메뉴 건너뛰기




Volumn 56, Issue 6, 2004, Pages 317-331

Structural and functional characterization of gene products encoded in the human genome by homology detection

Author keywords

Genome analysis; Homology detection; Protein domain folds; Protein evolution; Sequence analysis

Indexed keywords

ADENOSINE TRIPHOSPHATASE; GENE PRODUCT; GUANOSINE TRIPHOSPHATASE; HYDROLASE; PROTEIN KINASE; PROTEOME;

EID: 7044272774     PISSN: 15216543     EISSN: None     Source Type: Journal    
DOI: 10.1080/15216540400006105     Document Type: Review
Times cited : (4)

References (58)
  • 4
    • 0032424307 scopus 로고    scopus 로고
    • Structural assignments to the Mycoplasma genitalium proteins show extesive gene duplication and domain rearrangements
    • Teichmann, S. A., Park, J. and Chothia, C. (1998) Structural assignments to the Mycoplasma genitalium proteins show extesive gene duplication and domain rearrangements. Proc. Natl. Acad. Sci. USA 95, 14658-14663.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 14658-14663
    • Teichmann, S.A.1    Park, J.2    Chothia, C.3
  • 5
    • 0036145551 scopus 로고    scopus 로고
    • The CATH extended protein-family database providing structural annotations for genome sequences
    • Pearl, F. M., Lee, D., Bray, J. E., Buchan, D. W., Shepherd, A. J. and Orengo, C. A. (2002) The CATH extended protein-family database providing structural annotations for genome sequences. Protein Sci. 11, 233-244.
    • (2002) Protein Sci. , vol.11 , pp. 233-244
    • Pearl, F.M.1    Lee, D.2    Bray, J.E.3    Buchan, D.W.4    Shepherd, A.J.5    Orengo, C.A.6
  • 6
    • 0036601353 scopus 로고    scopus 로고
    • Trends in protein evolution inferred from sequence and structure analysis
    • Aravind, L., Mazumder, R., Vasudevan, S. and Koonin, E. V. (2002) Trends in protein evolution inferred from sequence and structure analysis. Curr. Opin. Struct. Biol. 12, 392-399.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 392-399
    • Aravind, L.1    Mazumder, R.2    Vasudevan, S.3    Koonin, E.V.4
  • 7
    • 0036314772 scopus 로고    scopus 로고
    • Studying genomes through the aeons: Protein families, pseudogenes and proteome evolution
    • Harrison, P. M. and Gerstein, M. (2002) Studying genomes through the aeons: protein families, pseudogenes and proteome evolution. J. Mol. Biol. 318, 1155-1174.
    • (2002) J. Mol. Biol. , vol.318 , pp. 1155-1174
    • Harrison, P.M.1    Gerstein, M.2
  • 8
    • 0033832615 scopus 로고    scopus 로고
    • Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
    • Huynen, M., Snel, B., Lathe, W, 3rd and Bork, P. (2000) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res. 10, 1204-1210.
    • (2000) Genome Res. , vol.10 , pp. 1204-1210
    • Huynen, M.1    Snel, B.2    Lathe III, W.3    Bork, P.4
  • 10
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson, W. R. and Lipman, D. J. (1988) Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85, 2444-2448.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 11
    • 0031302793 scopus 로고    scopus 로고
    • Distant homology recognition using structural classification of proteins
    • Murzin, A. G. and Bateman, A. (1997) Distant homology recognition using structural classification of proteins. Proteins Suppl 1, 105-112.
    • (1997) Proteins , Issue.SUPPL. 1 , pp. 105-112
    • Murzin, A.G.1    Bateman, A.2
  • 12
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia, C. and Lesk, A. M. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J. 5, 823-826.
    • (1986) EMBO J. , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 13
    • 0031020765 scopus 로고    scopus 로고
    • Protein evolution. How far can sequences diverge?
    • Chothia, C. and Gerstein, M. (1997) Protein evolution. How far can sequences diverge? Nature 385, 579-581.
    • (1997) Nature , vol.385 , pp. 579-581
    • Chothia, C.1    Gerstein, M.2
  • 14
    • 0032411225 scopus 로고    scopus 로고
    • How representative are the known structures of the proteins in a complete genome? A comprehensive structural census
    • Gerstein, M. (1998) How representative are the known structures of the proteins in a complete genome? A comprehensive structural census. Fold. Des. 3, 497-512.
    • (1998) Fold. Des. , vol.3 , pp. 497-512
    • Gerstein, M.1
  • 16
