{"id":28460,"date":"2015-10-05T13:46:08","date_gmt":"2015-10-05T11:46:08","guid":{"rendered":"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-2-multiple-sequence-alignment-of-protein-sequences\/"},"modified":"2021-06-18T15:05:01","modified_gmt":"2021-06-18T15:05:01","slug":"part-2-multiple-sequence-alignment-of-protein-sequences","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-2-multiple-sequence-alignment-of-protein-sequences\/?lang=it","title":{"rendered":"Parte 2: Allineamento multiplo di sequenze proteiche"},"content":{"rendered":"\n<div class=\"wp-block-group\"><div class=\"wp-block-group__inner-container is-layout-flow wp-block-group-is-layout-flow\">\n<div class=\"vf-tabs\"><ul class=\"vf-tabs__list\" data-vf-js-tabs=\"true\"><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-53c12c03-fd69-4c60-a98c-517e493c9be7\">Descrizione<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-3ca77dbd-92bb-40c5-90ff-80bab24f0706\">Compito<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-fb7f8c0d-e668-4b4b-a403-3125a01d76f8\">Sequenze<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-49802ed2-ad8e-4020-8ef1-38a6e6070f30\">MUSCLE<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-f3293f44-6770-44b4-aa21-2e837496da09\">Domande<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-52f5c833-db34-493c-919c-efbbcbcdb5cc\">Lista attivit\u00e1<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-53c12c03-fd69-4c60-a98c-517e493c9be7\"><h2>Descrizione<\/h2>\n<p>Complimenti! Svolgendo il tuo primo compito hai probabilmente capito che la tua proteina ignota era una rodopsina bovina \u2013 la molecola fotosensibile che si trova nella retina. Ora, vogliamo imparare qualcosa di pi\u00f9 riguardo alle proteine di questa famiglia e vedere se la bioinformatica possa essere di aiuto per trovare informazioni riguardo alla loro biochimica ed alla loro evoluzione.<\/p>\n\n\n\n<p>Per raggiungere questo scopo, creeremo un allineamento multiplo di sequenze. Questo significa che utilizzeremo molte sequenze amminoacidiche (che potresti ottenere, ad esempio, estrapolando informazioni dal risultato di BLAST) e le allineeremo in modo tale che i residui simili si trovino sempre uno sotto all\u2019altro.<\/p>\n\n\n\n<p>Nella sezione \u201cSequenze\u201d troverai un gruppo di sequenze pronte. La prima \u00e8 la rodopsina bovina con cui hai gi\u00e0 lavorato nella prima parte dell\u2019esercitazione. Utilizzeremo quindi l\u2019allineatore di sequenze multiple MUSCLE di EMBL-EBI per creare l\u2019allineamento.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-3ca77dbd-92bb-40c5-90ff-80bab24f0706\"><h2>Compito<\/h2>\n<p><strong>Procedi secondo le seguenti istruzioni:<\/strong><\/p>\n\n\n\n<p><strong>1. <\/strong>Utilizzando le sequenze disponibili nella sezione \u201cSequenze\u201d, allinea le 24 diverse opsine per compararle, utilizzando l\u2019allineatore di sequenze MUSCLE di EMBL-EBI<br><strong>2.