-
1
-
-
0035223823
-
Chapter 15: Comparative genome analysis
-
Edited by Baxevanis A, Ouellette F. New York: Wiley-Liss, Inc
-
Galperin MY, Koonin EV: Chapter 15: comparative genome analysis. In Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, edn 2. Edited by Baxevanis A, Ouellette F. New York: Wiley-Liss, Inc; 2001:359-392.
-
(2001)
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, edn 2
, pp. 359-392
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
3
-
-
0033055062
-
The use of gene clusters to infer functional coupling
-
Overbeek R., Fonstein M., D'Souza M., Pusch G.D., Maltsev N. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. U.S.A. 96:1999;2896-2901.
-
(1999)
Proc. Natl. Acad. Sci. U.S.A.
, vol.96
, pp. 2896-2901
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
4
-
-
0033523989
-
Protein interaction maps for complete genomes based on gene fusion events
-
Enright A.J., Iliopoulos I., Kyrpides N.C., Ouzounis C.A. Protein interaction maps for complete genomes based on gene fusion events. Nature. 402:1999;86-90.
-
(1999)
Nature
, vol.402
, pp. 86-90
-
-
Enright, A.J.1
Iliopoulos, I.2
Kyrpides, N.C.3
Ouzounis, C.A.4
-
5
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
Marcotte E.M., Pellegrini M., Ng H.L., Rice D.W., Yeates T.O., Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science. 285:1999;751-753.
-
(1999)
Science
, vol.285
, pp. 751-753
-
-
Marcotte, E.M.1
Pellegrini, M.2
Ng, H.L.3
Rice, D.W.4
Yeates, T.O.5
Eisenberg, D.6
-
6
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini M., Marcotte E.M., Thompson M.J., Eisenberg D., Yeates T.O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. U.S.A. 96:1999;4285-4288.
-
(1999)
Proc. Natl. Acad. Sci. U.S.A.
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
7
-
-
0034669669
-
Predicting regulons and their cis-regulatory motifs by comparative genomics
-
Manson McGuire A., Church G.M. Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucleic Acids Res. 28:2000;4523-4530.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 4523-4530
-
-
Manson McGuire, A.1
Church, G.M.2
-
9
-
-
0035085816
-
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context
-
Conserved 'gene strings' were used to infer functional coupling and to produce functional predictions for ∼90 clusters of orthologous groups including a probable archaeal equivalent of the eukaryotic exosome
-
Wolf Y.I., Rogozin I.B., Kondrashov A.S., Koonin E.V. Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res. 11:2001;356-372 Conserved 'gene strings' were used to infer functional coupling and to produce functional predictions for ∼90 clusters of orthologous groups including a probable archaeal equivalent of the eukaryotic exosome.
-
(2001)
Genome Res.
, vol.11
, pp. 356-372
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Kondrashov, A.S.3
Koonin, E.V.4
-
10
-
-
0036676469
-
Computational identification of operons in microbial genomes
-
Zheng Y., Szustakowski J.D., Fortnow L., Roberts R.J., Kasif S. Computational identification of operons in microbial genomes. Genome Res. 12:2002;1221-1230.
-
(2002)
Genome Res.
, vol.12
, pp. 1221-1230
-
-
Zheng, Y.1
Szustakowski, J.D.2
Fortnow, L.3
Roberts, R.J.4
Kasif, S.5
-
11
-
-
0037079680
-
A DNA repair system specific for thermophilic archaea and bacteria predicted by genomic context analysis
-
Makarova K.S., Aravind L., Grishin N.V., Rogozin I.B., Koonin E.V. A DNA repair system specific for thermophilic archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res. 30:2002;482-496.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 482-496
-
-
Makarova, K.S.1
Aravind, L.2
Grishin, N.V.3
Rogozin, I.B.4
Koonin, E.V.5
-
12
-
-
0343488601
-
A reconstruction of the metabolism of Methanococcus jannaschii from sequence data
-
Selkov E., Maltsev N., Olsen G.J., Overbeek R., Whitman W.B. A reconstruction of the metabolism of Methanococcus jannaschii from sequence data. Gene. 197:1997;GC11-GC26.
-
(1997)
Gene
, vol.197
-
-
Selkov, E.1
Maltsev, N.2
Olsen, G.J.3
Overbeek, R.4
Whitman, W.B.5
-
13
-
-
0031966808
-
Reconstruction of amino acid biosynthesis pathways from the complete genome sequence
-
Bono H., Ogata H., Goto S., Kanehisa M. Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res. 8:1998;203-210.
-
(1998)
Genome Res.
, vol.8
, pp. 203-210
-
-
Bono, H.1
Ogata, H.2
Goto, S.3
Kanehisa, M.4
-
14
-
-
0036081062
-
The KEGG databases at GenomeNet
-
This is an introduction to one of the most valuable public web-based resources. The core of this integration is a collection of pathways connected to individual compounds, reactions, functional roles (enzymes) and genes. Recent additions include microarray expression and protein-protein interactions data
-
Kanehisa M., Goto S., Kawashima S., Nakaya A. The KEGG databases at GenomeNet. Nucleic Acids Res. 30:2002;42-46 This is an introduction to one of the most valuable public web-based resources. The core of this integration is a collection of pathways connected to individual compounds, reactions, functional roles (enzymes) and genes. Recent additions include microarray expression and protein-protein interactions data.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 42-46
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Nakaya, A.4
-
15
-
-
0033215210
-
Pathway alignment: Application to the comparative analysis of glycolytic enzymes
-
Dandekar T., Schuster S., Snel B., Huynen M., Bork P. Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem. J. 343:1999;115-124.
-
(1999)
Biochem. J.
, vol.343
, pp. 115-124
-
-
Dandekar, T.1
Schuster, S.2
Snel, B.3
Huynen, M.4
Bork, P.5
-
16
-
-
0036119364
-
Comparative genome analysis and pathway reconstruction
-
Dandekar T., Sauerborn R. Comparative genome analysis and pathway reconstruction. Pharmacogenomics. 3:2002;245-256.
