Arylformamidase Methods: Difference between revisions
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An alignment of 2pbl and the protein of interest was performed using ClustalX. Default parameters were used. Residues of the catalytic triad were identified from the paper describing it and located in the sequence. Conservation of the residue and the surrounding sequence was observed. Note: in analysing conservation of the 2c7b catalytic triad with 2pbl, the clustalW alignment was found to differ from the alignment provided as part of the DALI results. | An alignment of 2pbl and the protein of interest was performed using ClustalX. Default parameters were used. Residues of the catalytic triad were identified from the paper describing it and located in the sequence. Conservation of the residue and the surrounding sequence was observed. Note: in analysing conservation of the 2c7b catalytic triad with 2pbl, the clustalW alignment was found to differ from the alignment provided as part of the DALI results. | ||
'''Structure''' | |||
The structure of arylfromamidase was obtained from RCSB Protein Data Bank (PDB ID: 2PBL). | |||
http://www.rcsb.org/pdb/home/home.do | |||
The predicted interaction arylformamidase with other proteins was determined using the STRING database (STRING: Search Tool for the Retrieval of Interacting Genes/Proteins). http://string.embl.de// | |||
The DALI database was used for the structural comparison of arylformamidase with other proteins. http://ekhidna.biocenter.helsinki.fi/dali_server/ | |||
PDBsum database was used to determine the secondary structure of arylformamidase. | |||
http://www.ebi.ac.uk/pdbsum/ | |||
[[Arylformamidase | Return to the main page...]] | [[Arylformamidase | Return to the main page...]] | ||
Revision as of 09:18, 3 June 2008
Literature search
A literature search was performed using the putative annotation ‘arylformamidase’. A paper by Pabarcus et al. 2007 was returned which, ironically, described the arylformamidase from Mus Musculus.
Conservation of Catalytic Triad
An alignment of 2pbl and the protein of interest was performed using ClustalX. Default parameters were used. Residues of the catalytic triad were identified from the paper describing it and located in the sequence. Conservation of the residue and the surrounding sequence was observed. Note: in analysing conservation of the 2c7b catalytic triad with 2pbl, the clustalW alignment was found to differ from the alignment provided as part of the DALI results.
Structure
The structure of arylfromamidase was obtained from RCSB Protein Data Bank (PDB ID: 2PBL). http://www.rcsb.org/pdb/home/home.do
The predicted interaction arylformamidase with other proteins was determined using the STRING database (STRING: Search Tool for the Retrieval of Interacting Genes/Proteins). http://string.embl.de//
The DALI database was used for the structural comparison of arylformamidase with other proteins. http://ekhidna.biocenter.helsinki.fi/dali_server/
PDBsum database was used to determine the secondary structure of arylformamidase. http://www.ebi.ac.uk/pdbsum/