<\/strong> Segui le istruzioni riportate nella sezione MUSCLE e cerca di rispondere alle domande della sezione \u201cDomande\u201d.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-fb7f8c0d-e668-4b4b-a403-3125a01d76f8\"><h2>Sequenze<\/h2>\n<p>Le tue sequenze iniziali:<\/p>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Bos_rho\nMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Homo_rho\nMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Homo_melan\nMNPPSGPRVPPSPTQEPSCMATPAPPSWWDSSQSSISSLGRLPSISPTAPGTWAAAWVPLPTVDVPDHAHYTLGTVILLVGLTGMLGNLTVIYTFCRSRSLRTPANMFIINLAVSDFLMSFTQAPVFFTSSLYKQWLFGETGCEFYAFCGALFGISSMITLTAIALDRYLVITRPLATFGVASKRRAAFVLLGVWLYALAWSLPPFFGWSAYVPEGLLTSCSWDYMSFTPAVRAYTMLLCCFVFFLPLLIIIYCYIFIFRAIRETGRALQTFGACKGNGESLWQRQRLQSECKMAKIMLLVILLFVLSWAPYSAVALVAFAGYAHVLTPYMSSVPAVIAKASAIHNPIIYAITHPKYRVAIAQHLPCLGVLLGVSRRHSRPYPSYRSTHRSTLTSHTSNLSWISIRRRQESLGSESEVGWTHMEAAAVWGAAQQANGRSLYGQGLEDLEAKAPPRPQGHEAETPGKTKGLIPSQDPRM<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Octopus_rho\nMVESTTLVNQTWWYNPTVDIHPHWAKFDPIPDAVYYSVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAFMKKWIFGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFLMIIFVWMWSIVWSVGPVFNWGAYVPEGILTSCSFDYLSTDPSTRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAKRLNAKELRKAQAGASAEMKLAKISMVIITQFMLSWSPYAIIALLAQFGPAEWVTPYAAELPVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKECEDANDAEEEVVASERGGESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGYPPQGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Mizuhopecten_Gqops\nMADNKSTLPGLPDINGTLNRSMTPNTGWEGPYDMSVHLHWTQFPPVTEEWHYIIGVYITIVGLLGIMGNTTVVYIFSNTKSLRSPSNLFVVNLAVSDLIFSAVNGFPLLTVSSFHQKWIFGSLFCQLYGFVGGVFGLMSINTLTAISIDRYVVITKPLQASQTMTRRKVHLMIVIVWVLSILLSIPPFFGWGAYIPEGFQTSCTFDYLTKTARTRTYIVVLYLFGFLIPLIIIGVCYVLIIRGVRRHDQKMLTITRSMKTEDARANNKRARSELRISKIAMTVTCLFIISWSPYAIIALIAQFGPAHWITPLVSELPMMLAKSSSMHNPVVYALSHPKFRKALYQRVPWLFCCCKPKEKADFRTSVCSKRSVTRTESVNSDVSSVISNLSDSTTTLGLTSEGATRANRETSFRRSVSIIKGDEDPCTHPDTFLLAYKEVEVGNLFDMTDDQNRRDSNLHSLYIPTRVQHRPTTQSLGTTPGGVYIVDNGQRVNGLTFNS<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Drosophila_rh6\nMASLHPPSFAYMRDGRNLSLAESVPAEIMHMVDPYWYQWPPLEPMWFGIIGFVIAILGTMSLAGNFIVMYIFTSSKGLRTPSNMFVVNLAFSDFMMMFTMFPPVVLNGFYGTWIMGPFLCELYGMFGSLFGCVSIWSMTLIAYDRYCVIVKGMARKPLTATAAVLRLMVVWTICGAWALMPLFGWNRYVPEGNMTACGTDYFAKDWWNRSYIIVYSLWVYLTPLLTIIFSYWHIMKAVAAHEKAMREQAKKMNVASLRNSEADKSKAIEIKLAKVALTTISLWFFAWTPYTIINYAGIFESMHLSPLSTICGSVFAKANAVCNPIVYGLSHPKYKQVLREKMPCLACGKDDLTSDSRTQATAEISESQA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Drosophila_rh2\nMERSHLPETPFDLAHSGPRFQAQSSGNGSVLDNVLPDMAHLVNPYWSRFAPMDPMMSKILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYYETWVLGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKILFIWMMAVFWTVMPLIGWSAYVPEGNLTACSIDYMTRMWNPRSYLITYSLFVYYTPLFLICYSYWFIIAAVAAHEKAMREQAKKMNVKSLRSSEDCDKSAEGKLAKVALTTISLWFMAWTPYLVICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVFGNTDEPKPDAPASDTETTSEADSKA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Xenopus_melanops\nMDLGKTVEYGTHRQDAIAQIDVPDQVLYTIGSFILIIGSVGIIGNMLVLYAFYRNKKLRTAPNYFIINLAISDFLMSATQAPVCFLSSLHREWILGDIGCNVYAFCGALFGITSMMTLLAISINRYIVITKPLQSIQWSSKKRTSQIIVLVWMYSLMWSLAPLLGWSSYVPEGLRISCTWDYVTSTMSNRSYTMMLCCCVFFIPLIVISHCYLFMFLAIRSTGRNVQKLGSYGRQSFLSQSMKNEWKMAKIAFVIIIVFVLSWSPYACVTLIAWAGHGKSLTPYSKTVPAVIAKASAIYNPIIYGIIHPKYRETIHKTVPCLRFLIREPKKDIFESSVRGSIYGRQSASRKKNSFISTVSTAETVSSHIWDNTPNGHWDRKSLSQTMSNLCSPLLQDPNSSHTLEQTLTWPDDPSPKEILLPSSLKSVTYPIGLESIVKDEHTNNSCVRNHRVDKSGGLDWIINATLPRIVIIPTSESNISETKEEHDNNSEEKSKRTEEEEDFFNFHVDTSLLNLEGLNSSTDLYEVVERFLS<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Platynereis_rops\nMSRSEVLVPGSMSLDGLLTTAHPIGNDSIETILHPYWQQFDIENTIPDSWHYAVAAWMTFFGILGVSGNLLVVWTFLKTKSLRTAPNMLLVNLAIGDMAFSAINGFPLLTISSINKRWVWGKLWRELYAFVGGIFGLMSINTLAWIAIDRFYVITNPLGAAQTMTKKRAFIILTIIWANASLWALAPFFGWGAYIPEGFQTSCTYDYLTQDMNNYTYVLGMYLFGFIFPVAIIFFCYLGIVRAIFAHHAEMMATAKRMGANTGKADADKKSEIQIAKVAAMTIGTFMLSWTPYAVVGVFGMIKPHSEMFIHPLLAEIPVMMAKASARYNPIIYALSHPKFRAEIDKHFPWLLCCCKPKPKAQLPSSTTKGSIASKTEADTSV<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Danio_melanops\nMSHHSSWRGHHCAPGDINCTAGFKESLGSRNYKLLHVPVHGPTHSHHHDPPHPFPTVDVPDHAHYIIGSVILIVGITGVIGNALVVYVFCRSRTLRTAGNMFIVNLAVADFLMSVTQSPVFFAASLHRRWVFGERPCELYAFCGALFGICSMMTLTAIAADRCLAITQPLALVSRVSRRKAGAVFVVVWLYSLGWSLPPFFGWSAYVPEGLQTSCSWDYMTFTPSVRAYTILLFVFVFFIPLGIIGSCYFAIFQTIRAAGKEIRELDCGETHKVYERMQNEWKMAKVALVVILLFIISWSPYSVVALTATAGYSHFLTPYMNSVPAVIAKASAIHNPIIYAITHPKYRVAIARYIPVLRPILRVKEKDLRSSFSSGSVSSRRPTLTSHQCSLGVSMGNAARANGRWGKTRLSSASDSDSCWTESEADGSSVSSLTFGRRVSTEISTDTVILSPGSSVSNASGQKSERAHKVVSVPVPSITFETDAADGESLSDGKALLGGN<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Sepia_rho\nMGRDIPDNETWWYNPTMEVHPHWKQFNQVPDAVYYSLGIFIGICGIIGCTGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFIKKWVFGMAACKVYGFIGGIFGLMSIMTMSMISIDRYNVIGRPMAASKKMSHRRAFLMIIFVWMWSTLWSIGPIFGWGAYVLEGVLCNCSFDYITRDSATRSNIVCMYIFAFCFPILIIFFCYFNIVMAVSNHEKEMAAMAKRLNAKELRKAQAGASAEMKLAKISIVIVTQFLLSWSPYAVVALLAQFGPIEWVTPYAAQLPVMFAKASAIHNPLIYSVSHPKFREAIAENFPWIITCCQFDEKEVEDDKDAETEIPATEQSGGESADAAQMKEMMAMMQKMQQQQAAYPPQGAYPPQGGYPPQGYPPPPAQGGYPPQGYPPPPQGYPPAQGYPPQGYPPPQGAPPQGAPPQAAPPQGVDNQAYQA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Takifugu_TMT\nMIVSNVSLSGCAGVNGAVCAAEGHQAGGSDRSTLTPTGNLVVSVFLGFIGTFGLVNNLLVLVLFCRYKMLRSPINLLLMNISISDLLVCVLGTPFSFAASTQGRWLIGEAGCVWYGFANSLFGVVSLISLAVLSFERYSTMMTPTEADPSNYCKVCLGITLSWVYSLVWTVPPLFGWSSYGPEGPGTTCSVNWTAKTTNSISYIICLFVFCLIVPFLVIVFCYGKLLCAIRQVSGINASTSRKREQRVLCMVVIMVICYLLCWLPYGVVALLATFGPPDLVTPEASIIPSVLAKSSTVINPIIYVFMNKQFYRCFLALLCCQDPRSGSSMKSSSKVATKAKGVTPTGQRRTDLLYMVASLGRPAATIPQLGPSFDATNDFTKPPSSDTIKPVVVSLAAHCDG<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Gallus_LWops\nMSSNSSQAPPNGTPGPFDGPQWPYQAPQSTYVGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCGSSVSLSNNINGFFVFGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCRPLGDFQFQRRHAVSGCAFTWGWALLWSTPPLLGWSSYVPEGLRTSCGPNWYTGGSNNNSYILSLFVTCFVLPLSLILFSYTNLLLTLRAAAAQQKEADTTQRAEREVTRMVIVMVMAFLLCWLPYSTFALVVATHKGIIIQPVLASLPSYFSKTATVYNPIIYVFMNKQFQSCLLEMLCCGYQPQRTGKASPGTPGPHADVTAAGLRNKVMPAHPV<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Xenopus_Parietops\nMDGNSTTPGIAVNLTVMPTIFPRSGYSILSFLMFLNAVFSICNNAIVILVTLKHPQLRNPINIFILNLSFSDLMMALCGTTIVVSTNYHGYFYLGKQFCIFQGFAVNYFGIVSLWSLTLLAYERYNVVCEPIGALKLSTKRGYQGLVFIWLFCLFWAIAPLFGWSSYGPEGVQTSCSIGWEERSWSNYSYIISYFLTCFIIPVGIIGFSYGSILRSLHQLNRKIEQQGGKTNPREEKRVVIMVLFMVLAFLICWLPYTVFALIVVINPQLYISPLAATLPTYFAKTSPVYNPIIYIFLNKQFRTYAVQCLTCGHINLDSLEEDTESVSAQAENMLTPKTNQVAPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Danio_MW4\nMNGTEGNNFYIPLSNRTGLARSPYEYPQYYLAEPWQFKLLAVYMFFLICLGFPINGLTLLVTAQHKKLRQPLNFILVNLAVAGTIMVCFGFTVTFYTAINGYFVLGPTGCAIEGFMATLGGEVALWSLVVLAVERYIVVCKPMGSFKFSASHAFAGCAFTWVMAMACAAPPLVGWPRYIPEGMQCSCGPDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQESESTQKAEREVTRMVILMVLGFLIAWTPYATVAAWIFFNKGAAFSAQFMAVPAFFSKTSALYNPVIYVLLNKQFRNCMLTTLFCGKNPLGDDESSTVSTSKTEVSSVSPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Danio_extraocular\nMNGTEGPNFYVPMSNRTGLVRSPFEEPQYYLAEPWQFSLLAAYMLFLILGSFPINALTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTVTLYTALHGYFLLGVTGCNIEGFFATLGGEIALWSLVVLAIERYIVVCKPMSTFRFGEKHAIIGVGFTWVMALTCAVPPLLGWSRYIPEGMQCSCGIDYYTPKPEVHNTSFVIYMFILHFSIPLLIIFFCYSRLLCTVRAAAAQQQESETTQRAEREVTRMVVVMVIAFLVCWVPYASVAWYIFANQGAEFGPVFMTVPAFFAKSAALYNPVIYIMLNRQFRNCMLSTVCCGKNPLAEDESSSAVSSKTQSSVVSSAQVSPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Latimeria_Rh2\nMNGTEGMNFYVPLSNRTGLVRSPFEYTQYYLAEPWKFSVLCAYMFLLIILGFPINFLTLLVTFKHKKLRQPLNYILVNLAVASLFMVVFGFTVTFYSSLNGYFVLGPMGCAMEGFFATLGGQVALWSLVVLAIERYIVVCKPMGNFRFASSHAIMGIAFTWIMALACAAPPLVGWSRYIPEGLQCSCGPDYYTLNPDFHNESYVMYLFLVHFLLPIIIIFFTYGRLICKVKEAAAQQQESASTQKAEKEVTRMVILMVIGFLTAWVPYASAAFWIFCNRGAEFTATLMTVPAFFSKSSCLFNPIIYVLLNKQFRNCMITTLCCGKNPLGDDDTSSAVSQSKTDVSSVSSSQVSPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Xenopus_green_ops\nMSKGRPDLRMEMPDEFYVPIPLETTNISSLSPFLVPQTHLGTPGIFMSISAFMLFTIIFGFPLNLLTIICTVKYKKLRSHLNYILVNLAVANLIVICFGSTTAFYSFSQMYFSLGTLACKIEGFTATLGGIIGLWSLAVVAFERFLVICKPMGNFTFRESHAVLGCILTWVIGLVAAIPPLLGWSRYIPEGLQCSCGPDWYTVNNKWNNESYVLFLFCFCFGFPLAIIVFSYGRLLLALHAVAKQQEQSATTQKAEREVTRMVIVMVVGFLVCWLPYASFALWAVTHRGELFDLRMSSVPSVFSKASTVYNPFIYIFMNRQFRSCMMKMIFCGKNPLGDDEETSVSGSTQVSSVSSSQIAPS<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Xenopus_violet_ops\nMLEEEDFYLFKNVSNVSPFDGPQYHIAPKWAFTLQAIFMGMVFLIGTPLNFIVLLVTIKYKKLRQPLNYILVNITVGGFLMCIFSIFPVFVSSSQGYFFFGRIACSIDAFVGTLTGLVTGWSLAFLAFERYIVICKPMGNFNFSSSHALAVVICTWIIGIVVSVPPFLGWSRYMPEGLQCSCGPDWYTVGTKYRSEYYTWFIFIFCFVIPLSLICFSYGRLLGALRAVAAQQQESASTQKAEREVSRMVIFMVGSFCLCYVPYAAMAMYMVTNRNHGLDLRLVTIPAFFSKSSCVYNPIIYSFMNKQFRGCIMETVCGRPMSDDSSVSSTSQRTEVSTVSSSQVSPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Gallus_blue_ops\nMHPPRPTTDLPEDFYIPMALDAPNITALSPFLVPQTHLGSPGLFRAMAAFMFLLIALGVPINTLTIFCTARFRKLRSHLNYILVNLALANLLVILVGSTTACYSFSQMYFALGPTACKIEGFAATLGGMVSLWSLAVVAFERFLVICKPLGNFTFRGSHAVLGCVATWVLGFVASAPPLFGWSRYIPEGLQCSCGPDWYTTDNKWHNESYVLFLFTFCFGVPLAIIVFSYGRLLITLRAVARQQEQSATTQKADREVTKMVVVMVLGFLVCWAPYTAFALWVVTHRGRSFEVGLASIPSVFSKSSTVYNPVIYVLMNKQFRSCMLKLLFCGRSPFGDDEDVSGSSQATQVSSVSSSHVAPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Danio_LWops\nMAEHWGDAIYAARRKGDETTREAMFTYTNSNNTKDPFEGPNYHIAPRWVYNVATVWMFFVVVASTFTNGLVLVATAKFKKLRHPLNWILVNLAIADLGETLFASTISVINQFFGYFILGHPMCIFEGYTVSVCGIAALWSLTVISWERWVVVCKPFGNVKFDAKWASAGIIFSWVWAAAWCAPPIFGWSRYWPHGLKTSCGPDVFSGSEDPGVQSYMVVLMITCCIIPLAIIILCYIAVYLAIHAVAQQQKDSESTQKAEKEVSRMVVVMIFAYCFCWGPYTFFACFAAANPGYAFHPLAAAMPAYFAKSATIYNPVIYVFMNRQFRVCIMQLFGKKVDDGSEVSTSKTEVSSVAPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Danio_SWops\nMDAWAVQFGNASKVSPFEGEQYHIAPKWAFYLQAAFMGFVFIVGTPMNGIVLFVTMKYKKLRQPLNYILVNISLAGFIFDTFSVSQVSVCAARGYYSLGYTLCSMEAAMGSIAGLVTGWSLAVLAFERYVVICKPFGSFKFGQGQAVGAVVFTWIIGTACATPPFFGWSRYIPEGLGTACGPDWYTKSEEYNSESYTYFLLITCFMMPMTIIIFSYSQLLGALRAVAAQQAESESTQKAEREVSRMVVVMVGSFVLCYAPYAVTAMYFANSDEPNKDYRLVAIPAFFSKSSSVYNPLIYAFMNKQFNACIMETVFGKKIDESSEVSSKTETSSVSA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Homo_MWops\nMAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFVLGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSSVSPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Danio_mel_rec1A\nMFMNGSSLNSSALDPSEQALQRPPWVTTTLGCFLIFTIVVDILGNLLVIFSVYRNKKLQNAGNIFVVSLAVADLVVAIYPYPLVLTSIFHRGWNLGYMHCQISGFLMGVSVIGSIFNITGIAINCYCYICHSLKYDKLYSDKNSVCYVLLIWALTVLAIVPNLFVGSLQYDPRVYSCTFEQSASSAYTIAVVFFHFILPIMIVTYCYLRIWVLVIQVRRRVKPDNRPKITPHDVRNFVTMFVVFVLFAVCWAPLNFIGLAVAISPERVVPLIPEWLFVASYFMAYFNSCLNAIVYGVLNQNFRREYKRIVVSVCTARIFFGESSNEAQERLKSKPSPLMTNNNQVKVDSV<\/pre>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-49802ed2-ad8e-4020-8ef1-38a6e6070f30\"><h2>MUSCLE<\/h2>\n<p><strong>1.<\/strong> Incolla tutte le sequenze amminoacidiche (comprensive del simbolo maggiore e del nome) tutte di seguito nella casella di ricerca (input box). (In alternativa puoi caricare <a href=\"http:\/\/emblog.embl.de\/ells\/wp-content\/uploads\/2014\/01\/FASTA_Opsins_part2.txt\" target=\"_blank\" rel=\"noreferrer noopener\">il file FASTA con la sequenza delle opsine<\/a> direttamente dal tuo computer).<\/p>\n\n\n\n<p><strong>2.<\/strong> Seleziona come formato output ClustalW<\/p>\n\n\n\n<p><strong>3.<\/strong> Invia le sequenze per l\u2019allineamento<\/p>\n\n\n\n<p><strong>4.<\/strong> A questo punto le varie opsine sono state allineate dal programma. Pu\u00f2 dare un\u2019occhiata al risultato nella sezione \u201cAlignment\u201d di MUSCLE e, per vedere meglio, scegli l\u2019opzione \u201cShow colors\u201d.