-
1
-
-
0003243559
-
MOLPHY: Programs for molecular phylogenetics. I. PROTML: Maximum-likelihood inference for protein phylogeny
-
I.O.S. Mathematics, Tokyo, Japan
-
Adachi, J., and M. Hasegawa. 1992. MOLPHY: programs for molecular phylogenetics. I. PROTML: maximum-likelihood inference for protein phylogeny. In Computer science monographs, vol. 27. I.O.S. Mathematics, Tokyo, Japan.
-
(1992)
Computer Science Monographs
, vol.27
-
-
Adachi, J.1
Hasegawa, M.2
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
3
-
-
0033574503
-
Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches
-
Aravind, L., and E. V. Koonin. 1999. Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J. Mol. Biol. 287:1023-1040.
-
(1999)
J. Mol. Biol.
, vol.287
, pp. 1023-1040
-
-
Aravind, L.1
Koonin, E.V.2
-
4
-
-
0017184389
-
A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding
-
Bradford, M. M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
-
(1976)
Anal. Biochem.
, vol.72
, pp. 248-254
-
-
Bradford, M.M.1
-
5
-
-
0000756509
-
Phosphoenolpyruvate carboxylase: A ubiquitous, highly regulated enzyme in plants
-
Chollet, R., J. Vidal, and M. H. O'Leary. 1996. Phosphoenolpyruvate carboxylase: a ubiquitous, highly regulated enzyme in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47:273-298.
-
(1996)
Annu. Rev. Plant Physiol. Plant Mol. Biol.
, vol.47
, pp. 273-298
-
-
Chollet, R.1
Vidal, J.2
O'Leary, M.H.3
-
6
-
-
0032420333
-
JPred: A consensus secondary structure prediction server
-
Cuff, J. A., M. E. Clamp, A. S. Siddiqui, M. Finlay, and G. J. Barton. 1998. JPred: a consensus secondary structure prediction server. Bioinformatics 14:892-893.
-
(1998)
Bioinformatics
, vol.14
, pp. 892-893
-
-
Cuff, J.A.1
Clamp, M.E.2
Siddiqui, A.S.3
Finlay, M.4
Barton, G.J.5
-
7
-
-
1842425027
-
Properties of GDP-mannose pyrophosphorylase, a critical enzyme and drug target in Leishmania mexicana
-
Davis, A. J., M. A. Perugini, B. J. Smith, J. D. Stewart, T. Ilg, A. N. Hodder, and E. Handman. 2004. Properties of GDP-mannose pyrophosphorylase, a critical enzyme and drug target in Leishmania mexicana. J. Biol. Chem. 279:12462-12468.
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 12462-12468
-
-
Davis, A.J.1
Perugini, M.A.2
Smith, B.J.3
Stewart, J.D.4
Ilg, T.5
Hodder, A.N.6
Handman, E.7
-
8
-
-
0029901637
-
Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods
-
Felsenstein, J. 1996. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol. 266:418-427.
-
(1996)
Methods Enzymol.
, vol.266
, pp. 418-427
-
-
Felsenstein, J.1
-
9
-
-
0014211361
-
Construction of phylogenetic trees
-
Fitch, W. M., and E. Margoliash. 1967. Construction of phylogenetic trees. Science 155:279-284.
-
(1967)
Science
, vol.155
, pp. 279-284
-
-
Fitch, W.M.1
Margoliash, E.2
-
10
-
-
0037468510
-
Maltodextrin-binding proteins from diverse bacteria and archaea are potent solubility enhancers
-
Fox, J. D., K. M. Routzahn, M. H. Bucher, and D. S. Waugh. 2003. Maltodextrin-binding proteins from diverse bacteria and archaea are potent solubility enhancers. FEBS Lett. 537:53-57.
-
(2003)
FEBS Lett.
