-
1
-
-
0027421793
-
Two global regulatory systems (Crp and Arc) control the cobalamin/propanediol regulon of Salmonella typhimurium
-
Ailion, M., T. A Bobik, and J. R. Roth. 1993. Two global regulatory systems (Crp and Arc) control the cobalamin/propanediol regulon of Salmonella typhimurium. J. Bacteriol. 175:7200-7208.
-
(1993)
J. Bacteriol.
, vol.175
, pp. 7200-7208
-
-
Ailion, M.1
Bobik, T.A.2
Roth, J.R.3
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F., T. L. Madden, A. A. Schäffer, 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
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
3
-
-
54849439082
-
Identification of the substrate radical intermediate derived from ethanolamine during catalysis by ethanolamine ammonia-lyase
-
Bender, G., R. R. Poyner, and G. H. Reed. 2008. Identification of the substrate radical intermediate derived from ethanolamine during catalysis by ethanolamine ammonia-lyase. Biochemistry 47:11360-11366.
-
(2008)
Biochemistry
, vol.47
, pp. 11360-11366
-
-
Bender, G.R.1
Poyner, R.2
Reed, G.H.3
-
4
-
-
0023894726
-
Selection of DNA binding sites by regulatory proteins. II. the bindingspecificity of cyclic AMP receptor protein to recognition sites
-
Berg, O. G., and P. H. von Hippel. 1988. Selection of DNA binding sites by regulatory proteins. II. The bindingspecificity of cyclic AMP receptor protein to recognition sites. J. Mol. Biol. 200:709-723.
-
(1988)
J. Mol. Biol.
, vol.200
, pp. 709-723
-
-
Berg, O.G.1
Von Hippel, P.H.2
-
5
-
-
20444491634
-
A review of long-branch attraction
-
Bergsten, J. 2005. A review of long-branch attraction. Cladistics 21:163-193.
-
(2005)
Cladistics
, vol.21
, pp. 163-193
-
-
Bergsten, J.1
-
6
-
-
0026503401
-
A single regulatory gene integrates control of vitamin B12 synthesis and propanediol degradation
-
Bobik, T. A., M. Ailion, and J. R. Roth. 1992. A single regulatory gene integrates control of vitamin B12 synthesis and propanediol degradation. J. Bacteriol. 174:2253-2266.
-
(1992)
J. Bacteriol.
, vol.174
, pp. 2253-2266
-
-
Bobik, T.A.1
Ailion, M.2
Roth, J.R.3
-
7
-
-
28044459168
-
Minimal functions and physiological conditions required for growth of Salmonella enterica on ethanolamine in the absence of the metabolosome
-
Brinsmade, S. R., T. Paldon, and J. C. Escalante-Semerena. 2005. Minimal functions and physiological conditions required for growth of Salmonella enterica on ethanolamine in the absence of the metabolosome. J. Bacteriol. 187:8039-8046.
-
(2005)
J. Bacteriol.
, vol.187
, pp. 8039-8046
-
-
Brinsmade, S.R.1
Paldon, T.2
Escalante-Semerena, J.C.3
-
8
-
-
0016593454
-
Evidence for the B12-dependent enzyme ethanolamine deaminase in Salmonella
-
Chang, G. W., and J. T. Chang. 1975. Evidence for the B12-dependent enzyme ethanolamine deaminase in Salmonella. Nature 254:150-151.
-
(1975)
Nature
, vol.254
, pp. 150-151
-
-
Chang, G.W.1
Chang, J.T.2
-
9
-
-
0036140266
-
A unifold, mesofold, and superfold model of protein fold use
-
Coulson, A. F., and J. Moult. 2002. A unifold, mesofold, and superfold model of protein fold use. Proteins 46:61-71.
-
(2002)
Proteins
, vol.46
, pp. 61-71
-
-
Coulson, A.F.1
Moult, J.2
-
10
-
-
2142738304
-
WebLogo: A sequence logo generator
-
Crooks, G. E., G. Hon, J. M. Chandonia, and S. E. Brenner. 2004. WebLogo: a sequence logo generator. Genome Res. 14:1188-1190.
