Additional file 1 of ConCysFind: a pipeline tool to predict conserved amino acids of protein sequences across the plant kingdom
Creators: name: Moore, Marten
name: Wesemann, Corinna
name: Gossmann, Nikolaj
name: Sahm, Arne
name: Krüger, Jan
name: Sczyrba, Alexander
name: Dietz, Karl-Josef
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: FOS: Computer and information sciences
subject: Plant Biology
subject: Computational Biology

description: Additional file 1: Figure 1. Phylogenetic tree of the plant species in database. The genomes of the given species are included in the default setting of ConCysFind. The phylogenetic tree of the selected 21 species was constructed following the Tree of Life Web Project [19] ( https://tolweb.org/tree/ ). The species are depicted as leaves with taxon description at the inner nodes. Here, the edges do not relate to evolutionary distances. Figure 2. Flow diagram of ConCysFind. Depicted are the working steps of the pipeline tool ConCysFind, sub-sectioned by the category of process. Input can be a single protein sequence in single letter code or multiple protein queries as UniProt ID and description in.tsv format. Optionally to the default database, a custom database of 21 species can be used. Each protein sequence 1…i is BLASTed for each species against the database resulting in a maximum of x BLAST hits per sequence i. A nine-times iteration is executed, eliminating close blast hits that do not carry the query AA with a BLAST score cut-off of 0.8 to obtain the nine best BLAST hits per species. A multiple alignment of each sequence i and all species is generated for each stored BLAST sequence. Following the multiple alignments, a phylogenetic tree for the whole protein sequence of each sequence i is constructed and subsequently the p value and score for each analysed AA is calculated. Lastly, for each AA a phylogenetic tree representing the individual conservation-score and p value is drawn. The outputs of the alignments and results are stored as.txt and the phylogenetic trees as.png in a subfolder. Figure 3. Output example of phylogenetic trees with conserved cysteines of known redox targets. (A) Phylogenetic tree of fully conserved Cys167 of the SAL1 phosphatase, a previously characterised target of functional oxidation and disulphide formation [24]. (B) Partial conservation of Cys241 of chloroplast redox sensor 2-cysteine peroxiredoxin in 21 plant species. Figure 4. Phylogenetic trees of partially conserved Cys388 and Cys404 of eRF1-1. (A) Cys388 is fully conserved within the green lineage, but not in red algae C. merolae and G. sulphuraria, resulting in 88% overall conservation. (B) With 77% overall conservation, Cys404 is the least conserved Cys of eRF1-1, as it is missing in red algae and two Micromonas representatives. Table 2. Input query. Consisting of 33 UniProt ID and their descriptions of translation elongation and termination factors, as well as 6 proteins previously described as being PTM-regulated. Table 3. ConCysFind parameters.