title: KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome.
abstract: BACKGROUND
  Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics.
  
  
  METHODS
  Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics.
  
  
  CONCLUSIONS
  We advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of evolutionary, developmental, metabolic, and environmental perspectives.
authors.affiliation: Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia.
authors.forename: Walter C
authors.initials: WC
authors.lastname: Dunlap
authors.forename: Antonio
authors.initials: A
authors.lastname: Starcevic
authors.forename: Damir
authors.initials: D
authors.lastname: Baranasic
authors.forename: Janko
authors.initials: J
authors.lastname: Diminic
authors.forename: Jurica
authors.initials: J
authors.lastname: Zucko
authors.forename: Ranko
authors.initials: R
authors.lastname: Gacesa
authors.forename: Madeleine Jh
authors.initials: MJ
authors.lastname: van Oppen
authors.forename: Daslav
authors.initials: D
authors.lastname: Hranueli
authors.forename: John
authors.initials: J
authors.lastname: Cullum
authors.forename: Paul F
authors.initials: PF
authors.lastname: Long
mesh_terms: D022126:Access to Information; D000818:Animals; D037421:Anthozoa / Q000235:genetics*; D003247:Conservation of Natural Resources; D057894:Coral Reefs; D057225:Data Mining; D030541:Databases, Genetic; D020407:Internet; D058977:Molecular Sequence Annotation / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid
references.citation: Mol Biol Evol. 2012 Aug;29(8):2019-29
references.pmid: 22337864
references.citation: PLoS One. 2009 Nov 25;4(11):e7509
references.pmid: 19946629
references.citation: Chemosphere. 2002 Jun;47(10):1059-64
references.pmid: 12137038
references.citation: Cell Stress Chaperones. 2009 Sep;14(5):469-76
references.pmid: 19214783
references.citation: Mol Cell Biol. 2011 Mar;31(5):1076-87
references.pmid: 21189285
references.citation: Biochem J. 2004 May 1;379(Pt 3):563-72
references.pmid: 14733615
references.citation: Cell Microbiol. 2009 Dec;11(12):1735-49
references.pmid: 19650828
references.citation: J Cell Biol. 1981 Dec;91(3 Pt 2):107s-124s
references.pmid: 6459326
references.citation: Microbiol Rev. 1995 Dec;59(4):604-22
references.pmid: 8531888
references.citation: Philos Trans R Soc Lond B Biol Sci. 2012 Jun 19;367(1596):1733-45
references.pmid: 22566679
references.citation: Mar Biotechnol (NY). 2009 Nov-Dec;11(6):771-85
references.pmid: 19459008
references.citation: Proc Natl Acad Sci U S A. 1999 May 25;96(11):5894-6
references.pmid: 10339513
references.citation: Comp Biochem Physiol B Biochem Mol Biol. 2009 Mar;152(3):249-59
references.pmid: 19110066
references.citation: Mol Biol Evol. 2012 Oct;29(10):3095-109
references.pmid: 22496439
references.citation: Biochem Biophys Res Commun. 1993 Feb 15;190(3):786-93
references.pmid: 8094957
references.citation: Ecology. 2009 Oct;90(10):2859-67
references.pmid: 19886494
references.citation: Science. 2007 Jul 6;317(5834):86-94
references.pmid: 17615350
references.citation: Dev Genes Evol. 2005 May;215(5):268-73
references.pmid: 15702325
references.citation: Proc Natl Acad Sci U S A. 1982 May;79(10):3162-6
references.pmid: 6285339
references.citation: Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14250-5
references.pmid: 12384570
references.citation: Nat Rev Neurosci. 2003 Aug;4(8):617-27
references.pmid: 12894237
references.citation: Mol Biol Evol. 2008 Apr;25(4):664-72
references.pmid: 18184723
references.citation: Environ Sci Technol. 2006 Nov 1;40(21):6537-46
references.pmid: 17144275
references.citation: Mol Cell. 2000 Aug;6(2):349-60
references.pmid: 10983982
references.citation: Dev Neurobiol. 2009 Mar;69(4):235-54
references.pmid: 19170043
references.citation: J Biol Chem. 1994 Jul 22;269(29):18723-6
references.pmid: 8034623
references.citation: J Immunol. 1996 May 1;156(9):3107-10
references.pmid: 8617930
references.citation: Mol Biol Cell. 2007 Sep;18(9):3463-71
references.pmid: 17596510
references.citation: Mol Microbiol. 2001 Mar;39(6):1572-84
references.pmid: 11260474
references.citation: BMC Genomics. 2009 Dec 23;10:627
references.pmid: 20030803
references.citation: Mar Pollut Bull. 2005 Feb;50(2):125-46
references.pmid: 15737355
references.citation: Dev Biol. 2009 Aug 1;332(1):2-24
references.pmid: 19465018
references.citation: Nat Rev Genet. 2011 Nov 15;13(1):7-13
references.pmid: 22083101
references.citation: Annu Rev Microbiol. 2012;66:325-47
references.pmid: 22746333
references.citation: J Biol Chem. 2010 Oct 15;285(42):31995-2002
references.pmid: 20685656
