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dbPSP: a curated database for protein phosphorylation sites in prokaryotes.

Pan Z, Wang B, Zhang Y, Wang Y, Ullah S, Jian R, Liu Z, Xue Y - Database (Oxford) (2015)

Bottom Line: With the dataset, the sequence preferences of the phosphorylation sites and functional annotations of the phosphoproteins were analyzed, while the results shows that there were obvious differences among the phosphorylation in bacteria, archaea and eukaryotes.All the phosphorylation sites were annotated with original references and other descriptions in the database, which could be easily accessed through user-friendly website interface including various search and browse options.Taken together, the dbPSP database provides a comprehensive data resource for further studies of protein phosphorylation in prokaryotes.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, University of Science and Technology of China, Hefei 230027, China, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China, and State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China School of Life Sciences, University of Science and Technology of China, Hefei 230027, China, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China, and State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China.

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Analyses of sequence preferences of phosphorylation sites in prokaryotes. The sequence preferences of phosphorylation sites in bacteria (A), archaea (B) and eukaryotes (C) were presented with WebLogo. The comparisons of sequence preferences for bacteria and archaea (D), bacteria and eukaryotes (E), archaea and eukaryotes (F).
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bav031-F5: Analyses of sequence preferences of phosphorylation sites in prokaryotes. The sequence preferences of phosphorylation sites in bacteria (A), archaea (B) and eukaryotes (C) were presented with WebLogo. The comparisons of sequence preferences for bacteria and archaea (D), bacteria and eukaryotes (E), archaea and eukaryotes (F).

Mentions: Previously, numerous studies on eukaryotes indicated that phosphorylation was mediated by linear motifs (5, 30). With the dataset collected in this study, we analysed the sequence preferences and motifs for Ser/Thr phosphorylation in bacteria (Figure 5A), archaea (Figure 5B) and eukaryotes (Figure 5C), while 10 092 eukaryotic Ser/Thr phosphorylation sites from phospho.ELM database were employed for comparison (31). As the sequence preferences illustrated by WebLogo (32), alanine and lysine has high frequencies around the phosphorylation sites in bacteria (Figure 5A) and archaea (Figure 5B), respectively, there were abundant serine and glutamic acid around the phosphorylated residues (Figure 5C). To further dissect the differences, pLogo was employed to pairwisely compare the sequence preferences (Figure 5D–F) (33). It was observed that positively charged residues including arginine and lysine were enriched around phosphorylated Ser/Thr in archaea than bacteria (Figure 5D) and eukaryotes (Figure 5F), while proline were over-presented in +1 position of the phosphorylation sites in eukaryotes than bacteria (Figure 5E) and archaea (Figure 5F). Taken together, obvious differences were observed among the sequence preferences of phosphorylation sites in the three domains of organisms.Figure 5.


dbPSP: a curated database for protein phosphorylation sites in prokaryotes.

Pan Z, Wang B, Zhang Y, Wang Y, Ullah S, Jian R, Liu Z, Xue Y - Database (Oxford) (2015)

Analyses of sequence preferences of phosphorylation sites in prokaryotes. The sequence preferences of phosphorylation sites in bacteria (A), archaea (B) and eukaryotes (C) were presented with WebLogo. The comparisons of sequence preferences for bacteria and archaea (D), bacteria and eukaryotes (E), archaea and eukaryotes (F).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4385273&req=5

bav031-F5: Analyses of sequence preferences of phosphorylation sites in prokaryotes. The sequence preferences of phosphorylation sites in bacteria (A), archaea (B) and eukaryotes (C) were presented with WebLogo. The comparisons of sequence preferences for bacteria and archaea (D), bacteria and eukaryotes (E), archaea and eukaryotes (F).
Mentions: Previously, numerous studies on eukaryotes indicated that phosphorylation was mediated by linear motifs (5, 30). With the dataset collected in this study, we analysed the sequence preferences and motifs for Ser/Thr phosphorylation in bacteria (Figure 5A), archaea (Figure 5B) and eukaryotes (Figure 5C), while 10 092 eukaryotic Ser/Thr phosphorylation sites from phospho.ELM database were employed for comparison (31). As the sequence preferences illustrated by WebLogo (32), alanine and lysine has high frequencies around the phosphorylation sites in bacteria (Figure 5A) and archaea (Figure 5B), respectively, there were abundant serine and glutamic acid around the phosphorylated residues (Figure 5C). To further dissect the differences, pLogo was employed to pairwisely compare the sequence preferences (Figure 5D–F) (33). It was observed that positively charged residues including arginine and lysine were enriched around phosphorylated Ser/Thr in archaea than bacteria (Figure 5D) and eukaryotes (Figure 5F), while proline were over-presented in +1 position of the phosphorylation sites in eukaryotes than bacteria (Figure 5E) and archaea (Figure 5F). Taken together, obvious differences were observed among the sequence preferences of phosphorylation sites in the three domains of organisms.Figure 5.

Bottom Line: With the dataset, the sequence preferences of the phosphorylation sites and functional annotations of the phosphoproteins were analyzed, while the results shows that there were obvious differences among the phosphorylation in bacteria, archaea and eukaryotes.All the phosphorylation sites were annotated with original references and other descriptions in the database, which could be easily accessed through user-friendly website interface including various search and browse options.Taken together, the dbPSP database provides a comprehensive data resource for further studies of protein phosphorylation in prokaryotes.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, University of Science and Technology of China, Hefei 230027, China, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China, and State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China School of Life Sciences, University of Science and Technology of China, Hefei 230027, China, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China, and State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China.

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