Phytanoyl-CoA method: Difference between revisions
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[[Phytanoyl-CoA abstract | Abstract]] | [[Phytanoyl-CoA intro| Introduction]] | [[Phytanoyl-CoA results| Results]] | [[Phytanoyl-CoA discussion| Discussion]] | [[Phytanoyl-CoA conclusion| Conclusion]] | [[Phytanoyl-CoA method| Method]] | [[Phytanoyl-CoA references| References]] | |||
===Multiple Sequence Alignment=== | ===Multiple Sequence Alignment=== | ||
The original fasta sequence for the Phytanoyl-CoA hydroxylase protein was searched against the non-redundant databases of blast. From these results 49 other sequences were selected for comparison based on low e-values and to include diverse organisms. From these 4 were removed due in inappropriate length leaving a total of 46 sequences including the target sequence. These were then aligned using the default setting in ClustalX. The final alignment from the postscript output can be seen in | The original fasta sequence for the Phytanoyl-CoA hydroxylase protein was searched against the non-redundant databases of blast. From these results 49 other sequences were selected for comparison based on low e-values and to include diverse organisms. From these 4 were removed due in inappropriate length leaving a total of 46 sequences including the target sequence. These were then aligned using the default setting in ClustalX. The final alignment from the postscript output can be seen in [[Phytanoyl-CoA results#Multiple Sequence Alignment|''figure 1.1-3'']]. | ||
===SCOP=== | |||
A search was made using the PDB number 2OPW as a query. A secondary structure match was conducted | |||
===Entrez Gene=== | |||
Entrez gene was searched with the PDB number 2OPW. This displayed both the genomic location and the different splicing details for isoforms a,b and c. | |||
===Phylogenetic Trees=== | |||
The original tree was obtained by submitting the alignment file obtained from Clustal to the Phylodendron Web Form found at http://iubio.bio.indiana.edu/treeapp/ The data was also bootstrapped using the seqboot function in Phylip. Using the neighbor and consensus programs a consensus tree file was obtained and also viewed using Phylodendron. The resulting [[Phytanoyl-CoA results#Phylogenetic trees|trees]] were annotated to highlight the division of species. | |||
===InterPro analysis=== | |||
The InterPro database (http://www.ebi.ac.uk/interpro/) was searched using the keyword ' ''Phytanoyl-CoA dioxygenase'' ' and returned the InterPro accession number IPR008775. Information on family ([[Phytanoyl-CoA results#Function Analysis|''figure 3.1'']]) was obtained from this accession number. | |||
===Secondary Structure Match analysis=== | |||
The PBD code for PhyD (2opw) was submitted to Profunc (http://www.ebi.ac.uk/thornton-srv/databases/profunc/index.html) on 03.05.2008. The results were finished on the 03.05.08 and Profunc's secondary structure matching analysis was used to show homology between 2opw and 2a1x. | |||
===Pymol analysis=== | |||
PDB files for PhyD (PDB code:2opw) and PhyH (PDB code:2a1x) were downloaded from the online protein databank (http://PDB.org). Cartoon and surface methods of visualization were used. Some animated GIF's were made for the purposes of presentation. | |||
For the structural comparisons, both proteins were loaded were overlayed. Surfaces were visualized in different colours for contrast. | |||
===Expression data=== | |||
Expression profiles of PhyH and PhyD were retrieved from symatlas (http://symatlas.gnf.org) by searching the accession terms PhyH and PhyHD respectively. | |||
[[Phytanoyl-CoA abstract | Abstract]] | [[Phytanoyl-CoA intro| Introduction]] | [[Phytanoyl-CoA results| Results]] | [[Phytanoyl-CoA discussion| Discussion]] | [[Phytanoyl-CoA conclusion| Conclusion]] | [[Phytanoyl-CoA method| Method]] | [[Phytanoyl-CoA references| References]] | [[Phytanoyl-CoA abstract | Abstract]] | [[Phytanoyl-CoA intro| Introduction]] | [[Phytanoyl-CoA results| Results]] | [[Phytanoyl-CoA discussion| Discussion]] | [[Phytanoyl-CoA conclusion| Conclusion]] | [[Phytanoyl-CoA method| Method]] | [[Phytanoyl-CoA references| References]] | ||
[[Phytanoyl-CoA dioxygenase domain containing 1 isoform a | Return to main page...]] | |||
Latest revision as of 01:11, 10 June 2008
Abstract | Introduction | Results | Discussion | Conclusion | Method | References
Multiple Sequence Alignment
The original fasta sequence for the Phytanoyl-CoA hydroxylase protein was searched against the non-redundant databases of blast. From these results 49 other sequences were selected for comparison based on low e-values and to include diverse organisms. From these 4 were removed due in inappropriate length leaving a total of 46 sequences including the target sequence. These were then aligned using the default setting in ClustalX. The final alignment from the postscript output can be seen in figure 1.1-3.
SCOP
A search was made using the PDB number 2OPW as a query. A secondary structure match was conducted
Entrez Gene
Entrez gene was searched with the PDB number 2OPW. This displayed both the genomic location and the different splicing details for isoforms a,b and c.
Phylogenetic Trees
The original tree was obtained by submitting the alignment file obtained from Clustal to the Phylodendron Web Form found at http://iubio.bio.indiana.edu/treeapp/ The data was also bootstrapped using the seqboot function in Phylip. Using the neighbor and consensus programs a consensus tree file was obtained and also viewed using Phylodendron. The resulting trees were annotated to highlight the division of species.
InterPro analysis
The InterPro database (http://www.ebi.ac.uk/interpro/) was searched using the keyword ' Phytanoyl-CoA dioxygenase ' and returned the InterPro accession number IPR008775. Information on family (figure 3.1) was obtained from this accession number.
Secondary Structure Match analysis
The PBD code for PhyD (2opw) was submitted to Profunc (http://www.ebi.ac.uk/thornton-srv/databases/profunc/index.html) on 03.05.2008. The results were finished on the 03.05.08 and Profunc's secondary structure matching analysis was used to show homology between 2opw and 2a1x.
Pymol analysis
PDB files for PhyD (PDB code:2opw) and PhyH (PDB code:2a1x) were downloaded from the online protein databank (http://PDB.org). Cartoon and surface methods of visualization were used. Some animated GIF's were made for the purposes of presentation.
For the structural comparisons, both proteins were loaded were overlayed. Surfaces were visualized in different colours for contrast.
Expression data
Expression profiles of PhyH and PhyD were retrieved from symatlas (http://symatlas.gnf.org) by searching the accession terms PhyH and PhyHD respectively.
Abstract | Introduction | Results | Discussion | Conclusion | Method | References