references.citation: Biochem Biophys Res Commun. 2004 Nov 19;324(3):1024-33
references.pmid: 15485657
references.citation: Annu Rev Pharmacol Toxicol. 2005;45:51-88
references.pmid: 15822171
references.citation: Appl Environ Microbiol. 2007 Apr;73(8):2673-81
references.pmid: 17308179
references.citation: J Infect Dis. 1990 Apr;161(4):626-33
references.pmid: 2181029
references.citation: Genome Biol. 2007;8(10):R226
references.pmid: 17958905
references.citation: Cell. 2012 Jan 20;148(1-2):24-8
references.pmid: 22265398
references.citation: Integr Comp Biol. 2010 Oct;50(4):662-74
references.pmid: 21558231
references.citation: Trends Genet. 2010 Apr;26(4):154-8
references.pmid: 20129693
references.citation: Nat Rev Mol Cell Biol. 2006 Sep;7(9):631-43
references.pmid: 16912714
references.citation: Comp Biochem Physiol A Mol Integr Physiol. 2007 Jan;146(1):9-25
references.pmid: 17101286
references.citation: J Biol Chem. 1997 Sep 19;272(38):23469-72
references.pmid: 9295278
references.citation: Environ Microbiol. 2008 Sep;10(9):2277-86
references.pmid: 18479440
references.citation: Nature. 1989 Aug 10;340(6233):467-8
references.pmid: 2755508
references.citation: Philos Trans R Soc Lond B Biol Sci. 2010 Feb 27;365(1540):671-8
references.pmid: 20083641
references.citation: Dev Comp Immunol. 2011 Oct;35(10):1098-101
references.pmid: 21527282
references.citation: Science. 2006 May 12;312(5775):857-8
references.pmid: 16690848
references.citation: J Biol Chem. 2003 May 2;278(18):16151-8
references.pmid: 12594219
references.citation: PLoS One. 2012;7(12):e47866
references.pmid: 23236347
references.citation: J Phys Chem A. 2009 Apr 23;113(16):4060-7
references.pmid: 19317477
references.citation: RNA Biol. 2010 May-Jun;7(3):276-81
references.pmid: 20484980
references.citation: Virology. 1991 Jul;183(1):1-11
references.pmid: 1711253
references.citation: Nature. 2011 Jul 24;476(7360):320-3
references.pmid: 21785439
references.citation: Mol Syst Biol. 2011 Oct 11;7:539
references.pmid: 21988835
references.citation: Mol Microbiol. 2003 Sep;49(5):1333-45
references.pmid: 12940991
references.citation: Genome Biol. 2007;8(4):R59
references.pmid: 17437634
references.citation: Nat Rev Microbiol. 2003 Nov;1(2):137-49
references.pmid: 15035043
references.citation: Curr Genet. 1997 Mar;31(3):235-40
references.pmid: 9065386
references.citation: Plant Physiol. 2006 Jun;141(2):312-22
references.pmid: 16760481
references.citation: Dis Aquat Organ. 2009 Nov 16;87(1-2):67-78
references.pmid: 20095242
references.citation: Mar Pollut Bull. 2005;51(5-7):507-23
references.pmid: 16115654
references.citation: Plant Cell Physiol. 2008 Apr;49(4):641-52
references.pmid: 18308760
references.citation: Nat Struct Biol. 2002 Apr;9(4):239-41
references.pmid: 11914728
references.citation: Science. 2011 Nov 11;334(6057):806-9
references.pmid: 22076378
references.citation: Aquat Toxicol. 2007 Nov 15;85(1):48-56
references.pmid: 17804091
references.citation: Zoology (Jena). 2003;106(2):109-16
references.pmid: 16351896
references.citation: Biol Bull. 2005 Feb;208(1):3-6
references.pmid: 15713806
references.citation: J Gen Virol. 2008 Oct;89(Pt 10):2359-2376
references.pmid: 18796704
references.citation: Biol Bull. 1990 Apr;178(2):175-186
references.pmid: 29314935
references.citation: Cell Mol Life Sci. 2006 Nov;63(22):2560-70
references.pmid: 16952052
references.citation: Mol Biol Evol. 2006 Jul;23(7):1437-43
references.pmid: 16675503
references.citation: Development. 2011 Jan;138(2):303-15
references.pmid: 21177343
references.citation: J Immunol. 2006 Jan 1;176(1):401-15
references.pmid: 16365434
references.citation: Trends Plant Sci. 2010 Jan;15(1):11-22
references.pmid: 19910236
references.citation: Environ Microbiol. 2010 May;12(5):1105-21
references.pmid: 20105222
references.citation: J Bacteriol. 1993 Nov;175(21):6737-44
references.pmid: 8226614
references.citation: Biochimie. 2007 Jun-Jul;89(6-7):812-8
references.pmid: 17570575
references.citation: PLoS Biol. 2007 Jun;5(6):e124
references.pmid: 17488183
references.citation: Biol Open. 2012 Feb 15;1(2):75-81
references.pmid: 23213399
references.citation: Adv Exp Med Biol. 2010;708:1-16
references.pmid: 21528690
references.citation: Curr Biol. 2007 Apr 17;17(8):706-10
references.pmid: 17379523
references.citation: Chembiochem. 2013 Aug 19;14(12):1407-9
references.pmid: 23821453
references.citation: Proc Natl Acad Sci U S A. 2004 Sep 21;101(38):13927-32
references.pmid: 15347812
references.citation: Mar Pollut Bull. 2003 Feb;46(2):187-96
references.pmid: 12586114
references.citation: Science. 1990 May 11;248(4956):705-11
references.pmid: 2185544
