DNA sequence analyses and in silico analysis.

Automatic annotation was performed online in the Rapid Annotation using Subsystem Technology (RAST) server (43). Correlations between gene and protein names reported in this work and locus tags in GenBank are shown in Table S6. A more thorough search and identification of CAZymes and sulfatases were carried out using hidden Markov model searches as described previously by Schultz-Johansen et al. (10). Selected gene sequences from RAST were imported into CLC Main Workbench 7.0 (Qiagen) for primer design. Similarity searches and predictions of conserved domains were performed by the use of BLASTp searches against the NCBI (https://www.ncbi.nlm.nih.gov) Protein Data Bank database (PDB), Swiss-Prot, and the nonredundant protein database (nr) and the Conserved Domain Database (CDD). Prediction of signal peptides and lipoproteins was performed with Pred-Lipo (44), SignalP 4.1 (45, 46), and LipoP 1.0 (47). All alignments were made in CLC Main Workbench 7.0, and phylogenetic trees were constructed in MEGA7 (48). Sequences were retrieved from the nonredundant database using C. echini A3^T genes or sequences from structurally determined proteins. In silico folding was performed using SWISS-MODEL (https://swissmodel.expasy.org) (51), and model quality was assessed using the QMEAN server (http://swissmodel.expasy.org/qmean) (52); models with QMEANDisCo values of <0.6 were discarded (51). Additionally, local quality estimate was used and only residues with a local quality score of >0.75 are discussed. Structural models were superimposed using the “super” function in PyMOL (The PyMOL Molecular Graphics System, Version 2.0; Schrödinger, LLC).

Correlation between names and function of proteins in this work and the corresponding genes in scaffold 5 of the Colwellia echini A3^T genome sequence, {"type":"entrez-nucleotide","attrs":{"text":"PJAI00000000.2","term_id":"1731532065","term_text":"PJAI00000000.2"}}PJAI00000000.2. Download Table S6, DOCX file, 0.01 MB.