메뉴 건너뛰기




Volumn 28, Issue 24, 2012, Pages 3203-3210

Assessing the relationship between conservation of function and conservation of sequence using photosynthetic proteins

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 84870805341     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts608     Document Type: Article
Times cited : (13)

References (41)
  • 1
    • 0033451741 scopus 로고    scopus 로고
    • Protein consensus sequence motifs
    • Aitken, A. (1999) Protein consensus sequence motifs. Mol. Biotechnol., 12, 241-253.
    • (1999) Mol. Biotechnol , vol.12 , pp. 241-253
    • Aitken, A.1
  • 2
    • 67849122320 scopus 로고    scopus 로고
    • Meme suite: Tools for motif discovery and searching
    • Bailey, T.L. et al. (2009) Meme suite: tools for motif discovery and searching. Nucleic Acids Res., 37, W202-W208.
    • (2009) Nucleic Acids Res , vol.37
    • Bailey, T.L.1
  • 3
    • 33747823564 scopus 로고    scopus 로고
    • Meme: Discovering and analyzing dna and protein sequence motifs
    • Bailey, T.L. et al. (2006)Meme: discovering and analyzing dna and protein sequence motifs. Nucleic Acids Res., 34, W369-W373.
    • (2006) Nucleic Acids Res , vol.34
    • Bailey, T.L.1
  • 4
    • 33845442570 scopus 로고    scopus 로고
    • Evaluation of biocreative assessment of task 2
    • Blaschke, C. et al. (2005) Evaluation of biocreative assessment of task 2. BMC Bioinformatics, 6 (Suppl. 1), S16.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Blaschke, C.1
  • 5
    • 0037255072 scopus 로고    scopus 로고
    • The swiss-prot protein knowledgebase and its supplement trembl in 2003
    • Boeckmann, B. et al. (2003) The swiss-prot protein knowledgebase and its supplement trembl in 2003. Nucleic Acids Res., 31, 365-370.
    • (2003) Nucleic Acids Res , vol.31 , pp. 365-370
    • Boeckmann, B.1
  • 6
    • 0031897589 scopus 로고    scopus 로고
    • Predicting functions from protein sequences-where are the bottlenecks?
    • Bork, P. and Koonin, E.V. (1998) Predicting functions from protein sequences-where are the bottlenecks? Nat. Genet., 18, 313-318.
    • (1998) Nat Genet , vol.18 , pp. 313-318
    • Bork, P.1    Koonin, E.V.2
  • 7
    • 0033119399 scopus 로고    scopus 로고
    • Errors in genome annotation
    • Brenner, S.E. (1999) Errors in genome annotation. Trends Genet., 15, 132-133.
    • (1999) Trends Genet , vol.15 , pp. 132-133
    • Brenner, S.E.1
  • 8
    • 58149191270 scopus 로고    scopus 로고
    • The universal protein resource (uniprot) 2009
    • Consortium, T.U. (2009) The universal protein resource (uniprot) 2009. Nucleic Acids Res., 37, D169-D174.
    • (2009) Nucleic Acids Res , vol.37
    • Consortium, T.U.1
  • 9
    • 77957025820 scopus 로고    scopus 로고
    • Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton
    • Cuvelier, M.L. et al. (2010) Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proc. Natl Acad. Sci. USA, 107, 14679-14684.
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 14679-14684
    • Cuvelier, M.L.1
  • 10
    • 0035424599 scopus 로고    scopus 로고
    • Intrinsic errors in genome annotation
    • Devos, D. and Valencia, A. (2001) Intrinsic errors in genome annotation. Trends Genet., 17, 429-431.
    • (2001) Trends Genet , vol.17 , pp. 429-431
    • Devos, D.1    Valencia, A.2
  • 11
    • 77955490026 scopus 로고    scopus 로고
    • Expansion of the protein repertoire in newly explored environments: Human gut microbiome specific protein families
    • Ellrott, K. et al. (2010) Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. PLoS Comput. Biol., 6, E1000798.
    • (2010) PLoS Comput. Biol , vol.6
    • Ellrott, K.1
  • 12
    • 0034178257 scopus 로고    scopus 로고
    • Homology a personal view on some of the problems
    • Fitch, W.M. (2000) Homology a personal view on some of the problems. Trends Genet., 16, 227-231.
    • (2000) Trends Genet , vol.16 , pp. 227-231
    • Fitch, W.M.1
  • 13
    • 67650720601 scopus 로고    scopus 로고
    • A HMGCR polymorphism is associated with relations between blood pressure and urinary sodium and potassium ratio in the Epic-Norfolk study
    • Freitas, R.N. et al. (2009) A HMGCR polymorphism is associated with relations between blood pressure and urinary sodium and potassium ratio in the Epic-Norfolk study. J. Am. Soc. Hypertens., 3, 238-244.
