Prediction of serine/threonine phosphorylation sites in bacteria proteins

Advances in Experimental Medicine and Biology

Volumn 827, Issue , 2015, Pages 275-285

  Li, Zhengpeng ^a   Wu, Ping ^a   Zhao, Yuanyuan ^b   Liu, Zexian ^c   Zhao, Wei ^c  

^a ANHUI SCIENCE AND TECHNOLOGY UNIVERSITY   (China)

^b HEFEI NORMAL UNIVERSITY   (China)

^c UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

Bacteria; CKSAAP; Phosphorylation; Prediction

Indexed keywords

PROTEIN SERINE THREONINE KINASE; BACTERIAL PROTEIN; SERINE; THREONINE;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; ENZYME PHOSPHORYLATION; MEASUREMENT ACCURACY; NONHUMAN; PREDICTIVE VALUE; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; VALIDATION PROCESS; WEB BROWSER; METABOLISM; PHOSPHORYLATION;

EUKARYOTA;

ALGORITHMS; BACTERIAL PROTEINS; PHOSPHORYLATION; SERINE; THREONINE;

EID: 84925284923     PISSN: 00652598     EISSN: 22148019     Source Type: Book Series    
DOI: 10.1007/978-94-017-9245-5_16     Document Type: Article

References (25)

1. Raju TN (2000) The nobel chronicles 1992: Fischer EH (b 1920), Krebs EG (b 1918). Lancet, 355:2004
2. Hunter T (2009) Tyrosine phosphorylation: 30 years and counting. Curr Opin Cell Biol 21:140–146
3. Johnson LN (2009) The regulation of protein phosphorylation. Biochem Soc Trans 37:627–641
4. Pawson T, Scott JD (2005) Protein phosphorylation in signaling—50 years and counting. Trends Biochem Sci 30:286–290
5. Cousin C, Derouiche A, Shi L, Pagot Y, Poncet S, Mijakovic I (2013) Protein-serine/ threonine/tyrosine kinases in bacterial signaling and regulation. FEMS Microbiol Lett 346(1):11–19
6. Cozzone AJ (1988) Protein-phosphorylation in prokaryotes. Annu Rev Microbiol 42:97–125
7. Ohlsen K, Donat S (2010) The impact of serine/threonine phosphorylation in staphylococcus aureus. Int J Med Microbiol 300:137–141
8. Deutscher J, Francke C, Postma PW (2006) How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev 70:939–1031
9. Hoch JA (2000) Two-component and phosphorelay signal transduction. Curr Opin Microbiol 3:165–170
10. Song C, Ye M, Liu Z, Cheng H, Jiang X, Han G, Songyang Z, Tan Y, Wang H, Ren J et al (2012) Systematic analysis of protein phosphorylation networks from phosphoproteomic data. Mol cell proteomics: MCP 11:1070–1083
11. Macek B, Mann M, Olsen JV (2009) Global and site-specific quantitative phosphoproteomics: principles and applications. Annu Rev Pharmacol Toxicol 49:199–221
12. Macek B, Gnad F, Soufi B, Kumar C, Olsen JV, Mijakovic I, Mann M (2008) Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/ Thr/Tyr phosphorylation. Mol cell proteomics: MCP 7:299–307
13. Macek B, Mijakovic I, Olsen JV, Gnad F, Kumar C, Jensen PR, Mann M (2007) The serine/ threonine/tyrosine phosphoproteome of the model bacterium bacillus subtilis. Mol cell proteomics: MCP 6:697–707
14. Ren J, Gao X, Liu Z, Cao J, Ma Q, Xue Y (2011) Computational analysis of phosphoproteomics: progresses and perspectives. Curr Protein Pept Sci 12:591–601
15. Xue Y, Gao X, Cao J, Liu Z, Jin C, Wen L, Yao X, Ren J (2010) A summary of computational resources for protein phosphorylation. Curr Protein Pept Sci 11:485–496
16. Miller ML, Soufi B, Jers C, Blom N, Macek B, Mijakovic I (2009) NetPhosBac—a predictor for Ser/Thr phosphorylation sites in bacterial proteins. Proteomics 9:116–125
17. Chen K, Jiang Y, Du L, Kurgan L (2009) Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs. J Comput Chem 30:163–172
18. Chen K, Kurgan LA, Ruan J (2007) Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs. BMC Struct Biol 7:25
19. Chen YZ, Tang YR, Sheng ZY, Zhang Z (2008) Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs. BMC Bioinformatics 9:101
20. Chen Z, Chen YZ, Wang XF, Wang C, Yan RX, Zhang Z (2011) Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs. PLoS ONE 6:e22930
21. Chen Z, Zhou Y, Song J (1834) Zhang Z (2013) hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties. Biochim Biophys Acta 8:1461–1467
22. Vacic V, Iakoucheva LM, Radivojac P (2006) Two sample logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics 22:1536–1537
23. Xue Y, Liu Z, Cao J, Ma Q, Gao X, Wang Q, Jin C, Zhou Y, Wen L, Ren J (2011) GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection. Protein Eng Des Sel 24:255–260
24. He Z, Yang C, Guo G, Li N, Yu W (2011) Motif-All: discovering all phosphorylation motifs. BMC Bioinformatics 12(Suppl 1):S22
25. Team RC (2012) R: a Language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria