== Known pombe gene losses == === Lipid metabolic process (mainly fatty acid oxidation?) === * YAT1 YAR035W carnitine O-acetyltransferase (human, CPT2) * CAT2 YML042W (human CRAT) * DCI1 YOR180C (human PECI) * POT1 (FOX3) YIL160C * TES1 YJR019C (human ACOT8) * POX1 YGL205W (human candidates ACOX1 and 2) * FAA2 YER015W (human ACSL1,5,6 ?) * PXA2 YKL188C (possible human ABCD4) * EHT1 YBR177c transporter * YBR041W (from Compara) * YDR287W (from Compara) * YDR294C (from Compara) * YHR046C (from Compara) * YJL153C (from Compara) * YLR118C (from Compara) * ECI1 YLR284C (human, PECI) * YMR210W similar to EEB1 and EHT1 medium-chain fatty acid metabolic process * YPL069C * EEB1 YPL095c medium-chain fatty acid ethyl ester biosynthesis during fermentation * YPL103C * TAZ1 YPR140W TAfaZzin (human , TAZ) * SPS19 YNL202W SPAC922.06 http://www.pantherdb.org/panther/family.do?clsAccession=PTHR24315:SF0 (no coompara) === TMA (translation machinery associated) === * TMA64 YDR117C (human LGTN) * TMA7 YLR262C-A ribosome associated (human TMA7) http://pfam.xfam.org/family/PF09072?type=Family#tabview=tab7 (no pombe family member) could not find with tblastn * STF2 YGR008C TMA10 paralog ( human SERBP1) (not in compara list) * TMA10 YLR327C STF2 paralog ( conserved in human SERBP1) (not in compara list) * YER176W === Nucleobase containing small molecule met === * YBR140C (from Compara) * YCR011C (from Compara) * YER155C (from Compara) check class * YIR027C (from Compara) * YKL088W (from Compara) * YKR072C (from Compara) CoA-synthesizing protein complex * YLR422W (from Compara) * YOL059W (from Compara) * YOL081W (from Compara) * YOR054C (from Compara) * YPL147W (from Compara) * YPR140W (from Compara) === Tryptophan degradation/ de novo NAD biosynthesis === * BNA1 YJR025c tryptophan met 3-hydroxyanthranilate 3,4-dioxygenase activity (human HAAO) * BNA2 YJR078W tryptophan 2,3-dioxygenase activity (human IDO2) * BNA4 YBL098W tryptophan met kynurenine 3-monooxygenase (human KMO) * BNA5 YLR231C tryptophan met kynureninase (human KYNU) * BNA6 YFR047C biosynthesis of NAD from tryptophan via kynurenine (human QPRT) (missing from compara) === Other cellular amino acid/derivative metabolic process === * YAL012W (from Compara) * YCL064C (from Compara) * YFL030W (from Compara) * YMR020W FMS1 (from Compara) * YNL040W possible FP (from Compara) * CYS4 YGR155W cystathionine beta-synthase (human CBS) ==== Urea metabolism ==== * YBR208C (from Compara) === Carbohydrate metabolic process === * YDL174C (from Compara) * YDR109C (from Compara) * YHL032C (from Compara) * YHR104W (from Compara) * YHR210C (from Compara) * YMR164C (from Compara) * YNR071C (from Compara) * YPR026W (from Compara) === Subset of carbohydrate , Glycogen metabolism === * GLC3 YEL011W glycogen branching enzyme (human GBE1) * GSY1 YFR015C (human GYS1) * GLG2 YJL137C * GLG1 YKR058W * GSY2 YLR258W (human GYS1) * GPH1 YPR160W glycogen debranching enzyme (human PYGB) * GDB1 YPR184W glycogen debranching enzyme (human AGL) === Transmembrane Transporters === * PFA4 YOL003C * AVT1 YJR001C * AVT2 YEL064C * FUN26 YAL022C (human SLC29A1,2,3,4) * YBR241C (from Compara) * YBR296C (from Compara) * YCR011C (from Compara) * YCR075C (from Compara) * YGL104C (from Compara) * YGR055W (from Compara) * YHL036W (from Compara) * YKL221W (from Compara) * YLR348C (from Compara) * YMR221C (from Compara) * YNL125C (from Compara) * YNL298W (from Compara) WHY IS THIS MAPPING HERE>=? * YOL119C (from Compara) * YOR079C (from Compara) * YOR306C (from Compara) * YPL147W (from Compara) * YPR021C (from Compara) * YPR192W AQY1 (from Compara) * YLL052C AQY2 * YLL053C * YOL075C (from Compara) predict carnitine === transcription and chromatin remodelleing complexes CHRAC and isw1-2 complexes === * ITC1 YGL133W CHRAC complex isw1-a complex (human BAZ1A,B) (no compara) * YPL216W ITC1 paralog (uncharacterised) (human BAZ1A,B) (no compara) * IOC3 YFR013W isw1-a (PWWP domain) (no compara REMOVE?) * IOC4 YMR044W isw1-b (PWWP domain) (no compara REMOVE?) * HHO1 YPL127C histone H1 (human H1F0) * YCL055W (from Compara) * YDR440W (from Compara) * YGL096W (from Compara) * YGL254W (from Compara) * YGR040W (from Compara) * YJL056C (from Compara) * YER040W (from Compara) * YKR034W (from Compara) * YKR099W (from Compara) * YMR164C (from Compara) * YNL239W (from Compara) * YPL177C (from Compara) == Chromosome organization == * ISW1 YBR245C isw1-a/b complex amily confirmed by compara (FP?) * ISW2 YOR304W CHRAC complex family confirmed by compara (FP?) * YDR096W (from Compara) * HOS1 YPR068C (from Compara) === Nucleocytoplsmic transport === * YKL068W (from Compara) (checked) * YMR047C (from Compara) (checked) * YNL298W (from Compara) (checked) === DNA recombination === * YBR186W (from Compara) * YDL154W (from Compara) * YFL003C (from Compara) * YFR038W (from Compara) * YGL251C (from Compara) * YPL164C (from Compara) === DNA repair === * YFL007W this isn't repair, cant figure why its mapping here * YOR386W (from Compara) * YDR054C (from Compara) * YGR109C (from Compara) * OGG1 YML060W "CBF3 complex" base excision repair protein (human OGG1) === DNA replication === * YDL101C (from Compara) === Miitotoic cell cycle regulation === (does not map here) * YPR120C (from Compara) === tRNA metabolic process === * TRM3 YDL112W (from Compara) checked * PUS6 YGR169C (from Compara) checked * RNY1 YPL123C (no compara) === Signalling === * YBR164C (from Compara) * YBR264C (from Compara) * YDL159W (from Compara) * YDR006C (from Compara) * YDR294C (from Compara) * YDR466W (from Compara) * YPL051W (from Compara) * YOR212W (from Compara) not annotated to signalling * YGR152C (from Compara) * YKL092C (from Compara) not annotated to signalling * PDE2 YOR360C high affinity 3',5'-cAMP phosphodiesterase (family has human members, but no pombe member http://pfam.xfam.org/family/PF00233?type=Family#tabview=tab7) === Mitochondrial organization === * COX23 YHR116w http://www.pantherdb.org/panther/family.do?clsAccession=PTHR13626 (has human) (no compara) * TOM6 YOR045W this paper links budding yeast to human, no pombe yet http://www.ncbi.nlm.nih.gov/pubmed/18331822 (no compara) === Proteases === * YCR045C (from Compara) (REMOVE?) * YCL057W (from Compara) * YFR006W (from Compara) * YOL057W === Proteasome assembly === * YGL004C (from Compara) === Misc === * move to above (in list) * YPC1 YBR183W paralog YDC1 (conserved in human ACER3) (no compara) * YDC1 YPL087W paralog YPC1 (conserved in human ACER3) (no compara) * SRN2 YLR119W Component of the ESCRT-I complex (no compara) * KXD1 YGL079W BLOC-1 complex (conserved in human KXD1) * SNN1 YNL086W BLOC-1 complex (conserved in human SNAPIN & BLOC1S6) * YKR013W (from Compara) === Unknown process === * AML1 YGR001C adenine methyltransferase, has human, (conserved in human N6AMT2) http://pfam.xfam.org/family/PF10237?type=Family#tabview=tab7 * YPL264C * YGR127W * YDL156W * YMR010W * YNR066C * YDR336W * YMR253C * YCR101C * YCR099C * YCL028W * YCR100C * YMR034C * YPL263C * YER004W * YMR132C * YPL162C * YJL132W * YFR016C * YFR018C * YGR001C * YHL021C * YJL078C * YJL079C * YMR114C * YMR110C === Compara false positive === * YLR087C (Compara false positive - yeast specific protein) * YGR023W fugal sepecific (low complexity) * YMR068W false positive fungal only ankyrin repeat * YLR332W fungal only serine rich * YOR195W fungal only http://pfam.xfam.org/family/PF12709?type=Family#tabview=tab7 * YDR235W http://www.pantherdb.org/panther/family.do?clsAccession=PTHR17204:SF23 * YNL016W http://www.pantherdb.org/panther/family.do?clsAccession=PTHR24622:SF45 * YIR019C * YDR054C delete is conserved in pombe * YDR519W domain only, check * YML078W domain only, check * removed from list to here to check: * YDL122W candidate for pombe Ubp11 http://www.pantherdb.org/panther/family.do?clsAccession=PTHR24006:SF412 * YJL073W possible fp, dnaj * FPS1 YLL043W (not sure about this) * YHR121W * YJL068C * YJR151C * YBL064C * YIL112W (should have pombe)