    • (2009) J. Am. Soc. Hypertens , vol.3 , pp. 238-244
    • Freitas, R.N.1
  • 14
    • 33744471138 scopus 로고    scopus 로고
    • New avenues in protein function prediction
    • Friedberg, I. et al. (2006) New avenues in protein function prediction. Protein Sci., 15, 1527-1529.
    • (2006) Protein Sci , vol.15 , pp. 1527-1529
    • Friedberg, I.1
  • 15
    • 33746664765 scopus 로고    scopus 로고
    • Can sequence determine function?
    • Gerlt, J.A. and Babbitt, P.C. (2000) Can sequence determine function? Genome Biol., 1, REVIEWS0005.
    • (2000) Genome Biol , vol.1
    • Gerlt, J.A.1    Babbitt, P.C.2
  • 16
    • 0037417809 scopus 로고    scopus 로고
    • Plant-like traits associated with metabolism of trypanosoma parasites
    • Hannaert, V. et al. (2003) Plant-like traits associated with metabolism of trypanosoma parasites. Proc Natl Acad. Sci. USA, 100, 1067-1071.
    • (2003) Proc Natl Acad. Sci. USA , vol.100 , pp. 1067-1071
    • Hannaert, V.1
  • 17
    • 35348926028 scopus 로고    scopus 로고
    • Quantitative assessment of protein function prediction from metagenomics shotgun sequences
    • Harrington, E.D. et al. (2007) Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proc. Natl Acad. Sci. USA, 104, 13913-13918.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 13913-13918
    • Harrington, E.D.1
  • 18
    • 13444250007 scopus 로고    scopus 로고
    • ADDA: A domain database with global coverage of the protein universe
    • Heger, A. et al. (2005) ADDA: a domain database with global coverage of the protein universe. Nucleic Acids Res., 33, D188-D191.
    • (2005) Nucleic Acids Res , vol.33
    • Heger, A.1
  • 19
    • 47149117822 scopus 로고    scopus 로고
    • Gene ontology annotations: What they mean and where they come from
    • Hill, D.P. et al. (2008) Gene ontology annotations: what they mean and where they come from. BMC Bioinformatics, 9 (Suppl. 5), S2.
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL. 5
    • Hill, D.P.1
  • 20
    • 34548434778 scopus 로고    scopus 로고
    • Functional representation of enzymes by specific peptides
    • Kunik, V. et al. (2007) Functional representation of enzymes by specific peptides. PLoS Comput. Biol., 3, E167.
    • (2007) PLoS Comput. Biol , vol.3
    • Kunik, V.1
  • 21
    • 36748998785 scopus 로고    scopus 로고
    • Assessment of predictions submitted for the casp7 function prediction category
    • Lopez, G. et al. (2007) Assessment of predictions submitted for the casp7 function prediction category. Proteins, 69 (Suppl. 8), 165-174.
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 165-174
    • Lopez, G.1
  • 22
    • 0036151083 scopus 로고    scopus 로고
    • Tools and resources for identifying protein families, domains and motifs
    • Mulder, N.J. and Apweiler, R. (2002) Tools and resources for identifying protein families, domains and motifs. Genome Biol., 3, REVIEWS2001.
    • (2002) Genome Biol , vol.3
    • Mulder, N.J.1    Apweiler, R.2
  • 24
    • 33746962182 scopus 로고    scopus 로고
    • Everest: Automatic identification and classification of protein domains in all protein sequences
    • Portugaly, E. et al. (2006) Everest: automatic identification and classification of protein domains in all protein sequences. BMC Bioinformatics, 7, 277.
    • (2006) BMC Bioinformatics , vol.7 , pp. 277
    • Portugaly, E.1
  • 25
    • 0034098729 scopus 로고    scopus 로고
    • Genome annotation assessment in drosophila melanogaster
    • Reese, M.G. et al. (2000) Genome annotation assessment in drosophila melanogaster. Genome Res., 10, 483-501.
    • (2000) Genome Res , vol.10 , pp. 483-501
    • Reese, M.G.1
  • 26
    • 45149115291 scopus 로고    scopus 로고
    • The 2006 automated function prediction meeting
    • Rodrigues, A.P. et al. (2007) The 2006 automated function prediction meeting. BMC Bioinformatics, 8 (Suppl. 4), S1-S4.
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 4
    • Rodrigues, A.P.1
  • 27
    • 0036308741 scopus 로고    scopus 로고
    • Enzyme function less conserved than anticipated
    • Rost, B. (2002) Enzyme function less conserved than anticipated. J. Mol. Biol., 318, 595-608.
    • (2002) J. Mol. Biol , vol.318 , pp. 595-608
    • Rost, B.1
  • 28
    • 0030879419 scopus 로고    scopus 로고
    • The HSSP database of protein structure-sequence alignments
    • Schneider, R. et al. (1997) The HSSP database of protein structure-sequence alignments. Nucleic Acids Res., 25, 226-230.
    • (1997) Nucleic Acids Res , vol.25 , pp. 226-230
    • Schneider, R.1
  • 29
    • 74549221383 scopus 로고    scopus 로고
    • Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies
    • Schnoes, A.M. et al. (2009) Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput. Biol., 5, E1000605.
