{"id":36135,"date":"2023-07-06T09:49:04","date_gmt":"2023-07-06T09:49:04","guid":{"rendered":"https:\/\/www.embl.org\/ells\/?post_type=teachingbase&#038;p=36135"},"modified":"2023-07-14T07:21:01","modified_gmt":"2023-07-14T07:21:01","slug":"part-3-multiple-sequence-alignment","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/the-mysterious-protein-a-bioinformatics-expedition\/part-3-multiple-sequence-alignment\/","title":{"rendered":"Part 3: Multiple sequence alignment"},"content":{"rendered":"\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-7598e4b0-bc8d-4747-9b2f-1cfbab5a5649\" data-vf-js-location-nearest-activation-target=\"\">Overview<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-023d5ea7-e7a8-4bf7-8217-721079a1aaa8\" data-vf-js-location-nearest-activation-target=\"\">Your task<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-f9ab8ab5-a1b8-4958-92c4-f8acc6e122d3\" data-vf-js-location-nearest-activation-target=\"\">Sequences<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-af77e21e-cc8e-41f0-aa74-7f112f133274\" data-vf-js-location-nearest-activation-target=\"\">Clustal Omega<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-d24452c0-50ca-4416-b035-2e5f70dc37dd\" data-vf-js-location-nearest-activation-target=\"\">Questions<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-059237fe-aeba-4999-ba07-b99de87ae8bf\" data-vf-js-location-nearest-activation-target=\"\">Activity navigation<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-7598e4b0-bc8d-4747-9b2f-1cfbab5a5649\"><h2>Overview<\/h2>\n<p>Well done! In Part 2 we discovered that our unknown protein is most likely rhodopsin \u2013 the photosensitive protein of the retina. Rhodopsins belong to a class of proteins called <a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/ells-glossary\/\" target=\"_blank\" rel=\"noreferrer noopener\">opsins<\/a>, which typically bind a chromophore called retinal.\u00a0<\/p>\n\n\n\n<p>Now we want to learn more about rhodopsins and utilise bioinformatics to explore their evolutionary changes. This will help us understand the evolution of our new species and identify any closely related species. We do this by performing a so-called <a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/ells-glossary\/\" target=\"_blank\" rel=\"noreferrer noopener\">multiple sequence alignment<\/a>, a technique that involves aligning numerous rhodopsin amino acid sequences from various species. The alignment ensures, if possible, that similar <a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/ells-glossary\/\" target=\"_blank\" rel=\"noreferrer noopener\">residues <\/a>are consistently positioned beneath each other. If this is the case for a big proportion of the amino acids, it would mean that the sequences are closely related.\u00a0\u00a0<\/p>\n\n\n\n<p>You can find a set of prepared sequences in the tab \u201cSequences\u201d. The first sequence (\u201c&gt;New species (Unknown)\u201d) corresponds to the rhodopsin you previously used. The other sequences correspond to rhodopsins from 20 different organisms, including human and common research organisms like fruit flies, house mice, rats and zebrafishes.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-023d5ea7-e7a8-4bf7-8217-721079a1aaa8\"><h2>Your task<\/h2>\n<p><strong>Please follow the steps outlined below:<\/strong><\/p>\n\n\n\n<p><strong>1. <\/strong>Using the sequences available in the \u201cSequences\u201d tab, align the rhodopsins from 21 different species for comparison using the EMBL-EBI Clustal Omega multiple sequences alignment tool.