== 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 catabolite repression/activation ====

  * DAL1 YIR027C (from Compara)  nitrogen catabolite repression
  * 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 

=== DNA recombination ===

  * MSH5 YDL154W  (from Compara)
  * MSH4 YFL003C (from Compara)
  * MLH3 YPL164C (from Compara)
  * HFM1 YGL251C (from Compara)

 === mRNA processing  ===

  * LSM12 YHR121W

 === 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

=== 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)

 === 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