-
(2002)
Pharmacogenomics
, vol.3
, pp. 245-256
-
-
Dandekar, T.1
Sauerborn, R.2
-
17
-
-
0036206041
-
Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586
-
Kapatral V., Anderson I., Ivanova N., Reznik G., Los T., Lykidis A., Bhattacharyya A., Bartman A., Gardner W., Grechkin G.et al. Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586. J. Bacteriol. 184:2002;2005-2018.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 2005-2018
-
-
Kapatral, V.1
Anderson, I.2
Ivanova, N.3
Reznik, G.4
Los, T.5
Lykidis, A.6
Bhattacharyya, A.7
Bartman, A.8
Gardner, W.9
Grechkin, G.10
-
18
-
-
0037039357
-
The genome sequence of the facultative intracellular pathogen Brucella melitensis
-
DelVecchio V.G., Kapatral V., Redkar R.J., Patra G., Mujer C., Los T., Ivanova N., Anderson I., Bhattacharyya A., Lykidis A.et al. The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc. Natl. Acad. Sci. U.S.A. 99:2002;443-448.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 443-448
-
-
DelVecchio, V.G.1
Kapatral, V.2
Redkar, R.J.3
Patra, G.4
Mujer, C.5
Los, T.6
Ivanova, N.7
Anderson, I.8
Bhattacharyya, A.9
Lykidis, A.10
-
19
-
-
0036798237
-
Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights
-
Bhattacharyya A., Stilwagen S., Reznik G., Feil H., Feil W.S., Anderson I., Bernal A., D'Souza M., Ivanova N., Kapatral V.et al. Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights. Genome Res. 12:2002;1556-1563.
-
(2002)
Genome Res.
, vol.12
, pp. 1556-1563
-
-
Bhattacharyya, A.1
Stilwagen, S.2
Reznik, G.3
Feil, H.4
Feil, W.S.5
Anderson, I.6
Bernal, A.7
D'Souza, M.8
Ivanova, N.9
Kapatral, V.10
-
20
-
-
0035281870
-
Metabolic modeling of microbial strains in silico
-
Covert M.W., Schilling C.H., Famili I., Edwards J.S., Goryanin I.I., Selkov E., Palsson B.O. Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 26:2001;179-186.
-
(2001)
Trends Biochem. Sci.
, vol.26
, pp. 179-186
-
-
Covert, M.W.1
Schilling, C.H.2
Famili, I.3
Edwards, J.S.4
Goryanin, I.I.5
Selkov, E.6
Palsson, B.O.7
-
21
-
-
0032702286
-
Microbial genomes and 'missing' enzymes: Redefining biochemical pathways
-
Cordwell S.J. Microbial genomes and 'missing' enzymes: redefining biochemical pathways. Arch. Microbiol. 172:1999;269-279.
-
(1999)
Arch. Microbiol.
, vol.172
, pp. 269-279
-
-
Cordwell, S.J.1
-
22
-
-
0033382609
-
Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes
-
Galperin M.Y., Koonin E.V. Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes. Genetica. 106:1999;159-170.
-
(1999)
Genetica
, vol.106
, pp. 159-170
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
23
-
-
0034916009
-
PubMed: Bridging the information gap
-
McEntyre J., Lipman D. PubMed: bridging the information gap. CMAJ. 164:2001;1317-1319.
-
(2001)
CMAJ
, vol.164
, pp. 1317-1319
-
-
McEntyre, J.1
Lipman, D.2
-
25
-
-
0037208159
-
The ERGO genome analysis and discovery system
-
Overbeek R., Larsen N., Walunas T., D'Souza M., Pusch G., Selkov E. Jr., Liolios K., Joukov V., Kaznadzey D., Anderson I.et al. The ERGO genome analysis and discovery system. Nucleic Acids Res. 31:2003;1-8.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 1-8
-
-
Overbeek, R.1
Larsen, N.2
Walunas, T.3
D'Souza, M.4
Pusch, G.5
Selkov E., Jr.6
Liolios, K.7
Joukov, V.8
Kaznadzey, D.9
Anderson, I.10
-
27
-
-
33746664765
-
Can sequence determine function?
-
reviews0005
-
Gerlt JA, Babbitt PC: Can sequence determine function? Genome Biol 2000, 1:reviews0005.
-
(2000)
Genome Biol
, vol.1
-
-
Gerlt, J.A.1
Babbitt, P.C.2
-
28
-
-
0035180870
-
Archaeal shikimate kinase, a new member of the GHMP-kinase family
-
Daugherty M., Vonstein V., Overbeek R., Osterman A. Archaeal shikimate kinase, a new member of the GHMP-kinase family. J. Bacteriol. 183:2001;292-300.
-
(2001)
J. Bacteriol.
, vol.183
, pp. 292-300
-
-
Daugherty, M.1
Vonstein, V.2
Overbeek, R.3
Osterman, A.4
-
29
-
-
0035162592
-
The COG database: New developments in phylogenetic classification of proteins from complete genomes
-
Tatusov R.L., Natale D.A., Garkavtsev I.V., Tatusova T.A., Shankavaram U.T., Rao B.S., Kiryutin B., Galperin M.Y., Fedorova N.D., Koonin E.V. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29:2001;22-28.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 22-28
-
-
Tatusov, R.L.1
Natale, D.A.2
Garkavtsev, I.V.3
Tatusova, T.A.4
Shankavaram, U.T.5
Rao, B.S.6
Kiryutin, B.7
Galperin, M.Y.8
Fedorova, N.D.9
Koonin, E.V.10
-
30
-
-
0035943350
-
SNAPping up functionally related genes based on context information: A colinearity-free approach
-
A modification of the chromosomal clustering analysis (termed similarity-neighborhood approach) is described, validated and illustrated with examples of application in genome annotation. The major distinction of this implementation is in removing any gene colinearity constraint from the original technique
-
Kolesov G., Mewes H.W., Frishman D. SNAPping up functionally related genes based on context information: a colinearity-free approach. J. Mol. Biol. 311:2001;639-656 A modification of the chromosomal clustering analysis (termed similarity-neighborhood approach) is described, validated and illustrated with examples of application in genome annotation. The major distinction of this implementation is in removing any gene colinearity constraint from the original technique.
