Difference between revisions of "3. Pick 5 protein sequences and predict their secondary structures using available prediction programs"

From Biolecture.org
imported>Jaehyeok Shin
(Created page with "<p>'H' - Helix, 'E' - Extended, 'B' - Buried, '-' - other types</p> <p>DSCR1(RCAN1) - Down Syndrome Critical Region 1, Regulator of Cal...")
 
imported>Jaehyeok Shin
 
(2 intermediate revisions by the same user not shown)
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<p>&#39;H&#39; - Helix, &#39;E&#39; - Extended, &#39;B&#39; - Buried,&nbsp;&#39;-&#39; - other types</p>
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<p><span style="font-family:arial,helvetica,sans-serif">I used Jpred 4 program <a href="http://www.compbio.dundee.ac.uk/jpred4/index.html">http://www.compbio.dundee.ac.uk/jpred4/index.html</a></span></p>
  
<p>DSCR1(RCAN1)&nbsp;- Down Syndrome Critical Region 1, Regulator of Calcineurin 1</p>
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<p><span style="font-family:arial,helvetica,sans-serif">&#39;H&#39; - Helix, &#39;E&#39; - Extended, &#39;B&#39; - Buried,&nbsp;&#39;-&#39; - other types</span></p>
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<p><span style="font-family:arial,helvetica,sans-serif">DSCR1(RCAN1)&nbsp;- Down Syndrome Critical Region 1, Regulator of Calcineurin 1</span></p>
  
 
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<pre>
 
<pre>
<code>MVYAKFESLFRTYDKDITFQYFKSFKRVRINFSNPFSAADARLQLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKQFLISPPASPPVGWKQVEDATPVINYDLLYAISKLGPGEKYELHAATDTTPSVVVHVCESDQEKEEEEEMERMRRPKPKIIQTRRPEYTPIHLS
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<span style="font-family:courier new,courier,monospace"><code>MVYAKFESLFRTYDKDITFQYFKSFKRVRINFSNPFSAADARLQLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKQFLISPPASPPVGWKQVEDATPVINYDLLYAISKLGPGEKYELHAATDTTPSVVVHVCESDQEKEEEEEMERMRRPKPKIIQTRRPEYTPIHLS
-HHHHHHHHHH-----EEEEE-----EEEEEE--HHHHHHHHHHH--------EEEEEE-------------------------------EEE---------HHHHHHHHH-------EE--------EEEEEE---------------------E---------------</code></pre>
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-HHHHHHHHHH-----EEEEE-----EEEEEE--HHHHHHHHHHH--------EEEEEE-------------------------------EEE---------HHHHHHHHH-------EE--------EEEEEE---------------------E---------------</code></span></pre>
  
 
<hr />
 
<hr />
<p>FMRP - Fragile X syndrome Mental Retardation Protein</p>
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<p><span style="font-family:arial,helvetica,sans-serif">FMRP - Fragile X syndrome Mental Retardation Protein</span></p>
  
