C1orf41 Methods
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 visualization of the protein structure was done using Pymol where, the surface and electrostatic surface distribution was analyzed. Scop 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.
Function
PDB-format file of c1orf41 was used to run Profunc server to get a summary of sequence and structural analysis of the protein (Laskowski et al, 2005). Besides that, string was used to determine the interaction of c1orf41 with other proteins. The information obtained from profunc server (Blast search, Gene Ontology and InterPro sequence motif), string, structural analysis and evolutionary analysis were combined to predict the function and mechanism of c1orf41. Scientific literature was used to support our finding and bring forth the function of c1orf41.
