{"id":19357,"date":"2015-10-05T13:45:15","date_gmt":"2015-10-05T11:45:15","guid":{"rendered":"http:\/\/emblog.embl.de\/ells\/?post_type=teachingbase&#038;p=19357"},"modified":"2021-06-18T15:02:38","modified_gmt":"2021-06-18T15:02:38","slug":"part-1-search-for-protein-identity","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-1-search-for-protein-identity\/","title":{"rendered":"Part 1: Search for protein identity"},"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-4e25ab7e-2c41-42d5-aa00-09c96f8b4be9\">Overview<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-056b45f6-2efd-4a4a-9bbe-8af6cbe7e751\">Your task<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-4ee0e8b2-ebdd-4d4e-905e-ae1e4235b011\">Sequence<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-a6dc31f5-7afe-43cb-9e43-f2728ace9ae5\">Protein BLAST<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-7a5ab492-eb0a-4cd9-9b74-10d11126f360\">Questions<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-36f3994d-b165-4987-a6b7-5098d466eec3\">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-4e25ab7e-2c41-42d5-aa00-09c96f8b4be9\"><h2>Overview<\/h2>\n<p>Imagine we have cloned a new gene and recently got the sequencing results. We were able to translate the nucleotide sequence into an amino acid sequence. However, we do not know anything about the function of our gene. We will therefore try to find very similar sequences in a database containing known protein sequences to see whether our protein resembles any known sequences and their functions.<\/p>\n\n\n\n<p>To start the activity, just follow the instructions in the &#8220;Your Task&#8221; tab and try to answer the activity questions.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-056b45f6-2efd-4a4a-9bbe-8af6cbe7e751\"><h2>Your task<\/h2>\n<p><strong>Proceed as described below:<\/strong><\/p>\n\n\n\n<p><strong>1.&nbsp;&nbsp;&nbsp;<\/strong>The \u201cSequence\u201d tab contains the amino acid sequence of the unknown protein \u201cBovine_Protein\u201d.<br><strong>2. &nbsp;<\/strong>&nbsp;Copy the sequence and follow the instructions on the \u201cProtein BLAST\u201d tab to search for the identity of the protein.<br><strong>3.<\/strong>&nbsp;&nbsp; Follow the instructions in the \u201cProtein BLAST\u201d tab and 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-4ee0e8b2-ebdd-4d4e-905e-ae1e4235b011\"><h2>Sequence<\/h2>\n<p>Your input sequence:<\/p>\n\n\n\n<pre class=\"wp-block-code vf-u-text--break\"><code>Bovine_Protein\nMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA<\/code><\/pre>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-a6dc31f5-7afe-43cb-9e43-f2728ace9ae5\"><h2>Protein BLAST<\/h2>\n<p><strong>1.&nbsp;<\/strong>&nbsp; Access the Protein BLAST (Basic Local Alignment Search Tool) tool below.<br><strong>2.&nbsp;&nbsp;&nbsp;<\/strong>Paste your amino acid sequence (including greater-than symbol and sequence name) in the query box. Enter a descriptive job title (such as \u201cUnknown Protein\u201d). In the&nbsp; \u201cParameters\u201d field ensure \u201cblastp\u201d is selected. Run the search by hitting \u201cSubmit\u201d.<br><strong>3.<\/strong>&nbsp;&nbsp; Looking at the data table, try and answer the task questions.<\/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\/sss\/ncbiblast\/\" 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-7a5ab492-eb0a-4cd9-9b74-10d11126f360\"><h2>Questions<\/h2>\n<p><strong>1.<\/strong>&nbsp;&nbsp; Which protein gives the best hit in the protein database?<br><strong>2.<\/strong>&nbsp;&nbsp; What percentage of identity does your \u201cunknown protein\u201d share with the best hit?<br><strong>3.<\/strong>&nbsp;&nbsp; What is the known biological function of the best hit? (Click on the link in the second column of the results table (DB:ID) and scroll to \u201cGeneral annotation (Comments)\u201d.)<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-36f3994d-b165-4987-a6b7-5098d466eec3\"><h2>Activity navigation<\/h2>\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/\" data-type=\"teachingbase\" data-id=\"3942\">Introductory page<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-1-search-for-protein-identity\/\" data-type=\"teachingbase\" data-id=\"19357\">Part 1: Search for protein identity<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-2-multiple-sequence-alignment-of-protein-sequences\/\" data-type=\"teachingbase\" data-id=\"19359\"><strong>Part 2: Multiple sequence alignment of protein sequences<\/strong><\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-3-phylogenetic-analysis-of-aligned-protein-sequences\/\" data-type=\"teachingbase\" data-id=\"19361\">Part 3: Phylogenetic analysis of aligned protein sequences<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-4-topological-and-structural-analysis-of-proteins\/\" data-type=\"teachingbase\" data-id=\"19363\">Part 4: Topological and structural analysis of proteins<\/a><\/li><\/ul>\n<\/section>\n<\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"featured_media":1660,"parent":3942,"menu_order":4,"template":"","class_list":["post-19357","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/19357","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\/3942"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media\/1660"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=19357"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}