    • 0033597176 scopus 로고    scopus 로고
    • The relationship between protein structure and function a comprehensive survey with application to the yeast genome
    • Hegyi, H. and Gerstein, M. (1999) The relationship between protein structure and function a comprehensive survey with application to the yeast genome. J. Mol. Biol. 288, 147-164.
    • (1999) J. Mol. Biol. , vol.288 , pp. 147-164
    • Hegyi, H.1    Gerstein, M.2
  • 17
    • 0034595501 scopus 로고    scopus 로고
    • Enhanced genome annotation using structural profiles in the program 3D-PSSM
    • Kelley, L. A., MacCallum, R. M. and Sternberg, M. J. (2000) Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299, 499-520.
    • (2000) J. Mol. Biol. , vol.299 , pp. 499-520
    • Kelley, L.A.1    MacCallum, R.M.2    Sternberg, M.J.3
  • 18
    • 0033117760 scopus 로고    scopus 로고
    • Predicting structures for genome proteins
    • Fischer, D. and Eisenberg, D. (1999) Predicting structures for genome proteins. Curr. Opin. Struct. Biol. 9, 208-211.
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 208-211
    • Fischer, D.1    Eisenberg, D.2
  • 20
    • 0035059281 scopus 로고    scopus 로고
    • Genomic-scale comparison of sequence-and structure-based methods of function prediction: Does structure provide additional insight?
    • Fetrow, J. S., Siew, N., Di Gennaro, J. A., Martinez-Yamout, M., Dyson, J. H. and Skolnick, J. (2001) Genomic-scale comparison of sequence-and structure-based methods of function prediction: Does structure provide additional insight? Protein Sci. 10, 1005-1014.
    • (2001) Protein Sci. , vol.10 , pp. 1005-1014
    • Fetrow, J.S.1    Siew, N.2    Di Gennaro, J.A.3    Martinez-Yamout, M.4    Dyson, J.H.5    Skolnick, J.6
  • 22
    • 0028181441 scopus 로고
    • Hidden Markov models in computational biology. Applications to protein modeling
    • Krogh, A., Brown, M., Mian, I. S., Sjolander. K. and Haussler, D. (1994) Hidden Markov models in computational biology. Applications to protein modeling. J. Mol. Biol. 235, 1510-1531.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1510-1531
    • Krogh, A.1    Brown, M.2    Mian, I.S.3    Sjolander, K.4    Haussler, D.5
  • 23
    • 0031844330 scopus 로고    scopus 로고
    • Fold and function predictions for Mycoplasma genitalium proteins
    • Rychlewski, L., Zhang, B. and Godzik, A. (1998) Fold and function predictions for Mycoplasma genitalium proteins. Fold Des. 3, 229-238.
    • (1998) Fold Des. , vol.3 , pp. 229-238
    • Rychlewski, L.1    Zhang, B.2    Godzik, A.3
  • 24
    • 0029997801 scopus 로고    scopus 로고
    • Applying motif and profile searches
    • Bork, P. and Gibson, T. J. (1996) Applying motif and profile searches. Methods Enzymol. 266, 162-184.
    • (1996) Methods Enzymol. , vol.266 , pp. 162-184
    • Bork, P.1    Gibson, T.J.2
  • 26
    • 0036087098 scopus 로고    scopus 로고
    • SUPFAM-a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: Implications for structural genomics and function annotation in genomes
    • Pandit, S. B., Gosar, D., Abhiman, S., Sujatha, S., Dixit, S. S., Mhatre, N. S., Sowdhamini, R. and Srinivasan, N. (2002) SUPFAM-a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes. Nucl Acids Res. 30, 289-293.
    • (2002) Nucl Acids Res. , vol.30 , pp. 289-293
    • Pandit, S.B.1    Gosar, D.2    Abhiman, S.3    Sujatha, S.4    Dixit, S.S.5    Mhatre, N.S.6    Sowdhamini, R.7    Srinivasan, N.8
  • 28
    • 4644275573 scopus 로고    scopus 로고
    • Enhanced functional and structural domain assignments using remote similarity detection procedures for proteins encoded in the genome of Mycobacterium tuberculosis H37Rv
    • in press
    • Namboori, S., Mhatre, N., Sujatha, S., Srinivasan, N. and Pandit, S. B. (2004) Enhanced functional and structural domain assignments using remote similarity detection procedures for proteins encoded in the genome of Mycobacterium tuberculosis H37Rv J. of Biosci. (in press).
    • (2004) J. of Biosci.
    • Namboori, S.1    Mhatre, N.2    Sujatha, S.3    Srinivasan, N.4    Pandit, S.B.5
  • 29
    • 0038438514 scopus 로고    scopus 로고
    • IMPALA: Matching a protein sequence against a collection of PS1-BLAST-constructed position-specific score matrices