-
(2001)
J. Mol. Biol.
, vol.311
, pp. 639-656
-
-
Kolesov, G.1
Mewes, H.W.2
Frishman, D.3
-
31
-
-
0037052935
-
Connected gene neighborhoods in prokaryotic genomes
-
Clustering of genes on the chromosome was extended to larger gene neighborhoods (superoperons), revealing new functional links between proteins, including a hypothesized 'genomic hitchhiking' phenomenon possibly related to maintaining optimal expression levels for large ensembles of genes
-
Rogozin I.B., Makarova K.S., Murvai J., Czabarka E., Wolf Y.I., Tatusov R.L., Szekely L.A., Koonin E.V. Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res. 30:2002;2212-2223 Clustering of genes on the chromosome was extended to larger gene neighborhoods (superoperons), revealing new functional links between proteins, including a hypothesized 'genomic hitchhiking' phenomenon possibly related to maintaining optimal expression levels for large ensembles of genes.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 2212-2223
-
-
Rogozin, I.B.1
Makarova, K.S.2
Murvai, J.3
Czabarka, E.4
Wolf, Y.I.5
Tatusov, R.L.6
Szekely, L.A.7
Koonin, E.V.8
-
32
-
-
0034666108
-
STRING: A web-server to retrieve and display the repeatedly occurring neighbourhood of a gene
-
This paper describes a convenient web-based implementation of the chromosomal gene-clustering technique
-
Snel B., Lehmann G., Bork P., Huynen M.A. STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res. 28:2000;3442-3444 This paper describes a convenient web-based implementation of the chromosomal gene-clustering technique.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 3442-3444
-
-
Snel, B.1
Lehmann, G.2
Bork, P.3
Huynen, M.A.4
-
33
-
-
0034084865
-
Who's your neighbor? New computational approaches for functional genomics
-
One of the earliest comprehensive reviews summarizing principles and applications of major techniques in comparative genomics going beyond sequence comparison. The functional prediction of an alternative thymidilate synthase (Thy1) was experimentally confirmed later and cited in this review
-
Galperin M.Y., Koonin E.V. Who's your neighbor? New computational approaches for functional genomics. Nat. Biotechnol. 18:2000;609-613 One of the earliest comprehensive reviews summarizing principles and applications of major techniques in comparative genomics going beyond sequence comparison. The functional prediction of an alternative thymidilate synthase (Thy1) was experimentally confirmed later and cited in this review.
-
(2000)
Nat. Biotechnol.
, vol.18
, pp. 609-613
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
34
-
-
0034306448
-
Gene context conservation of a higher order than operons
-
Lathe W.C. III, Snel B., Bork P. Gene context conservation of a higher order than operons. Trends Biochem. Sci. 25:2000;474-479.
-
(2000)
Trends Biochem. Sci.
, vol.25
, pp. 474-479
-
-
Lathe W.C. III1
Snel, B.2
Bork, P.3
-
36
-
-
0037197886
-
The identification of functional modules from the genomic association of genes
-
Snel B., Bork P., Huynen M.A. The identification of functional modules from the genomic association of genes. Proc. Natl. Acad. Sci. U.S.A. 99:2002;5890-5895.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 5890-5895
-
-
Snel, B.1
Bork, P.2
Huynen, M.A.3
-
37
-
-
0036533931
-
Identifying functional links between genes using conserved chromosomal proximity
-
Yanai I., Mellor J.C., DeLisi C. Identifying functional links between genes using conserved chromosomal proximity. Trends Genet. 18:2002;176-179.
-
(2002)
Trends Genet.
, vol.18
, pp. 176-179
-
-
Yanai, I.1
Mellor, J.C.2
DeLisi, C.3
-
38
-
-
0034669517
-
Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools
-
Kyrpides N.C., Ouzounis C.A., Iliopoulos I., Vonstein V., Overbeek R. Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools. Nucleic Acids Res. 28:2000;4573-4576.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 4573-4576
-
-
Kyrpides, N.C.1
Ouzounis, C.A.2
Iliopoulos, I.3
Vonstein, V.4
Overbeek, R.5
-
40
-
-
0034027595
-
Computational genetics: Finding protein function by nonhomology methods
-
Genome context analysis techniques ('domain fusion, conserved gene position and gene co-inheritance and co-expression') are reviewed in the context of their application in genome-wide predictions of functions for proteins without characterized homologs
-
Marcotte E.M. Computational genetics: finding protein function by nonhomology methods. Curr. Opin. Struct. Biol. 10:2000;359-365 Genome context analysis techniques ('domain fusion, conserved gene position and gene co-inheritance and co-expression') are reviewed in the context of their application in genome-wide predictions of functions for proteins without characterized homologs.
-
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 359-365
-
-
Marcotte, E.M.1
-
41
-
-
0034940467
-
Genes linked by fusion events are generally of the same functional category: A systematic analysis of 30 microbial genomes
-
Yanai I., Derti A., DeLisi C. Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. Proc. Natl. Acad. Sci. U.S.A. 98:2001;7940-7945.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 7940-7945
-
-
Yanai, I.1
Derti, A.2
DeLisi, C.3
-
42
-
-
0033832615
-
Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
-
Huynen M., Snel B., Lathe W. iii, Bork P. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res. 10:2000;1204-1210.
-
(2000)
Genome Res.
, vol.10
, pp. 1204-1210
-
-
Huynen, M.1
Snel, B.2
Lathe W. III3
Bork, P.4
-
43
-
-
0036081482
-
Predictome: A database of putative functional links between proteins
-
This paper describes one of the first web-based public resources providing a collection of predicted functional links between proteins (from 44 genomes) computed by a combination of genome context analysis techniques and protein-protein interaction data. The relative impact and potential synergy between all of these techniques is quantitatively evaluated and illustrated using the TCA cycle
-
Mellor J.C., Yanai I., Clodfelter K.H., Mintseris J., DeLisi C. Predictome: a database of putative functional links between proteins. Nucleic Acids Res. 30:2002;306-309 This paper describes one of the first web-based public resources providing a collection of predicted functional links between proteins (from 44 genomes) computed by a combination of genome context analysis techniques and protein-protein interaction data. The relative impact and potential synergy between all of these techniques is quantitatively evaluated and illustrated using the TCA cycle.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 306-309
-
-
Mellor, J.C.1
Yanai, I.2
Clodfelter, K.H.3
Mintseris, J.4
DeLisi, C.5
-
44
-
-
2242447089
-
Whole-genome analysis of photosynthetic prokaryotes
-
Raymond J., Zhaxybayeva O., Gogarten J.P., Gerdes S.Y., Blankenship R.E. Whole-genome analysis of photosynthetic prokaryotes. Science. 298:2002;1616-1620.