references.citation: Nature. 2005 Sep 29;437(7059):681-6
references.pmid: 16193043
references.citation: Annu Rev Microbiol. 2008;62:93-111
references.pmid: 18429691
references.citation: Chembiochem. 2012 Mar 5;13(4):531-3
references.pmid: 22278966
references.citation: Cell. 2011 Apr 29;145(3):423-34
references.pmid: 21496894
references.citation: J Exp Biol. 2011 Jan 15;214(Pt 2):303-11
references.pmid: 21177950
references.citation: Mar Biotechnol (NY). 2011 Oct;13(5):992-1002
references.pmid: 21318259
references.citation: Ecol Appl. 2010 Apr;20(3):840-50
references.pmid: 20437968
references.citation: Aquat Toxicol. 2009 Jul 26;93(4):188-95
references.pmid: 19501419
references.citation: ISME J. 2007 Oct;1(6):492-501
references.pmid: 18043651
references.citation: Cell. 1997 Jun 27;89(7):1067-76
references.pmid: 9215629
references.citation: Sci Total Environ. 2000 Mar 20;247(2-3):313-32
references.pmid: 10803558
references.citation: J Appl Toxicol. 2013 Dec;33(12):1407-15
references.pmid: 22886929
references.citation: Biochem Biophys Res Commun. 2005 Dec 23;338(3):1607-16
references.pmid: 16288726
references.citation: Nature. 2010 May 6;465(7294):110-4
references.pmid: 20400946
references.citation: Proc Natl Acad Sci U S A. 1997 Sep 30;94(20):10541-6
references.pmid: 9380671
references.citation: Biochemistry. 2008 Dec 9;47(49):13004-15
references.pmid: 19006326
references.citation: Science. 1998 Sep 4;281(5382):1519-23
references.pmid: 9727980
references.citation: J Exp Biol. 2005 Jun;208(Pt 11):2157-65
references.pmid: 15914659
references.citation: J Biol Chem. 1996 Aug 23;271(34):20399-405
references.pmid: 8702776
references.citation: Annu Rev Genet. 1988;22:631-77
references.pmid: 2853609
references.citation: PLoS One. 2007 Jan 24;2(1):e153
references.pmid: 17252055
references.citation: Mol Ecol. 2008 Sep;17(17):3952-71
references.pmid: 18662230
references.citation: Proc Natl Acad Sci U S A. 1992 Nov 1;89(21):10449-53
references.pmid: 1438232
references.citation: Comp Biochem Physiol C Toxicol Pharmacol. 2012 Mar;155(2):275-80
references.pmid: 21963688
references.citation: Cell. 1997 Apr 4;89(1):149-58
references.pmid: 9094723
references.citation: Trends Biochem Sci. 2006 May;31(5):243-7
references.pmid: 16595176
references.citation: J Biol Chem. 2002 Oct 11;277(41):38294-304
references.pmid: 12161444
references.citation: Annu Rev Physiol. 2005;67:225-57
references.pmid: 15709958
references.citation: Cell. 2005 Sep 9;122(5):669-82
references.pmid: 16125763
references.citation: Microbiol Mol Biol Rev. 2012 Jun;76(2):229-61
references.pmid: 22688813
references.citation: ISME J. 2007 May;1(1):78-91
references.pmid: 18043616
references.citation: Diabetes. 2009 Feb;58(2):344-51
references.pmid: 19008341
references.citation: Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):11013-8
references.pmid: 15256601
references.citation: Biofactors. 2009 Jan-Feb;35(1):14-20
references.pmid: 19319841
references.citation: Integr Comp Biol. 2005 Aug;45(4):631-8
references.pmid: 21676810
references.citation: Proc Natl Acad Sci U S A. 2007 May 15;104 Suppl 1:8627-33
references.pmid: 17494762
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37
references.pmid: 21593126
references.citation: Mar Biotechnol (NY). 2009 Jan-Feb;11(1):118-23
references.pmid: 18661183
references.citation: PLoS One. 2011;6(10):e26914
references.pmid: 22046408
references.citation: ISME J. 2008 Jan;2(1):67-73
references.pmid: 18059488
references.citation: Cell Microbiol. 2008 Dec;10(12):2377-86
references.pmid: 18549454
references.citation: Genes Dev. 1994 Aug 1;8(15):1817-28
references.pmid: 7958859
references.citation: BMC Biol. 2010 Jan 18;8:4
references.pmid: 20082688
references.citation: Front Physiol. 2012 Jan 02;2:116
references.pmid: 22232607
references.citation: Cell Res. 2010 Jul;20(7):812-25
references.pmid: 20479784
references.citation: Science. 2008 Jul 25;321(5888):560-3
references.pmid: 18653892
references.citation: Nature. 2004 Mar 4;428(6978):66-70
references.pmid: 14999280
references.citation: Proc Natl Acad Sci U S A. 2013 Jan 22;110(4):1387-92
references.pmid: 23297204
references.citation: Redox Rep. 2010;15(3):98-114
references.pmid: 20594413
references.citation: Dis Aquat Organ. 2006 Mar 23;69(1):101-10
references.pmid: 16703772
references.citation: Nature. 2010 Mar 25;464(7288):592-6
references.pmid: 20228792
references.citation: Plant Cell Environ. 2009 Feb;32(2):170-7
references.pmid: 19021889
references.citation: Mar Genomics. 2010 Mar;3(1):51-62
references.pmid: 21798197
references.citation: Future Microbiol. 2007 Jun;2(3):335-44
references.pmid: 17661707
