Lec17+notes

Lec17+notes - Protein homology (see Lecture 4!) Proteins...

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1 Protein homology (see Lecture 4!) Proteins with very similar sequences likely fold the same Proteins with very similar sequences likely function the same Proteins with less similar sequences *may* fold the same Similar folds *may* imply similar function (but not always) Identity at key residues implies similar function Proteins with even less similar sequences can fold the same (but may not at all!) Common folds do not necessarily imply common function With a large amount of sequence data, many comparisons can be made!
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2 How to find proteins similar to a given protein? Large database of protein sequences at NCBI Online search tool using BLAST, a search algorithm Submit a search form, get back a list of “hits” The list will have links to other info about the similar protein The user tries to decide what can be concluded…
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3 BLOSUM (BLOCK SUBSTITUTION MATRIX) Alignments are scored using a substitution matrix
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4 Let’s try to do it! You have a mystery sequence that predicts a protein: >mysterious protein MASDTPGFYVDKLNKYSQIHKVKIIYKEISVTGPPHDRRFTFQVIIEEREFPEGEGRSKQEAKNNAAKLA VEILDNENKVDSHTDASEQGLIEGNYIGLVNSFAQKENLPVNFELCDPDSQLPHRFICKCKIGQTTYGTG FGANKKEAKQLAAKNAYQKLSEKSPSKTGFVTSLSSDFSSSSSITSNSASQSASGRDFEDIFMNGLREKR KSGVKVPSDDVLRNKYTLDDRFSKDFEDIEEIGSGGFGQVFKAKHRIDGKTYAIKRITYNTKKAKREVQA LAELNHANIVQYRVCWEGEDYDYDPENSTNGDTSRYKTRCLFIQMEFCDKGTLQQWLEKRNRSQEDKALV LELFEQIVTGVDYIHSKGLIHRDLKPGNIFLVDEKHIKIGDFGLATALENDGNPRTKYTGTPQYMSPEQK SSLVEYGKEVDIFALGLILAELLHICKTDSEKIEFFQLLRNGIFSDDIFDNKEKSLLQKLLSSKPRERPN TSEILKTLAEWKNISEKKKRNTC This is a FASTA file:
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Lec17+notes - Protein homology (see Lecture 4!) Proteins...

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