, vol.537
, pp. 53-57
-
-
Fox, J.D.1
Routzahn, K.M.2
Bucher, M.H.3
Waugh, D.S.4
-
11
-
-
0033168449
-
Variation and evolution of the citric-acid cycle: A genomic perspective
-
Huynen, M. A., T. Dandekar, and P. Bork. 1999. Variation and evolution of the citric-acid cycle: a genomic perspective. Trends Microbiol. 7:281-291.
-
(1999)
Trends Microbiol.
, vol.7
, pp. 281-291
-
-
Huynen, M.A.1
Dandekar, T.2
Bork, P.3
-
12
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
-
(1992)
Comput. Appl. Biosci.
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
13
-
-
0033514310
-
Three-dimensional structure of phosphoenolpyruvate carboxylase: A proposed mechanism for allosteric inhibition
-
Kai, Y., H. Matsumura, T. Inoue, K. Terada, Y. Nagara, T. Yoshinaga, A. Kihara, K. Tsumura, and K. Izui. 1999. Three-dimensional structure of phosphoenolpyruvate carboxylase: a proposed mechanism for allosteric inhibition. Proc. Natl. Acad. Sci. USA 96:823-828.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 823-828
-
-
Kai, Y.1
Matsumura, H.2
Inoue, T.3
Terada, K.4
Nagara, Y.5
Yoshinaga, T.6
Kihara, A.7
Tsumura, K.8
Izui, K.9
-
14
-
-
0037763823
-
Phosphoenolpyruvate carboxylase: Three-dimensional structure and molecular mechanisms
-
Kai, Y., H. Matsumura, and K. Izui. 2003. Phosphoenolpyruvate carboxylase: three-dimensional structure and molecular mechanisms. Arch. Biochem. Biophys. 414:170-179.
-
(2003)
Arch. Biochem. Biophys.
, vol.414
, pp. 170-179
-
-
Kai, Y.1
Matsumura, H.2
Izui, K.3
-
15
-
-
0025181359
-
Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
-
Kishino, H., T. Miyata, and M. Hasegawa. 1990. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J. Mol. Evol. 31:151-160.
-
(1990)
J. Mol. Evol.
, vol.31
, pp. 151-160
-
-
Kishino, H.1
Miyata, T.2
Hasegawa, M.3
-
17
-
-
0043011009
-
Comparative genomics of archaea: How much have we learned in six years, and what's next?
-
Makarova, K. S., and E. V. Koonin. 2003. Comparative genomics of archaea: how much have we learned in six years, and what's next? Genome Biol. 4:115.
-
(2003)
Genome Biol.
, vol.4
, pp. 115
-
-
Makarova, K.S.1
Koonin, E.V.2
-
18
-
-
1542543651
-
Filling a gap in the central metabolism of archaea: Prediction of a novel aconitase by comparative-genomic analysis
-
Makarova, K. S., and E. V. Koonin. 2003. Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis. FEMS Microbiol. Lett. 227:17-23.
-
(2003)
FEMS Microbiol. Lett.
, vol.227
, pp. 17-23
-
-
Makarova, K.S.1
Koonin, E.V.2
-
20
-
-
0036899531
-
Crystal structures of C4 form maize and quaternary complex of E. coli phosphoenolpyruvate carboxylases
-
Matsumura, H., Y. Xie, S. Shirakata, T. Inoue, T. Yoshinaga, Y. Ueno, K. Izui, and Y. Kai. 2002. Crystal structures of C4 form maize and quaternary complex of E. coli phosphoenolpyruvate carboxylases. Structure 10:1721-1730.
-
(2002)
Structure
, vol.10
, pp. 1721-1730
-
-
Matsumura, H.1
Xie, Y.2
Shirakata, S.3
Inoue, T.4
Yoshinaga, T.5
Ueno, Y.6
Izui, K.7
Kai, Y.8
-
21
-
-
0034546359
-
A stable archaeal pyruvate carboxylase from the hyperthermophile Methanococcus jannaschii
-
Mukhopadhyay, B., V. J. Patel, and R. S. Wolfe. 2000. A stable archaeal pyruvate carboxylase from the hyperthermophile Methanococcus jannaschii. Arch. Microbiol. 174:406-414.