-
(2002)
Science
, vol.298
, pp. 1616-1620
-
-
Raymond, J.1
Zhaxybayeva, O.2
Gogarten, J.P.3
Gerdes, S.Y.4
Blankenship, R.E.5
-
45
-
-
0033918228
-
Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes
-
McGuire A.M., Hughes J.D., Church G.M. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res. 10:2000;744-757.
-
(2000)
Genome Res.
, vol.10
, pp. 744-757
-
-
McGuire, A.M.1
Hughes, J.D.2
Church, G.M.3
-
46
-
-
0037188521
-
Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics
-
van Nimwegen E., Zavolan M., Rajewsky N., Siggia E.D. Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics. Proc. Natl. Acad. Sci. U.S.A. 99:2002;7323-7328.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 7323-7328
-
-
Van Nimwegen, E.1
Zavolan, M.2
Rajewsky, N.3
Siggia, E.D.4
-
47
-
-
0035162782
-
RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12
-
Salgado H., Santos-Zavaleta A., Gama-Castro S., Millan-Zarate D., Diaz-Peredo E., Sanchez-Solano F., Perez-Rueda E., Bonavides-Martinez C., Collado-Vides J. RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res. 29:2001;72-74.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 72-74
-
-
Salgado, H.1
Santos-Zavaleta, A.2
Gama-Castro, S.3
Millan-Zarate, D.4
Diaz-Peredo, E.5
Sanchez-Solano, F.6
Perez-Rueda, E.7
Bonavides-Martinez, C.8
Collado-Vides, J.9
-
48
-
-
0036797992
-
Conservation of the biotin regulon and the BirA regulatory signal in eubacteria and archaea
-
Rodionov D.A., Mironov A.A., Gelfand M.S. Conservation of the biotin regulon and the BirA regulatory signal in eubacteria and archaea. Genome Res. 12:2002;1507-1516.
-
(2002)
Genome Res.
, vol.12
, pp. 1507-1516
-
-
Rodionov, D.A.1
Mironov, A.A.2
Gelfand, M.S.3
-
49
-
-
2242446202
-
Comparative genomics of thiamin biosynthesis in procaryotes: New genes and regulatory mechanisms
-
Rodionov D.A., Vitreschak A.G., Mironov A.A., Gelfand M.S. Comparative genomics of thiamin biosynthesis in procaryotes: new genes and regulatory mechanisms. J. Biol. Chem. 277:2002;48949-48959.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 48949-48959
-
-
Rodionov, D.A.1
Vitreschak, A.G.2
Mironov, A.A.3
Gelfand, M.S.4
-
50
-
-
0037100667
-
Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation
-
An extensive cross-genome analysis of occurrences of a conserved regulatory element (RFN) involved with riboflavin biosynthesis allowed the authors to implicate several uncharacterized genes as potential riboflavin transporters. Similar results were obtained by this group by extending the approach to biotin- and thiamin-related conserved regulatory elements (as described in their publications cited in this review)
-
Vitreschak A.G., Rodionov D.A., Mironov A.A., Gelfand M.S. Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res. 30:2002;3141-3151 An extensive cross-genome analysis of occurrences of a conserved regulatory element (RFN) involved with riboflavin biosynthesis allowed the authors to implicate several uncharacterized genes as potential riboflavin transporters. Similar results were obtained by this group by extending the approach to biotin- and thiamin-related conserved regulatory elements (as described in their publications cited in this review).
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 3141-3151
-
-
Vitreschak, A.G.1
Rodionov, D.A.2
Mironov, A.A.3
Gelfand, M.S.4
-
52
-
-
0036600834
-
Evolution of protein structures and functions
-
Kinch L.N., Grishin N.V. Evolution of protein structures and functions. Curr. Opin. Struct. Biol. 12:2002;400-408.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 400-408
-
-
Kinch, L.N.1
Grishin, N.V.2
-
53
-
-
0036084625
-
SCOP database in 2002: Refinements accommodate structural genomics
-
Lo Conte L., Brenner S.E., Hubbard T.J., Chothia C., Murzin A.G. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res. 30:2002;264-267.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 264-267
-
-
Lo Conte, L.1
Brenner, S.E.2
Hubbard, T.J.3
Chothia, C.4
Murzin, A.G.5
-
54
-
-
0000515691
-
HMM-based databases in InterPro
-
Bateman A., Haft D.H. HMM-based databases in InterPro. Brief Bioinform. 3:2002;236-245.
-
(2002)
Brief Bioinform.
, vol.3
, pp. 236-245
-
-
Bateman, A.1
Haft, D.H.2
-
55
-
-
0036084361
-
The PROSITE database, its status in 2002
-
Falquet L., Pagni M., Bucher P., Hulo N., Sigrist C.J., Hofmann K., Bairoch A. The PROSITE database, its status in 2002. Nucleic Acids Res. 30:2002;235-238.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 235-238
-
-
Falquet, L.1
Pagni, M.2
Bucher, P.3
Hulo, N.4
Sigrist, C.J.5
Hofmann, K.6
Bairoch, A.7
-
56
-
-
0035175010
-
The Stanford microarray database
-
Sherlock G., Hernandez-Boussard T., Kasarskis A., Binkley G., Matese J.C., Dwight S.S., Kaloper M., Weng S., Jin H., Ball C.A.et al. The Stanford microarray database. Nucleic Acids Res. 29:2001;152-155.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 152-155
-
-
Sherlock, G.1
Hernandez-Boussard, T.2
Kasarskis, A.3
Binkley, G.4
Matese, J.C.5
Dwight, S.S.6
Kaloper, M.7
Weng, S.8
Jin, H.9
Ball, C.A.10
-
57
-
-
0034747028
-
DIP: The database of interacting proteins: 2001 update
-
Xenarios I., Fernandez E., Salwinski L., Duan X.J., Thompson M.J., Marcotte E.M., Eisenberg D. DIP: the database of interacting proteins: 2001 update. Nucleic Acids Res. 29:2001;239-241.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 239-241
-
-
Xenarios, I.1
Fernandez, E.2
Salwinski, L.3
Duan, X.J.4
Thompson, M.J.5
Marcotte, E.M.6
Eisenberg, D.7
-
58
-
-
0034761603
-
Selection analyses of insertional mutants using subgenic-resolution arrays
-
Badarinarayana V., Estep P.W. III, Shendure J., Edwards J., Tavazoie S., Lam F., Church G.M. Selection analyses of insertional mutants using subgenic-resolution arrays. Nat. Biotechnol. 19:2001;1060-1065.
