1887

Abstract

The predicted extracellular proteins of the bacterium were analysed to gain insight into the mechanisms underlying interactions of this bacterium with its environment. Extracellular proteins play important roles in processes ranging from probiotic effects in the gastrointestinal tract to degradation of complex extracellular carbon sources such as those found in plant materials, and they have a primary role in the adaptation of a bacterium to changing environmental conditions. The functional annotation of extracellular proteins was improved using a wide variety of bioinformatics methods, including domain analysis and phylogenetic profiling. At least 12 proteins are predicted to be directly involved in adherence to host components such as collagen and mucin, and about 30 extracellular enzymes, mainly hydrolases and transglycosylases, might play a role in the degradation of substrates by to sustain its growth in different environmental niches. A comprehensive overview of all predicted extracellular proteins, their domains composition and their predicted function is provided through a database at http://www.cmbi.ru.nl/secretome, which could serve as a basis for targeted experimental studies into the function of extracellular proteins.

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2006-11-01
2019-11-15
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vol. , part 11, pp. 3175 - 3183

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vol. , part 11, pp. 3175 - 3183

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vol. , part 11, pp. 3175 - 3183

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Multiple sequence alignment of Repeat_5. Residues were coloured using the default ClustalX colouring scheme: conserved A, C, F, H, I, L, M, V, W,Y or P residues are coloured blue, while conserved S or T residues are in green. Conserved positively charged residues and negatively charged residues are coloured red and magenta, respectively. Exact details can be found in the ClustalX manual (Thompson et al., 1997; see main paper for reference details). The number following the locus tags indicate the start position of the domain in the complete protein sequence. Multiple sequence alignment of the WY domain and the transglycosylase-like domain from the PFAM database (PF06737). Residues were coloured using the default ClustalX colouring scheme: conserved A, C, F, H, I, L, M, V, W, Y or P residues are coloured blue, while columns with conserved S or T residues are in green. Conserved positively charged residues and negatively charged residues are coloured red and magenta, respectively. Exact details can be found in the ClustalX manual (Thompson et al., 1997). An asterisk indicates the conserved Glu residue. Multiple sequence alignment of the CSH domain. Residues were coloured using the default ClustalX colouring scheme: conserved A, C, F, H, I, L, M,V,W,Y or P residues are coloured blue, while columns with conserved S or T residues are in green. Conserved positively charged residues and negatively charged residues are coloured red and magenta, respectively. Exact details can be found in the ClustalX manual (Thompson et al., 1997).The numbers following the locus tags indicate the start position of the domain in the complete protein sequence. Asterisks indicate the conserved catalytic residues Ser, Asp and His of these alpha/beta hydrolases. Table S1 lists all proteins predicted to be extracellular, Tables S2-S13 list proteins classified by function and anchor type, Tables S14-S17 list identified PFAM domains, and Table S18 lists groups of genes with similar phylogenetic distributions. [ Excel file] (102 kb) The CLUSTAL_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 4876-4882.

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