references.citation: J Innate Immun. 2009;1(4):291-300
references.pmid: 20375587
references.citation: Toxicon. 2009 Dec 15;54(8):1162-73
references.pmid: 19232527
references.citation: J Cell Biol. 1999 Jul 12;146(1):141-8
references.pmid: 10402466
references.citation: J Bacteriol. 2000 Dec;182(24):6940-9
references.pmid: 11092854
references.citation: Bioessays. 2000 Jan;22(1):10-5
references.pmid: 10649285
references.citation: Proc Natl Acad Sci U S A. 2008 Nov 18;105(46):17867-71
references.pmid: 19004808
references.citation: Nat Rev Mol Cell Biol. 2009 Feb;10(2):104-15
references.pmid: 19165213
references.citation: J Exp Biol. 2009 Sep 1;212(17):2760-6
references.pmid: 19684208
references.citation: Cell. 2001 Dec 28;107(7):843-54
references.pmid: 11779461
references.citation: Int J Dev Biol. 2006;50(1):63-70
references.pmid: 16323079
references.citation: Gene. 2012 Mar 15;496(1):1-7
references.pmid: 22285376
references.citation: J Exp Biol. 2006 Jun;209(Pt 12):2328-36
references.pmid: 16731809
references.citation: Biochim Biophys Acta. 2004 May 27;1663(1-2):117-26
references.pmid: 15157614
references.citation: Microbiology (Reading). 2008 Mar;154(Pt 3):693-704
references.pmid: 18310016
references.citation: Trends Genet. 2005 Dec;21(12):633-9
references.pmid: 16226338
references.citation: PLoS One. 2008;3(11):e3718
references.pmid: 19005565
references.citation: Annu Rev Biochem. 1995;64:141-69
references.pmid: 7574478
references.citation: Cell. 2001 Oct 19;107(2):137-48
references.pmid: 11672522
references.citation: Science. 2007 Dec 14;318(5857):1737-42
references.pmid: 18079392
references.citation: Biosystems. 2004 Aug-Oct;76(1-3):75-87
references.pmid: 15351132
references.citation: Annu Rev Biochem. 1991;60:321-47
references.pmid: 1679318
references.citation: Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):9905-9
references.pmid: 21636790
references.citation: Proteins. 2002 Jul 1;48(1):1-14
references.pmid: 12012333
references.citation: Annu Rev Microbiol. 2002;56:289-314
references.pmid: 12142488
references.citation: Annu Rev Physiol. 1998;60:73-103
references.pmid: 9558455
references.citation: J Exp Biol. 2010 Mar 15;213(6):934-45
references.pmid: 20190118
references.citation: Philos Trans R Soc Lond B Biol Sci. 2009 Oct 12;364(1531):2881-95
references.pmid: 19720651
references.citation: Mol Biol Evol. 2011 Jan;28(1):699-706
references.pmid: 20829345
references.citation: Biochim Biophys Acta. 2010 Mar-Apr;1799(3-4):257-65
references.pmid: 19682612
references.citation: Proc Natl Acad Sci U S A. 2008 Oct 7;105(40):15576-80
references.pmid: 18832159
references.citation: Proc Natl Acad Sci U S A. 2000 Mar 14;97(6):2886-91
references.pmid: 10694572
references.citation: ISME J. 2012 Jun;6(6):1159-65
references.pmid: 22189494
references.citation: Biochem Biophys Res Commun. 2003 Aug 29;308(3):586-95
references.pmid: 12914791
references.citation: Appl Environ Microbiol. 2012 May;78(9):3136-44
references.pmid: 22344646
references.citation: J Biol Chem. 1983 Oct 10;258(19):12064-8
references.pmid: 6352705
references.citation: J Exp Biol. 2005 Mar;208(Pt 5):843-8
references.pmid: 15755882
references.citation: J Clin Invest. 2007 Apr;117(4):1068-77
references.pmid: 17404621
references.citation: Circ Res. 2008 Mar 28;102(6):703-10
references.pmid: 18239138
references.citation: BMC Genomics. 2008 Nov 14;9:540
references.pmid: 19014561
references.citation: J Mol Evol. 2006 Jul;63(1):95-107
references.pmid: 16770683
references.citation: Crit Rev Biochem Mol Biol. 2003;38(2):121-42
references.pmid: 12749696
references.citation: Annu Rev Genet. 2009;43:95-118
references.pmid: 19659442
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12115-20
references.pmid: 16880384
references.citation: J Bacteriol. 1988 Apr;170(4):1575-81
references.pmid: 2832369
references.citation: PLoS One. 2011 Jan 24;6(1):e16095
references.pmid: 21283671
references.citation: Trends Genet. 2009 Sep;25(9):404-13
references.pmid: 19716618
references.citation: Aging Cell. 2007 Aug;6(4):505-14
references.pmid: 17521387
references.citation: Mar Environ Res. 2001 Feb;51(1):17-27
references.pmid: 11125701
references.citation: Nat Rev Microbiol. 2007 May;5(5):355-62
references.pmid: 17384666
references.citation: Mol Biol Evol. 2000 Dec;17(12):1956-70
references.pmid: 11110912
references.citation: ISME J. 2012 Apr;6(4):835-46
references.pmid: 22158392
references.citation: Nat Rev Mol Cell Biol. 2010 Aug;11(8):545-55
references.pmid: 20628411
references.citation: Nature. 2011 Mar 17;471(7338):368-72
references.pmid: 21368762
references.citation: J Toxicol Environ Health A. 2006 Jan 8;69(1-2):175-84