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 1060-1065
-
-
Badarinarayana, V.1
Estep P.W. III2
Shendure, J.3
Edwards, J.4
Tavazoie, S.5
Lam, F.6
Church, G.M.7
-
59
-
-
0036334571
-
From genetic footprinting to antimicrobial drug targets: Examples in cofactor biosynthetic pathways
-
Gerdes S.Y., Scholle M.D., D'Souza M., Bernal A., Baev M.V., Farrell M., Kurnasov O.V., Daugherty M.D., Mseeh F., Polanuyer B.M.et al. From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways. J. Bacteriol. 184:2002;4555-4572.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 4555-4572
-
-
Gerdes, S.Y.1
Scholle, M.D.2
D'Souza, M.3
Bernal, A.4
Baev, M.V.5
Farrell, M.6
Kurnasov, O.V.7
Daugherty, M.D.8
Mseeh, F.9
Polanuyer, B.M.10
-
60
-
-
0036247948
-
Inhibitors of fatty acid synthesis as antimicrobial chemotherapeutics
-
Heath R.J., White S.W., Rock C.O. Inhibitors of fatty acid synthesis as antimicrobial chemotherapeutics. Appl. Microbiol. Biotechnol. 58:2002;695-703.
-
(2002)
Appl. Microbiol. Biotechnol.
, vol.58
, pp. 695-703
-
-
Heath, R.J.1
White, S.W.2
Rock, C.O.3
-
61
-
-
0034780806
-
Bacterial fatty acid biosynthesis: Targets for antibacterial drug discovery
-
Campbell J.W., Cronan J.E. Jr. Bacterial fatty acid biosynthesis: targets for antibacterial drug discovery. Annu. Rev. Microbiol. 55:2001;305-332.
-
(2001)
Annu. Rev. Microbiol.
, vol.55
, pp. 305-332
-
-
Campbell, J.W.1
Cronan J.E., Jr.2
-
62
-
-
0034644010
-
A triclosan-resistant bacterial enzyme
-
Heath R.J., Rock C.O. A triclosan-resistant bacterial enzyme. Nature. 406:2000;145-146.
-
(2000)
Nature
, vol.406
, pp. 145-146
-
-
Heath, R.J.1
Rock, C.O.2
-
63
-
-
0037160079
-
A new mechanism for anaerobic unsaturated fatty acid formation in Streptococcus pneumoniae
-
Further exploration of the extended cluster of fatty acid biosynthetic genes in S. pneumoniae enabled the discovery of a 'missing pathway', including a new enzyme and regulatory mechanism
-
Marrakchi H., Choi K.H., Rock C.O. A new mechanism for anaerobic unsaturated fatty acid formation in Streptococcus pneumoniae. J. Biol. Chem. 277:2002;44809-44816 Further exploration of the extended cluster of fatty acid biosynthetic genes in S. pneumoniae enabled the discovery of a 'missing pathway', including a new enzyme and regulatory mechanism.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 44809-44816
-
-
Marrakchi, H.1
Choi, K.H.2
Rock, C.O.3
-
64
-
-
0036282337
-
The enigmatic Escherichia coli fadE gene is yafH
-
A missing gene for acyl-CoA dehydrogenase was elucidated on the basis of evidence from microarrays and the analysis of regulatory sites, and experimental verification
-
Campbell J.W., Cronan J.E. Jr. The enigmatic Escherichia coli fadE gene is yafH. J. Bacteriol. 184:2002;3759-3764 A missing gene for acyl-CoA dehydrogenase was elucidated on the basis of evidence from microarrays and the analysis of regulatory sites, and experimental verification.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 3759-3764
-
-
Campbell, J.W.1
Cronan J.E., Jr.2
-
65
-
-
0035497843
-
Study of regulation of long-chain fatty acid metabolism using computer analysis of complete bacterial genomes
-
Sadovskaya N.S., Laikova O.N., Mironov A.A., Gelfand M.S. Study of regulation of long-chain fatty acid metabolism using computer analysis of complete bacterial genomes. Mol. Biol. 35:2001;862-866.
-
(2001)
Mol. Biol.
, vol.35
, pp. 862-866
-
-
Sadovskaya, N.S.1
Laikova, O.N.2
Mironov, A.A.3
Gelfand, M.S.4
-
67
-
-
0036152610
-
Cloning and characterization of a novel human pantothenate kinase gene
-
Ni X., Ma Y., Cheng H., Jiang M., Ying K., Xie Y., Mao Y. Cloning and characterization of a novel human pantothenate kinase gene. Int. J. Biochem. Cell Biol. 34:2002;109-115.
-
(2002)
Int. J. Biochem. Cell Biol.
, vol.34
, pp. 109-115
-
-
Ni, X.1
Ma, Y.2
Cheng, H.3
Jiang, M.4
Ying, K.5
Xie, Y.6
Mao, Y.7
-
68
-
-
0020842362
-
A bifunctional enzyme complex in coenzyme A biosynthesis: Purification of pantetheine phosphate adenylyltransferase and dephospho-CoA kinase
-
Worrall D.M., Tubbs P.K. A bifunctional enzyme complex in coenzyme A biosynthesis: purification of pantetheine phosphate adenylyltransferase and dephospho-CoA kinase. Biochem. J. 215:1983;153-157.
