranded DNA binding (GO:0003697) # cellular_component 20100607: node_PTN000005477 is found in cytoplasm (GO:0005737) 20140506: Eukaryota_PTN000005479 is found in mitochondrial matrix (GO:0005759) 20100607: Eukaryota_PTN000005559 is found in peroxisomal matrix (GO:0005782) 20140506: Bacteria _PTN000005641 is NOT found in mitochondrial matrix (GO:0005759) # biological_process 20100607: node_PTN000005477 participates in misfolded or incompletely synthesized protein catabolic process (GO:0006515) 20100607: Eukaryota_PTN000005479 participates in mitochondrion organization (GO:0007005) 20100607: Eukaryota_PTN000005479 participates in chaperone-mediated protein complex assembly (GO:0051131) 20100607: Eukaryota_PTN000005559 participates in protein processing (GO:0016485) 20140506: Eukaryota_PTN000005559 participates in protein targeting to peroxisome (GO:0006625) 20100607: Bacteria _PTN000005641 does NOT participate in mitochondrion organization (GO:0007005) # PRUNED 07 May 2016: Archaea_PTN000799469 has been pruned from tree # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES 23 Mar 2016: Archaea_PTN000799469 has been pruned from tree 14 Mar 2016: Archaea_PTN000799469 has been pruned from tree MF - PMID:15606774 gives active site residues (serine) at MSA position 1812 - Hs not Mm binds mitochondrial heavy strand promoter (PMID:12657466) [no up-propagation] - single-stranded RNA binding because the specificity is the same as for the mito DNA binding, annotated to same ancestor CC - Arabidopsis LonP2 "cytosol" annotation is from an HTP paper and is the only one to "cytosol." There are several annotations to "cytoplasm" or to organellar children of cytoplasm, which are not in cytosol. - PG Fixed CC to match BP: LONP2 subgroup annotated to peroxisomal matrix, and LONP1 subgroup to mitochondrial matrix. BP - Do not propagate "ATP catabolic process" from mouse Lonp1, which is already annotated to "ATP-dependent peptidase activity" under MF. Questions for MOD's - Human LONP2: The "protein processing" IMP from PMID 18281296 appears to refer to the removal of the peroxisome-targeting signal PTS1. Would a more specific annotation to the child term "signal peptide processing" (GO:0006465) be appropriate? If not, how about "protein maturation by peptide bond cleavage" (GO:0051605)? (SF # 3012766) Response, July 29, 2010 7:53:51 AM EDT: I have changed the annotation to signal peptide processing. // PG disputed the annotation May 6, 2014: Fig 5 LONP cleaves AOX (low acitivity); moreover, much more than the signal peptide appears to be removed (it removes 20kDa). Used to develop PAINT SOP, April 2010 Revised 2010 Dec 22, MSL Reviewed PG 2014-05-06 # 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).