Bioinformatics: Multiple Sequence Alignment Lab, science homework help

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Fuhturf95

Science

Description

Assignment: 

In this lab, we are comparing sequences of phosphoglycerate kinase amongst different organisms. 

Procedure:

1. Visit http://www.ebi.ac.uk/Tools/msa/clustalo/

2. Copy & Paste alignment sequences into input box (You will find this attached as "4NG4 Multisequence")

3. Click Submit

4. Right Click "Download Alignment File" --> "Download Linked File"

5. Visit http://consurf.tau.ac.il

6. Click Amino Acids --> Is there a protein structure ? Yes --> PDB ID: 4NG4 --> Click "Next" --> Chain A --> MSA to upload ? Yes --> Choose File: Upload the file you downloaded from Clustal Omega --> Query Sequence Name: sp|P0A799|PGK_ECOLI --> Tree file to upload ? No --> Uncheck send link to email --> Click "Submit" & wait for results

After getting results from Consurf, use Jmol or Chimera to: 

1) produce the overall 3D structure (capture/screenshot this image)

2) produce an image of least conserved regions and most conserved regions (capture/screenshot this image)

***NOTE: The molecule will be in space filling mode color coded by conservation with the most conserved regions in maroon and the least conserved regions in blue. ***

ALSO, If Jmol doesn't work you may have to download Chimera !