-
(2000)
Arch. Microbiol.
, vol.174
, pp. 406-414
-
-
Mukhopadhyay, B.1
Patel, V.J.2
Wolfe, R.S.3
-
22
-
-
0034982772
-
Oxaloacetate synthesis in the methanarchaeon Methanosarcina barkeri: Pyruvate carboxylase genes and a putative Escherichia coli-type bifunctional biotin protein ligase gene (bpl/birA) exhibit a unique organization
-
Mukhopadhyay, B., E. Purwantini, C. L. Kreder, and R. S. Wolfe. 2001. Oxaloacetate synthesis in the methanarchaeon Methanosarcina barkeri: pyruvate carboxylase genes and a putative Escherichia coli-type bifunctional biotin protein ligase gene (bpl/birA) exhibit a unique organization. J. Bacteriol. 183:3804-3810.
-
(2001)
J. Bacteriol.
, vol.183
, pp. 3804-3810
-
-
Mukhopadhyay, B.1
Purwantini, E.2
Kreder, C.L.3
Wolfe, R.S.4
-
23
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A. G., S. E. Brenner, T. Hubbard, and C. Chothia. 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
-
24
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame, C., D. G. Higgins, and J. Heringa. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302:205-217.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
25
-
-
3242763774
-
The phosphoenolpyruvate carboxylase from Methanothermobacter thermautotrophicus has a novel structure
-
Patel, H. M., J. L. Kraszewski, and B. Mukhopadhyay. 2004. The phosphoenolpyruvate carboxylase from Methanothermobacter thermautotrophicus has a novel structure. J. Bacteriol. 186:5129-5137.
-
(2004)
J. Bacteriol.
, vol.186
, pp. 5129-5137
-
-
Patel, H.M.1
Kraszewski, J.L.2
Mukhopadhyay, B.3
-
26
-
-
0030861417
-
Biochemical relationship of phosphoenolpyruvate carboxylases (PEPCs) from thermophilic archaea
-
Sako, Y., K. Takai, T. Nishizaka, and Y. Ishida. 1997. Biochemical relationship of phosphoenolpyruvate carboxylases (PEPCs) from thermophilic archaea. FEMS Microbiology Lett. 153:159-165.
-
(1997)
FEMS Microbiology Lett.
, vol.153
, pp. 159-165
-
-
Sako, Y.1
Takai, K.2
Nishizaka, T.3
Ishida, Y.4
-
27
-
-
0030603147
-
Purification and characterization of phosphoenolpyruvate carboxylase from the hyperthermophilic archaeon Methanothermus sociabilis
-
Sako, Y., K. Takai, A. Uchida, and Y. Ishida. 1996. Purification and characterization of phosphoenolpyruvate carboxylase from the hyperthermophilic archaeon Methanothermus sociabilis. FEBS Lett. 392:148-152.
-
(1996)
FEBS Lett.
, vol.392
, pp. 148-152
-
-
Sako, Y.1
Takai, K.2
Uchida, A.3
Ishida, Y.4
-
28
-
-
0037494947
-
Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides
-
Schut, G. J., S. D. Brehrn, S. Datta, and M. W. Adams. 2003. Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides. J. Bacteriol. 185:3935-3947.
-
(2003)
J. Bacteriol.
, vol.185
, pp. 3935-3947
-
-
Schut, G.J.1
Brehrn, S.D.2
Datta, S.3
Adams, M.W.4
-
29
-
-
0002094581
-
Anabolic pathways in methanogens
-
J. G. Ferry (ed.), Chapman and Hall, New York, N.Y.
-
Simpson, P. G., and W. B. Withman. 1993. Anabolic pathways in methanogens, p. 445-472. In J. G. Ferry (ed.), Methanogenesis: ecology, physiology, biochemistry, and genetics. Chapman and Hall, New York, N.Y.