-
(2004)
Genome Res.
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
11
-
-
0000122573
-
PHYLIP - Phylogeny inference package
-
version 3.2
-
Felsenstein, J. 1989. PHYLIP - phylogeny inference package (version 3.2). Cladistics 5:164-166.
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
12
-
-
63149194170
-
Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis
-
Fox, K. A., A. Ramesh, J. E. Stearns, A. Bourgogne, A. Reyes-Jara, W. C. Winkler, and D. A. Garsin. 2009. Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis. Proc. Natl. Acad. Sci. USA 106:4435-4440.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 4435-4440
-
-
Fox, K.A.1
Ramesh, A.2
Stearns, J.E.3
Bourgogne, A.4
Reyes-Jara, A.5
Winkler, W.C.6
Garsin, D.A.7
-
13
-
-
0034330226
-
Comparative analysis of regulatory patterns in bacterial genomes
-
Gelfand, M. S., P. S. Novichkov, E. S. Novichkova, and A. A. Mironov. 2000. Comparative analysis of regulatory patterns in bacterial genomes. Brief. Bioinform. 1:357-371.
-
(2000)
Brief. Bioinform.
, vol.1
, pp. 357-371
-
-
Gelfand, M.S.1
Novichkov, P.S.2
Novichkova, E.S.3
Mironov, A.A.4
-
14
-
-
0003763748
-
-
2nd ed., Wiley, New York, NY.
-
Johnson, N. L., S. Kotz, and A. W. Kemp. 1992. Univariate discrete distributions, 2nd ed., p. 266-269. Wiley, New York, NY.
-
(1992)
Univariate Discrete Distributions
, pp. 266-269
-
-
Johnson, N.L.1
Kotz, S.2
Kemp, A.W.3
-
15
-
-
0032851358
-
The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins
-
Kofoid, E., C. Rappleye, I. Stojiljkovic, and J. Roth. 1999. The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. J. Bacteriol. 181:5317-5329.
-
(1999)
J. Bacteriol.
, vol.181
, pp. 5317-5329
-
-
Kofoid, E.1
Rappleye, C.2
Stojiljkovic, I.3
Roth, J.4
-
16
-
-
21844471754
-
Systematic association of genes to phenotypes by genome and literature mining
-
Korbel, J. O., T. Doerks, L. J. Jensen, C. Perez-Iratxeta, S. Kaczanowski, S. D. Hooper, M. A. Andrade, and P. Bork. 2005. Systematic association of genes to phenotypes by genome and literature mining. PLoS Biol. 3:e134.
-
(2005)
PLoS Biol.
, vol.3
-
-
Korbel, J.O.1
Doerks, T.2
Jensen, L.J.3
Perez-Iratxeta, C.4
Kaczanowski, S.5
Hooper, S.D.6
Andrade, M.A.7
Bork, P.8
-
17
-
-
33845873289
-
Interactive Tree of Life (iTOL): An online tool for phylogenetic tree display and annotation
-
DOI 10.1093/bioinformatics/btl529
-
Letunic, I., and P. Bork. 2007. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23:127-128. (Pubitemid 46017867)
-
(2007)
Bioinformatics
, vol.23
, Issue.1
, pp. 127-128
-
-
Letunic, I.1
Bork, P.2
-
18
-
-
65449187899
-
Detection of biochemical pathways by probabilistic matching of phyletic vectors
-
Li, H., D. M. Kristensen, M. K. Coleman, and A. Mushegian. 2009. Detection of biochemical pathways by probabilistic matching of phyletic vectors. PLoS ONE 4:e5326.
-
(2009)
PLoS ONE
, vol.4
-
-
Li, H.1
Kristensen, D.M.2
Coleman, M.K.3
Mushegian, A.4
-
20
-
-
0034147960
-
Genome-Explorer: Software for analysis of complete bacterial genomes
-
Mironov, A. A., N. P. Vinokurova, and M. S. Gelfand. 2000. Genome-Explorer: software for analysis of complete bacterial genomes. Mol. Biol. 34:222-231.
