Computational protocol: Klebsiella pneumoniae yggG Gene Product: A Zinc-Dependent Metalloprotease

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Protocol publication

[…] YggG protein sequence was subjected to a series of BLAST search against non-redundant database (NR) and PDB for template selection. Its structure prediction was done using MODELLER 9v8 []. 20 models were generated randomly and the best Discrete Optimized Potential Energy (DOPE) scoring model was selected. Verification of the built model was done using PROCHECK.The domain family analysis was performed using Pfam protein families database []. ClustalW2 [] was used to perform the multiple sequence alignment with related metalloproteases. Transmembrane region of YggG protein was predicted and compared to other metalloproteases under the same peptidase M48 family by using TMpred []. […]

Pipeline specifications

Software tools MODELLER, PROCHECK, Clustal W, TMpred
Databases Pfam
Applications Protein structure analysis, Membrane protein analysis
Organisms Klebsiella pneumoniae, Escherichia coli
Diseases Pneumonia
Chemicals Isopropyl Thiogalactoside, Zinc, Zinc Acetate