-
(1993)
Methanogenesis: Ecology, Physiology, Biochemistry, and Genetics
, pp. 445-472
-
-
Simpson, P.G.1
Withman, W.B.2
-
30
-
-
0037007150
-
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens
-
Slesarev, A. I., K. V. Mezhevaya, K. S. Makarova, N. N. Polushin, O. V. Shcherbinina, V. V. Shakhova, G. I. Belova, L. Aravind, D. A. Natale, I. B. Rogozin, R. L. Tatusov, Y. I. Wolf, K. O. Stetter, A. G. Malykh, E. V. Koonin, and S. A. Kozyavkin. 2002. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc. Natl. Acad. Sci. USA 99:4644-4649.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 4644-4649
-
-
Slesarev, A.I.1
Mezhevaya, K.V.2
Makarova, K.S.3
Polushin, N.N.4
Shcherbinina, O.V.5
Shakhova, V.V.6
Belova, G.I.7
Aravind, L.8
Natale, D.A.9
Rogozin, I.B.10
Tatusov, R.L.11
Wolf, Y.I.12
Stetter, K.O.13
Malykh, A.G.14
Koonin, E.V.15
Kozyavkin, S.A.16
-
31
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
Tatusov, R. L., N. D. Fedorova, J. D. Jackson, A. R. Jacobs, B. Kiryutin, E. V. Koonin, D. M. Krylov, R. Mazumder, S. L. Mekhedov, A. N. Nikolskaya, B. S. Rao, S. Smirnov, A. V. Sverdlov, S. Vasudevan, Y. I. Wolf, J. J. Yin, and D. A. Natale. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 41
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Kiryutin, B.5
Koonin, E.V.6
Krylov, D.M.7
Mazumder, R.8
Mekhedov, S.L.9
Nikolskaya, A.N.10
Rao, B.S.11
Smirnov, S.12
Sverdlov, A.V.13
Vasudevan, S.14
Wolf, Y.I.15
Yin, J.J.16
Natale, D.A.17
-
32
-
-
0015406695
-
Phosphoenolpyruvate carboxylase of Escherichia coli: Alteration of allosteric properties by photooxidation
-
Teraoka, H., K. Izui, and H. Katsuki. 1972. Phosphoenolpyruvate carboxylase of Escherichia coli: alteration of allosteric properties by photooxidation. Arch. Biochem. Biophys. 152:821-827.
-
(1972)
Arch. Biochem. Biophys.
, vol.152
, pp. 821-827
-
-
Teraoka, H.1
Izui, K.2
Katsuki, H.3
-
33
-
-
0000613752
-
Multiple forms of plant phosphoenolpyruvate carboxylase associated with different metabolic pathways
-
Ting, I. P., and C. B. Osmond. 1973. Multiple forms of plant phosphoenolpyruvate carboxylase associated with different metabolic pathways. Plant Physiol. 51:448-453.
-
(1973)
Plant Physiol.
, vol.51
, pp. 448-453
-
-
Ting, I.P.1
Osmond, C.B.2
-
34
-
-
0142138858
-
The unique features of glycolytic pathways in Archaea
-
Verhees, C. H., S. W. Kengen, J. E. Tuininga, G. J. Schut, M. W. Adams, W. M. De Vos, and J. Van Der Oost. 2003. The unique features of glycolytic pathways in Archaea. Biochem. J. 375:231-246.
-
(2003)
Biochem. J.
, vol.375
, pp. 231-246
-
-
Verhees, C.H.1
Kengen, S.W.2
Tuininga, J.E.3
Schut, G.J.4
Adams, M.W.5
De Vos, W.M.6
Van Der Oost, J.7
-
35
-
-
0017709116
-
Oxidoreductases involved in cell carbon synthesis of Methanobacterium thermoautotrophicum
-
Zeikus, J. G., G. Fuchs, W. Kenealy, and R. K. Thauer. 1977. Oxidoreductases involved in cell carbon synthesis of Methanobacterium thermoautotrophicum. J. Bacteriol. 132:604-613.
-
(1977)
J. Bacteriol.
, vol.132
, pp. 604-613
-
-
Zeikus, J.G.1
Fuchs, G.2
Kenealy, W.3
Thauer, R.K.4
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