 
<pre>
 
<pre>
<code>MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPDRQIPFHDVRFPPPVGYNKDINESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKPATKDTFHKIKLDVPEDLRQMCAKEAAHKDFKKAVGAFSVTYDPENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLIMRNEEASKQLESSRQLASRFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEEIMPPNSLPSNNSRVGPNAPEEKKHLDIKENSTHFSQPNSTKVQRVLVASSVVAGESQKPELKAWQGMVPFVFVGTKDSIANATVLLDYHLNYLKEVDQLRLERLQIDEQLRQIGASSRPPPNRTDKEKSYVTDDGQGMGRGSRPYRNRGHGRRGPGYTSGTNSEASNASETESDHRDELSDWSLAPTEEERESFLRRGDGRRRGGGGRGQGGRGRGGGFKGNDDHSRTDNRPRNPREAKGRTTDGSLQIRVDCNNERSVHTKTLQNTSSEGSRLRTGKDRNQKKEKPDSVDGQQPLVNGVP
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<span style="font-family:arial,helvetica,sans-serif"><code>MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPDRQIPFHDVRFPPPVGYNKDINESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKPATKDTFHKIKLDVPEDLRQMCAKEAAHKDFKKAVGAFSVTYDPENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLIMRNEEASKQLESSRQLASRFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEEIMPPNSLPSNNSRVGPNAPEEKKHLDIKENSTHFSQPNSTKVQRVLVASSVVAGESQKPELKAWQGMVPFVFVGTKDSIANATVLLDYHLNYLKEVDQLRLERLQIDEQLRQIGASSRPPPNRTDKEKSYVTDDGQGMGRGSRPYRNRGHGRRGPGYTSGTNSEASNASETESDHRDELSDWSLAPTEEERESFLRRGDGRRRGGGGRGQGGRGRGGGFKGNDDHSRTDNRPRNPREAKGRTTDGSLQIRVDCNNERSVHTKTLQNTSSEGSRLRTGKDRNQKKEKPDSVDGQQPLVNGVP
---EEEEEE-----EEEEEEEEE---EEEEEE-------------------------------EEEEEE----------EEEEEEEE----EEEEEE-------EEEEE----------------EEEEEEE--HHHHHHHH-HHHHHHHHH---EEEEEE-----EEEEEE-----EEEEEH-HEEE----HHHHHHHHHHHHHHHHHHHHHHH----EEEEE-----HHHH------HHHHHHH----EEEE------EEEEEE--HHHHHHHHHHHHHHHEEEEE------EEE----HHHHHHH----EEEEEE-------------------HHHHHHHHHHHHHHHHHHH------EEE----------------------------------EEEEEEE--HHHHHHHHHHHHHHHHHHH-HHHHHEE-------------------EE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------</code></pre>
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---EEEEEE-----EEEEEEEEE---EEEEEE-------------------------------EEEEEE----------EEEEEEEE----EEEEEE-------EEEEE----------------EEEEEEE--HHHHHHHH-HHHHHHHHH---EEEEEE-----EEEEEE-----EEEEEH-HEEE----HHHHHHHHHHHHHHHHHHHHHHH----EEEEE-----HHHH------HHHHHHH----EEEE------EEEEEE--HHHHHHHHHHHHHHHEEEEE------EEE----HHHHHHH----EEEEEE-------------------HHHHHHHHHHHHHHHHHHH------EEE----------------------------------EEEEEEE--HHHHHHHHHHHHHHHHHHH-HHHHHEE-------------------EE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------</code></span></pre>
  
 
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<p>Death associated protein kinase 3</p>
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<p><span style="font-family:arial,helvetica,sans-serif">Death associated protein kinase 3</span></p>
  
 
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<pre>
<code>MSTFRQEDVEDHYEMGEELGSGQFAIVRKCRQKGTGKEYAAKFIKKRRLSSSRRGVSREEIEREVNILREIRHPNIITLHDIFENKTDVVLILELVSGGELFDFLAEKESLTEDEATQFLKQILDGVHYLHSKRIAHFDLKPENIMLLDKNVPNPRIKLIDFGIAHKIEAGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGETKQETLTNISAVNYDFDEEYFSNTSELAKDFIRRLLVKDPKRRMTIAQSLEHSWIKAIRRRNVRGEDSGRKPERRRLKTTRLKEYTIKSHSSLPPNNSYADFERFSKVLEEAAAAEEGLRELQRSRRLCHEDVEALAAIYEEKEAWYREESDSLGQDLRRLRQELLKTEALKRQAQEEAKGALLGTSGLKRRFSRLENRYEALAKQVASEMRFVQDLVRALEQEKLQGVECGLR
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<span style="font-family:arial,helvetica,sans-serif"><code>MSTFRQEDVEDHYEMGEELGSGQFAIVRKCRQKGTGKEYAAKFIKKRRLSSSRRGVSREEIEREVNILREIRHPNIITLHDIFENKTDVVLILELVSGGELFDFLAEKESLTEDEATQFLKQILDGVHYLHSKRIAHFDLKPENIMLLDKNVPNPRIKLIDFGIAHKIEAGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGETKQETLTNISAVNYDFDEEYFSNTSELAKDFIRRLLVKDPKRRMTIAQSLEHSWIKAIRRRNVRGEDSGRKPERRRLKTTRLKEYTIKSHSSLPPNNSYADFERFSKVLEEAAAAEEGLRELQRSRRLCHEDVEALAAIYEEKEAWYREESDSLGQDLRRLRQELLKTEALKRQAQEEAKGALLGTSGLKRRFSRLENRYEALAKQVASEMRFVQDLVRALEQEKLQGVECGLR
------------EEEEEEEEE---EEEEEEEE----EEEEEEEEE--------HHHHHHHHHHHHHHHHH-----EEEEEEEE----EEEEEEEE----HHHHHHHH-----HHHHHHHHHHHHHHHHHHHH---EEE-----EEEE---------EEEEE---EEEE----EEEEE------HHHHHH----------HHHHHHHHHHHHH---------HHHHHHHHH---------------HHHHHHHHHHH---------HHHHHH---------------------------------------------------------------------HHHHHH------------HHHH-----------HHHHHHHHH-----HHHHHH---------------HHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH-----------</code></pre>
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------------EEEEEEEEE---EEEEEEEE----EEEEEEEEE--------HHHHHHHHHHHHHHHHH-----EEEEEEEE----EEEEEEEE----HHHHHHHH-----HHHHHHHHHHHHHHHHHHHH---EEE-----EEEE---------EEEEE---EEEE----EEEEE------HHHHHH----------HHHHHHHHHHHHH---------HHHHHHHHH---------------HHHHHHHHHHH---------HHHHHH---------------------------------------------------------------------HHHHHH------------HHHH-----------HHHHHHHHH-----HHHHHH---------------HHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH-----------</code></span></pre>
  
