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]] | [[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=== | ||
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===Phylogenetic Trees=== | ===Phylogenetic Trees=== | ||
The | 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'' ' | |||
===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). Files were uploaded into PyMol molecular graphics system and atructural alignments were constructed using inbuilt commands. | |||
===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...]] | [[Phytanoyl-CoA dioxygenase domain containing 1 isoform a | Return to main page...]] | ||
Revision as of 01:00, 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.
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 '
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). Files were uploaded into PyMol molecular graphics system and atructural alignments were constructed using inbuilt commands.
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
