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compgenomics:modul3 [2025/05/17 13:37] – ingocompgenomics:modul3 [2025/09/23 13:26] (current) – felix
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-==== Analysis ====+===== Analysis =====
  
 In this exercise, we will extract the sequences of a subset of orthologs for two PCD gene families from [[https://ebersberger-46-155.biologie.uni-frankfurt.de/phyloppcd/|our interactive webtool]]. We will align these sequences and calculate a phylogenetic tree. This tree will then help us to better understand the evolutionary history of the gene family In this exercise, we will extract the sequences of a subset of orthologs for two PCD gene families from [[https://ebersberger-46-155.biologie.uni-frankfurt.de/phyloppcd/|our interactive webtool]]. We will align these sequences and calculate a phylogenetic tree. This tree will then help us to better understand the evolutionary history of the gene family
  
-=== Task 1: GH27_QRW17738.1 ===+==== Task 1: GH27_QRW17738.1 ====
  
   - Extract the sequences of GH27_QRW17738.1 orthologs for the following taxa:<WRAP>   - Extract the sequences of GH27_QRW17738.1 orthologs for the following taxa:<WRAP>
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   - Align the sequences using [[https://www.ebi.ac.uk/jdispatcher/msa/clustalo|ClustalOmega]]   - Align the sequences using [[https://www.ebi.ac.uk/jdispatcher/msa/clustalo|ClustalOmega]]
   - Inspect the distance tree generated by ClustalOmega. What can you learn?   - Inspect the distance tree generated by ClustalOmega. What can you learn?
 +
 +
 +=== Shortcut to Sequence file ===
  
 <hidden GH27_QRW17738.fa> <hidden GH27_QRW17738.fa>
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-=== Task 2: GH28_QRW23661.1 ===+==== Task 2: GH28_QRW23661.1 ====
  
   - Repeat the analysis using GH28_QRW23661.1 and the following taxon set:<WRAP>   - Repeat the analysis using GH28_QRW23661.1 and the following taxon set:<WRAP>
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 </file></WRAP> </file></WRAP>
  
