Expansin homologues in actinobacterial genomes from South Africa


Hit sequences for putative expansins (or expansin domains) are reported from an exemplary genome screening. 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. The first or last available amino acid position in a contig was used to extend the hits in case of a missing start or stop codon, respectively.

The five extended hit sequences correspond to five actinobacterial genomes from different habitats in South Africa: (1) Rooibos (Aspalathus linearis) plant material, Clanwilliam; (2) Sediments collected from the banks of the Gamka River, Swartberg Mountain Range; (3) Marine ascidian collected from Algoa Bay; (4) Sediment from the roots of a giant quiver tree, Worcester; (5) Wild garlic plant material, Wellington.

DOI https://doi.org/10.18419/darus-699
Related Identifier https://doi.org/10.1002/prot.26001
Metadata Access https://darus.uni-stuttgart.de/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=doi:10.18419/darus-699
Creator Buchholz, Patrick C. F. (Universität Stuttgart)
Publisher DaRUS
Contributor Pleiss, Jürgen; Le Roes-Hill, Marilize (Cape Peninsula University of Technology, South Africa)
Publication Year 2020
Rights CC BY 4.0; info:eu-repo/semantics/openAccess; http://creativecommons.org/licenses/by/4.0
OpenAccess true
Contact Pleiss, Jürgen (Universität Stuttgart)
Resource Type Dataset
Format application/octet-stream
Size 1368; 4073
Version 1.1
Discipline Life Sciences; Medicine