Changes between Version 67 and Version 68 of OrthologInventoriesNoPom


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Timestamp:
Oct 3, 2014, 1:52:26 PM (6 years ago)
Author:
vw253
Comment:

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  • OrthologInventoriesNoPom

    v67 v68  
    11
    2  == Known pombe gene losses ==
    3 
    4 === Lipid metabolic process (mainly fatty acid oxidation?) ===
    52 
    6   * YAT1 YAR035W carnitine O-acetyltransferase (human, CPT2)
    7   * YBR041W (from Compara)
    8   * EHT1 YBR177c medium-chain fatty acid metabolic process
    9   * YDR287W (from Compara)
    10   * YDR294C (from Compara)
    11   * FAA2 YER015W (human ACSL1,5,6 ?)
    12   * POX1  YGL205W (human candidates ACOX1 and 2)
    13   * YHR046C  (from Compara)
    14   * POT1 (FOX3)  YIL160C
    15   * YJL153C (from Compara)
    16   * TES1 YJR019C  (human ACOT8)
    17   * YLR118C (from Compara)
    18   * ECI1 YLR284C  (human, PECI)
    19   * CAT2 YML042W  (human CRAT)
    20   * YMR210W similar to EEB1 and EHT1 medium-chain fatty acid metabolic process
    21   * DCI1  YOR180C (human PECI)
    22   * YPL069C
    23   * EEB1 YPL095c medium-chain fatty acid ethyl ester biosynthesis during fermentation
    24   * YPL103C
    25   * TAZ1 YPR140W TAfaZzin (human , TAZ)
    26   * SPS19 YNL202W SPAC922.06 http://www.pantherdb.org/panther/family.do?clsAccession=PTHR24315:SF0 (no coompara)
    27  
    28 
    29 === TMA (translation machinery associated) ===
    30 
    31   * TMA64 YDR117C (human LGTN)
    32   * 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
    33   * STF2 YGR008C  TMA10 paralog ( human SERBP1) (not  in compara list)
    34   * TMA10 YLR327C STF2 paralog ( conserved in human SERBP1)  (not in compara list)
    35 
    36 
    37  === nucleobase containing small molecule met  ===
    38 
    39   * YBR140C (from Compara)
    40   * YCR011C (from Compara)
    41   * YER155C (from Compara) check class
    42   * YIR027C (from Compara)
    43   * YKL088W (from Compara)
    44   * YKR072C (from Compara) CoA-synthesizing protein complex
    45   * YLR422W (from Compara)
    46   * YOL059W (from Compara)
    47   * YOL075C (from Compara)
    48   * YOL081W (from Compara)
    49   * YOR054C (from Compara)
    50   * YPL147W (from Compara)
    51   * YPR140W (from Compara)
    52 
    53   === Tryptophan degradation/ de novo NAD biosynthesis ===
    54 
    55   * BNA1 YJR025c tryptophan met 3-hydroxyanthranilate 3,4-dioxygenase activity (human HAAO)
    56   * BNA2 YJR078W tryptophan 2,3-dioxygenase activity (human IDO2)
    57   * BNA4 YBL098W tryptophan met kynurenine 3-monooxygenase (human KMO)
    58   * BNA5 YLR231C tryptophan met  kynureninase (human KYNU)
    59   * BNA6 YFR047C biosynthesis of NAD from tryptophan via kynurenine  (human QPRT) (missing from compara)
    60 
    61   === Other cellular amino acid/derivative  metabolic process ===
    62  
    63   * YAL012W (from Compara)