<br><strong>2.<\/strong> Follow the instructions in the \u201cClustal Omega\u201d tab.<br><strong>3. <\/strong>Try to answer the questions in the \u201cQuestions\u201d tab.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-f9ab8ab5-a1b8-4958-92c4-f8acc6e122d3\"><h2>Sequences<\/h2>\n<pre class=\"wp-block-code vf-u-text--break\"><code>\n>New species (Unknown) \nMNGTEGPFGYIPMSNATGLVRSPYDYPQYYLVPPWGYACLAAYMFLLILTGFPVNFLTLY\nVTIEHKKLRSPLNYILLNLAVADLFMVIGGFTTTMWTSLBGYFVFGRMGCNIEGFFATLG\nGEIALWSLVVLSMERWIVVCKPISNFRFGENHAVMGVAFSWFMAAACAVPPLVGWSRYIP\nEGMQCSCGIDYYTRAEGFNNESFVIYMFVVFFTCPLTIITFCYGRLVCTVKEAAAQQQES\nETTQRAEREVTRMVIITFVAFLACWVPYASVAWYIFTHQGSEFGPVFMTIPAFFAKSSAV\nYNPVIYICLNKQFRHCMITTLCCGKNPFEEEEGSTTASKTEASSVCSVSPHA\n\n>Drosophila melanogaster (Fruit fly)\nMASLHPPSFAYMRDGRNLSLAESVPAEIMHMVDPYWYQWPPLEPMWFGIIGFVIAILGTM\nSLAGNFIVMYIFTSSKGLRTPSNMFVVNLAFSDFMMMFTMFPPVVLNGFYGTWIMGPFLC\nELYGMFGSLFGCVSIWSMTLIAYDRYCVIVKGMARKPLTATAAVLRLMVVWTICGAWALM\nPLFGWNRYVPEGNMTACGTDYFAKDWWNRSYIIVYSLWVYLTPLLTIIFSYWHIMKAVAA\nHEKAMREQAKKMNVASLRNSEADKSKAIEIKLAKVALTTISLWFFAWTPYTIINYAGIFE\nSMHLSPLSTICGSVFAKANAVCNPIVYGLSHPKYKQVLREKMPCLACGKDDLTSDSRTQA\nTAEISESQA\n\n>Sus scrofa (Wild boar)\nMNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFMLIVLGFPINFLTLY\nVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG\nGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIP\nEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFSIPLVIIFFCYGQLVFTVKEAAAQQQES\nATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSDFGPIFMTIPAFFAKSASI\nYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTTSKTETSQVAPA\n\n>Bos taurus (Cattle)\nMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY\nVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG\nGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP\nEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQES\nATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAV\nYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA\n\n>Homo sapiens (Human)\nMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY\nVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG\nGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP\nEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES\nATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI\nYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\n\n>Mus musculus (House mouse) \nMNGTEGPNFYVPFSNVTGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY\nVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG\nGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVVFTWIMALACAAPPLVGWSRYIP\nEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES\nATTQKAEKEVTRMVIIMVIFFLICWLPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSI\nYNPVIYIMLNKQFRNCMLTTLCCGKNPLGDDDASATASKTETSQVAPA\n\n>Gallus gallus (Red junglefowl)\nMNGTEGQDFYVPMSNKTGVVRSPFEYPQYYLAEPWKFSALAAYMFMLILLGFPVNFLTLY\nVTIQHKKLRTPLNYILLNLVVADLFMVFGGFTTTMYTSMNGYFVFGVTGCYIEGFFATLG\nGEIALWSLVVLAVERYVVVCKPMSNFRFGENHAIMGVAFSWIMAMACAAPPLFGWSRYIP\nEGMQCSCGIDYYTLKPEINNESFVIYMFVVHFMIPLAVIFFCYGNLVCTVKEAAAQQQES\nATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTNQGSDFGPIFMTIPAFFAKSSAI\nYNPVIYIVMNKQFRNCMITTLCCGKNPLGDEDTSAGKTETSSVSTSQVSPA\n\n>Cricetulus griseus (Chinese