    • Schaffer, A. A., Wolf, Y. I., Ponting, C. P., Koonin, E. V., Aravind, L. and Altschul, S. F. (1999) IMPALA: matching a protein sequence against a collection of PS1-BLAST-constructed position-specific score matrices. Bioinformatics 15, 1000-1011.
    • (1999) Bioinformatics , vol.15 , pp. 1000-1011
    • Schaffer, A.A.1    Wolf, Y.I.2    Ponting, C.P.3    Koonin, E.V.4    Aravind, L.5    Altschul, S.F.6
  • 30
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy, S. R. (1998) Profile hidden Markov models. Bioinformatics 14, 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 31
    • 0345504211 scopus 로고    scopus 로고
    • Benchmarking PSI-BLAST in genome annotation
    • Muller, A., MacCallum, R. M. and Sternberg, M. J. (1999) Benchmarking PSI-BLAST in genome annotation. J. Mol. Biol. 293, 1257-1271.
    • (1999) J. Mol. Biol. , vol.293 , pp. 1257-1271
    • Muller, A.1    MacCallum, R.M.2    Sternberg, M.J.3
  • 32
    • 0034695414 scopus 로고    scopus 로고
    • Identification of related proteins on family, superfamily and fold level
    • Lindahl, E. and Eloffson, A. (2000) Identification of related proteins on family, superfamily and fold level. J. Mol. Biol. 295, 613-625.
    • (2000) J. Mol. Biol. , vol.295 , pp. 613-625
    • Lindahl, E.1    Eloffson, A.2
  • 33
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • Jones. D. T. (1999) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287, 797-815.
    • (1999) J. Mol. Biol. , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 34
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie, J. U., Luthy, R. and Eisenberg, D. (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253, 164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 35
    • 0037020194 scopus 로고    scopus 로고
    • Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster
    • Zbdonov, E. M., von Mering, C., Letunic, I., Torrents, D., Suyuma, M., Copley, R. R. et al. (2002) Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 298, 149-159.
    • (2002) Science , vol.298 , pp. 149-159
    • Zbdonov, E.M.1    Von Mering, C.2    Letunic, I.3    Torrents, D.4    Suyuma, M.5    Copley, R.R.6
  • 36
    • 0037197886 scopus 로고    scopus 로고
    • The identification of functional modules from the genomic association of genes
    • Snel, B., Bork, P. and Huynen, M. A. (2002) The identification of functional modules from the genomic association of genes. Proc. Natl. Acad. Sci. USA 99, 5890-5895.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 5890-5895
    • Snel, B.1    Bork, P.2    Huynen, M.A.3
  • 38
    • 0036853192 scopus 로고    scopus 로고
    • Structural characterization of the human proteome
    • Muller, A., MacCallum, R. M. and Sternberg, M. J. (2002) Structural characterization of the human proteome. Genome Res. 12, 1625-1641.
    • (2002) Genome Res. , vol.12 , pp. 1625-1641
    • Muller, A.1    MacCallum, R.M.2    Sternberg, M.J.3
  • 39
    • 0033941641 scopus 로고    scopus 로고
    • Protein fold recognition using sequence profiles and its application in structural genomics
    • Koonin, E. V., Wolf, Y. I. and Arvind, L. (2000) Protein fold recognition using sequence profiles and its application in structural genomics. Adv. Prot. Chem. 54, 245-275.
    • (2000) Adv. Prot. Chem. , vol.54 , pp. 245-275
    • Koonin, E.V.1    Wolf, Y.I.2    Arvind, L.3
  • 43
    • 0035175268 scopus 로고    scopus 로고
    • PALI-a database of Phylogeny and ALIgnment of homologous protein structures
    • Balaji, S., Sujatha, S., Kumar, S. S. C. and Srinivasan, N. (2001) PALI-a database of Phylogeny and ALIgnment of homologous protein structures. Nucleic Acids Res. 29, 61-65.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 61-65
    • Balaji, S.1    Sujatha, S.2    Kumar, S.S.C.3    Srinivasan, N.4
  • 44
    • 0037246028 scopus 로고    scopus 로고
    • Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database
    • Gowri, V. S., Pandit, S. B., Karthik, P. S., Srinivasan, N. and Balaji, S. (2003) Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database. Nucl. Acids Res. 31, 486-488.
    • (2003) Nucl. Acids Res. , vol.31 , pp. 486-488
    • Gowri, V.S.1    Pandit, S.B.2    Karthik, P.S.3    Srinivasan, N.4    Balaji, S.5
  • 45
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A. G., Brenner, S. E., Hubbard, T. and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 46
