{"id":19439,"date":"2015-10-05T20:01:59","date_gmt":"2015-10-05T18:01:59","guid":{"rendered":"http:\/\/emblog.embl.de\/ells\/?post_type=teachingbase&#038;p=19439"},"modified":"2021-06-17T17:48:23","modified_gmt":"2021-06-17T17:48:23","slug":"step-4-comparison-of-amino-acid-sequences","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-4-comparison-of-amino-acid-sequences\/","title":{"rendered":"Step 4: Comparison of amino acid sequences"},"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-06938b10-94be-46c6-be96-2fffd279c159\">Overview<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-8a733a57-5480-4758-911e-46ffc6af953b\">Your task<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-d194c45f-37fc-4601-8ab3-de9b4974a4a3\">MUSCLE<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-1285552d-049a-4c11-bd79-cfaa40a8f7a7\">Amino acid sequences<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-7eb8e73c-ae74-4cfe-822f-3c7775beeee2\">Questions<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-f9fcf67e-c0d4-45cc-b8bc-959d4ee50b10\">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-06938b10-94be-46c6-be96-2fffd279c159\"><h2>Overview<\/h2>\n<p>In this part of the activity, we will feed two of the protein sequences which we have generated in the previous step into the EMBL-EBI MUSCLE alignment tool to check the similarity between these two fluorescent proteins. A sequence alignment based on the amino acid sequence gives a stronger hint towards their similarity than a nucleotide sequence. The alignment allows us to visualise additions, deletions or exchanges within the amino acid sequences. It also allows to find amino acid residues or stretches which have been strongly conserved during evolution.<\/p>\n\n\n\n<p>After completing this task, you will have produced a multiple sequence alignment on protein level and you will be able to roughly estimate where and what the differences between our two sequences are.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-8a733a57-5480-4758-911e-46ffc6af953b\"><h2>Your task<\/h2>\n<p><strong>Proceed as described below:<\/strong><\/p>\n\n\n\n<ol class=\"wp-block-list\"><li>Copy all of the amino acid sequences which are provided under the tab \u201cAmino acid sequences\u201d (i.e. select and copy the whole block of sequences) (shortcut Ctrl. + C).<\/li><li>Paste the amino acid sequences into the MUSCLE search box (shortcut Ctrl. + V).<\/li><li>Follow the instructions in the tab \u201cMUSCLE\u201d to align your sequences.<\/li><li>Have a look at the alignment and try to answer the task questions.<\/li><\/ol>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-d194c45f-37fc-4601-8ab3-de9b4974a4a3\"><h2>MUSCLE<\/h2>\n<ol class=\"wp-block-list\"><li>Copy all of the amino acid sequences which are provided under the tab \u201cAmino acid sequences\u201d (i.e. select and copy the whole block of sequences) (shortcut Ctrl. + C).<\/li><li>Paste the amino acid sequences into the MUSCLE search box (shortcut Ctrl. + V).<\/li><li>In the \u201cSTEP 2\u201d section ensure that \u201c<strong>Output Format<\/strong>\u201d is set at&nbsp;<strong>\u201cClustalW\u201d<\/strong>.<\/li><li>Just click on the large&nbsp;<strong>\u201cSubmit<\/strong>\u201d button and your alignment will be processed.<\/li><li>You will see the results after a few seconds.<\/li><li>Have a look at the alignment and try to answer the questions in the \u201cQuestions\u201d tab<\/li><\/ol>\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-1285552d-049a-4c11-bd79-cfaa40a8f7a7\"><h2>Amino acid sequences<\/h2>\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nProtein sequence 1<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<pre class=\"wp-block-preformatted\"><span style=\"word-break:break-all\"<\/span>&gt;Protein_Sequence1_AVGFP_1\nMSKGEELFTGVVPVLVELDGDVNGQKFSVSGEGEGDATYGKLTLNFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFYKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKMEYNYNSHNVYIMGDKPKNGIKVNFKIRHNIKDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMILLEFVTAARITHGMDELYK<\/pre>\n\n<\/div>\n<\/details>\n\n\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nProtein sequence 2<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<pre class=\"wp-block-preformatted\"><span style=\"word-break:break-all\"<\/span>&gt;Protein_Sequence2_GFPm_1\nMSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFGYGVQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK<\/pre>\n\n<\/div>\n<\/details>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-7eb8e73c-ae74-4cfe-822f-3c7775beeee2\"><h2>Questions<\/h2>\n<p>Have a look at the protein alignment and try to answer the following questions:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>How do you know whether the amino acid residues in the individual sequences are the same or not compared to the other aligned sequences?<\/li><li>Do you think there many corresponding amino acids? Are there more similarities compared to the respective nucleotide alignments?<\/li><li>What do you think are the reasons for these changes?<\/li><\/ul>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-f9fcf67e-c0d4-45cc-b8bc-959d4ee50b10\"><h2>Activity navigation<\/h2>\n<p><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/\">GFP treasure hunt<\/a><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/gfp-treasure-hunt-introduction\/\">GFP treasure hunt introduction<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-1-database-search\/\">Step 1: Database search<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-2-comparison-of-nucleotide-sequences\/\">Step 2: Comparison of nucleotide sequences<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-3-translation-of-mrnas\/\">Step 3: Translation of mRNAs<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-4-comparison-of-amino-acid-sequences\/\">Step 4: Comparison of amino acid sequences<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-5-structure-of-gfp\/\"><strong>Step 5: Structure of GFP<\/strong><\/a><\/li><\/ul>\n<\/section>\n<\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"featured_media":1664,"parent":5012,"menu_order":2,"template":"","class_list":["post-19439","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/19439","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\/5012"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media\/1664"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=19439"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}