 
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<p>Calcineurin</p>
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<p><span style="font-family:arial,helvetica,sans-serif">Calcineurin</span></p>
  
 
<pre>
 
<pre>
<code>MGVEIETISPGDGRTFPKKGQTCVVHYTGMLQNGKKFDSSRDRNKPFKFRIGKQEVIKGFEEGAAQMSLGQRAKLTCTPDVAYGATGHPGVIPPNATLIFDVELLNLE
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<span style="font-family:arial,helvetica,sans-serif"><code>MGVEIETISPGDGRTFPKKGQTCVVHYTGMLQNGKKFDSSRDRNKPFKFRIGKQEVIKGFEEGAAQMSLGQRAKLTCTPDVAYGATGHPGVIPPNATLIFDVELLNLE
--EEEEEEEE-----------EEEEEEEEEE----EEEE------EEEEEE----HHHHHHHHH-------EEEEEE--------------------EEEEEEEEE--</code></pre>
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--EEEEEEEE-----------EEEEEEEEEE----EEEE------EEEEEE----HHHHHHHHH-------EEEEEE--------------------EEEEEEEEE--</code></span></pre>
  
 
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<hr />
<p>Fc region of Immunoglobluin G</p>
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<p><span style="font-family:arial,helvetica,sans-serif">Fc region of Immunoglobluin G</span></p>
  
<p>&nbsp;</p>
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<pre>
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<code>MDWTWRFLFVVAAATGVQSQMQVVQSGAEVKKPGSSVTVSCKASGGTFSNYAISWVRQAPGQGLEWMGGIIPLFGTPTYSQNFQGRVTITADKSTSTAHMELISLRSEDTAVYYCATDRYRQANFDRARVGWFDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
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--HHHHHHHHHHHH------EEEEE----EEE----EEEEEEE--------EEEEEEE------EEEEEE----------------EEEE-------EEEEE---------EEEE------------------EE-----EEEE------------------------EEEEEEE--------EEEE-----EE--EEEEE---------EEEEEE---------EEEEEEE-------EEE----------------------------------------------EEEEEE-------EEEEEE---------------------EEEEEEEE----------EEEEEE-------EEEEEEEE--------EEEEE------------EEEEEEE------EEEEEE--------------------EEEEEEEEEE---------EEEEEEEE------EEEEEEE-----</code></pre>
  
<p>&nbsp;</p>
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<p><span style="font-family:arial,helvetica,sans-serif">&nbsp;</span></p>

Latest revision as of 11:15, 15 June 2016

I used Jpred 4 program http://www.compbio.dundee.ac.uk/jpred4/index.html

'H' - Helix, 'E' - Extended, 'B' - Buried, '-' - other types

DSCR1(RCAN1) - Down Syndrome Critical Region 1, Regulator of Calcineurin 1


<span style="font-family:courier new,courier,monospace"><code>MVYAKFESLFRTYDKDITFQYFKSFKRVRINFSNPFSAADARLQLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKQFLISPPASPPVGWKQVEDATPVINYDLLYAISKLGPGEKYELHAATDTTPSVVVHVCESDQEKEEEEEMERMRRPKPKIIQTRRPEYTPIHLS
-HHHHHHHHHH-----EEEEE-----EEEEEE--HHHHHHHHHHH--------EEEEEE-------------------------------EEE---------HHHHHHHHH-------EE--------EEEEEE---------------------E---------------</code></span>