    • 18444402182 scopus 로고    scopus 로고
    • The Ensembl genome database project
    • Hubbard et al. (2002) The Ensembl genome database project. Nucl. Acids Res. 30, 38-41.
    • (2002) Nucl. Acids Res. , vol.30 , pp. 38-41
    • Hubbard1
  • 47
    • 0034022925 scopus 로고    scopus 로고
    • OMIM passes the 1000-disease-gene mark
    • Antonarakis, S. E. and McKusick, V. A. (2000) OMIM passes the 1000-disease-gene mark. Nat. Genet. 25, 11.
    • (2000) Nat. Genet. , vol.25 , pp. 11
    • Antonarakis, S.E.1    McKusick, V.A.2
  • 48
    • 0033957834 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
    • Bairoch, A. and Apweiler, R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucl. Acids Res. 28, 45-48.
    • (2000) Nucl. Acids Res. , vol.28 , pp. 45-48
    • Bairoch, A.1    Apweiler, R.2
  • 50
    • 0038549051 scopus 로고    scopus 로고
    • The repertoire of protein kinases encoded in the draft version of the human genome: Atypical variations and uncommon domain combinations
    • Krupa, A. and Srinivasan, N. (2002) The repertoire of protein kinases encoded in the draft version of the human genome: atypical variations and uncommon domain combinations. Genome Biol. 3, 0066.1-0066.14.
    • (2002) Genome Biol. , vol.3
    • Krupa, A.1    Srinivasan, N.2
  • 51
    • 0030029513 scopus 로고    scopus 로고
    • AcrAB efflux pump plays a major role in the antibiotic resistance phenotype of Escherichia coli multiple-antibiotic-resistance (Mar) mutants
    • Okusu, H., Ma, D. and Nikaido, H. (1996) AcrAB efflux pump plays a major role in the antibiotic resistance phenotype of Escherichia coli multiple-antibiotic-resistance (Mar) mutants. J. Bacteriol. 178, 306-308.
    • (1996) J. Bacteriol. , vol.178 , pp. 306-308
    • Okusu, H.1    Ma, D.2    Nikaido, H.3
  • 52
    • 0024468746 scopus 로고
    • The Drosophila patched gene encodes a putative membrane protein required for segmental patterning
    • Hooper, J. E. and Scott, M. P. (1989) The Drosophila patched gene encodes a putative membrane protein required for segmental patterning. Cell 59, 751-765.
    • (1989) Cell , vol.59 , pp. 751-765
    • Hooper, J.E.1    Scott, M.P.2
  • 53
    • 0028140309 scopus 로고
    • SecD and SecF are required for the proton electrochemical gradient stimulation of preprotein translocation
    • Arkowitz, R. A. and Wickner, W. (1994) SecD and SecF are required for the proton electrochemical gradient stimulation of preprotein translocation. EMBO J. 13, 954-963.
    • (1994) EMBO J. , vol.13 , pp. 954-963
    • Arkowitz, R.A.1    Wickner, W.2
  • 55
    • 0034709561 scopus 로고    scopus 로고
    • Molecular identification and characterization of novel members of the human organic anion transporter (OATP) family
    • Tamai, I., Nezu, J., Uchino, H., Sai, Y., Oku, A., Shimane, M. and Tsuji, A. (2000) Molecular identification and characterization of novel members of the human organic anion transporter (OATP) family. Biochem. Biophys. Res. Commun. 273, 251-260.
    • (2000) Biochem. Biophys. Res. Commun. , vol.273 , pp. 251-260
    • Tamai, I.1    Nezu, J.2    Uchino, H.3    Sai, Y.4    Oku, A.5    Shimane, M.6    Tsuji, A.7
  • 56
    • 0036226647 scopus 로고    scopus 로고
    • Dual function of the tRNA (m(5)U54) methyltransferase in tRNA maturation
    • Johansson, M. J. and Bystrom, A. S. (2002) Dual function of the tRNA (m(5)U54) methyltransferase in tRNA maturation. RNA 8, 324-335.
    • (2002) RNA , vol.8 , pp. 324-335
    • Johansson, M.J.1    Bystrom, A.S.2
  • 57
    • 0035800737 scopus 로고    scopus 로고
    • Identification of the catalytic residues of bifunctional glycogen debranching enzyme
    • Nakayama, A., Yamamoto, K. and Tabata, S. (2001) Identification of the catalytic residues of bifunctional glycogen debranching enzyme. J. Biol. Chem. 276, 28824-28828.
    • (2001) J. Biol. Chem. , vol.276 , pp. 28824-28828
    • Nakayama, A.1    Yamamoto, K.2    Tabata, S.3
  • 58
    • 0027609916 scopus 로고
    • SETOR: Hardware lighted three-dimensional-solid model representations of macromolecules
    • Evans, S. V. (1993) SETOR: hardware lighted three-dimensional-solid model representations of macromolecules. J Mol. Graph. 11, 134-138.
    • (1993) J Mol. Graph. , vol.11 , pp. 134-138
    • Evans, S.V.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.