Changes between Version 66 and Version 67 of OrthologInventoriesNoPom


Ignore:
Timestamp:
Oct 3, 2014, 1:50:01 PM (6 years ago)
Author:
vw253
Comment:

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  • OrthologInventoriesNoPom

    v66 v67  
    2424  * YPL103C
    2525  * TAZ1 YPR140W TAfaZzin (human , TAZ)
     26  * SPS19 YNL202W SPAC922.06 http://www.pantherdb.org/panther/family.do?clsAccession=PTHR24315:SF0 (no coompara)
    2627 
    2728
     
    3435
    3536
    36 === nucleobase containing small molecule met  ===
     37 === nucleobase containing small molecule met  ===
    3738
    3839  * YBR140C (from Compara)
     
    4344  * YKR072C (from Compara) CoA-synthesizing protein complex
    4445  * YLR422W (from Compara)
    45  * YOL059W (from Compara)
    46  * YOL075C (from Compara)
    47  * YOL081W (from Compara)
    48  * YOR054C (from Compara)
    49  * YPL147W (from Compara)
    50  * YPR140W (from Compara)
    51 
    52  === Tryptophan degradation/ de novo NAD biosynthesis ===
     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 ===
    5354
    5455  * BNA1 YJR025c tryptophan met 3-hydroxyanthranilate 3,4-dioxygenase activity (human HAAO)
     
    5859  * BNA6 YFR047C biosynthesis of NAD from tryptophan via kynurenine  (human QPRT) (missing from compara)
    5960
    60  === Other cellular amino acid/derivative  metabolic process ===
    61  
    62  ==== urea metabolism ====
    63 
    64   * YBR208C (from Compara)
    65  
    66 
     61  === Other cellular amino acid/derivative  metabolic process ===
     62 
    6763  * YAL012W (from Compara)
    6864  * YCL064C (from Compara)
     
    7167  * YNL040W possible FP (from Compara)
    7268  * CYS4 YGR155W cystathionine beta-synthase (human CBS)
     69
     70  ==== urea metabolism ====
     71
     72  * YBR208C (from Compara)
    7373
    7474 === Carbohydrate metabolic process ===
     
    115115  * YPR021C (from Compara)
    116116  * YPR192W  AQY1 (from Compara)
    117 
    118  ===  trancription and chromatin remodelleing complexes CHRAC and isw1-2 complexes ===
     117  * PXA2 YKL188C (possible human ABCD4)
     118 
     119
     120 ===  transcription and chromatin remodelleing complexes CHRAC and isw1-2 complexes ===
    119121
    120122  * ITC1  YGL133W CHRAC complex isw1-a  complex (human BAZ1A,B) (no compara)
     
    177179  * TRM3  YDL112W (from Compara) checked
    178180  * PUS6 YGR169C (from Compara) checked
     181  * RNY1  YPL123C (no compara)
    179182
    180183  ===  meotic cell cycle -===
     
    195198  * YGR152C (from Compara)
    196199  * 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)
    197206
    198207  === proteases ===
    199208
    200   * YCR045C (from Compara) (REMOVE)
     209  * YCR045C (from Compara) (REMOVE?)
    201210 
    202211 === proteasome assembly ===
     
    204213  * YGL004C (from Compara)
    205214
    206 
     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 
    207226  === Compara false positive ===
    208227 
     
    214233  * YDR235W http://www.pantherdb.org/panther/family.do?clsAccession=PTHR17204:SF23
    215234  * YNL016W http://www.pantherdb.org/panther/family.do?clsAccession=PTHR24622:SF45
    216  * YIR019C
    217  
    218   * YDL122W candidate for pombe  Ubp11 http://www.pantherdb.org/panther/family.do?clsAccession=PTHR24006:SF412
     235  * YIR019C
    219236  * YDR054C delete  is conserved in pombe
    220237  * YDR519W domain only, check
    221238  * YML078W domain only, check
    222 
    223 
    224 
    225  === misc ===
    226  
    227   * YPC1 YBR183W paralog YDC1 (conserved in human ACER3)
    228   * YDC1 YPL087W paralog YPC1  (conserved in human ACER3)
    229   * AML1  YGR001C adenine methyltransferase, has human, (conserved in human  N6AMT2) http://pfam.xfam.org/family/PF10237?type=Family#tabview=tab7
    230   * 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)
    231   * YJL073W possible fp, dnaj
     239  * removed from list to here
    232240
    233241to check:
    234   * SRN2 YLR119W Component of the ESCRT-I complex
     242  * YDL122W candidate for pombe  Ubp11 http://www.pantherdb.org/panther/family.do?clsAccession=PTHR24006:SF412
     243  * YJL073W possible fp, dnaj 
    235244  * FPS1 YLL043W (not sure about this)
    236245
    237   === Mitochondrial ===
    238 
    239   * COX23 YHR116w http://www.pantherdb.org/panther/family.do?clsAccession=PTHR13626 (has human)
    240   * TOM6 (small)  this paper links budding yeast to human, no pombe yet http://www.ncbi.nlm.nih.gov/pubmed/18331822
    241 
    242 
    243  === peroxisomal proteins and  components of the fatty acid oxidation pathway
    244 
    245   * PXA2 YKL188C (possible human ABCD4)
    246   * SPS19 YNL202W SPAC922.06
    247 
    248  === BLOC1 complex (involved in endosomal maturation)  ===   
    249 
    250   * KXD1 YGL079W BLOC-1 complex (conserved in human KXD1)
    251   * SNN1 YNL086W  BLOC-1 complex (conserved in human SNAPIN & BLOC1S6)
    252   * CNL1 YDR357C BLOC-1 complex  ( NONE detected but most likely conserved)
    253   * VAB2 YEL005C  BLOC-1 complex  ( NONE detected but most likely conserved)
    254   * BLI1 YKL061W  BLOC-1 complex ( NONE detected but most likely conserved)
    255   * BLS1 YLR408C  BLOC-1 complex  ( NONE  detected but most likely conserved)
    256  
    257  Other human members SNAP25,47, BLOC1S1,2,3,4,5  SYX12,DTNBP1, K7ELZO, PI4K2A
    258 
    259  === biotin synthesis enzymes ===
    260  
    261 check bio1,5,6,7,8
    262   * BIO4 YNR057C
    263   * BIO3 YNR058W
    264   * BIO5 YNR056C
    265   * BIO6 YAR069W-A (NOT IN 288C)
    266   * BIO7 YHR214W-G (NOT IN 288C) pseudogenic, highly degraded
    267   * BIO8 YHR214W-F  (NOT IN 288C) pseudogenic, highly degraded
    268 
    269  ==  To check==
    270 
    271   * DLS1 YJL065C   DSL1 complex http://www.pantherdb.org/panther/family.do?clsAccession=PTHR10252 with YBR278w
     246
     247 
     248
     249
     250  ==  Yeast/ ascomycete specific complex members May be conserved but not yet detected ==
     251
    272252  * STE18 YJR086W gamma subunit of G protein (check)
    273   * YJL055W involved in the metabolism of purine and pyrimidine base analogues
    274   * YDl156W (WD repeat)
    275   * HPA2 YPL123C
    276 
    277   ==  Yeast/ ascomycete specific complex members May be conserved but not yet detected ==
    278 
    279253  * MGR1 YCL044C iAAA protease complex subunit (saccharomycetes only)
    280254  * RSF1 YMR030W (yeast only)