-=== Summary and Discussion ===+=== Shortcut to Sequence file === 
 + 
 +<hidden GH28_QRW23661.1.fa> 
 +<file> 
 +>WP_367284634.1 glycoside hydrolase family 28 protein [Arcicella rosea] 
 +MKKRISLLIAISSAMFCNSLVAQKTPTYSWKNLPKIVQPTFAKDTFNVTKFGAKPDGITLNTQAINDAIT 
 +ACSKKGGGVVLVPNGMWLTGPIVLKSNVNLHIRKAATLLFTEDKSQYPLVEGSYEGKSAARNQSPISATN 
 +QENIAITGQGIIDGSGDVWRAVNKAQLTESEWNAKKASGGVLKANGLTWYPSEQFMKASVENRSMLLKDG 
 +VSLQSFADMKDFLRPNLLVITKCKKVLLEGVTFQNSPAWCLHPLMSENLTLRNLTIKNPEYAHNGDGMDI 
 +ESCKNFLVDGCTIDVGDDAICIKSGKDEEGRKRGMPTENGIIRNCIVYNGHGGFVVGSEMSGGARNIFVY 
 +DCTFAGTDKGLRFKSVRGRGGIVENIYAKNIFMKDIAQEAIFFDMYYFVKFATDSPRDERPVVNEGTPIF 
 +RNMKFENIVCKGANKGIFVRGLSEMPIQNIQMSNIVLDTKIGAEFIDASNITLEKVTLISENTKPVISVN 
 +NSDGLTFNTIQYKANAELLFAIAGERSKAIQILQTDSSKAQKQIEFTEGATKEAITVSTGK 
 +>GH28_QRW23661.1|PYROR@242507@000002495_2|XP_003719232.1|1 
 +MKLSSLLAMLGVATTATAFMPADRPRNAQEFRAKHPVARRADSGCRRRFTPRASTHDLDDVSAEFEQAVRDANNGGTVHLPKDQLFVIGKPLDLTFLNDIHVKLEGTIRFTNDTPYWQANAFYHPFQRSLMFWKWGGKDIKIYGEGVLDGNGQRWWNEFSGLEILDPDNPYLRPVLFYAENTTNLHVEGIFMKDSPVWHNFVVTSKDVTYKDVIIEAISNNATSPPKNSDFFNSLNVDGVTVERVWVNIGDDCFSPKSNTSNVHVNTMYCNGTHGQSMGSLGQYEGEVSIVENVLIENVALLNGDNGARLKIWAGESVGSGWIRNVTFRNFYAANLDFVARLDSCYFNIPSETCNRFPSKMSIQDITFENFSGTTSGKNGDAVARLTCSTSPDAVCENVVFKNFNITSPCGGAPVVICDGITGLQHGCVAFDSAEAKAAMDNKCKAPVASIEPPWPVRDWRNSK 
 +>GH28_QRW23661.1|RHISO@456999@016906535_1|XP_043183898.1|1 
 +MLSAILAVALGAAVALASKTGVKTQTCIVPSHGNVNISDTPAVHATFKKCGKGGHIIFSENTNYTLRELTTMTPCIGCTVQLEGTIQMADNITYWLKNETTNTPNITAETFPHLVYYPFQDTVAYLILKDWSHSTLVSKTGKGLIDGLGQLWWDAAVGQQILLPGTLRRPVLFTLDGANNVTVDNVTMRNPANWFNWVTDSSNVVYKNIRLSALSANKNPPANADGWDTYRTSHFELRDSHIVSGDDCFAFKPNSTYITIENVYCQNSHGVSVGSLAQYPGVLDIVEHVKVKNVTFVGNGDSSSNGARIKIWSGPVGSAIVNDIHYEDLRVENVTNPLVVDSCYFSSAYCATGKPVATITNVTVTNITGTSTGKVVSSIICPEGSTCDIKLKNVNIVPKTGVAPVYRCFSVASEDLGVNCTYPTIVNGAFKWPA 
 +>GH28_QRW23661.1|PROLA@2754530@002105105_1|XP_040722516.1|1 
 +MLPQHCAIAAAWLQLLSLGYATAQGLSISSSHLLTSNAAVKPNPTEANVAPKVCSIKANMNGISKDLLQAAQACKSNGHIIIEAGDSLIDNVVVMADLKDVTISIQGTLHLKADPVFWAQNAYKHDLVNFQNSSAAILFRDCEGLKFGGAEVFKTGSTIIGYGAPFWSAYLADNTIMRPNLVTLQRCTNCEISNLRFLDTPKWAMYVTDSDHVNIHDMMIQSIGGSVMAMNTDGIDIRNSTNVEFHNNYIDNTDDCVAIKGMCSNIYVHDIICGSKTAGVAIGSLGNIVGVNEFVKDVVIQDVLISGTPRGGIRIKIWPGNRVKAKELLGGGGLADVHNITASRIHTSDNSQALYIDTCYSLGRTNSNCYGYPSLGTITDVTIDGIYGTSPTGSFGHVLCSNPSKCQNIKINNVIMATAVDTASGIGTTAVLNTVGVPPSILSGAPADIGLFDLSLPNGCYLERAAYATDSTPVPYFAPKPRDRPLGYLDGVPKTPADCLQPGSKWWLAQGQPSDFTLSTTSYKPPVYPKVHLSQIPASRVKVSPAFPKNG 
