wiki:OrthologInventoriesNoPom

Version 63 (modified by vw253, 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)
  • YBR041W (from Compara)
  • EHT1 YBR177c medium-chain fatty acid metabolic process
  • YDR287W (from Compara)
  • YDR294C (from Compara)
  • FAA2 YER015W (human ACSL1,5,6 ?)
  • POX1 YGL205W (human candidates ACOX1 and 2)
  • YHR046C (from Compara)
  • POT1 (FOX3) YIL160C
  • YJL153C (from Compara)
  • TES1 YJR019C (human ACOT8)
  • YLR118C (from Compara)
  • ECI1 YLR284C (human, PECI)
  • CAT2 YML042W (human CRAT)
  • YMR210W similar to EEB1 and EHT1 medium-chain fatty acid metabolic process
  • DCI1 YOR180C (human PECI)
  • YPL069C
  • EEB1 YPL095c medium-chain fatty acid ethyl ester biosynthesis during fermentation
  • YPL103C
  • TAZ1 YPR140W TAfaZzin (human , TAZ)

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)

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)
  • YOL075C (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

urea metabolism

  • YBR208C (from Compara)

  • YAL012W (from Compara)
  • YCL064C (from Compara)
  • YFL030W (from Compara)
  • YMR020W (from Compara)
  • YNL040W possible FP (from Compara)
  • CYS4 YGR155W cystathionine beta-synthase (human CBS)

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

  • 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)

trancription 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)

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)

replication

  • YDL101C (from Compara)

mitotoic cell cycle regulation=== (does not map here)

  • YPR120C (from Compara)

tRNA metabolic process

  • TRM3 YDL112W (from Compara) checked
  • PUS6 YGR169C (from Compara) checked

meotic cell cycle -

  • YIL112W (from Compara) check classification

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

proteases

  • YCR045C (from Compara) (REMOVE)

proteasome assembly

  • YGL004C (from Compara)

Compara false positive

misc

to check:

  • SRN2 YLR119W Component of the ESCRT-I complex
  • FPS1 YLL043W (not sure about this)

Mitochondrial

peroxisomal proteins and components of the fatty acid oxidation pathway

  • PXA2 YKL188C (possible human ABCD4)
  • SPS19 YNL202W SPAC922.06

BLOC1 complex (involved in endosomal maturation)

  • KXD1 YGL079W BLOC-1 complex (conserved in human KXD1)
  • SNN1 YNL086W BLOC-1 complex (conserved in human SNAPIN & BLOC1S6)
  • CNL1 YDR357C BLOC-1 complex ( NONE detected but most likely conserved)
  • VAB2 YEL005C BLOC-1 complex ( NONE detected but most likely conserved)
  • BLI1 YKL061W BLOC-1 complex ( NONE detected but most likely conserved)
  • BLS1 YLR408C BLOC-1 complex ( NONE detected but most likely conserved)

Other human members SNAP25,47, BLOC1S1,2,3,4,5 SYX12,DTNBP1, K7ELZO, PI4K2A

biotin synthesis enzymes

check bio1,5,6,7,8

  • BIO4 YNR057C
  • BIO3 YNR058W
  • BIO5 YNR056C
  • BIO6 YAR069W-A (NOT IN 288C)
  • BIO7 YHR214W-G (NOT IN 288C) pseudogenic, highly degraded
  • BIO8 YHR214W-F (NOT IN 288C) pseudogenic, highly degraded

To check

Yeast/ ascomycete specific complex members May be conserved but not yet detected

  • MGR1 YCL044C iAAA protease complex subunit (saccharomycetes only)
  • RSF1 YMR030W (yeast only)
  • AIM23 YJL131C? mitochondrial IF3 (saccharomycetes only) ​http://pfam.xfam.org/family/PF14877?type=Family#tabview=tab7
  • SPP381 YBR152W (ascomycota only)
  • SHE1 YBL031W (ascomycota only)
  • NTC20 YBR188C (ascomycota only)
  • UTP8 YGR128C ​http://pfam.xfam.org/family/PF10395?type=Family#tabview=tab7 (ascomycota only)
  • NVJ1 YHR195W nuclear envelope protein (saccharomycetes only) (confirmed with PSI-blast)
  • VID22 YLR373C is paralog of ENV11 (ascomycota only)
  • ENV11 YGR071C is paralog of VID22 (ascomycota only)
  • TMA10 YLR327C ribosome associated (ascomycete only)
  • TMA16 YOR252W ribosome associated (ascomycete only)
  • TMA17 YDL110C (ascomycete only)
  • TMA24 YOL111C (ascomycete only variant or RAD23 paralog)
  • TMA108 YIL137C
  • PEX8 YGR077C (yeast only)
  • PEX21 YGR239C (yeast only)
  • ATG23 YLR431C (yeast only)
  • ATG21 YPL100W (ATG18 releated)
  • ATG27 YJL178C mainly fungal but som metazoa. no human or pombe detected ​http://pfam.xfam.org/family/PF09451?type=Family#tabview=tab7

  • there are also 64 essential genes in budding yeast which do not appear to have a fission yeast ortholog