Changes between Version 50 and Version 51 of OrthologInventoriesNoPom


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Timestamp:
Oct 2, 2014, 4:20:23 PM (6 years ago)
Author:
vw253
Comment:

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  • OrthologInventoriesNoPom

    v50 v51  
    11
    22 == Known pombe gene losses ==
     3
     4=== Lipid metabolic process (mainly fatty acid oxidation?) ===
     5 
     6  * YAT1 YAR035W carnitine O-acetyltransferase (conserved in human, CPT2)
     7  * YBR041W (from compara)
     8  * EHT1 YBR177c medium-chain fatty acid metabolic process
     9  * YDR096W (from Compara)
     10  * YDR287W (from Compara)
     11  * YDR294C (from Compara)
     12  * FAA2 YER015W (human ACSL1,5,6 ?)
     13  * POX1  YGL205W (human candidates ACOX1 and 2)
     14  * YHR046C  (from Compara)
     15  * POT1 (FOX3)  YIL160C
     16  * YJL153C (from Compara)
     17  * TES1 YJR019C  (conserved in human, ACOT8)
     18  * YLR118C (from Compara)
     19  * ECI1 YLR284C  (conserved in human, PECI)
     20  * CAT2 YML042W  (conserved in human, CRAT)
     21  * YMR210W similar to EEB1 and EHT1 medium-chain fatty acid metabolic process
     22  * DCI1  YOR180C (conserved in human, PECI)
     23  * YPL069C
     24  * EEB1 YPL095c medium-chain fatty acid ethyl ester biosynthesis during fermentation
     25  * YPL103C
     26  * TAZ1 YPR140W TAfaZzin (conserved in human , TAZ)
     27 
     28
     29=== TMA (translation machinery associated) ===
     30
     31  * TMA64 YDR117C (conserved in 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 ( conserved in 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)
     42  * YGR152C (from Compara)
     43  * YIR027C (from Compara)
     44  * YKL088W (from Compara)
     45  * YKL092C (from Compara)
     46  * YKR072C (from Compara)
     47  * YLR422W (from Compara)
     48 * YOL059W (from Compara)
     49 * YOL075C (from Compara)
     50 * YOL081W (from Compara)
     51 * YOR054C (from Compara)
     52 * YOR212W (from Compara)
     53 * YPL147W (from Compara)
     54 * YPR140W (from Compara)
     55
     56=== Tryptophan degradation/ de novo NAD biosynthesis ===
     57
     58  * BNA1 YJR025c tryptophan met 3-hydroxyanthranilate 3,4-dioxygenase activity (conserved in human HAAO)
     59  * BNA2 YJR078W tryptophan 2,3-dioxygenase activity (conserved in human IDO2)
     60  * BNA4 YBL098W tryptophan met kynurenine 3-monooxygenase (conserved in human, KMO)
     61  * BNA5 YLR231C tryptophan met  kynureninase (conserved in human, KYNU)
     62  * BNA6 YFR047C biosynthesis of NAD from tryptophan via kynurenine  (conserved in human, QPRT) (missing from compara)
     63
     64=== Carbohydrate metabolic process ===
     65
     66  * YDL174C (from Compara)
     67  * YDR109C (from Compara)
     68  * YHL032C (from Compara)
     69  * YHR104W (from Compara)
     70  * YHR210C (from Compara)
     71  * YMR164C (from Compara)
     72  * YNR071C (from Compara)
     73  * YPR026W (from Compara)
     74
     75=== subset of carbohydrate , Glycogen metabolism ===
     76
     77  * GLC3 YEL011W glycogen branching enzyme (conserved in human GBE1)
     78  * GSY1 YFR015C (conserved in human GYS1)
     79  * GLG2 YJL137C 
     80  * GLG1 YKR058W 
     81 * GSY2 YLR258W (conserved in human GYS1)
     82  * GPH1 YPR160W glycogen debranching enzyme (conserved in human PYGB)
     83  * GDB1 YPR184W glycogen debranching enzyme (conserved in human AGL)
     84 
     85  * FPS1 YLL043W (not sure about this)
    386
    487 === misc ===
     
    689  * YAT1 YAR035W carnitine O-acetyltransferase (conserved in human, CPT2)
    790  * CYS4 YGR155W cystathionine beta-synthase (conserved in human, CBS)
    8   * TAZ1 YPR140W TAfaZzin (conserved in human , TAZ)
    991  * YPC1 YBR183W paralog YDC1 (conserved in human ACER3)
    1092  * YDC1 YPL087W paralog YPC1  (conserved in human ACER3)
     
    1799  * SRN2 YLR119W Component of the ESCRT-I complex
    18100
    19  === TMA (translation machinery associated) ===
    20 
    21   * TMA64 YDR117C (conserved in human, LGTN)
    22   * 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
    23   * STF2 YGR008C  TMA10 paralog ( conserved in human SERBP1)
    24   * TMA10 YLR327C STF2 paralog ( conserved in human SERBP1)
    25  
    26   === Glycogen metabolism ===
    27 
    28   * GLC3 YEL011W glycogen branching enzyme (conserved in human GBE1)
    29   * GDB1 YPR184W glycogen debranching enzyme (conserved in human AGL)
    30   * GPH1 YPR160W glycogen debranching enzyme (conserved in human PYGB)
    31   * GSY1 YFR015C (conserved in human GYS1)
    32   * GSY2 YLR258W (conserved in human GYS1)
    33   * FPS1 YLL043W (not sure about this)
    34   * GLG1 YKR058W  (not sure about this)
    35   * GLG2 YJL137C  (not sure about this)
    36 
    37101  === Mitochondrial ===
    38102
     
    40104  * TOM6 (small)  this paper links budding yeast to human, no pombe yet http://www.ncbi.nlm.nih.gov/pubmed/18331822
    41105
    42  === Tryptophan degradation/ de novo NAD biosynthesis ===
    43 
    44   * BNA1 YJR025c tryptophan met 3-hydroxyanthranilate 3,4-dioxygenase activity (conserved in human HAAO)
    45   * BNA2 YJR078W tryptophan 2,3-dioxygenase activity (conserved in human IDO2)
    46   * BNA4 YBL098W tryptophan met kynurenine 3-monooxygenase (conserved in human, KMO)
    47   * BNA5 YLR231C tryptophan met  kynureninase (conserved in human, KYNU)
    48   * BNA6 YFR047C biosynthesis of NAD from tryptophan via kynurenine  (conserved in human, QPRT)
    49106
    50107 === peroxisomal proteins and  components of the fatty acid oxidation pathway
    51108
    52   * PXA2 YKL188C (possible human ABCD4)
    53   * POX1  YGL205W (human candidates ACOX1 and 2)
    54   * DCI1  YOR180C (conserved in human, PECI)
    55   * ECI1 YLR284C  (conserved in human, PECI)
    56   * FAA2 YER015W (human ACSL1,5,6 ?)
    57   * TES1 YJR019C  (conserved in human, ACOT8)
    58   * CAT2 YML042W  (conserved in human, CRAT)
    59 
    60   * EEB1 YPL095c medium-chain fatty acid ethyl ester biosynthesis during fermentation
    61   * EHT1 YBR177c medium-chain fatty acid metabolic process
    62   * YMR210W similar to EEB1 and EHT1 medium-chain fatty acid metabolic process
    63   * POT1 (FOX3)  YIL160C
     109  * PXA2 YKL188C (possible human ABCD4)
    64110  * SPS19 YNL202W SPAC922.06
    65111