Version 52 (modified by 3 years ago) (diff) | ,
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Known pombe gene losses
YML029W missing Hrd1 complex subunit
Lipid metabolic process
Carnitine
- YAT1 YAR035W carnitine O-acetyltransferase (human, CPT2)
- CAT2 YML042W (human CRAT)
- YOL075C (from Compara) transporter predict carnitine
Fatty acid oxidation
- 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
- YMR210W similar to EEB1 and EHT1 medium-chain fatty acid metabolic process
- ECI1 YLR284C (human, PECI)
- YPL147W (from Compara)
- EEB1 YPL095c medium-chain fatty acid ethyl ester biosynthesis during fermentation
- SPS19 YNL202W SPAC922.06 http://www.pantherdb.org/panther/family.do?clsAccession=PTHR24315:SF0 (no coompara)
CoA synthesissing protein complex
- CAB3 YKL088W (from Compara)
- VHS3 YOR054C (from Compara) coenzyme-A
- SIS2 YKR072C (from Compara) CoA-synthesizing protein complex
Inositol
- INM2 YDR287W (from Compara)
- INM1 YHR046C (from Compara)
- INO1 YJL153C (from Compara)
Ceramide
- YPC1 YBR183W paralog YDC1 (conserved in human ACER3) (no compara) ceramide
- YDC1 YPL087W paralog YPC1 (conserved in human ACER3) (no compara) ceramide
- DPL1 YDR294C (from Compara) sphingolipid
Amino acid
Tryptophan degradation
- 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)
- BNA7 YDR428C
Sulfur amino acid metabolic process
- CYC3 YAL012W (from Compara)
- CHA1 YCL064C (from Compara)
- AGX1 YFL030W (from Compara)
- CYS4 YGR155W cystathionine beta-synthase (human CBS)
- MUP3 YHL036W (from Compara) methionine transporter
- MUP1 YGR055W (from Compara) methionine transporter
Carbohydrate metabolic process
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)
Glycerol metabolism
- GUT1 YHL032C (from Compara)
- GPD2 YOL059W (from Compara)
- YHR104W (from Compara) NOT ANNOTATED AS GLYEROL
Transcription related
Nitrogen metabolism
- DAL1 YIR027C (from Compara) nitrogen catabolite repression (Enzyme is known to be present in pombe, see function predictions
???
- DAL80 YKR034W (from Compara) nitrogen catabolite repression
- GLN3 YER040W (from Compara)
- AVT1 YJR001C amino acid transporter, move closer to other cluster?
Isw1 complex
- ISW1 YBR245C isw1-a/b complex amily confirmed by compara
- ITC1 YGL133W isw1-a complex (human BAZ1A,B) (no compara)
- ISW2 YOR304W CHRAC complex family confirmed by compara
- YPL216W ITC1 paralog (uncharacterised) (human BAZ1A,B) (no compara)
- GIS1 YGL096W (from Compara)
- CMR1 YDL156W (human WDR76 ortholog)
DNA recombination
- MSH5 YDL154W (from Compara)
- MSH4 YFL003C (from Compara)
- MLH3 YPL164C (from Compara)
- HFM1 YGL251C (from Compara)
Signalling
Dock GEF associated
- DCK1 YLR422W (from Compara)
- YCR100C
- YCR101C
Camp mediated signalling (some role inglycogen metabolism?)