Hamster)\nMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY\nVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG\nGEIALWSLVVLAIERYVVICKPMSNFRFGENHAIMGVVFTWIMALACAAPPLVGWSRYIP\nEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIVIFFCYGQLVFTVKEAAAQQQES\nATTQKAEKEVTRMVILMVVFFLICWFPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSI\nYNPVIYIMMNKQFRNCMLTTLCCGKNILGDDEASATASKTETSQVAPA\n\n>Canis lupus familiaris (Dog)\nMNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY\nVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNVEGFFATLG\nGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP\nEGMQCSCGIDYYTLKPEINNESFVIYMFVVHFAIPMIVIFFCYGQLVFTVKEAAAQQQES\nATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSDFGPIFMTLPAFFAKSSSI\nYNPVIYIMMNKQFRNCMITTLCCGKNPLGDDEASASASKTETSQVAPA\n\n>Danio rerio (Zebrafish)\nMNGTEGPAFYVPMSNATGVVRSPYEYPQYYLVAPWAYGLLAAYMFFLIITGFPVNFLTLY\nVTIEHKKLRTPLNYILLNLAIADLFMVFGGFTTTMYTSLHGYFVFGRLGCNLEGFFATLG\nGEMGLWSLVVLAIERWMVVCKPVSNFRFGENHAIMGVAFTWVMACSCAVPPLVGWSRYIP\nEGMQCSCGVDYYTRTPGVNNESFVIYMFIVHFFIPLIVIFFCYGRLVCTVKEAAAQQQES\nETTQRAEREVTRMVIIMVIAFLICWLPYAGVAWYIFTHQGSEFGPVFMTLPAFFAKTSAV\nYNPCIYICMNKQFRHCMITTLCCGKNPFEEEEGASTTASKTEASSVSSSSVSPA\n\n>Rattus norvegicus (Brown rat)\nMNGTEGPNFYVPFSNITGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY\nVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG\nGEIGLWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP\nEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES\nATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQGSNFGPIFMTLPAFFAKTASI\nYNPIIYIMMNKQFRNCMLTSLCCGKNPLGDDEASATASKTETSQVAPA\n\n>Delphinus delphis (Short-beaked common dolphin)\nMNGTEGLNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSVLAAYMFLLIVLGFPINFLTLY\nVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSLHAYFVFGPTGCNLEGFFATLG\nGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWIMAMACAAPPLVGWSRYIP\nEGMQCSCGIDYYTLSPEVNNESFVIYMFVVHFTIPLVIIFFCYGQLVFTVKEAAAQQQES\nATTQKAEKEVTRMVIIMVVAFLICWVPYASVAFYIFTHQGSDFGPIFMTIPSFFAKSSSI\nYNPVIYIMMNKQFRNCMLTTLCCGRNPLGDDEASTTASKTETSQVAPA\n\n>Mesoplodon bidens (Sowerby's beaked whale)\nMNGTEGLNFYVPFSNHTGVVRSPFEYPQYYLAEPWQFSVLAAYMFLLIMLGFPINFLTLY\nVTVQHKKLRTPLNYILLNLAVANLFMVLGGFTTTLYTSMHAYFIFGPTGCNLEGFFATLG\nGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWIMALACAAPPLVGWSRYIP\nEGMQCSCGVDYYTPSPEVNNESFVVYMFVVHFSIPMVIIFFCYGQLVFTVKEAAAQQQES\nATTQKAEKEVTRMVVIMVVAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPSFFAKSSAI\nYNPVIYIMMNKQFRNCMLTTLCCGRNPLGDDEVSTTASKTETSQVAPA\n\n>Phoca vitulina (Harbor seal)\nMNGTEGPNFYVPFSNKTGVVRSPFEFPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY\nVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG\nGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVGFTWVMALACAAPPLVGWSRYIP\nEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES\nATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKAASI\nYNPVIYIMMNKQFRTCMITTLCCGKNPLGDDEVSASASKTETSQVAPA\n\n>Scyliorhinus canicula (Catshark)\nMNGTEGENFYIPMSNKTGVVRSPFDYPQYYLAEPWKFSVLAAYMFFLIIAGFPVNFLTLY\nVTIQHKKLRQPLNYILLNLAVADLFMIFGGFPSTMITSMNGYFVFGPSGCNFEGFFATLG\nGEIGLWSLVVLAIERYVVVCKPMSNFRFGSQHAFMGVGLTWIMAMACAFPPLVGWSRYIP\nEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFSIPLTIIFFCYGRLVCTVKEAAAQQQES\nETTQRAEREVTRMVIIMVIAFLICWLPYASVAFFIFCNQGSEFGPIFMTIPAFFAKAASL\nYNPLIYILMNKQFRNCMITTICCGKNPFEEEESTSASASKTEASSVSSSQVAPA\n\n>Carassius auratus (Goldfish)\nMNGTEGDMFYVPMSNATGIVRSPYDYPQYYLVAPWAYACLAAYMFFLIITGFPVNFLTLY\nVTIEHKKLRTPLNYILLNLAISDLFMVFGGFTTTMYTSLHGYFVFGRVGCNPEGFFATLG\nGEMGLWSLVVLAFERWMVVCKPVSNFRFGENHAIMGVVFTWFMACTCAVPPLVGWSRYIP\nEGMQCSCGVDYYTRPQAYNNESFVIYMFIVHFIIPLIVIFFCYGRLVCTVKEAAAQHEES\nETTQRAEREVTRMVVIMVIGFLICWIPYASVAWYIFTHQGSEFGPVFMTLPAFFAKTAAV\nYNPCIYICMNKQFRHCMITTLCCGKNPFEEEEGASTTASKTEASSVSSSSVSPA\n\n>Lithobates