Computational protocol: Genome-guided insight into the methylotrophy of Paracoccus aminophilus JCM 7686

Similar protocols

Protocol publication

[…] The putative function of particular genes was assigned using BLAST programs (Altschul et al., ) and PRIAM tool (Claudel-Renard et al., ) as previously described (Heinl et al., ). Metabolic pathways were recognized and described using Pathway tools (Karp et al., ), the MetaCyc database (Caspi et al., ) and GenDB 2.0 (Meyer et al., ). For the identification of methylotrophy-linked genes/proteins a BLASTn/BLASTp analysis comparing the sequence of each gene/protein with the genome/proteome of a particular Paracoccus strain was performed. Strict cutoff values were applied for this analysis: e < 10−40, 70% for minimal query coverage and sequence identity of at least 45%. […]

Pipeline specifications

Software tools PRIAM, Pathway Tools, GenDB, BLASTN, BLASTP
Application Protein sequence analysis
Organisms Paracoccus aminophilus, Paracoccus denitrificans PD1222
Chemicals Methanol, Carbon, Dimethylformamide