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Pipeline publication

[…] ry was used to identify links to a truncated AvrB query (gi|149242490, range 55–128 and range 212–321) lacking the inserted upper lobe domain. Domain organization was assessed using the conserved domain database CDD with a cutoff of 0.003., To visualize the relationships between identified fido sequences, all against all pair-wise sequence similarities for collected sequences (fic, doc, and AvrB) were calculated using BLAST implementation (-pval 0.1) with the CLANS application . Sequences were clustered in two-dimensional space with a P-value cutoff of (1E-05) until node movement became negligible (rounds). Resulting clusters were used to constructed multiple sequence alignments using the MAFFT program (version 6, L-ins-I strategy, default parameters with no homologs , ) with manual adjustments. The multiple alignments of each group were merged into a global alignment using structure superpositions, secondary structure predictions (JPRED), hydrophobicity patterns, and paired BLAST hit alignments as guides., DaliLite was used to determine the closest structural neighbors in the PDB database. For each query, all pairwise comparisons were then ranked in order of descending Z-score to determine the closest structural neighbors., CG9523 was amplified off of a plasmid containing the coding region of CG9523 (kindly provided by Helmut Kramer) using VENT polymerase. The PCR product was restriction digested, ligated into pET28a, and transformed into E. coli (DH5a, Invitrogen). Positive clones were confirmed by DNA sequence analysis. Histidine to alanine mutants of VopS and CG9523 were generated using the Stratagene QuikChangeTM site-directed mutagenesis kit, according to the manufacturer's instructions. […]

Pipeline specifications

Software tools MAFFT, JPred, DaliLite
Databases CDD