-
(1983)
Biochem. J.
, vol.215
, pp. 153-157
-
-
Worrall, D.M.1
Tubbs, P.K.2
-
69
-
-
0037077259
-
Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics
-
This paper provides an illustration of projection of function from prokaryotes to eukaryotes. The key evidence for identification of a missing human gene was provided by a protein fusion event
-
Daugherty M., Polanuyer B., Farrell M., Scholle M., Lykidis A., de Crecy-Lagard V., Osterman A. Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics. J. Biol. Chem. 277:2002;21431-21439 This paper provides an illustration of projection of function from prokaryotes to eukaryotes. The key evidence for identification of a missing human gene was provided by a protein fusion event.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 21431-21439
-
-
Daugherty, M.1
Polanuyer, B.2
Farrell, M.3
Scholle, M.4
Lykidis, A.5
De Crecy-Lagard, V.6
Osterman, A.7
-
70
-
-
0037151056
-
Molecular cloning of CoA synthase. The missing link in CoA biosynthesis
-
Zhyvoloup A., Nemazanyy I., Babich A., Panasyuk G., Pobigailo N., Vudmaska M., Naidenov V., Kukharenko O., Palchevskii S., Savinska L.et al. Molecular cloning of CoA synthase. The missing link in CoA biosynthesis. J. Biol. Chem. 277:2002;22107-22110.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 22107-22110
-
-
Zhyvoloup, A.1
Nemazanyy, I.2
Babich, A.3
Panasyuk, G.4
Pobigailo, N.5
Vudmaska, M.6
Naidenov, V.7
Kukharenko, O.8
Palchevskii, S.9
Savinska, L.10
-
71
-
-
0036646536
-
Identification and characterization of the gene encoding the human phosphopantetheine adenylyltransferase and dephospho-CoA kinase bifunctional enzyme (CoA synthase)
-
Aghajanian S., Worrall D.M. Identification and characterization of the gene encoding the human phosphopantetheine adenylyltransferase and dephospho-CoA kinase bifunctional enzyme (CoA synthase). Biochem. J. 365:2002;13-18.
-
(2002)
Biochem. J.
, vol.365
, pp. 13-18
-
-
Aghajanian, S.1
Worrall, D.M.2
-
72
-
-
18544403253
-
Identification, evolution, and essentiality of the mevalonate pathway for isopentenyl diphosphate biosynthesis in Gram-positive cocci
-
Wilding E.I., Brown J.R., Bryant A.P., Chalker A.F., Holmes D.J., Ingraham K.A., Iordanescu S., So C.Y., Rosenberg M., Gwynn M.N. Identification, evolution, and essentiality of the mevalonate pathway for isopentenyl diphosphate biosynthesis in Gram-positive cocci. J. Bacteriol. 182:2000;4319-4327.
-
(2000)
J. Bacteriol.
, vol.182
, pp. 4319-4327
-
-
Wilding, E.I.1
Brown, J.R.2
Bryant, A.P.3
Chalker, A.F.4
Holmes, D.J.5
Ingraham, K.A.6
Iordanescu, S.7
So, C.Y.8
Rosenberg, M.9
Gwynn, M.N.10
-
73
-
-
0037019823
-
Genetics of isoprenoid biosynthesis in Paracoccus zeaxanthinifaciens
-
Humbelin M., Thomas A., Lin J., Li J., Jore J., Berry A. Genetics of isoprenoid biosynthesis in Paracoccus zeaxanthinifaciens. Gene. 297:2002;129-139.
-
(2002)
Gene
, vol.297
, pp. 129-139
-
-
Humbelin, M.1
Thomas, A.2
Lin, J.3
Li, J.4
Jore, J.5
Berry, A.6
-
74
-
-
0033793828
-
Biosynthesis of isoprenoids via mevalonate in archaea: The lost pathway
-
Traditional and new techniques of comparative genome analysis were elegantly applied for metabolic reconstruction and identification of missing gene candidates in the archaeal version of the mevalonate pathway
-
Smit A., Mushegian A. Biosynthesis of isoprenoids via mevalonate in archaea: the lost pathway. Genome Res. 10:2000;1468-1484 Traditional and new techniques of comparative genome analysis were elegantly applied for metabolic reconstruction and identification of missing gene candidates in the archaeal version of the mevalonate pathway.
-
(2000)
Genome Res.
, vol.10
, pp. 1468-1484
-
-
Smit, A.1
Mushegian, A.2
-
76
-
-
0033813444
-
Evidence of a role for LytB in the nonmevalonate pathway of isoprenoid biosynthesis
-
Cunningham F.X. Jr., Lafond T.P., Gantt E. Evidence of a role for LytB in the nonmevalonate pathway of isoprenoid biosynthesis. J. Bacteriol. 182:2000;5841-5848.
-
(2000)
J. Bacteriol.
, vol.182
, pp. 5841-5848
-
-
Cunningham F.X., Jr.1
Lafond, T.P.2
Gantt, E.3
-
77
-
-
2242429820
-
Isoprenoid biosynthesis through the methylerythritol phosphate pathway: The (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase (GcpE) is a [4Fe-4S] protein
-
In vitro experiments provided the ultimate confirmation of the predicted enzymatic role of the gcpE gene product in the nonmevalonate pathway, and implicated Fe-S clusters and an unknown regeneration system in its mode of action
-
Seemann M., Bui B.T., Wolff M., Tritsch D., Campos N., Boronat A., Marquet A., Rohmer M. Isoprenoid biosynthesis through the methylerythritol phosphate pathway: the (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase (GcpE) is a [4Fe-4S] protein. Angew. Chem. Int. Ed. Engl. 41:2002;4337-4339 In vitro experiments provided the ultimate confirmation of the predicted enzymatic role of the gcpE gene product in the nonmevalonate pathway, and implicated Fe-S clusters and an unknown regeneration system in its mode of action.
-
(2002)
Angew. Chem. Int. Ed. Engl.
