Computational protocol: A Putative Type II Secretion System Is Involved in Cellulose Utilization in Cytophaga hutchisonii

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Protocol publication

[…] To search for the presence of homologous T2SS genes in C. hutchinsonii genome, the well-characterized T2SS protein sequences from several Proteobacteria members and the InterPro and Pfam numbers for T2S-D (IPR004846, PF00263), T2S-E (IPR001482, PF00437), T2S-F (IPR018076, PF00482), T2S-G (IPR013545, PF08334), T2S-L (IPR024230, PF05134), T2S-M (IPR007690, PF04612), and T2S-C (IPR024961, PF11356) were used as queries. Multiple sequence alignments were performed using Clustal W (Larkin et al., ). Pfam domain identification and secondary structural analysis was carried out using the Pfam 31.0 tool (http://pfam.xfam.org/) and the PSIPRED Server (http://bioinf.cs.ucl.ac.uk/psipred/), respectively (Jones, ; Finn et al., ). HHpred analyses of protein sequences were undertaken using the server available online (https://toolkit.tuebingen.mpg.de; Soding et al., ). […]

Pipeline specifications

Software tools Clustal W, PSIPRED, HHPred
Databases Pfam
Application Protein structure analysis
Organisms Cytophaga hutchinsonii
Chemicals Cellobiose