 +>GH28_QRW23661.1|RHAZE@28612@001687245_1|XP_017491101.1|1 
 +LNPVVVQINDSSHIIVSDLTFINSPWFTVAPYRSEYVTIDHVTVKNPSNAPNTDGIHPEACHHVVISNCFVSTGDDGIVITSETDKNTNAKYSSENITVNHCTVHSGHGGIVIGSAISGDVRDIHAHNLHFEGTLRGVRLKSTRDHGGIVENIYIKDITMKNISDEGITISAFYDVKNFDPHNIPSKTFDVSKTPTFRNIHLTNVTGDSKLGLQIVGLPEKHFDKIELKQVHLVAKKEEIIVNADHVLKENFIYKIDKHLHDN 
 +>GH28_QRW23661.1|BRACO@38358@014529535_1|XP_037032572.1|0 
 +MKNLITIATFIGSVLTSQLLPLPTQFFSSRLGDSAPLDKKFIVENCDYNGRLLAFSIENCTDTEGICNIVTKREYNVNITFEPSVSTSNLIWRVIFNINGQDQVLVERPIYEHVQPGVTYTLFNTFAFGFENEGLSFPATFQIIDASTERAEICHSAVLDVNSWHMVPEILSRIKAPIFPDRDFDITTYGAVPDGETDNTEAFSRAIVHCHLLGGGRVVVPPGVFLSSAITLLSNVNLHLKEGSTILFTQNTTAYPNVFTRLGGLELINFSPFIYAFGAENIALTGSGVLNGNADCEHWWPWKGRNNNLELLCGIIEGFPTEEADVAALTEMAERNVPVEERIFGEGHFMRPVFVQPYNSKNILIEGVTFLRSPNWILNPVLCENVIVRGVTINSTGPNSDGCNPESSKDVLIENVKFITGDDCIAVKSGRNADGRRINVKSENIVIQNCEMENGHGGFTIGSEISGGAQNIFCQNCSMNSPQLEQGLRFKNNAVRGGLIEDIYIRNIHIPELYTGTSASRGMVLSIDFFYEEGPNGNYPPVVRNVDIRNVTALKSNYALYLRGFPTDQITNVRLYDCHFNGVVRGSVIEHVENLGLFNVTVNGDVIEVPAV 
 +>GH28_QRW23661.1|SPOLI@69820@002706865_1|XP_022836218.1|1 
 +MFCNSLVAQKTPTYSWKNLPKIVQPTFAKDTFNVTKFGAKPDGITLNTQAINDAITACSKKGGGVVLVPNGMWLTGPIVLKSNVNLHIRKAATLLFTEDKSQYPLVEGSYEGKSAARNQSPISATNQENIAITGQGIIDGSGDVWRAVNKAQLTESEWNAKKASGGVLKANGLTWYPSEQFMKASVENRSMLLKDGVSLQSFADMKDFLRPNLLVITKCKKVLLEGVTFQNSPAWCLHPLMSENLTLRNLTIKNPEYAHNGDGMDIESCKNFLVDGCTIDVGDDAICIKSGKDEEGRKRGMPTENGIIRNCIVYNGHGGFVVGSEMSGGARNIFVYDCTFAGTDKGLRFKSVRGRGGIVENIYAKNIFMKDIAQEAIFFDMYYFVKFATDSPRDERPVVNEGTPIFRNMKFENIVCKGANKGIFVRGLSEMPIQNIQMSNIVLDTKIGAEFIDASNITLEKVTLISENTKPVISVNNSDGLTFNTIQYKANAELLFAIAGERSKAIQILQTDSSKAQKQIEFTEGATKEAITVSTGK 
 +</file> 
 +</hidden> 
 + 
 + 
 + 
 +==== Summary and Discussion ====
  
   * Why are there plant cell wall degrading enzymes in animals?   * Why are there plant cell wall degrading enzymes in animals?
   * Why is GH28 of //Spodoptera litura// identical to a bacterial sequence? What are the consequences given the assumptions stated above?   * Why is GH28 of //Spodoptera litura// identical to a bacterial sequence? What are the consequences given the assumptions stated above?
  
-{{ :compgenomics:cellulase_all.extended.fa.gz |}}+==== Supplementary Data === 
 + 
 +{{ :compgenomics:cellulase_all.extended.fa.gz |all_cellulase_sequences.fa.gz}}
  
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