, vol.41
, pp. 4337-4339
-
-
Seemann, M.1
Bui, B.T.2
Wolff, M.3
Tritsch, D.4
Campos, N.5
Boronat, A.6
Marquet, A.7
Rohmer, M.8
-
78
-
-
0035909959
-
Studies on the nonmevalonate pathway to terpenes: The role of the GcpE (IspG) protein
-
Hecht S., Eisenreich W., Adam P., Amslinger S., Kis K., Bacher A., Arigoni D., Rohdich F. Studies on the nonmevalonate pathway to terpenes: the role of the GcpE (IspG) protein. Proc. Natl. Acad. Sci. U.S.A. 98:2001;14837-14842.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A
, vol.98
, pp. 14837-14842
-
-
Hecht, S.1
Eisenreich, W.2
Adam, P.3
Amslinger, S.4
Kis, K.5
Bacher, A.6
Arigoni, D.7
Rohdich, F.8
-
79
-
-
0037126065
-
Biosynthesis of terpenes: Studies on 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase
-
This paper provides experimental verification of the last step in the nonmevalonate pathway, which produces a mixture of both critical isoprenoids (IPP and DMAPP). The step is driven by the product of lytB gene assisted by several cofactors, and probably one or more unidentified proteins
-
Adam P., Hecht S., Eisenreich W., Kaiser J., Grawert T., Arigoni D., Bacher A., Rohdich F. Biosynthesis of terpenes: studies on 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase. Proc. Natl. Acad. Sci. U.S.A. 99:2002;12108-12113 This paper provides experimental verification of the last step in the nonmevalonate pathway, which produces a mixture of both critical isoprenoids (IPP and DMAPP). The step is driven by the product of lytB gene assisted by several cofactors, and probably one or more unidentified proteins.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 12108-12113
-
-
Adam, P.1
Hecht, S.2
Eisenreich, W.3
Kaiser, J.4
Grawert, T.5
Arigoni, D.6
Bacher, A.7
Rohdich, F.8
-
80
-
-
0035235055
-
Biosynthesis of riboflavin
-
Bacher A., Eberhardt S., Eisenreich W., Fischer M., Herz S., Illarionov B., Kis K., Richter G. Biosynthesis of riboflavin. Vitam. Horm. 61:2001;1-49.
-
(2001)
Vitam. Horm.
, vol.61
, pp. 1-49
-
-
Bacher, A.1
Eberhardt, S.2
Eisenreich, W.3
Fischer, M.4
Herz, S.5
Illarionov, B.6
Kis, K.7
Richter, G.8
-
81
-
-
0036203061
-
The pyrimidine nucleotide reductase step in riboflavin and F(420) biosynthesis in archaea proceeds by the eukaryotic route to riboflavin
-
A combination of comparative genomics and experimental techniques is applied to characterize missing genes in archaeal riboflavin biosynthesis
-
Graupner M., Xu H., White R.H. The pyrimidine nucleotide reductase step in riboflavin and F(420) biosynthesis in archaea proceeds by the eukaryotic route to riboflavin. J. Bacteriol. 184:2002;1952-1957 A combination of comparative genomics and experimental techniques is applied to characterize missing genes in archaeal riboflavin biosynthesis.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 1952-1957
-
-
Graupner, M.1
Xu, H.2
White, R.H.3
-
82
-
-
0036829021
-
Biosynthesis of riboflavin in archaea studies on the mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase of Methanococcus jannaschii
-
Fischer M., Romisch W., Schiffmann S., Kelly M., Oschkinat H., Steinbacher S., Huber R., Eisenreich W., Richter G., Bacher A. Biosynthesis of riboflavin in archaea studies on the mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase of Methanococcus jannaschii. J. Biol. Chem. 277:2002;41410-41416.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 41410-41416
-
-
Fischer, M.1
Romisch, W.2
Schiffmann, S.3
Kelly, M.4
Oschkinat, H.5
Steinbacher, S.6
Huber, R.7
Eisenreich, W.8
Richter, G.9
Bacher, A.10
-
83
-
-
0036832419
-
Biosynthesis of vitamin B2
-
Kaiser J., Schramek N., Eberhardt S., Puttmer S., Schuster M., Bacher A. Biosynthesis of vitamin B2. Eur. J. Biochem. 269:2002;5264-5270.
-
(2002)
Eur. J. Biochem.
, vol.269
, pp. 5264-5270
-
-
Kaiser, J.1
Schramek, N.2
Eberhardt, S.3
Puttmer, S.4
Schuster, M.5
Bacher, A.6
-
84
-
-
0033230755
-
A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes
-
Gelfand M.S., Mironov A.A., Jomantas J., Kozlov Y.I., Perumov D.A. A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. Trends Genet. 15:1999;439-442.
-
(1999)
Trends Genet.
, vol.15
, pp. 439-442
-
-
Gelfand, M.S.1
Mironov, A.A.2
Jomantas, J.3
Kozlov, Y.I.4
Perumov, D.A.5
-
85
-
-
18744396047
-
Sensing small molecules by nascent RNA. A mechanism to control transcription in bacteria
-
Mironov A.S., Gusarov I., Rafikov R., Lopez L.E., Shatalin K., Kreneva R.A., Perumov D.A., Nudler E. Sensing small molecules by nascent RNA. A mechanism to control transcription in bacteria. Cell. 111:2002;747-756.
-
(2002)
Cell
, vol.111
, pp. 747-756
-
-
Mironov, A.S.1
Gusarov, I.2
Rafikov, R.3
Lopez, L.E.4
Shatalin, K.5
Kreneva, R.A.6
Perumov, D.A.7
Nudler, E.8
-
87
-
-
0001302597
-
Inactivation of the ypaA gene in Bacillus subtilis: Analysis of the resulting phenotypic expression
-
Kreneva R.A., Gel'fand M.S., Mironov A.A., Iomantas Iu A., Kozlov Iu I., Mironov A.S., Perumov D.A. Inactivation of the ypaA gene in Bacillus subtilis: analysis of the resulting phenotypic expression. Russian J. Genet. 36:2000;972-974.
-
(2000)
Russian J. Genet.
