Sequence analysis of Lactobacillus reuteri ATCC PTA 6475.

In order to identify genes encoding cell wall anchor domain proteins (Marraffini et al., 2006), the genome sequence and identified proteins of strain ATCC PTA 6475, hereafter called 6475 (previously named MM4-1A; GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"ACGX02000000","term_id":"324979114","term_text":"gb||ACGX02000000"}}ACGX02000000, sequences {"type":"entrez-nucleotide-range","attrs":{"text":"ACGX02000001-ACGX02000007","start_term":"ACGX02000001","end_term":"ACGX02000007","start_term_id":"324979101","end_term_id":"324977012"}}ACGX02000001-ACGX02000007), were reanalysed after the preliminary analysis made by Saulnier et al. (2011). The sorting motif LPxTG was searched for manually in the protein sequences, and YSIRK-G/S signal sequences (pfam04650), cell wall anchor domains (TIGR01167) and other protein domains were searched for in GenBank and with blastp at the National Center for Biotechnology Information website (http://www.ncbi.nlm.nih.gov). Secretion signal peptides were predicted with SignalP 4.1 (http://www.cbs.dtu.dk/services/SignalP) (Petersen et al., 2011) and transmembrane helices were predicted with tmhmm 2.0 (http://www.cbs.dtu.dk/services/TMHMM). Repeats in the protein sequences were identified using radar (http://www.ebi.ac.uk/Tools/pfa/radar).