references.pmid: 16291569
references.citation: FEMS Microbiol Ecol. 2009 May;68(2):152-63
references.pmid: 19302548
references.citation: Virology. 2006 Jan 5;344(1):119-30
references.pmid: 16364743
references.citation: Mar Drugs. 2012 Aug;10(8):1812-1851
references.pmid: 23015776
references.citation: J Exp Biol. 2006 Jul;209(Pt 14):2804-10
references.pmid: 16809471
references.citation: Mar Pollut Bull. 2012;65(10-12):506-15
references.pmid: 22284701
references.citation: Arch Toxicol. 2005 Apr;79(4):183-91
references.pmid: 15526190
references.citation: Cell. 1995 Oct 20;83(2):207-18
references.pmid: 7585938
references.citation: Cell. 1999 Jan 22;96(2):271-90
references.pmid: 9988221
references.citation: Curr Biol. 2003 Dec 16;13(24):2190-5
references.pmid: 14680636
references.citation: PLoS One. 2011;6(5):e20013
references.pmid: 21637757
references.citation: Nat Rev Genet. 2007 Apr;8(4):272-85
references.pmid: 17363976
references.citation: Cell. 1987 Jan 30;48(2):271-9
references.pmid: 3802195
references.citation: ISME J. 2013 Jan;7(1):13-27
references.pmid: 22791238
references.citation: J Biol Chem. 2005 Dec 16;280(50):41236-42
references.pmid: 16246842
references.citation: Mar Environ Res. 2001 Sep;52(3):289-99
references.pmid: 11570808
references.citation: Biol Bull. 2008 Jun;214(3):233-54
references.pmid: 18574101
references.citation: BMC Evol Biol. 2007 Apr 04;7:55
references.pmid: 17408485
references.citation: Nature. 2004 Aug 12;430(7001):741
references.pmid: 15306799
references.citation: Genes Cells. 2004 Dec;9(12):1151-66
references.pmid: 15569148
references.citation: Physiol Rev. 2002 Apr;82(2):373-428
references.pmid: 11917093
references.citation: Bioinformatics. 2012 Jun 15;28(12):i84-9
references.pmid: 22689783
references.citation: Mol Cell Proteomics. 2012 Jun;11(6):M111.015487
references.pmid: 22351649
references.citation: Trends Ecol Evol. 1990 May;5(5):149-55
references.pmid: 21232343
references.citation: PLoS One. 2012;7(3):e32859
references.pmid: 22396797
references.citation: Proc Biol Sci. 2008 Dec 7;275(1652):2687-93
references.pmid: 18700208
references.citation: Sci Rep. 2011;1:160
references.pmid: 22355675
references.citation: Trends Biochem Sci. 2005 Nov;30(11):642-9
references.pmid: 16182531
references.citation: Curr Opin Plant Biol. 2011 Jun;14(3):267-74
references.pmid: 21450514
references.citation: Mol Membr Biol. 2003 Apr-Jun;20(2):105-15
references.pmid: 12851068
references.citation: J Neurosci. 2004 Nov 17;24(46):10454-65
references.pmid: 15548660
references.citation: Physiol Rev. 2011 Jan;91(1):119-49
references.pmid: 21248164
references.citation: J Virol. 2003 Oct;77(19):10179-85
references.pmid: 12970403
references.citation: Trends Genet. 2005 Oct;21(10):536-9
references.pmid: 16098631
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12529-33
references.pmid: 16888041
references.citation: PLoS One. 2011;6(9):e25072
references.pmid: 21949855
references.citation: Proc Natl Acad Sci U S A. 1994 Aug 16;91(17):8137-41
references.pmid: 8058769
references.citation: Dev Biol. 2006 Dec 1;300(1):366-84
references.pmid: 17097629
references.citation: BMC Genomics. 2011 Nov 29;12:585
references.pmid: 22126435
references.citation: Science. 2011 Jan 14;331(6014):175
references.pmid: 21233378
references.citation: Environ Health Perspect. 2002 Oct;110 Suppl 5:745-8
references.pmid: 12426124
references.citation: Nature. 2009 Jun 25;459(7250):1091-7
references.pmid: 19458617
references.citation: Cell Microbiol. 2004 Nov;6(11):1027-40
references.pmid: 15469432
references.citation: J Biol Chem. 2005 Apr 8;280(14):13560-7
references.pmid: 15653680
references.citation: Sci Rep. 2012;2:240
references.pmid: 22355753
references.citation: J Biol Chem. 2005 Jan 14;280(2):1369-75
references.pmid: 15522876
references.citation: Aquat Toxicol. 2010 Apr 15;97(2):125-33
references.pmid: 20089320
references.citation: Biochemistry. 1997 Jun 10;36(23):6885-95
references.pmid: 9188683
references.citation: Development. 2012 Jan;139(2):347-57
references.pmid: 22159579
references.citation: J Bacteriol. 1992 Feb;174(4):1081-5
references.pmid: 1735703
references.citation: J Biol Chem. 2008 Sep 12;283(37):25475-25484
references.pmid: 18617510
references.citation: Environ Microbiol. 2007 Nov;9(11):2707-19
references.pmid: 17922755
references.citation: Plant Cell. 2007 Jan;19(1):369-87
references.pmid: 17237353
references.citation: Cell. 1990 Oct 5;63(1):11-22
references.pmid: 2208275
references.citation: Mol Cell Biol. 2004 Nov;24(22):10083-98
references.pmid: 15509808
references.citation: Plant Physiol. 2003 Mar;131(3):1209-19
references.pmid: 12644671
