wiki:PombeGeneLosses

Version 52 (modified by vw253, 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?)

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

Compara false positive

  • YGR109C (from Compara)
  • removed from list to here

  • YKR043C present in yeast/ protazoa/dicty