<\/p>\n\n\n\n<p><strong>5.<\/strong> Per fare analisi un po\u2019 pi\u00f9 raffinate, utilizzeremo il programma JalView con cui gli allineamenti si possono guardare e modificare. Per farlo, clicca sul tasto destro del mouse sul pulsante \u201cResults Summary\u201d e scegli di aprire il risultato in una nuova scheda del browser (\u201capri in una nuova scheda\u201d). Nella nuova scheda del browser apri l\u2019allineamento usando \u201cJalView\u201d. La nuova scheda ci serve solamente per far si che JalView rimanga aperto mentre lavoriamo nella scheda precedente; tutti i passaggi successivi puoi portarli avanti nella scheda iniziale.<\/p>\n\n\n\n<p class=\"has-text-align-left\"><strong><strong>6.<\/strong> <\/strong>Assicurati di poter vedere tutte e 24 le sequenze una sotto all\u2019altra aggiustando le dimensioni della finestra (utilizza il cursore per portare la finestra in alto ed allargarla).<\/p>\n\n\n\n<div class=\"wp-block-image wp-image-4944\"><figure class=\"vf-figure  | vf-figure--align vf-figure--align-centered  size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"170\" height=\"157\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/ells\/wp-content\/uploads\/2021\/05\/IdentityScale_Web.png\" alt=\"\" class=\"wp-image-1440\"\/><figcaption class=\"vf-figure__caption\">Identity Scale<\/figcaption><\/figure><\/div>\n\n\n\n<div class=\"wp-block-image wp-image-4943\"><figure class=\"vf-figure  | vf-figure--align vf-figure--align-centered  size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"435\" height=\"203\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/ells\/wp-content\/uploads\/2021\/05\/HydrophobicityScale_Web.png\" alt=\"\" class=\"wp-image-1439\" srcset=\"https:\/\/www.embl.org\/ells\/wp-content\/uploads\/2021\/05\/HydrophobicityScale_Web.png 435w, https:\/\/www.embl.org\/ells\/wp-content\/uploads\/2021\/05\/HydrophobicityScale_Web-300x140.png 300w\" sizes=\"auto, (max-width: 435px) 100vw, 435px\" \/><figcaption class=\"vf-figure__caption\">Hydrophobicity Scale<\/figcaption><\/figure><\/div>\n\n\n\n<p>In JalView si possono selezionare diversi criteri di colorazionedell\u2019allineamento (vai su \u201cColour\u201d per selezionarli). Ad esempio, puoi colorare in base alla percentuale di identit\u00e0 o in base a quanto sono idrofobici i singoli residui amminoacidici.<\/p>\n\n\n\n<p><strong>7.<\/strong> Infondo alla pagina di JalView, puoi vedere i punteggi di allineamento rappresentati come barre di identit\u00e0\/similarit\u00e0 di sequenza. Noti nessuna peculiarit\u00e0? Cerca di rispondere a questa domanda che ti viene posta nella sezione \u201cDomande\u201d.<\/p>\n\n\n\n<p><strong>Nota:<\/strong> Quando hai finito questa parte, non chiudere la pagina di JalView, perch\u00e9 ci servir\u00e0 per il prossimo esercizio.