references.citation: Genome Biol. 2008;9(7):229
references.pmid: 18671835
references.citation: Appl Environ Microbiol. 2012 Sep;78(17):6377-9
references.pmid: 22729548
references.citation: Cell Death Differ. 2009 Feb;16(2):195-207
references.pmid: 19023332
references.citation: PLoS One. 2008 Jan 23;3(1):e1456
references.pmid: 18213365
references.citation: Biochim Biophys Acta. 2010 Aug;1804(8):1666-75
references.pmid: 19879981
references.citation: Biol Bull. 2009 Apr;216(2):131-7
references.pmid: 19366924
references.citation: J Biol Chem. 2005 Oct 7;280(40):34178-85
references.pmid: 16100115
references.citation: BMC Genomics. 2009 May 12;10:219
references.pmid: 19435504
references.citation: Environ Toxicol Chem. 2006 Dec;25(12):3181-7
references.pmid: 17220087
references.citation: Cell Mol Life Sci. 1999 Oct 30;56(5-6):507-22
references.pmid: 11212301
references.citation: J Biol Chem. 2001 Jun 1;276(22):19160-5
references.pmid: 11278543
references.citation: Science. 2004 Aug 13;305(5686):997-1000
references.pmid: 15310901
references.citation: Trends Microbiol. 1994 Jun;2(6):187-92
references.pmid: 7916248
references.citation: EMBO J. 1988 Jul;7(7):2117-30
references.pmid: 3138113
references.citation: Proc Natl Acad Sci U S A. 2004 Jan 20;101(3):881-5
references.pmid: 14709675
references.citation: Biol Bull. 2012 Apr;222(2):88-92
references.pmid: 22589399
references.citation: Methods Mol Biol. 2008;440:3-14
references.pmid: 18369933
references.citation: Science. 2003 Aug 15;301(5635):929-33
references.pmid: 12920289
references.citation: PLoS One. 2010 Apr 28;5(4):e10379
references.pmid: 20442851
references.citation: Nat Struct Mol Biol. 2008 Mar;15(3):218-20
references.pmid: 18319735
references.citation: Cell. 2003 Feb 7;112(3):369-77
references.pmid: 12581526
references.citation: J Biol Chem. 2000 Aug 18;275(33):25057-60
references.pmid: 10816601
references.citation: Neuron. 1998 Sep;21(3):479-80
references.pmid: 9768835
references.citation: Adv Exp Med Biol. 2012;738:46-59
references.pmid: 22399373
references.citation: Curr Top Dev Biol. 2009;88:63-101
references.pmid: 19651302
references.citation: PLoS One. 2009;4(3):e4865
references.pmid: 19283069
references.citation: PLoS One. 2010 Sep 21;5(9):e12805
references.pmid: 20877728
references.citation: Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2533-7
references.pmid: 18268342
references.citation: Int Rev Cell Mol Biol. 2012;293:123-48
references.pmid: 22251560
references.citation: Plant Cell Environ. 2008 May;31(5):679-94
references.pmid: 18315536
references.citation: J Biol Chem. 1995 Oct 6;270(40):23860-6
references.pmid: 7559564
references.citation: Mol Cell Biol. 1990 May;10(5):2214-23
references.pmid: 2183024
references.citation: J Biol Chem. 2000 Jun 2;275(22):16414-9
references.pmid: 10748051
references.citation: Eukaryot Cell. 2006 Sep;5(9):1517-31
references.pmid: 16963634
references.citation: J Bacteriol. 2000 Nov;182(22):6499-502
references.pmid: 11053396
references.citation: Dev Comp Immunol. 2008;32(12):1582-92
references.pmid: 18599120
references.citation: Development. 2006 Mar;133(5):957-66
references.pmid: 16469972
references.citation: Gene. 1999 Feb 18;227(2):157-67
references.pmid: 10023047
references.citation: Science. 2010 Sep 24;329(5999):1653-6
references.pmid: 20813918
references.citation: Trends Ecol Evol. 2008 May;23(5):268-75
references.pmid: 18378040
references.citation: Curr Opin Microbiol. 2003 Apr;6(2):140-5
references.pmid: 12732303
references.citation: Integr Comp Biol. 2003 Aug;43(4):542-8
references.pmid: 21680462
references.citation: Nature. 2000 Jan 6;403(6765):41-5
references.pmid: 10638745
references.citation: FEBS J. 2006 Sep;273(18):4186-98
references.pmid: 16907933
references.citation: Cold Spring Harb Perspect Biol. 2011 Aug 01;3(8):a003947
references.pmid: 21746798
references.citation: Mol Biol Evol. 2012 Jun;29(6):1545-56
references.pmid: 22319135
references.citation: PLoS One. 2008 Feb 27;3(2):e1584
references.pmid: 18301735
references.citation: Mol Biol Evol. 2011 Jan;28(1):153-61
references.pmid: 20660083
references.citation: J Immunol. 2006 Sep 1;177(5):3260-5
references.pmid: 16920966
references.citation: Autophagy. 2009 Feb;5(2):211-6
references.pmid: 19066451
references.citation: J Biol Chem. 2000 Aug 4;275(31):23583-8
references.pmid: 10811655
references.citation: Toxicon. 2002 Feb;40(2):111-24
references.pmid: 11689232
references.citation: Mol Microbiol. 1992 Sep;6(18):2557-63
references.pmid: 1447969
references.citation: Dev Comp Immunol. 2009 Apr;33(4):559-69
references.pmid: 19013190
references.citation: Bull Environ Contam Toxicol. 2008 Dec;81(6):553-7
