C1orf41 Methods: Difference between revisions
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'''Evolution''' | |||
The sequence of the c1orf41 was obtained from National Center for Biotechnology Information (NCBI) webpage and was used to find homologues of this protein using Blastp non-redundant protein database. Amino acid Sequence of homolgues with E-value of less than 1e-16 was retrieved and aligned using Clustalx to find conserved regions. Homologues which showed poor alignment were discarded from further investigation. From the sequence alignment, a phylogenetic tree was constructed to observe the evolutionary relationship of this protein with its homologues. The ensure the reliability of the evolutionary tree, bootstrap was performed with 100 replicates. | The sequence of the c1orf41 was obtained from National Center for Biotechnology Information (NCBI) webpage and was used to find homologues of this protein using Blastp non-redundant protein database. Amino acid Sequence of homolgues with E-value of less than 1e-16 was retrieved and aligned using Clustalx to find conserved regions. Homologues which showed poor alignment were discarded from further investigation. From the sequence alignment, a phylogenetic tree was constructed to observe the evolutionary relationship of this protein with its homologues. The ensure the reliability of the evolutionary tree, bootstrap was performed with 100 replicates. | ||
Revision as of 09:52, 10 June 2009
Evolution
The sequence of the c1orf41 was obtained from National Center for Biotechnology Information (NCBI) webpage and was used to find homologues of this protein using Blastp non-redundant protein database. Amino acid Sequence of homolgues with E-value of less than 1e-16 was retrieved and aligned using Clustalx to find conserved regions. Homologues which showed poor alignment were discarded from further investigation. From the sequence alignment, a phylogenetic tree was constructed to observe the evolutionary relationship of this protein with its homologues. The ensure the reliability of the evolutionary tree, bootstrap was performed with 100 replicates.
Structure
The structure was of c1orf41 was obtained from Protein Data Bank (PDB) under the id 1TVG. The visualisation of the protein structure was done using Pymol where, the surface and electrostatic surface distribution was analysied. Scope and PDBsum were used to learn more about the secondary structure of the protein. Next a structural similarity search was performed using DALI. The domain of the protein was identified using Pfam. Pfam was used to look for the common domain of the proteins from the DALI result by making searches using the FASTA sequence of 1gog (galactose oxidase), 2bzd (bacterial sialidase) and 2vca (alpha-N-acetylglucosaminidase). CastP was used to identify the surface clefts that are possible ligand binding positions. Nest analysis by Profunc was used to look for motifs that are commonly found in regions that are functionally important in proteins.
