三种分析蛋白结构域(Domains)的方法

1、三种分析蛋白结构域(Domains)的方法三种分析蛋白结构域(Domains)的方法1,SMARAH,蛋白结构和功能分析SMARTSSMART(aSimpleModularArchitectureResearchTool)allowstheidentificationandannotationofgeneticallymobiledomainsandtheanalysisofdomainarchitectures.Morethan500domainfamiliesfoundinsignalling,extracellularandchromatin-associatedproteinsared

2、etectable.Thesedomainsareextensivelyannotatedwithrespecttophyleticdistributions,functionalclass,tertiarystructuresandfunctionallyimportantresidues.Eachdomainfoundinanon-redundantproteindatabaseaswellassearchparametersandtaxonomicinformationarestoredinarelationaldatabasesystem.Userinterfacestothisdat

3、abaseallowsearchesforproteinscontainingspecificcombinationsofdomainsindefinedtaxa.Forallthedetails,pleaserefertothepublicationsonSMART.SMARTttp:smart.embl-heidelberg.de/),可以说是蛋白结构预测和功能分析的工具集合。简单点说，就是集合了一些工具，可以预测蛋白的一些二级结构。如跨膜区(Transmembranesegments)，复合螺旋区(coiledcoilregions),信号肽(Signalpeptides),蛋白结构域(

4、PFAMdomains 等。SMART?该知道的1,SMAR 有两种不同的模式：normal 或 genomic主要是用的数据库不一样。 NormalSMART,用的数据库 Swiss-Prot,SP-TrEMBL 和stableEnsemblproteomes。GenomicSMART,用全基因组序列。详细列表：http:smart.embl-heidelberg.de/smart/listgenomes.pl2,一些名词解释http:smart.embl-heidelberg.de/help/smartglossary.shtmlSMAR 进行时可以直接用各个数据库蛋白的ID。 如Unip

5、rot/EnsemblID/Accessionnumber(ACC)。或是直接蛋白序列。运行 SMAR 也可选择 signalpeptides、PFAMdomains 等的预测，勾上就是。看下图SequenceanalysisYoumayuseeitheraUnjprutXEnsemtilsequenceidentifier(ID)/accessionnumberCACC)orsequenceitselftorequestttieSMARTsemceSequenceIDorACC(Q8N9N1SequencelUGJJrrTVGLAVCJTPHEVCTmSSFLNSQGRLNSCHFSTmGI

6、QMFQALNVKPRELLRHGRCPPTSLIRCHmYFRHDLFI,KPVFLLTFLTFSULHLCLLL3APSQIYISVfHLFSLPlCRFCLGlIDYIYLGLLKTLPTFPSVRSFPSVmiVFIKKTHKTmL1VPST1mFLCFTLQ 工 TQKSYLYFLQFl5Y5PLMAL5HPURF555TIISMI?ksiyS5TF5P51T1SequenceSMARTIResetHMMERsearchesoftheSMARTdatabaseoccurbydefault.YoumayalsafindSMARGESctuH!用3l.(1QQe)PfW!.的拉耻我.Sa

7、i.廿狷95.阳舁不部4Letuniaet.值口值)岫c相 E 刖熠住s.ctai:10.1093/t*arflgknfipeMESETUPFAQABOUTGLOSSARYWHAFSHEWFEEDSACKutlierhomologiesandhomologuesofknownstructurePFAMdomainssignalpeptidesinternalrepeatsMriq迎p(rt 日indisorderSMARTS运行后的结果用图表表示。其实运行后的结果都有明确的解释详细请看下Mouseoverdomainundefinedregionformoreinfo;clickanittog

8、otodetainedarinatation;TransmemtiranesegmentsaspredictedbytheWWW2program(I).colledcoilregionsderpeptidesdeterminedbytheprogram().Introrpc-sitiorsareindicatedwithvertical不同结构的预测由不同的工具完成。如果你想了解更多，可访问去该工具的网站。跨膜区(Transmembranesegments),TMHMM2ogram。(用表示)复合螺旋区(coiledcoilregions),Coils2program0(用表示)信号肽(Sig

9、nalpeptides),SignalPprogram。()蛋白结构域(PFAM,PFAM等等。不止这几个的。其它不一一列举。因为都是详细的说明。点击图标链接，就能看到该区域的序列，或是一些详细的描述。如上图的跨膜区，点击进去就是该跨膜区从开始到结束的序列。面。SMARMGST1_HUMAN(P1ISshutEet司I,(ISaajPnciG.刖.凡初.SQtwsa95.5637-5364Leitunicetsi.WjtctefccsWs,田 m,doi：!10二!1。4内krSSHOMESETLIPFAQABOUTOLOSARYWHATStJEWFEEDBACKtransferase1Dom

10、ainswithinHomosapiensproteinNDUA6HUMAN(P5lpeptidesdeterminedbythe3ra/Fprogram().Hitsonlyfoundby日LASTareIndicated网.DisorderedregionsdetectedbyDisEtdBL().另外，不一定所有预测的区域都会用在图示里看到。一般 SMART 勺显示顺序是SMARTPFAMPROSPEROrepeatsSignalpeptideTransmembraneCoiledcoilUnstructuredregionsLowcomplexity。另夕卜其它不用图解显示的区域，在底

11、下的表格也有详细说明。2,Sanger 的 Pfam 数据库网址：http:/pfam.sanger.ac.uk/目前的版本：Pfam23.0(July2008,10340families)ThePfamdatabaseisalargecollectionofproteinfamilies,eachrepresentedbymultiplesequencealignmentsandhiddenMarkovmodels(HMMs).SMARcovered时domainsreindicatedbyHOMESETUPFAQABOUTGLOSSARYUVHATSNEWFEEDBACKSehuitset

12、al,口gq盯Fee用礼AcMSa5szi35.我口.科 gbfturicet3l.pOOGJM除田间?武号fifey34,如MouseoverdomainJundefinedr&gionformoreirtfo;clickonittogotodetailedannotation;TramsmembranesegmentsaspredictedbtheTAfK/WM?program:!),tailedcoilregionsdePfam23,0(July2008,10340families)ThePfamdatabaseisalrgscollectioncfproteinfamilies

13、jeachrepresentedalignmentsandhiddenMarkovmodels(HMMs),PdDreANALYZEYOURPROTEINSEQUENCEIP5steyourprateinsecjuenceheretnfinBL&USK1V&CtFSftpsDtmELCKSLreiTIIinSKESITTSKUirRlHklEETEEIETCITSEnnEntEDFIFEPDQ三resultspage.jrsearchsequence(7siqnificaritsnd9insiqnifitrit),Voudidnotehoosetoicethatyousubmi

14、tted,Pfamdomainsonanawsequence.VIEWAGLAMVIEWASEQUENCEVIEWASTRUCTUREKEYWORDSEARCHJUMPTOSLQATSEnnmiKLTTLIJIJnjvuipmlorumnsiLS?THfPmSFT?H?BLTDLFllPTSDIIT?FlilLTKLBr?CE?FFLCSTSLPEF?VRUnQtELTIT?KI?V?ETII?TTKD1wrwcmrTHTII-TeuwTHUUU PiiTLimnThissearchwillu*且且bothglobalandlocalmode1.0.You匚匚君君nsetyour口口 件件se

15、archp自自r4mEtEirm宿宿searcheshere-QUICKLINKS3,NCBI 的 CDD(ConservedDomainDatabase)数据库网址：/Structure/cdd/wrpsb.cgiProteinsoftencontainseveralmodulesordomains,eachwithadistinctevolutionaryoriginandfunction.NCBIsConservedDomainDatabaseisacollectionofmultiplesequencealignmentsforanc

16、ientdomainsandfull-lengthproteins.Conserveddomainsoni胴生良心掘我%112x21LocdlquerysequiGraphicalsummary)12505H113li1i111I1i11Queryse?,3i.b3,hdih卜 Kj.七 it-eQplwbictinFcoredorainphosphotQinebindingpodketAiL.tkRhdrphob:bIndiri-gpockdkphffffph-fftryrflffMTBbindingFochsSearchforsimilardomainarListofdomainhitsQ

17、Defi|rtiQn+cjQDIy,FLCMFhosEM迎即跑Migdomain,Phosphoinositide-specificiphospholi+gd00275,C22,Proteinkirase|consepedregion2,subgroup.Ca2+45lndingmotii+lcd01246,PH_PLC,PhospholipaseC(PLC)pleckstrlnhomology(PH)domair,Thereare-+HQ248aPLCF,Phcspholipase%catalyticdGm9in,Phosphoiricsitide-specificphohaliFHcdOOI73,SH2,Srcfiomology2domains;Signaltransdudian,invclvedinrecognitiun3豺+cd00173,8H21Srchomology2domains;Signalinnsducti