    64   * YCL064C (from Compara)
    65   * YFL030W (from Compara)
    66   * YMR020W FMS1  (from Compara)
    67   * YNL040W possible FP (from Compara)
    68   * CYS4 YGR155W cystathionine beta-synthase (human CBS)
    69 
    70   ==== urea metabolism ====
    71 
    72   * YBR208C (from Compara)
    73 
    74  === Carbohydrate metabolic process ===
    75 
    76   * YDL174C (from Compara)
    77   * YDR109C (from Compara)
    78   * YHL032C (from Compara)
    79   * YHR104W (from Compara)
    80   * YHR210C (from Compara)
    81   * YMR164C (from Compara)
    82   * YNR071C (from Compara)
    83   * YPR026W (from Compara)
    84 
    85 === subset of carbohydrate , Glycogen metabolism ===
    86 
    87   * GLC3 YEL011W glycogen branching enzyme (human GBE1)
    88   * GSY1 YFR015C (human GYS1)
    89   * GLG2 YJL137C 
    90   * GLG1 YKR058W 
    91   * GSY2 YLR258W (human GYS1)
    92   * GPH1 YPR160W glycogen debranching enzyme (human PYGB)
    93   * GDB1 YPR184W glycogen debranching enzyme (human AGL)
    94  
    95 
    96  === Transmembrane Transporters ===
    97 
    98   * FUN26 YAL022C (human SLC29A1,2,3,4)
    99   * YBR241C (from Compara)
    100   * YBR296C (from Compara)
    101   * YCR011C (from Compara)
    102   * YCR075C (from Compara)
    103   * YGL104C (from Compara)
    104   * YGR055W (from Compara)
    105   * YHL036W (from Compara)
    106   * YKL221W (from Compara)
    107   * YLR348C (from Compara)
    108   * YMR221C (from Compara)
    109   * YNL125C (from Compara)
    110   * YNL298W (from Compara) WHY IS THIS MAPPING HERE>=?
    111   * YOL119C (from Compara)
    112   * YOR079C (from Compara)
    113   * YOR306C (from Compara)
    114   * YPL147W (from Compara)
    115   * YPR021C (from Compara)
    116   * YPR192W  AQY1 (from Compara)
    117   * PXA2 YKL188C (possible human ABCD4)
    118  
    119 
    120  ===  transcription and chromatin remodelleing complexes CHRAC and isw1-2 complexes ===
    121 
    122   * ITC1  YGL133W CHRAC complex isw1-a  complex (human BAZ1A,B) (no compara)
    123   * YPL216W ITC1 paralog (uncharacterised) (human BAZ1A,B) (no compara)
    124   * IOC3 YFR013W isw1-a (PWWP domain) (no compara REMOVE?)
    125   * IOC4 YMR044W isw1-b (PWWP domain) (no compara REMOVE?)
    126   * HHO1 YPL127C histone H1  (human  H1F0) 
    127   * YCL055W (from Compara)
    128   * YDR440W (from Compara)
    129   * YGL096W (from Compara)
    130   * YGL254W (from Compara)
    131   * YGR040W (from Compara)
    132   * YJL056C (from Compara)
    133   * YER040W (from Compara)
    134   * YKR034W (from Compara)
    135   * YKR099W (from Compara)
    136   * YMR164C (from Compara)
    137   * YNL239W (from Compara)
    138   * YPL177C (from Compara)
    139 
    140  == chromosome organization ==
    141   * ISW1 YBR245C isw1-a/b  complex amily  confirmed by compara (FP?)
    142   * ISW2  YOR304W CHRAC complex family  confirmed by compara (FP?)
