Difference between revisions of "Task 9 Lab Journal (MSUD)"

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==Visualizatin of mutant structures==
  
==Visualizatin of mutant structures==
 
In order to get the position of mutations in PDB structure 2BFF, we have aligned the SEQRES sequence of 2BFF to reference sequence of BCKDHA using Needleman Wunsch algorithm.
  
In order to get the position of mutations in PDB structure 2BFF, we have aligned the SEQRES sequence of 2BFF to reference sequence of BCKDHA using Needleman Wunsch algorithm.
  +
The position of mutations should be shifted 45 residues back. Alignment is shown below:
  +
  +
<nowiki>NP_000700.1 1 MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDD 50
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|||||
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SEQUENCE 1 ---------------------------------------------SSLDD 5
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  +
NP_000700.1 51 KPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKE 100
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||||||||||||||||||||||||||||||||||||||||||||||||||
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SEQUENCE 6 KPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKE 55
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  +
NP_000700.1 101 KVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDN 150
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||||||||||||||||||||||||||||||||||||||||||||||||||
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SEQUENCE 56 KVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDN 105
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NP_000700.1 151 TDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER 200
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||||||||||||||||||||||||||||||||||||||||||||||||||
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SEQUENCE 106 TDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER 155
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NP_000700.1 201 HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGF 250
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||||||||||||||||||||||||||||||||||||||||||||||||||
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SEQUENCE 156 HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGF 205
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NP_000700.1 251 NFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG 300
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||||||||||||||||||||||||||||||||||||||||||||||||||
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SEQUENCE 206 NFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG 255
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NP_000700.1 301 NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDE 350
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||||||||||||||||||||||||||||||||||||||||||||||||||
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SEQUENCE 256 NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDE 305
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NP_000700.1 351 VNYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERK 400
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|.||||||||||||||||||||||||||||||||||||||||||||||||
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SEQUENCE 306 VGYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERK 355
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NP_000700.1 401 PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK 445
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|||||||||||||||||||||||||||||||||||||||||||||
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SEQUENCE 356 PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK 400</nowiki>

Revision as of 12:33, 12 July 2013

Visualizatin of mutant structures

In order to get the position of mutations in PDB structure 2BFF, we have aligned the SEQRES sequence of 2BFF to reference sequence of BCKDHA using Needleman Wunsch algorithm. The position of mutations should be shifted 45 residues back. Alignment is shown below: 

NP_000700.1        1 MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDD     50
                                                                  |||||
SEQUENCE           1 ---------------------------------------------SSLDD      5

NP_000700.1       51 KPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKE    100
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE           6 KPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKE     55

NP_000700.1      101 KVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDN    150
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE          56 KVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDN    105

NP_000700.1      151 TDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER    200
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE         106 TDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER    155

NP_000700.1      201 HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGF    250
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE         156 HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGF    205

NP_000700.1      251 NFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG    300
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE         206 NFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG    255

NP_000700.1      301 NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDE    350
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE         256 NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDE    305

NP_000700.1      351 VNYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERK    400
                     |.||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE         306 VGYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERK    355

NP_000700.1      401 PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK    445
                     |||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE         356 PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK    400
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