Version 9 (modified by 6 years ago) (diff) | ,
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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
- FAT1 YBR041W (from Compara) transporter
- 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)