references.pmid: 18820822
references.citation: Emerg Infect Dis. 1998 Oct-Dec;4(4):551-60
references.pmid: 9866731
references.citation: Dev Biol. 2003 Aug 1;260(1):191-206
references.pmid: 12885564
references.citation: BMC Genomics. 2013 Apr 08;14:228
references.pmid: 23565725
references.citation: Genome Biol. 2006;7(7):R64
references.pmid: 16867185
references.citation: J Virol. 1999 Aug;73(8):6500-5
references.pmid: 10400745
references.citation: Annu Rev Genet. 2009;43:143-66
references.pmid: 19659441
references.citation: Arch Biochem Biophys. 1998 Dec 1;360(1):10-4
references.pmid: 9826423
references.citation: Mol Biol Evol. 2010 Dec;27(12):2879-89
references.pmid: 20627874
references.citation: Biotechnol Lett. 2005 Jul;27(14):1011-5
references.pmid: 16132846
references.citation: J Biol Chem. 1992 Dec 15;267(35):25589-96
references.pmid: 1460054
references.citation: Mol Ecol Resour. 2011 Mar;11(2):328-34
references.pmid: 21429140
references.citation: Annu Rev Immunol. 2001;19:623-55
references.pmid: 11244049
references.citation: J Struct Biol. 2003 Jan;141(1):77-83
references.pmid: 12576022
references.citation: Proc Natl Acad Sci U S A. 2008 Nov 11;105(45):17442-6
references.pmid: 18988740
references.citation: Annu Rev Plant Physiol Plant Mol Biol. 1999 Jun;50:277-303
references.pmid: 15012211
references.citation: BMC Biol. 2012 Mar 05;10:17
references.pmid: 22390726
references.citation: Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18413-8
references.pmid: 19017800
references.citation: Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):2168-73
references.pmid: 22308434
references.citation: Pharm Acta Helv. 2000 Mar;74(2-3):265-72
references.pmid: 10812968
references.citation: Proc Biol Sci. 2007 Dec 22;274(1629):3079-85
references.pmid: 17925275
references.citation: RNA. 2000 Mar;6(3):449-57
references.pmid: 10744028
references.citation: Evol Dev. 1999 Jul-Aug;1(1):16-23
references.pmid: 11324016
references.citation: J Physiol. 2003 Oct 15;552(Pt 2):335-44
references.pmid: 14561818
references.citation: Dev Biol. 1998 Jul 15;199(2):216-25
references.pmid: 9698441
references.citation: J Virol. 1993 Apr;67(4):2168-74
references.pmid: 8445726
references.citation: Environ Microbiol. 2006 Dec;8(12):2068-73
references.pmid: 17107548
references.citation: PLoS One. 2010 Nov 12;5(11):e13975
references.pmid: 21103042
references.citation: Cell Signal. 2011 Apr;23(4):609-20
references.pmid: 20959140
references.citation: Mol Mar Biol Biotechnol. 1995 Mar;4(1):36-42
references.pmid: 7749464
references.citation: ISME J. 2011 Sep;5(9):1471-83
references.pmid: 21451583
references.citation: Proc Natl Acad Sci U S A. 1995 Apr 25;92(9):3784-8
references.pmid: 7731983
references.citation: Mar Biotechnol (NY). 2001 Sep;3(5):501-8
references.pmid: 14961344
references.citation: Nature. 2007 May 24;447(7143):396-8
references.pmid: 17522671
references.citation: Trends Microbiol. 2009 Dec;17(12):554-62
references.pmid: 19822428
references.citation: Environ Microbiol. 2009 Jan;11(1):268-76
references.pmid: 19125818
references.citation: Mar Pollut Bull. 2005;51(1-4):9-22
references.pmid: 15757704
references.citation: Neuron. 2001 May;30(2):301-3
references.pmid: 11394990
references.citation: PLoS One. 2012;7(4):e34659
references.pmid: 22509341
references.citation: J Virol. 2009 Oct;83(20):10761-9
references.pmid: 19656871
references.citation: PLoS One. 2011;6(12):e28634
references.pmid: 22216101
references.citation: Trends Immunol. 2007 Oct;28(10):449-54
references.pmid: 17855167
references.citation: Curr Opin Genet Dev. 2009 Dec;19(6):613-9
references.pmid: 19897356
references.citation: Clin Microbiol Rev. 2005 Apr;18(2):247-63
references.pmid: 15831824
references.citation: J Virol. 1985 Aug;55(2):347-51
references.pmid: 2410629
references.citation: BMC Genet. 2011 Nov 01;12:94
references.pmid: 22044657
references.citation: BMC Evol Biol. 2012 Nov 12;12:217
references.pmid: 23145489
references.citation: Nature. 2003 Aug 14;424(6950):741
references.pmid: 12917674
references.citation: Mol Cell Biol. 1993 Jul;13(7):4331-41
references.pmid: 8321235
references.citation: Cell Cycle. 2003 Nov-Dec;2(6):585-90
references.pmid: 14512774
references.citation: Biochemistry. 2004 Mar 2;43(8):2297-308
references.pmid: 14979726
references.citation: Cell Res. 2000 Sep;10(3):169-77
references.pmid: 11032169
references.citation: Cell Biol Toxicol. 2008 Dec;24(6):483-502
references.pmid: 18956243
references.citation: Oncogene. 2003 Dec 8;22(56):9041-7
references.pmid: 14663482
references.citation: J Cell Sci. 1994 Jun;107 ( Pt 6):1545-50