- IRA1 YBR140C (from Compara)
- IRA2 YOL081W (from Compara)
- 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)
- YPL263C (kelch repeat unknown function, clusters with string)
tRNA metabolic process
- TRM3 YDL112W (from Compara) checked
- PUS6 YGR169C (from Compara) checked
- RNY1 YPL123C (no compara)
- YNL040W (from Compara) checked
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)
- ECM32 YER176W
- TMA16
Nucleocytoplsmic transport
- YKL068W (from Compara) (checked)
- YMR047C (from Compara) (checked)
- YNL298W (from Compara) (checked)
Proteases
- YCL057W (from Compara)
- YFR006W (from Compara)
Transmembrane Transporters
- PFA4 YOL003C
- AVT2 YEL064C
- FUN26 YAL022C (human SLC29A1,2,3,4)
- YBR241C (from Compara)
- YBR296C (from Compara)
- YCR011C (from Compara)
- YCR075C (from Compara)
- YGL104C (from Compara)
- YKL221W (from Compara)
- YLR348C (from Compara)
- YMR221C (from Compara)
- YNL125C (from Compara)
- YOL119C (from Compara)
- YOR079C (from Compara)
- YOR306C (from Compara)
- YPL147W (from Compara)
- YPR021C (from Compara)
- YPR192W AQY1 (from Compara)
- YLL052C AQY2
- YLL053C
CHECKED TO HERE
misc transcription and chromatin remodelleing
- DOT1 YDR440W (from Compara) histone methyltransferase activity (H3-K79 specific)
- HHO1 YPL127C histone H1 (human H1F0)
- YCL055W (from Compara)
- YGL254W (from Compara)
- YJL056C (from Compara)
- YKR099W (from Compara)
- YMR164C (from Compara)
- YNL239W (from Compara)
- YPL177C (from Compara)
- YDR096W (from Compara)
- HOS1 YPR068C (from Compara)
- HOS4 YIL112W
- RBS! YDL189W (appears to be conserved with no pombe, see panther)
misc DNA metabolism
- YBR186W (from Compara)
- YFR038W (from Compara)
- YFL007W this isn't repair, cant figure why its mapping here
- YOR386W (from Compara)
- YDR054C (from Compara)
- OGG1 YML060W "CBF3 complex" base excision repair protein (human OGG1)
- YDL101C (from Compara)
misc Signalling
- YBR164C (from Compara)
- STE7 YDL159W (from Compara)
- SOK1 YDR006C (from Compara)
- DPL1 YDR294C (from Compara)
- YPL051W (from Compara)
- YOR212W (from Compara) not annotated to signalling
- YGR152C (from Compara)
- YKL092C (from Compara) not annotated to signalling
Misc
- DLD1 YDL174C (from Compara) lactate dehydrogenase
- YNR071C (from Compara) aldose-1-epimerase family
- YHR210C (from Compara) aldose-1-epimerase family
- YDR109C (from Compara) sugar kinase
- FMS1 YMR020W (from Compara) pantathoate/ spermidine met
- KXD1 YGL079W BLOC-1 complex (conserved in human KXD1)
- SNN1 YNL086W BLOC-1 complex (conserved in human SNAPIN & BLOC1S6)
- APT1 YLR118C (from Compara) depalmitolation
- BTS1 YPL069C terpenoid
- YPL103C N-acylethanomine
- TAZ1 YPR140W TAfaZzin (human , TAZ)
- SRN2 YLR119W Component of the ESCRT-I complex (no compara)
- YJL068C
- PRX1 YBL064C
- YKR013W (from Compara)
- YGL004C (from Compara)
- YCR011C (from Compara)
- YER155C (from Compara) check class
- YPR140W (from Compara)
- YBR208C (from Compara)
- YMR164C (from Compara)
- YPR026W (from Compara)
- YJL073W possible fp, dnaj
- FPS1 YLL043W (not sure about this)
Unknown process
- AML1 YGR001C adenine methyltransferase, has human, (conserved in human N6AMT2) http://pfam.xfam.org/family/PF10237?type=Family#tabview=tab7
- YPL264C
- YGR127W
- YMR010W
- YNR066C
- YDR336W
- YMR253C
- YCR099C
- YCL028W
- YMR034C
- 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
- YNL298W (from Compara) (homolog only) (possibly has pombe ortholog)
- YCR045C (from Compara) (homolog only)
- YOL057W (from Compara) (homolog only)
- YBR264C (from Compara) (homolog only)
- PKH3 YDR466W (from Compara) (homolog only)
- DAN4 YJR151C
- YGR040W (from Compara)
- YDL122W candidate for pombe Ubp11 http://www.pantherdb.org/panther/family.do?clsAccession=PTHR24006:SF412
- YPR120C (from Compara)
- YGR109C (from Compara)
- removed from list to here
- YKR043C present in yeast/ protazoa/dicty