, vol.36
, pp. 972-974
-
-
Kreneva, R.A.1
Gel'fand, M.S.2
Mironov, A.A.3
Iomantas Iu, A.4
Kozlov Iu, I.5
Mironov, A.S.6
Perumov, D.A.7
-
88
-
-
0036005602
-
Elucidation of methanogenic coenzyme biosyntheses: From spectroscopy to genomics
-
Graham D.E., White R.H. Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics. Nat. Prod. Rep. 19:2002;133-147.
-
(2002)
Nat. Prod. Rep.
, vol.19
, pp. 133-147
-
-
Graham, D.E.1
White, R.H.2
-
89
-
-
0034797059
-
2+)-dependent acid phosphatases
-
Clustering of genes on the chromosome provided key evidence for identification and experimental verification of the novel gene (comB) in the biosynthesis of coenzyme M cofactor. The broad conservation of comB homologs beyond methanogenic species illustrates an evolutionary recruitment of 'old genes' into 'new pathways'
-
2+)-dependent acid phosphatases. Eur. J. Biochem. 268:2001;5176-5188 Clustering of genes on the chromosome provided key evidence for identification and experimental verification of the novel gene (comB) in the biosynthesis of coenzyme M cofactor. The broad conservation of comB homologs beyond methanogenic species illustrates an evolutionary recruitment of 'old genes' into 'new pathways'.
-
(2001)
Eur. J. Biochem.
, vol.268
, pp. 5176-5188
-
-
Graham, D.E.1
Graupner, M.2
Xu, H.3
White, R.H.4
-
90
-
-
0033941879
-
Identification of the Escherichia coli nicotinic acid mononucleotide adenylyltransferase gene
-
Mehl R.A., Kinsland C., Begley T.P. Identification of the Escherichia coli nicotinic acid mononucleotide adenylyltransferase gene. J. Bacteriol. 182:2000;4372-4374.
-
(2000)
J. Bacteriol.
, vol.182
, pp. 4372-4374
-
-
Mehl, R.A.1
Kinsland, C.2
Begley, T.P.3
-
91
-
-
0036947230
-
Ribosylnicotinamide kinase domain of nadr protein: Identification and implications in NAD biosynthesis
-
Kurnasov O.V., Polanuyer B.M., Ananta S., Sloutsky R., Tam A., Gerdes S.Y., Osterman A.L. Ribosylnicotinamide kinase domain of nadr protein: identification and implications in NAD biosynthesis. J. Bacteriol. 184:2002;6906-6917.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 6906-6917
-
-
Kurnasov, O.V.1
Polanuyer, B.M.2
Ananta, S.3
Sloutsky, R.4
Tam, A.5
Gerdes, S.Y.6
Osterman, A.L.7
-
92
-
-
0037067753
-
Identification of the tRNA-dihydrouridine synthase family
-
A synergistic application of several genome context analysis techniques allowed the authors to implicate, experimentally verify and characterize members of a new family of enzymes involved in critical tRNA modification pathways
-
Bishop A.C., Xu J., Johnson R.C., Schimmel P., de Crecy-Lagard V. Identification of the tRNA-dihydrouridine synthase family. J. Biol. Chem. 277:2002;25090-25095 A synergistic application of several genome context analysis techniques allowed the authors to implicate, experimentally verify and characterize members of a new family of enzymes involved in critical tRNA modification pathways.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 25090-25095
-
-
Bishop, A.C.1
Xu, J.2
Johnson, R.C.3
Schimmel, P.4
De Crecy-Lagard, V.5
-
93
-
-
0036782099
-
Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 Å resolution
-
Kuhn P., Lesley S.A., Mathews I.I., Canaves J.M., Brinen L.S., Dai X., Deacon A.M., Elsliger M.A., Eshaghi S., Floyd R.et al. Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 Å resolution. Proteins. 49:2002;142-145.
-
(2002)
Proteins
, vol.49
, pp. 142-145
-
-
Kuhn, P.1
Lesley, S.A.2
Mathews, I.I.3
Canaves, J.M.4
Brinen, L.S.5
Dai, X.6
Deacon, A.M.7
Elsliger, M.A.8
Eshaghi, S.9
Floyd, R.10
-
94
-
-
0034704090
-
The enoyl-[acyl-carrier-protein] reductases FabI and FabL from Bacillus subtilis
-
Heath R.J., Su N., Murphy C.K., Rock C.O. The enoyl-[acyl-carrier-protein] reductases FabI and FabL from Bacillus subtilis. J. Biol. Chem. 275:2000;40128-40133.
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 40128-40133
-
-
Heath, R.J.1
Su, N.2
Murphy, C.K.3
Rock, C.O.4
-
95
-
-
0035813109
-
Identification of the human methylmalonyl-CoA racemase gene based on the analysis of prokaryotic gene arrangements. Implications for decoding the human genome
-
One of the first reports in which a eukaryotic missing gene (involved in propionyl-CoA metabolism) was characterized by projection from the clusters on prokaryotic chromosomes. The authors express a well-justified enthusiasm about the potential of such an approach in the functional analysis of human genome
-
Bobik T.A., Rasche M.E. Identification of the human methylmalonyl-CoA racemase gene based on the analysis of prokaryotic gene arrangements. Implications for decoding the human genome. J. Biol. Chem. 276:2001;37194-37198 One of the first reports in which a eukaryotic missing gene (involved in propionyl-CoA metabolism) was characterized by projection from the clusters on prokaryotic chromosomes. The authors express a well-justified enthusiasm about the potential of such an approach in the functional analysis of human genome.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 37194-37198
-
-
Bobik, T.A.1
Rasche, M.E.2
-
96
-
-
0037025191
-
An alternative flavin-dependent mechanism for thymidylate synthesis
-
Myllykallio H., Lipowski G., Leduc D., Filee J., Forterre P., Liebl U. An alternative flavin-dependent mechanism for thymidylate synthesis. Science. 297:2002;105-107.
-
(2002)
Science
, vol.297
, pp. 105-107
-
-
Myllykallio, H.1
Lipowski, G.2
Leduc, D.3
Filee, J.4
Forterre, P.5
Liebl, U.6
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