references.pmid: 7962196
references.citation: Cell. 2008 Jun 27;133(7):1145-8
references.pmid: 18585349
references.citation: Chem Rev. 2011 Sep 14;111(9):5768-83
references.pmid: 21793530
references.citation: Comp Biochem Physiol C Toxicol Pharmacol. 2007 Jan;144(4):348-55
references.pmid: 17208054
references.citation: PLoS One. 2007 Jun 06;2(6):e506
references.pmid: 17551586
references.citation: Cell. 2009 Feb 20;136(4):763-76
references.pmid: 19239894
references.citation: Cell. 2011 Apr 29;145(3):459-69
references.pmid: 21529717
references.citation: Am Nat. 2003 Oct;162(4 Suppl):S51-62
references.pmid: 14583857
references.citation: Methods Enzymol. 2011;496:399-422
references.pmid: 21514473
references.citation: Nature. 2004 Jun 24;429(6994):827-33
references.pmid: 15215854
references.citation: Plant Physiol. 2006 Nov;142(3):911-22
references.pmid: 17028153
references.citation: Annu Rev Immunol. 1993;11:571-611
references.pmid: 8476573
references.citation: FEBS Lett. 2005 Mar 28;579(9):1983-7
references.pmid: 15792807
references.citation: J Biol Chem. 2011 Mar 18;286(11):9856-64
references.pmid: 21245135
references.citation: Mol Cell. 2010 Jun 25;38(6):864-78
references.pmid: 20620956
references.citation: Mol Aspects Med. 2009 Dec;30(6):423-30
references.pmid: 19560485
references.citation: Immunol Cell Biol. 2012 Nov;90(10):945-54
references.pmid: 22801575
references.citation: Appl Environ Microbiol. 1990 Feb;56(2):352-6
references.pmid: 2306088
references.citation: Appl Environ Microbiol. 2007 May;73(9):2976-81
references.pmid: 17351090
references.citation: Eur J Biochem. 2000 Oct;267(20):6102-9
references.pmid: 11012661
references.citation: Annu Rev Genet. 1993;27:437-96
references.pmid: 8122909
references.citation: Mol Ecol. 2010 Apr;19(8):1515-7
references.pmid: 20456235
references.citation: Toxicon. 2009 Dec 15;54(8):1031-7
references.pmid: 19576920
references.citation: Subcell Biochem. 2007;44:115-41
references.pmid: 18084892
references.citation: Toxicon. 2013 Sep;71:11-7
references.pmid: 23688393
references.citation: Nature. 1990 Feb 8;343(6258):536-40
references.pmid: 2105471
references.citation: Cell Stress Chaperones. 2011 Jan;16(1):69-80
references.pmid: 20821176
references.citation: Appl Environ Microbiol. 2007 Sep;73(17):5642-7
references.pmid: 17586663
references.citation: Proc Natl Acad Sci U S A. 1998 Dec 22;95(26):15849-54
references.pmid: 9861059
references.citation: Science. 2002 Apr 26;296(5568):733-5
references.pmid: 11976454
references.citation: Bioinformatics. 2010 Oct 15;26(20):2629-30
references.pmid: 20739309
references.citation: BMC Bioinformatics. 2009 Dec 15;10:421
references.pmid: 20003500
references.citation: Mol Biol Evol. 2013 Jan;30(1):167-76
references.pmid: 22936719
references.citation: Cell. 2006 Jan 27;124(2):315-29
references.pmid: 16439206
references.citation: Environ Microbiol. 2008 Nov;10(11):2979-90
references.pmid: 18707612
references.citation: Plant Physiol. 2008 Jul;147(3):1239-50
references.pmid: 18502976
references.citation: Science. 2007 Oct 19;318(5849):467-70
references.pmid: 17947585
references.citation: Toxicon. 2012 Sep 15;60(4):551-7
references.pmid: 22465017
references.citation: Mol Cell Proteomics. 2013 Feb;12(2):312-29
references.pmid: 23152539
references.citation: J Biol Chem. 2002 Aug 2;277(31):28271-9
references.pmid: 12145319
references.citation: Proc R Soc Lond B Biol Sci. 1979 Apr 11;204(1155):131-9
references.pmid: 36618
references.citation: Mol Ecol. 2009 Jul;18(14):3062-75
references.pmid: 19538339
references.citation: Cell. 2005 Dec 16;123(6):1079-92
references.pmid: 16360037
references.citation: Mar Biotechnol (NY). 2013 Apr;15(2):244-51
references.pmid: 22875536
references.citation: J Bacteriol. 2005 May;187(9):3188-200
references.pmid: 15838046
references.citation: Curr Biol. 2002 Oct 15;12(20):1773-8
references.pmid: 12401173
references.citation: J Med Chem. 2006 Feb 9;49(3):1191-7
references.pmid: 16451083
references.citation: J Bacteriol. 1991 Jul;173(14):4247-53
references.pmid: 1906060
references.citation: Mol Pharmacol. 2006 Nov;70(5):1469-80
references.pmid: 16887934
references.citation: Annu Rev Biochem. 2005;74:481-514
references.pmid: 15952895
references.citation: PLoS One. 2007 Nov 28;2(11):e1213
references.pmid: 18043729
references.citation: Mar Pollut Bull. 2005 Nov;50(11):1448-51
references.pmid: 16271374
references.citation: Science. 2008 Feb 15;319(5865):948-52
references.pmid: 18276889
references.citation: J Cell Biol. 1995 Dec;131(6 Pt 1):1517-27
references.pmid: 8522608
references.citation: Cell Microbiol. 2006 Dec;8(12):1985-93
references.pmid: 16879456