catesbeianus (American bullfrog)\nMNGTEGPNFYVPMSNKTGIVRSPFEYPQYYLAEPWKYSVLAAYMFLLILLGLPINFMTLY\nVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTITMYTSLHGYFVFGQTGCYFEGFFATLG\nGEIALWSLVVLAIERYIVVCKPMSNFRFGENHAMMGVAFTWIMALACAVPPLFGWSRYIP\nEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFLIPLIIISFCYGRLVCTVKEAAAQQQES\nATTQKAEKEVTRMVVIMVIFFLICWVPYAYVAFYIFTHQGSEFGPIFMTVPAFFAKSSAI\nYNPVIYIMLNKQFRNCMITTLCCGKNPFGDEDASSAATSKTEATSVSTSQVSPA\n\n>Bufo bufo (Common toad)\nMNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLY\nVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLG\nGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIP\nEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQES\nATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSI\nYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTEASSVSSSQVSPA\n\n>Oryzias latipes (Japanese rice fish)\nMNGTEGPYFNVPMVNTTGIVRSPYEYPQYYLVSPAAYAALGAYMFFLILVGFPINFLTLY\nVTLEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVLGRLGCNLEGFFATLG\nGEIGLWSLVVLAIERWVVVCKPISNFRFGENHAIMGLVFTWIMAASCAVPPLVGWSRYIP\nEGMQCSCGVDYYTRAEGFNNESFVVYMFVCHFLIPLIVVFFCYGRLLCAVKEAAAAQQES\nETTQRAEREVTRMVVIMVIGFLVCWLPYASVAWYIFTNQGSEFGPLFMTIPAFFAKSSSI\nYNPAIYICMNKQFRNCMITTLCCGKNPFEEEEGASTTASKTEASSVSSSSVSPA\n\n>Sardina pilchardus (Pilchard)\nMNGTEGPFFYIPMSNATGLVRSPYDYPQYYLVPPWGYACLAAYMFLLILTGFPVNFLTLY\nVTIEHKKLRSPLNYILLNLAVADLFMVIGGFTTTMWTSLNGYFVFGRMGCNIEGFFATLG\nGEIALWSLVVLSMERWIVVCKPISNFRFGENHAVMGVAFSWFMAAACAVPPLVGWSRYIP\nEGMQCSCGIDYYTRAEGFNNESFVIYMFVVHFTCPLTIITFCYGRLVCTVKEAAAQQQES\nETTQRAEREVTRMVIIMFVAFLACWVPYASVAWYIFTHQGSEFGPVFMTIPAFFAKSSAV\nYNPVIYICLNKQFRHCMITTLCCGKNPFEEEEGSTTASKTEASSVCSVSPA\n\n>Lacunicambarus ludovicianus (Painted devil crayfish)\nLHMIHLHWYQYPPMNPMMYPLLLVFMLITGILCLAGNFVTIWVFMNTKSLRTPANLLVVN\nLAMSDFLMMFTMFPPMMITCYYHTWTLGATFCEVYAFLGNLCGCASIWTMVFITFDRYNV\nIVKGVAGEPLSTKKASLWILTVWVLSFTWCVAPFFGWNRYVPEGNLTGCGTDYLSEDILS\nRSYLYIYSTWVYFLPLAITIYCYVFIIKAVAAHEKGMRDQAKKMGIKSLRNEEAQKTSAE\nCRLAKIAMTTVALWFIAWTPYLLINWVGMFARSYLSPVYTIWGYVFAKANAVYNPIVYAI\nS<\/code><\/pre>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-af77e21e-cc8e-41f0-aa74-7f112f133274\"><h2>Clustal Omega<\/h2>\n<ol class=\"wp-block-list\">\n<li><\/li>\n<\/ol>\n\n\n\n<ol class=\"wp-block-list\">\n<li><\/li>\n<\/ol>\n\n\n\n<p><strong>1.<\/strong> Paste all the amino acid sequences, including greater-than symbols and species names, into the input box in the window below. (Alternatively, upload <a href=\"https:\/\/drive.google.com\/file\/d\/1KDqNuCz0dGR0WpanujVZ0HUd2xMJz0B2\/view?usp=sharing\" target=\"_blank\" rel=\"noreferrer noopener\">this FASTA file<\/a> containing the sequences from your computer.)<\/p>\n\n\n\n<p><strong>2.<\/strong> Select \u201cClustalW with character counts\u201d as the output format.<\/p>\n\n\n\n<p><strong>3.<\/strong> Submit the sequences for alignment.<\/p>\n\n\n\n<p><strong>4.<\/strong> The multiple rhodopsin sequences have now been aligned. You can view the results in the \u201cAlignment\u201d tab and for a better visualisation, click on \u201cShow Colors\u201d.&nbsp;<\/p>\n\n\n\n<p><strong>5.<\/strong> Download or copy the aligned amino acid sequences for the next task (including \u201cCLUSTAL O(1.2.4) multiple sequence alignment\u201d).