<\/p>\n\n\n<div\n  class=\"vf-embed vf-embed--custom-ratio\"\n\n  style=\"--vf-embed-max-width: 100%;\n    --vf-embed-custom-ratio-x: 640;\n    --vf-embed-custom-ratio-y: 360;\"\n><iframe loading=\"lazy\" width=\"640\" height=\"360\" src=\"https:\/\/www.ebi.ac.uk\/Tools\/msa\/muscle\/\" frameborder=\"0\" allow=\"accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/div>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-f3293f44-6770-44b4-aa21-2e837496da09\"><h2>Domande<\/h2>\n<p><strong>1.<\/strong> Cosa puoi dedurre dall\u2019allineamento?<br><strong>2.<\/strong> Ci sono regioni della sequenza pi\u00f9 conservati di altri? Se s\u00ec, quanti? Qual\u2019\u00e8 la loro caratteristica biochimica?(sono residui basici, acidi, idrofobici o idrofilici?)<br><strong>3.<\/strong> Ci sono residui conservati o brevi sequenze conservati in tutte le sequenze? Attenzione, una delle sequenze, \u201cDanio_mel_rec1A\u201d, non \u00e8 una opsina ma una molecola evolutivamente correlata (e questo sar\u00e0 rilevante per la prossima parte dell\u2019esercitazione).<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-52f5c833-db34-493c-919c-efbbcbcdb5cc\"><h2>Lista attivit\u00e1<\/h2>\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/?lang=it\" data-type=\"teachingbase\" data-id=\"28423\">Esploriamo l\u2019evoluzione delle proteine sensibili alla luce<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-1-search-for-protein-identity\/?lang=it\" data-type=\"teachingbase\" data-id=\"28446\">Parte 1: Ricerca per identit\u00e0 di proteine<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-2-multiple-sequence-alignment-of-protein-sequences\/?lang=it\" data-type=\"teachingbase\" data-id=\"28460\">Parte 2: Allineamento multiplo di sequenze proteiche<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-3-phylogenetic-analysis-of-aligned-protein-sequences\/?lang=it\" data-type=\"teachingbase\" data-id=\"28480\"><strong>Parte 3: Analisi filogenetica delle sequenze proteiche allineate<\/strong><\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-4-topological-and-structural-analysis-of-proteins\/?lang=it\" data-type=\"teachingbase\" data-id=\"28503\">Parte 4: Analisi topologica e strutturale delle proteine<\/a><\/li><\/ul>\n<\/section>\n<\/div><\/div>\n\n\n\n<p><\/p>\n\n\n\n<p><\/p>\n<\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"featured_media":28461,"parent":28423,"menu_order":3,"template":"","class_list":["post-28460","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/28460","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase"}],"about":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/types\/teachingbase"}],"up":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/28423"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media\/28461"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=28460"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}