-
(2000)
Mol. Biol.
, vol.34
, pp. 222-231
-
-
Mironov, A.A.1
Vinokurova, N.P.2
Gelfand, M.S.3
-
21
-
-
0029167899
-
Biogenesis and ultrastructure of carboxysomes from wild type and mutants of Synechococcus sp. strain PCC 7942
-
Orus, M. I., M. L. Rodriguez, F. Martinez, and E. Marco. 1995. Biogenesis and ultrastructure of carboxysomes from wild type and mutants of Synechococcus sp. strain PCC 7942. Plant Physiol. 107:1159-1166.
-
(1995)
Plant Physiol.
, vol.107
, pp. 1159-1166
-
-
Orus, M.I.1
Rodriguez, M.L.2
Martinez, F.3
Marco, E.4
-
22
-
-
0028170314
-
Vitamin B12 repression of the cob operon in Salmonella typhimurium: Translational control of the cbiA gene
-
Richter-Dahlfors, A. A., S. Ravnum, and D. I. Andersson. 1994. Vitamin B12 repression of the cob operon in Salmonella typhimurium: translational control of the cbiA gene. Mol. Microbiol. 13:541-553.
-
(1994)
Mol. Microbiol.
, vol.13
, pp. 541-553
-
-
Richter-Dahlfors, A.A.1
Ravnum, S.2
Andersson, D.I.3
-
23
-
-
33847264343
-
Enrichment or depletion of a GO category within a class of genes: Which test?
-
Rivals, I., L. Personnaz, L. Taing, and M. C. Potier. 2007. Enrichment or depletion of a GO category within a class of genes: which test? Bioinformatics 23:401-407.
-
(2007)
Bioinformatics
, vol.23
, pp. 401-407
-
-
Rivals, I.1
Personnaz, L.2
Taing, L.3
Potier, M.C.4
-
24
-
-
0142071742
-
Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes
-
Rodionov, D. A., A. G. Vitreschak, A. A. Mironov, and M. S. Gelfand. 2003. Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J. Biol. Chem. 278:41148-41159.
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 41148-41159
-
-
Rodionov, D.A.1
Vitreschak, A.G.2
Mironov, A.A.3
Gelfand, M.S.4
-
25
-
-
0029882437
-
In vitro analysis of the interactions between the PocR regulatory protein and the promoter region of the cobalamin biosynthetic (cob) operon of Salmonella typhimurium LT2
-
Rondon, M. R., and J. C. Escalante-Semerena. 1996. In vitro analysis of the interactions between the PocR regulatory protein and the promoter region of the cobalamin biosynthetic (cob) operon of Salmonella typhimurium LT2. J. Bacteriol. 178:2196-2203.
-
(1996)
J. Bacteriol.
, vol.178
, pp. 2196-2203
-
-
Rondon, M.R.1
Escalante-Semerena, J.C.2
-
26
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
DOI 10.1093/bioinformatics/btg180
-
Ronquist, F., and J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. (Pubitemid 37038874)
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
27
-
-
0024075956
-
Ethanolamine utilization in Salmonella typhimurium
-
Roof, D. M., and J. R. Roth. 1988. Ethanolamine utilization in Salmonella typhimurium. J. Bacteriol. 170:3855-3863.
-
(1988)
J. Bacteriol.
, vol.170
, pp. 3855-3863
-
-
Roof, D.M.1
Roth, J.R.2
-
28
-
-
0024393078
-
12-dependent ethanolamine utilization in Salmonella typhimurium
-
12-dependent ethanolamine utilization in Salmonella typhimurium. J. Bacteriol. 171:3316-3323.
