Hypothetical protein References

REFERENCES

Evolution:

• Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice. Nucl. Acids Res. 22: 4673-4680.

• Tamura, K., Dudley, J., Nei, M. and Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.

• Strimmer, K. and von Haeseler, A. (1996) Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13: 964-969

Function

• Turner, M., Woodberry, T., Hafner L.M., & Giffard, P.M., (1999), The bspA Locus of Lactobacillus fermentum BR11 Encodes an L-Cystine Uptake System, Journal of Bacteriology, 181(7): 2192-2198.

• Ryu, K.S., Kim, C., Kim, I., Yoo, S., Choi, B.S. and Park, C. (2004) NMR Application Probes a Novel and Ubiquitous Family of Enzymes That Alter Monosaccharide Configuration. J. Biol. Chem., 279(17): 25544-25548.

• Park, D., Ryu, K.S., Choi, D., Kwak, J. and Park, C. (2007) Characterization and role of fucose mutarotase in mammalian cells. Glycobiology. 17(9):955-962

• Igarashi Y, Aoki KF, Mamitsuka H, Kuma K, and Kanehisa M, 2004. ‘The Evolutionary Repertoires of the Eukaryotic-Type ABC Transporters in Terms of the Phylogeny of ATP-binding Domains in Eukaryotes and Prokaryotes’, Molecular Biology and Evolution, vol. 21 no. 11, pp. 2149-2160.

• Jensen et al. (2009) "STRING 8--a global view on proteins and their functional interactions in 630 organisms." Nucleic Acids Res. 37(Database issue):D412-6. Epub 2008 Oct 21.

• Laskowski R A, Watson J D, Thornton J M (2005). ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res., 33, W89-W93.

Structure

• Dundas J., Ouyang Z., Tseng T., Binkowski A., Turpaz Y., & Liang J. (2006). CASTp: computed atas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucl. Acids Res., 34:W116-W118.

• EMBL EBI. (2008). Protein Quaternary Structure entry: 1ogd. Retrieved 01 06, 2009, from EMBL EBI: http://www.ebi.ac.uk/pdbe/pqs/pqs-bin/macmol.pl?filename=1ogD

• EMBL EBI. (2007). PDBsum entry: 2ob5. Retrieved 12 05, 2009, from EMBL EBI: PDBsum: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=2ob5

• EMBL EBI. (2007). PDBsum entry: 2ob5. Retrieved 12 05, 2009, from EMBL EBI: PDBsum: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=2ob5

• EMBL EBI. (2007). PDBsum entry: 2ob5. Retrieved 12 05, 2009, from EMBL EBI: PDBsum: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=2ob5

• Holm L., & Sander C. (1993). Protein Structure Comparison by Alignment of Distance Matrices (Dali ver. 2.0). J.Mol.Biol , 233 (1), 123-138.

• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD - Visual Molecular Dynamics. J. Molec. Graphics , 14 (1), 33-38.

• Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540

• RCSB. (2009). RCSB PDB : Structure Explorer - 2ob5. Retrieved 04 05, 2009, from RCSB Protein Data Bank: http://www.pdb.org/pdb/explore/explore.do?structureId=2OB5

• RCSB. (2009). RCSB PDB : Structure Explorer - 3e7n. Retrieved 06 05, 2009, from RCSB Protein Data Bank: http://www.pdb.org/pdb/explore/explore.do?structureId=3E7N

• RCSB. (2009). RCSB PDB : Structure Explorer - 1ogd. Retrieved 06 05, 2009, from RCSB Protein Data Bank:

• Kim M., Shin J., Lee W., Lee H. & Oh B. (2003) “Crystal Structures of RbsD Leading to the Identification of Cytoplasmic Sugar-binding Proteins with a Novel Folding Architecture” J. Biol. Chem. 278(30) pp. 28173–28180.

• Roberts, E., Eargle, J., Wright, D., & Luthey-Schulten, Z. (2006). MultiSeq: Unifying sequence and structure data for evolutionary analysis. BMC Bioinformatics , 7 (382), 1-11.

• Sanger Institute. (2001). Pfam: RbsD_FucU. Retrieved 14 05, 2009, from Pfam, Sanger Institute: http://pfam.sanger.ac.uk/family?acc=PF05025

• Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332.

• Wallace A C, Laskowski R A & Thornton J M (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Prot. Eng., 8, 127-134.

Abstract | Introduction | Method | Results | Discussion | Conclusion | References

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