<\/p>\n\n\n\n<p><strong>Note:<\/strong> The output of multiple sequence alignments also contains an additional line underneath the last sequence that gives information about how conserved a specific residue is. Here\u2019s how to interpret this:<\/p>\n\n\n\n<p>&#8211; Asterisk (<strong>*<\/strong>):&nbsp; fully conserved residue (identical in all sequences)<br>&#8211; Colon (<strong>:<\/strong>): strongly conserved residue<br>&#8211; Period (<strong>.<\/strong>): semi-conserved residue<br>&#8211; Empty (<strong> <\/strong>): non-conserved residue<\/p>\n\n\n\n<div class=\"vf-embed vf-embed--16x9 | vf-u-margin__bottom--400\"\n>\n<iframe src=\"https:\/\/www.ebi.ac.uk\/Tools\/msa\/clustalo\/\" frameborder=\"0\" controls allowfullscreen><\/iframe><\/div>\n\n\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-d24452c0-50ca-4416-b035-2e5f70dc37dd\"><h2>Questions<\/h2>\n<p><strong>1.<\/strong> What can you deduce from the alignment? Are there any notable differences in the length of the sequences?<br><strong>2.<\/strong> Which species possesses the longest rhodopsin amino acid sequence?<br><strong>3.<\/strong>&nbsp;Are there any conserved residues or parts of the sequences present in all the species? Are there some parts that are found solely in one or a few species?<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-059237fe-aeba-4999-ba07-b99de87ae8bf\"><h2>Activity navigation<\/h2>\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/the-mysterious-protein-a-bioinformatics-expedition\/\">Introductory<\/a><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/the-mysterious-protein-a-bioinformatics-expedition\/\" target=\"_blank\" rel=\"noreferrer noopener\"> <\/a><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/the-mysterious-protein-a-bioinformatics-expedition\/\">page<\/a><\/li>\n\n\n\n<li><a href=\"http:\/\/embl.org\/ells\/teachingbase\/part-1-from-dna-to-protein-sequence\/\" target=\"_blank\" rel=\"noreferrer noopener\">Part 1: From DNA to protein sequence<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-2-protein-identity-and-function\/\" data-type=\"URL\" data-id=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-2-protein-identity-and-function\/\" target=\"_blank\" rel=\"noreferrer noopener\">Part 2: Protein identity and function<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-3-multiple-sequence-alignment\/\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>Part 3: Multiple sequence alignment&nbsp;<\/strong><\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-4-phylogenetic-analysis\/\" data-type=\"URL\" data-id=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-4-phylogenetic-analysis\/\" target=\"_blank\" rel=\"noreferrer noopener\">Part 4: Phylogenetic analysis&nbsp;<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-5-structural-analysis\/\" data-type=\"URL\" data-id=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-5-structural-analysis\/\" target=\"_blank\" rel=\"noreferrer noopener\">Part 5: Structural analysis<\/a><\/li>\n<\/ul>\n<\/section>\n<\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"featured_media":36177,"parent":36087,"menu_order":3,"template":"","class_list":["post-36135","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/36135","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\/36087"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media\/36177"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=36135"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}