-
(1989)
J. Bacteriol.
, vol.171
, pp. 3316-3323
-
-
Roof, D.M.1
Roth, J.R.2
-
29
-
-
0026657140
-
Autogenous regulation of ethanolamine utilization by a transcriptional activator of the eut operon in Salmonella typhimurium
-
Roof, D. M., and J. R. Roth. 1992. Autogenous regulation of ethanolamine utilization by a transcriptional activator of the eut operon in Salmonella typhimurium. J. Bacteriol. 174:6634-6643.
-
(1992)
J. Bacteriol.
, vol.174
, pp. 6634-6643
-
-
Roof, D.M.1
Roth, J.R.2
-
30
-
-
0026100921
-
A workbench for multiple alignment construction and analysis
-
Schuler, G. D., S. F. Altschul, and D. J. Lipman. 1991. A workbench for multiple alignment construction and analysis. Proteins 9:180-190.
-
(1991)
Proteins
, vol.9
, pp. 180-190
-
-
Schuler, G.D.1
Altschul, S.F.2
Lipman, D.J.3
-
31
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
DOI 10.1093/bioinformatics/bti125
-
Söding, J. 2005. Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960. (Pubitemid 40467915)
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 951-960
-
-
Soding, J.1
-
32
-
-
33745586769
-
8, TIM-barrel fold and radical catalytic site structural features
-
DOI 10.1002/prot.20997
-
Sun, L., and K. Warncke. 2006. Comparative model of EutB from coenzyme B12-dependent ethanolamine ammonia-lyase reveals a beta8alpha8, TIM-barrel fold and radical catalytic site structural features. Proteins 64:308-319. (Pubitemid 43993641)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.64
, Issue.2
, pp. 308-319
-
-
Sun, L.1
Warncke, K.2
-
33
-
-
43949084713
-
12-dependent ethanolamine ammonia-lyase
-
DOI 10.1021/bi702366e
-
Sun, L., O. A. Groover, J. M. Canfield, and K. Warncke. 2008. Critical role of arginine 160 of the EutB protein subunit for active site structure and radical catalysis in coenzyme B12-dependent ethanolamine ammonia-lyase. Biochemistry 47:5523-5535. (Pubitemid 351705163)
-
(2008)
Biochemistry
, vol.47
, Issue.20
, pp. 5523-5535
-
-
Sun, L.1
Groover, O.A.2
Canfield, J.M.3
Warncke, K.4
-
34
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov, R. L., E. V. Koonin, and D. J. Lipman. 1997. A genomic perspective on protein families. Science 278:631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
35
-
-
0031574072
-
The CLUSTAL-X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
-
Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 4876-4882
-
-
Thompson, J.D.1
Gibson, T.J.2
Plewniak, F.3
Jeanmougin, F.4
Higgins, D.G.5
-
36
-
-
0042834096
-
Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element
-
Vitreschak, A. G., D. A. Rodionov, A. A. Mironov, and M. S. Gelfand. 2003. Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element. RNA 9:1084-1097.
-
(2003)
RNA
, vol.9
, pp. 1084-1097
-
-
Vitreschak, A.G.1
Rodionov, D.A.2
Mironov, A.A.3
Gelfand, M.S.4
-
37
-
-
18544379948
-
The crystal structure of coenzyme B12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol
-
Yamanishi, M., M. Yunoki, T. Tobimatsu, H. Sato, J. Matsui, A. Dokiya, Y. Iuchi, K. Oe, K. Suto, N. Shibata, Y. Morimoto, N. Yasuoka, and T. Toraya. 2002. The crystal structure of coenzyme B12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol. Eur. J. Biochem. 269:4484-4494.
-
(2002)
Eur. J. Biochem.
, vol.269
, pp. 4484-4494
-
-
Yamanishi, M.1
Yunoki, M.2
Tobimatsu, T.3
Sato, H.4
Matsui, J.5
Dokiya, A.6
Iuchi, Y.7
Oe, K.8
Suto, K.9
Shibata, N.10
Morimoto, Y.11
Yasuoka, N.12
Toraya, T.13
|