Biomedical Engineering Reference
In-Depth Information
CLUSTAL W (1.83) multiple sequence alignment for 1CQD
PDBB_model_default_chain_A LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSE
PDBB_model_default_chain_B LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSE
PDBB_model_default_chain_C LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSE
1CQD_model_default_chain_D LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSE
PDBB_model_default_chain_D LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSE
1CQD_model_default_chain_C LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSE
1CQD_model_default_chain_B LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSE
1CQD_model_default_chain_A LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSE
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PDBB_model_default_chain_A QQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTV
PDBB_model_default_chain_B QQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTV
PDBB_model_default_chain_C QQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTV
1CQD_model_default_chain_D QQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTV
PDBB_model_default_chain_D QQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTV
1CQD_model_default_chain_C QQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTV
1CQD_model_default_chain_B QQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTV
1CQD_model_default_chain_A QQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTV
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PDBB_model_default_chain_A
NAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFT
PDBB_model_default_chain_B
NAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFT
PDBB_model_default_chain_C
NAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFT
1CQD_model_default_chain_D
NAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFT
PDBB_model_default_chain_D
NAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFT
1CQD_model_default_chain_C
NAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFT
1CQD_model_default_chain_B NAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFT
1CQD_model_default_chain_A NAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFT
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PDBB_model_default_chain_A GSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENP
PDBB_model_default_chain_B GSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENP
PDBB_model_default_chain_C GSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENP
1CQD_model_default_chain_D GSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENP
PDBB_model_default_chain_D GSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENP
1CQD_model_default_chain_C GSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENP
1CQD_model_default_chain_B GSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENP
1CQD_model_default_chain_A GSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENP
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PDBB_model_default_chain_A DGKCGITRFASYPVKK
PDBB_model_default_chain_B DGKCGITRFASYPVKK
PDBB_model_default_chain_C
DGKCGITRFASYPVKK
1CQD_model_default_chain_D
DGKCGITRFASYPVKK
PDBB_model_default_chain_D
DGKCGITRFASYPVKK
1CQD_model_default_chain_C
DGKCGITRFASYPVKK
1CQD_model_default_chain_B
DGKCGITRFASYPVKK
1CQD_model_default_chain_A
DGKCGITRFASYPVKK
Fig. 11 The Clustal-W file chains are identified by colors and show alignment matches between
1CQD (control file) and PDBB (minimized output)
used for the sequence between the known structure and the minimized structure. The
STRAP software followed the structural trace through to the C-termini and takes the
C-termini of both files to compare. No regions were ignored or skipped (i.e., even
loops were carefully considered and aligned). The alignment was constructed with
the primary aim of maximizing the aligned positions between structures, provided
that there was a rational basis for the alignment. Excellent alignment was achieved.
5 Discussion
The implementation of the ab intio model as a geometry solution was considered
since other approaches for protein modelling were fraught with difficulty due
mainly to insufficient computation resources. The complexity of the protein
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