FMRP - Fragile X syndrome Mental Retardation Protein

<span style="font-family:arial,helvetica,sans-serif"><code>MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPDRQIPFHDVRFPPPVGYNKDINESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKPATKDTFHKIKLDVPEDLRQMCAKEAAHKDFKKAVGAFSVTYDPENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLIMRNEEASKQLESSRQLASRFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEEIMPPNSLPSNNSRVGPNAPEEKKHLDIKENSTHFSQPNSTKVQRVLVASSVVAGESQKPELKAWQGMVPFVFVGTKDSIANATVLLDYHLNYLKEVDQLRLERLQIDEQLRQIGASSRPPPNRTDKEKSYVTDDGQGMGRGSRPYRNRGHGRRGPGYTSGTNSEASNASETESDHRDELSDWSLAPTEEERESFLRRGDGRRRGGGGRGQGGRGRGGGFKGNDDHSRTDNRPRNPREAKGRTTDGSLQIRVDCNNERSVHTKTLQNTSSEGSRLRTGKDRNQKKEKPDSVDGQQPLVNGVP
---EEEEEE-----EEEEEEEEE---EEEEEE-------------------------------EEEEEE----------EEEEEEEE----EEEEEE-------EEEEE----------------EEEEEEE--HHHHHHHH-HHHHHHHHH---EEEEEE-----EEEEEE-----EEEEEH-HEEE----HHHHHHHHHHHHHHHHHHHHHHH----EEEEE-----HHHH------HHHHHHH----EEEE------EEEEEE--HHHHHHHHHHHHHHHEEEEE------EEE----HHHHHHH----EEEEEE-------------------HHHHHHHHHHHHHHHHHHH------EEE----------------------------------EEEEEEE--HHHHHHHHHHHHHHHHHHH-HHHHHEE-------------------EE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------</code></span>

Death associated protein kinase 3

<span style="font-family:arial,helvetica,sans-serif"><code>MSTFRQEDVEDHYEMGEELGSGQFAIVRKCRQKGTGKEYAAKFIKKRRLSSSRRGVSREEIEREVNILREIRHPNIITLHDIFENKTDVVLILELVSGGELFDFLAEKESLTEDEATQFLKQILDGVHYLHSKRIAHFDLKPENIMLLDKNVPNPRIKLIDFGIAHKIEAGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGETKQETLTNISAVNYDFDEEYFSNTSELAKDFIRRLLVKDPKRRMTIAQSLEHSWIKAIRRRNVRGEDSGRKPERRRLKTTRLKEYTIKSHSSLPPNNSYADFERFSKVLEEAAAAEEGLRELQRSRRLCHEDVEALAAIYEEKEAWYREESDSLGQDLRRLRQELLKTEALKRQAQEEAKGALLGTSGLKRRFSRLENRYEALAKQVASEMRFVQDLVRALEQEKLQGVECGLR
------------EEEEEEEEE---EEEEEEEE----EEEEEEEEE--------HHHHHHHHHHHHHHHHH-----EEEEEEEE----EEEEEEEE----HHHHHHHH-----HHHHHHHHHHHHHHHHHHHH---EEE-----EEEE---------EEEEE---EEEE----EEEEE------HHHHHH----------HHHHHHHHHHHHH---------HHHHHHHHH---------------HHHHHHHHHHH---------HHHHHH---------------------------------------------------------------------HHHHHH------------HHHH-----------HHHHHHHHH-----HHHHHH---------------HHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH-----------</code></span>

Calcineurin

<span style="font-family:arial,helvetica,sans-serif"><code>MGVEIETISPGDGRTFPKKGQTCVVHYTGMLQNGKKFDSSRDRNKPFKFRIGKQEVIKGFEEGAAQMSLGQRAKLTCTPDVAYGATGHPGVIPPNATLIFDVELLNLE
--EEEEEEEE-----------EEEEEEEEEE----EEEE------EEEEEE----HHHHHHHHH-------EEEEEE--------------------EEEEEEEEE--</code></span>

Fc region of Immunoglobluin G

<code>MDWTWRFLFVVAAATGVQSQMQVVQSGAEVKKPGSSVTVSCKASGGTFSNYAISWVRQAPGQGLEWMGGIIPLFGTPTYSQNFQGRVTITADKSTSTAHMELISLRSEDTAVYYCATDRYRQANFDRARVGWFDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
--HHHHHHHHHHHH------EEEEE----EEE----EEEEEEE--------EEEEEEE------EEEEEE----------------EEEE-------EEEEE---------EEEE------------------EE-----EEEE------------------------EEEEEEE--------EEEE-----EE--EEEEE---------EEEEEE---------EEEEEEE-------EEE----------------------------------------------EEEEEE-------EEEEEE---------------------EEEEEEEE----------EEEEEE-------EEEEEEEE--------EEEEE------------EEEEEEE------EEEEEE--------------------EEEEEEEEEE---------EEEEEEEE------EEEEEEE-----</code>