    • (2009) PLoS Comput. Biol , vol.5
    • Schnoes, A.M.1
  • 30
    • 0036228634 scopus 로고    scopus 로고
    • Predicting gene ontology functions from prodom and cdd protein domains
    • Schug, J. et al. (2002) predicting gene ontology functions from prodom and cdd protein domains. Genome Res., 12, 648-655.
    • (2002) Genome Res , vol.12 , pp. 648-655
    • Schug, J.1
  • 31
    • 70249108768 scopus 로고    scopus 로고
    • Photosystem i gene cassettes are present in marine virus genomes
    • Sharon, I. et al. (2009) Photosystem I gene cassettes are present in marine virus genomes. Nature, 461, 258-262.
    • (2009) Nature , vol.461 , pp. 258-262
    • Sharon, I.1
  • 32
    • 0001290045 scopus 로고    scopus 로고
    • Prosite: A documented database using patterns and profiles as motif descriptors
    • Sigrist, C.J. et al. (2002) Prosite: a documented database using patterns and profiles as motif descriptors. Brief. Bioinform., 3, 265-274.
    • (2002) Brief. Bioinform , vol.3 , pp. 265-274
    • Sigrist, C.J.1
  • 33
    • 0030925920 scopus 로고    scopus 로고
    • Pfam: A comprehensive database of protein domain families based on seed alignments
    • Sonnhammer, E.L. et al. (1997) Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins, 28, 405-420.
    • (1997) Proteins , vol.28 , pp. 405-420
    • Sonnhammer, E.L.1
  • 34
    • 30344440806 scopus 로고    scopus 로고
    • The prediction of protein function at CASP6
    • Soro, S. and Tramontano, A. (2005) The prediction of protein function at CASP6. Proteins, 61 (Suppl. 7), 201-213.
    • (2005) Proteins , vol.61 , Issue.SUPPL. 7 , pp. 201-213
    • Soro, S.1    Tramontano, A.2
  • 35
    • 0042902833 scopus 로고    scopus 로고
    • The COG database: An updated version includes eukaryotes
    • Tatusov, R.L. et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4, 41.
    • (2003) BMC Bioinformatics , vol.4 , pp. 41
    • Tatusov, R.L.1
  • 36
    • 0142106373 scopus 로고    scopus 로고
    • How well is enzyme function conserved as a function of pairwise sequence identity? J
    • Tian, W. and Skolnick, J. (2003) How well is enzyme function conserved as a function of pairwise sequence identity? J. Mol. Biol., 333, 863-882.
    • (2003) Mol. Biol , vol.333 , pp. 863-882
    • Tian, W.1    Skolnick, J.2
  • 37
    • 0036776101 scopus 로고    scopus 로고
    • Sequence landmark patterns identify and characterize protein families
    • Wade, R.H. (2002) Sequence landmark patterns identify and characterize protein families. Structure, 10, 1329-1336.
    • (2002) Structure , vol.10 , pp. 1329-1336
    • Wade, R.H.1
  • 38
    • 40749111548 scopus 로고    scopus 로고
    • Confunc-functional annotation in the twilight zone
    • Wass, M.N. and Sternberg, M.J. (2008) Confunc-functional annotation in the twilight zone. Bioinformatics, 24, 798-806.
    • (2008) Bioinformatics , vol.24 , pp. 798-806
    • Wass, M.N.1    Sternberg, M.J.2
  • 39
    • 34248216996 scopus 로고    scopus 로고
    • Making the connections-the crucial role of metabolite transporters at the interface between chloroplast and cytosol
    • Weber, A.P. and Fischer, K. (2007) Making the connections-the crucial role of metabolite transporters at the interface between chloroplast and cytosol. FEBS Lett., 581, 2215-2222.
    • (2007) FEBS Lett , vol.581 , pp. 2215-2222
    • Weber, A.P.1    Fischer, K.2
  • 40
    • 77955979374 scopus 로고    scopus 로고
    • Using affinity propagation combined post-processing to cluster protein sequences
    • Yang, F. et al. (2010) Using affinity propagation combined post-processing to cluster protein sequences. Protein Pept. Lett., 17, 681-689.
    • (2010) Protein Pept. Lett , vol.17 , pp. 681-689
    • Yang, F.1
  • 41
    • 28644449137 scopus 로고    scopus 로고
    • Putative novel photosynthetic reaction centre organizations in marine aerobic anoxygenic photosynthetic bacteria: Insights from metagenomics and environmental genomics
    • Yutin, N. and Beja, O. (2005) Putative novel photosynthetic reaction centre organizations in marine aerobic anoxygenic photosynthetic bacteria: insights from metagenomics and environmental genomics. Environ. Microbiol., 7, 2027-2033.
    • (2005) Environ. Microbiol , vol.7 , pp. 2027-2033
    • Yutin, N.1    Beja, O.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.