Expansin homologues in actinobacterial genomes from South Africa (doi:10.18419/darus-699)

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Expansin homologues in actinobacterial genomes from South Africa

doi:10.18419/darus-699

DaRUS

2020-04-09

1

Buchholz, Patrick C. F., 2020, "Expansin homologues in actinobacterial genomes from South Africa", https://doi.org/10.18419/darus-699, DaRUS, V1

Expansin homologues in actinobacterial genomes from South Africa

doi:10.18419/darus-699

Buchholz, Patrick C. F. (Universität Stuttgart)

Le Roes-Hill, Marilize (Cape Peninsula University of Technology, South Africa)

DaRUS

Pleiss, Jürgen

Buchholz, Patrick C. F.

2020-03-06

https://doi.org/10.18419/darus-699

Medicine, Health and Life Sciences, protein sequence, amino acid sequence, genome mining, nucleic acid sequence, DNA sequence

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 (<i>Aspalathus linearis</i>) 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.

Lohoff, Caroline, 2020, "Profile hidden Markov models of the ExED", <a href="https://doi.org/10.18419/darus-623">doi:10.18419/darus-623</a>, DaRUS

Lohoff C., Buchholz P. C. F., Le Roes-Hill M. & Pleiss J. (2020). The Expansin Engineering Database: a navigation and classification tool for expansins and homologues. Proteins: Structure, Function, and Bioinformatics 89:2.

10.1002/prot.26001

Lohoff C., Buchholz P. C. F., Le Roes-Hill M. & Pleiss J. (2020). The Expansin Engineering Database: a navigation and classification tool for expansins and homologues. Proteins: Structure, Function, and Bioinformatics 89:2.

Coil D, Jospin G, Darling AE. A5-miseq: An updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics. 2015;31:587-589. <a href="doi:10.1093/bioinformatics/btu661">doi:10.1093/bioinformatics/btu661</a>

Label:

hits_aa.fasta

Text:

FASTA file of protein sequences (amino acid symbols). The numbers in the headers correspond to the hits mentioned in the Supporting Information file from Lohoff et al. 2020.

application/octet-stream

Label:

hits_nt.fasta

Text:

FASTA file of nucleic acid sequences. The numbers in the headers correspond to the hits mentioned in the Supporting Information file from Lohoff et al. 2020.

application/octet-stream