Expansin homologues in actinobacterial genomes from South Africa

Five actinobacterial genomes were selected to show the application of the Expansin Engineering Database (ExED) for the identification of expansin domains. The original nucleic acid sequences were translated by the standard codon usage table implemented in the transeq tool from the EMBOSS software suite.

The hmmscan tool from the HMMER software suite was used to scan the translated amino acid sequences with profile hidden Markov models (profile HMMs) representing the N- and C-terminal expansin domains. The hits from hmmscan were filtered by a minimal domain-based score of 35 and a minimal coverage of 75% (defined as the ratio of hit length without insertions divided by the length of the profile HMM). The matches for the profile HMMs of both expansin domains were extended to find the adjacent start methionine and stop codon along the contig sequence of each match.