    143   * YDR096W (from Compara)
    144   * HOS1 YPR068C (from Compara)
    145 
    146   === nucleocytoplsmic transport  ===
    147 
    148   * YKL068W (from Compara) (checked)
    149   * YMR047C (from Compara) (checked)
    150   * YNL298W (from Compara) (checked)
    151 
    152   === DNA recombination ===
    153 
    154   * YBR186W (from Compara)
    155   * YDL154W  (from Compara)
    156   * YFL003C (from Compara)
    157   * YFR038W (from Compara)
    158   * YGL251C (from Compara)
    159   * YPL164C (from Compara)
    160 
    161  === repair ===
    162 
    163   * YFL007W this isn't repair, cant figure why its mapping here
    164   * YOR386W  (from Compara)
    165   * YDR054C  (from Compara)
    166   * YGR109C (from Compara)
    167   * OGG1 YML060W "CBF3 complex"  base excision repair protein (human OGG1)
    168 
    169   === replication ===
    170  
    171   * YDL101C (from Compara)
    172  
    173  === mitotoic cell cycle regulation=== (does not map here)
    174  
    175   * YPR120C (from Compara)
    176 
    177  === tRNA metabolic process ===
    178  
    179   * TRM3  YDL112W (from Compara) checked
    180   * PUS6 YGR169C (from Compara) checked
    181   * RNY1  YPL123C (no compara)
    182 
    183   ===  meotic cell cycle -===
    184  
    185   * YIL112W (from Compara)  check classification
    186  
    187  
    188   === signalling ===
    189 
    190   * YBR164C (from Compara)
    191   * YBR264C (from Compara)
    192   * YDL159W (from Compara)
    193   * YDR006C (from Compara)
    194   * YDR294C (from Compara)
    195   * YDR466W (from Compara)
    196   * YPL051W (from Compara)
    197   *  YOR212W (from Compara) not annotated to signalling
    198   * YGR152C (from Compara)
    199   * YKL092C (from Compara) not annotated to signalling
    200   * 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)
    201  
    202  === Mitochondrial ===
    203 
    204   * COX23 YHR116w http://www.pantherdb.org/panther/family.do?clsAccession=PTHR13626 (has human) (no compara)
    205   * TOM6 YOR045W  this paper links budding yeast to human, no pombe yet http://www.ncbi.nlm.nih.gov/pubmed/18331822 (no compara)
    206 
    207   === proteases ===
    208 
    209   * YCR045C (from Compara) (REMOVE?)
    210  
    211  === proteasome assembly ===
    212 
    213   * YGL004C (from Compara)
    214 
    215   === misc ===
    216   move to above (in list)
    217   * YPC1 YBR183W paralog YDC1 (conserved in human ACER3) (no compara)
    218   * YDC1 YPL087W paralog YPC1  (conserved in human ACER3) (no compara)
    219   * SRN2 YLR119W Component of the ESCRT-I complex  (no compara)
    220   * KXD1 YGL079W BLOC-1 complex (conserved in human KXD1)
    221   * SNN1 YNL086W  BLOC-1 complex (conserved in human SNAPIN & BLOC1S6)
    222   === Unknown process ===
    223  
    224  * AML1  YGR001C adenine methyltransferase, has human, (conserved in human  N6AMT2) http://pfam.xfam.org/family/PF10237?type=Family#tabview=tab7
    225  
    226   === Compara false positive ===
    227  
    228   * YLR087C (Compara false positive - yeast specific protein)
    229   * YGR023W fugal sepecific  (low complexity)
    230   * YMR068W  false positive fungal only ankyrin repeat
    231   * YLR332W  fungal only  serine rich
    232   * YOR195W fungal only http://pfam.xfam.org/family/PF12709?type=Family#tabview=tab7
    233   * YDR235W http://www.pantherdb.org/panther/family.do?clsAccession=PTHR17204:SF23
    234   * YNL016W http://www.pantherdb.org/panther/family.do?clsAccession=PTHR24622:SF45
    235   * YIR019C
    236   * YDR054C delete  is conserved in pombe
    237   * YDR519W domain only, check
    238   * YML078W domain only, check
    239   * removed from list to here
    240 
    241 to check:
    242   * YDL122W candidate for pombe  Ubp11 http://www.pantherdb.org/panther/family.do?clsAccession=PTHR24006:SF412
    243   * YJL073W possible fp, dnaj 
    244   * FPS1 YLL043W (not sure about this)
    245 
    246 
    2473 
    2484