Version 40 (modified by 7 years ago) (diff) | ,
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Known pombe gene losses
misc
- YAT1 YAR035W carnitine O-acetyltransferase (conserved in human, CPT2)
- CYS4 YGR155W cystathionine beta-synthase (conserved in human, CBS)
- TAZ1 YPR140W TAfaZzin (conserved in human , TAZ)
- YPC1 YBR183W paralog YDC1 (conserved in human ACER3)
- YDC1 YPL087W paralog YPC1 (conserved in human ACER3)
- HHO1 YPL127C histone H1 (conserved in human H1F0)
- AML1 adenine methyltransferase, has human, (conserved in human N6AMT2) http://pfam.xfam.org/family/PF10237?type=Family#tabview=tab7
- 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)
- OGG1 YML060W "CBF3 complex" base excision repair protein (conserved in human OGG1)
- TMA64 YDR117C (conserved in 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
to check:
- SRN2 YLR119W Component of the ESCRT-I complex
Glycogen metabolism
- GLC3 YEL011W glycogen branching enzyme (conserved in human GBE1)
- GDB1 YPR184W glycogen debranching enzyme (conserved in human AGL)
- GPH1 YPR160W glycogen debranching enzyme (conserved in human PYGB)
- GSY1 YFR015C (conserved in human GYS1)
- GSY2 YLR258W (conserved in human GYS1)
- FPS1 YLL043W (not sure about this)
- GLG1 YKR058W (not sure about this)
- GLG2 YJL137C (not sure about this)
Mitochondrial
- COX23 yhr116w http://www.pantherdb.org/panther/family.do?clsAccession=PTHR13626 (has human)
- TOM6 (small) this paper links budding yeast to human, no pombe yet http://www.ncbi.nlm.nih.gov/pubmed/18331822
Tryptophan degradation/ de novo NAD biosynthesis
- BNA1 YJR025c tryptophan met 3-hydroxyanthranilate 3,4-dioxygenase activity (conserved in human HAAO)
- BNA2 YJR078W tryptophan 2,3-dioxygenase activity (conserved in human IDO2)
- BNA4 YBL098W tryptophan met kynurenine 3-monooxygenase (conserved in human, KMO)
- BNA5 YLR231C tryptophan met kynureninase (conserved in human, KYNU)
- BNA6 YFR047C biosynthesis of NAD from tryptophan via kynurenine (conserved in human, QPRT)
peroxisomal proteins and components of the fatty acid oxidation pathway
- PXA2 YKL188C (possible human ABCD4)
- POX1 YGL205W (human candidates ACOX1 and 2)
- DCI1 YOR180C (conserved in human, PECI)
- ECI1 YLR284C (conserved in human, PECI)
- FAA2 YER015W (human ACSL1,5,6 ?)
- TES1 YJR019C (conserved in human, ACOT8)
- CAT2 YML042W (conserved in human, CRAT)
- EEB1 YPL095c medium-chain fatty acid ethyl ester biosynthesis during fermentation
- EHT1 YBR177c medium-chain fatty acid metabolic process
- YMR210W similar to EEB1 and EHT1 medium-chain fatty acid metabolic process
- POT1 (FOX3) YIL160C
- SPS19 YNL202W SPAC922.06
Autophagy and vesicle transport
- ATG21 YPL100W
- ATG23 YLR431C
- ATG27 YJL178C
BLOC1 complex (involved in endosomal maturation)
- KXD1 YGL079W BLOC-1 complex (conserved in human KXD1)
- CNL1 YDR357C BLOC-1 complex
- VAB2 YEL005C ( NONE immediately detected but most likely conserved)
- BLI1 YKL061W ( NONE immediately detected but most likely conserved)
- BLS1 YLR408C ( NONE immediately detected but most likely conserved)
- SNN1 YNL086W
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
May be conserved but not yet detected
to check:
- STE18 YJR086W gamma subunit of G protein (check)
- YJL055W involved in the metabolism of purine and pyrimidine base analogues
- YDl156W (WD repeat)
- YGR008C
- FUN26 YAL022C
- DLS1 YJL065C DSL1 complex
- ITC1 YGL133W CHRAC complex
- ISW1 YBR245C isw1-a complex
- ISW2 YOR304W CHRAC complex
- HPA2 YPL123C
- 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)
- there are also 64 essential genes in budding yeast which do not appear to have a fission yeast ortholog
Examples of distant orthologs not picked up by most ortholog predictors
- Sfr1 / MEI5 http://pfam.sanger.ac.uk/family/PF10376 (conserved to human)
- Rum1 / SIC1
- ipk1 / IPK1 (orthoMcl only)
- orc6 / ORC6 pfam.sanger.ac.uk/family/PF05460
- APC13 / YDR260C http://pfam.sanger.ac.uk/protein/O74358
- SPCC622.10c -> A. gossypii AGL158C (fasta) which is is syntentic ortholog of S. cerevisiae YDR166C
- rrn10/ RRN10 (small) (fungal only) http://pfam.sanger.ac.uk/family/PF05234
- SPCC553.01c/ YGR042W (to human) http://pfam.sanger.ac.uk/family/PF10382
- Sds3 /YIL084C (KOGS only) http://pfam.sanger.ac.uk/family/PF08598
- Swi5/SAE3 http://pfam.sanger.ac.uk/family/PF07061
- Sus1/SUS1 (OrthoMcl? only) http://pfam.sanger.ac.uk/family/PF10163
- Mediator complex subunits (add details)
- Atp15/ATP15 (KOGS only) http://pfam.sanger.ac.uk/family/PF04627
- SPCC297.06c / YKL142W http://pfam.sanger.ac.uk/family/PF07957
- See also ortholog table releases