Unformatted Attachment Preview

>sp|P0A799|PGK_ECOLI SNAMSENKMKALPFLSMSNLNLHNKRVMIREDLNVPMKNGKITNDERIVRALPT IQKAIEQKARVMILSHLGRPEEGKFEKEFSLAPVARLLSKKLNQKVPLINDWLKG VAVEPGQAILCENVRFNKGENENNTELAKRMAELCDIFVMDAFATAHRAQAST AGVAAYAKLACAGPLLISEVEALSRALENPQKPLVAVVGGSKVSTKIHLLENLLD KVDQLIVGGGIANTFLKAQGYSIGKSLCENEWLDAAQQFWEKAAEKNVSLPLPV DVIVADELSEDAKATVKNIDAVTSNESIFDVGPNTSATYAKLMAQAGTIVWNGPI GVFEIEAFSQGTRALAQAVAKSTAYSIVGGGDTLAALDKFNLTDQMSYVSTAGG AFLEFLEGKILPAIKILTQRAKEY >sp|Q3T0P6|PGK1_BOVIN MSLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKYCLDSG AKSVVLMSHLGRPDGVPMPDKYSLQPVAVELKSLLGKDVLFLKDCVGPEVEKA CADPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPTKIEAFRASLSKLGDVY VNDAFGTAHRAHSSMVGVNLPKKAGGFLMKKELNYFAKALESPERPFLAILGG AKVADKIQLISNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGSKIVKDL MSKADKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSK KYAEAVARAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGD TATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSSV >sp|P00558|PGK1_HUMAN MSLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNG AKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKA CANPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIEAFRASLSKLGDVY VNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGG AKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDL MSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSK KYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDT ATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI >sp|Q7SIB7|PGK1_PIG MSLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAIPSIKFCLDNG AKSVVLMSHLGRPDGIPMPDKYSLEPVAVELKSLPGKDVLFLKDCVGPEVEKA CADPAAGSVILLENLRFHVEEEGKGKDASGSKVKADPAKIEAFRASLSKLGDVY VNDAFGTAHRAHSSMVGVNLPKKAGGFLMKKELNYFAKALESPERPFLAILGG AKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGSKIVKDL MSKAEKNGVKITLPVDFVTADKFDENAKIGQATVASGIPAGWMGLDCGPESSK KYSEAVARAKQIVWNGPVGVFEWEAFAQGTKALMDEVVKATSRGCITIIGGGD TATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNV >sp|P09041|PGK2_MOUSE MALSAKLTLDKVDLKGKRVIMRVDFNVPMKNNQITNNQRIKAAIPSIKHCLDNGA KSVVLMSHLGRPDGIPMPDKYSLEPVADELKSLLNKDVIFLKDCVGPEVEQACA NPDNGSIILLENLRFHVEEEGKGKDSSGKKISADPAKVEAFQASLSKLGDVYVN DAFGTAHRAHSSTVGVNLPQKASGFLMKKELDYFSKALEKPERPFLAILGGAKV KDKIQLIKNMLDKVNFMIIGGGMAYTFLKELKNMQIGASLFDEEGATIVKEIMEKA EKNGVKIVFPVDFVTGDKFDENAKVGQATIESGIPSGWMGLDCGPESIKINAQIV AQAKLIVWNGPIGVFEWDAFAKGTKALMDEVVKATSNGCVTIIGGGDTATCCAK WGTEDKVSHVSTGGGASLELLEGKILPGVEALSNM >sp|P51903|PGK_CHICK MSLSNKLTLDKVDVKGKRVVMRVDFNVPMKDHKITNNQRIKAAVPTIKHCLDHG AKSVVLMSHLGRPDGVPMPDKFSFSPVAVELKALLGREVSFLKDCVGPEVEKA CANPANGSVILLENLRFHVEEEGKGKDASGNKIKADAAKVEAFRASLSKLGDVY VNDAFGTAHRAHSSMVGVHLPQKAAGFLMKKELDYFAKALESPERPFLAILGG AKVQDKIQLISNMLDKVNEMIIGGGMAFTFLKVLNNMQIGNSLFDEEGSKIVKDL MAKAEKNGVKITLPVDFITADKFDEHAQTGEATVASGIPAGWMGLDCGPESVK KFVEVVGRAKQIVWNGPVGVFEWDKFSKGTKALMDKVVEVTGKGCITIIGGGD TATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSSV >sp|P12782|PGKH_WHEAT MASTAAPPAALVARRAASASVAAPLRGAGLAAGCQPARSLAFAAGADPRLAVH VASRCRAASAARGTRAVATMAKKSVGDLTAADLEGKRVLVRADLNVPLDDNQ NITDDTRIRAAIPTIKYLLSNGAKVILTSHLGRPKGVTPKFSLAPLVPRLSELLGIEV KKAEDVIGPEVEKLVADLANGAVLLLENVRFYKEEEKNDPEFAKKLASLADLFVN DAFGTAHRAHASTEGVTKFLKPSVAGFLLQKELDYLDGAVSNPKRPFAAIVGGS KVSSKIGVIESLLEKCDILLLGGGMIFTFYKAQGLSVGSSLVEEDKLELATSLLAK AKAKGVSLLLPSDVIIADKFAPDANSQTVPASAIPDGWMGLDIGPDSVKTFNDAL DTTQTIIWNGPMGVFEFDKFAVGTESIAKKLAELSKKGVTTIIGGGDSVAAVEKV GVADVMSHISTGGGASLELLEGKELPGVVALDEGVMTRSVTV >sp|P00559|PGK1_HORSE MSLSNKLTLDKLNVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNG AKSVVLMSHLGRPDVGPMPDKYSLQPVAVELKSLLGKDVLFLKDCVGPEVEKA CADPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIETFRASLSKLGDVY VNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGG AKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKNL MSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGTESSK KYAEAVARAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGD TATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNV >sp|P16617|PGK1_RAT MSLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNG AKSVVLMSHLGRPDGVPMPDKYSLEPVAAELKSLLGKDVLFLKDCVGSEVENA CANPAAGTVILLENLRFHVEEEGKGKDASGNKVKAEPAKIDAFRASLSKLGDVY VNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGG AKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLYDEEGAKIVKDL MAKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGTESSK KYAEAVARAKQIVWNGPVGVFEWEAFARGTKSLMDEVVKATSRGCITIIGGGD TATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNV >sp|Q11CR7|PGK_CHESB MAGFKTLDDLKDVAGKRVLLRVDLNVPVKDGEVTDTTRIERVAPTITELSDKGA KVILLAHFGRPKGKPDAEASLQPIAHAVEAVLDRRVHFASSCIGEPAKKAVDEM TGGDILLLENTRFHAGEEKNDPEFTKALAANGDIYVNDAFSAAHRAHASTEGLA HLLPAYAGRTIQAELEALQRGLGDPKRPVVAIVGGAKVSTKIDLLTNLVKKVDCL VIGGGMANTFLAARGTSVGKSLCEHDLRETAKQIMIDAAEAGCAIILPVDAVVAR KFEAGAETETVDIDAVPEDAMILDVGPKSVEKVKEWLDRADTLVWNGPLGAFE LSPFDKATMEVAKYAARRTRESLLVSVAGGGDTVAALNQADVSDDFSYVSTAG GAFLEWMEGKDLPGVAALQK >sp|Q01604|PGK_DROME MAFNKLSIENLDLAGKRVLMRVDFNVPIKEGKITSNQRIVAALDSIKLALSKKAKS VVLMSHLGRPDGNKNIKYTLAPVAAELKTLLGQDVIFLSDCVGSEVEAACKDPA PGSVILLENVRFYVEEEGKGLDASGGKVKADPAKVKEFRASLAKLGDVYVNDA FGTAHRAHSSMMGDGFEQRAAGLLLNKELKYFSQALDKPPNPFLAILGGAKVA DKIQLIENLLDKVNEMIIGGGMAFTFLKVLNNMKIGGSLFDEEGSKIVEKLVEKAK KNNVQLHLPVDFVCGDKFAENAAVSEATVEAGIPDGHMGLDVGPKTRELFAAPI ARAKLIVWNGPPGVFEFPNFANGTKSIMDGVVAATKNGTVSIIGGGDTASCCAK WNTEALVSHVSTGGGASLELLEGKTLPGVAALTSA
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Explanation & Answer

Dear student,I have modelled the proteins according to the default settings in both Clustal Omega and ConSurf with the data file you provided me with their sequences and the instructions provided in the assignment specifications.Please find enclosed a zip file with all the results obtained from the Co...

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