Computational protocol: Expression and efficient secretion of a functional chitinase from Chromobacterium violaceum in Escherichia coli

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Protocol publication

[…] Searches for homologous proteins on public sequence databases were performed using BLASTp []. Signal peptide and signal peptidase cleavage sites were predicted using SignalP version 3.0 []. The theoretical isoelectric point (pI) and molecular weight (Mw) were predicted using Compute pI/Mw on the ExPASy Proteomics Server []. The presence and delimitation of protein domains was accomplished using the Conserved Domain Database (CDD) []. Multiple amino acid sequence alignments were generated using ClustalW []. The identity between a pair of aligned sequences was calculated as the number of identical residues divided by the number of aligned positions, excluding the sites with gaps, and expressed as a percentage. Structural alignments based on comparisons of 3D structures deposited in the Protein Data Bank (PDB) were obtained from the Dali database []. The functional domains were named following the nomenclature adopted by the Carbohydrate-Active enZymes (CAZy) database []. […]

Pipeline specifications

Software tools BLASTP, SignalP, Clustal W, DALI
Databases CAZy CDD ExPASy
Application Protein structure analysis
Organisms Escherichia coli, Chromobacterium violaceum, Chromobacterium violaceum ATCC 12472, Thiocystis violascens, Escherichia coli BL21(DE3)