-
1
-
-
84870604440
-
Genome context as a predictive tool for identifying regulatory targets of the TetR family transcriptional regulators
-
doi:10.1371/journal.pone.0050562
-
Ahn, S. K., Cuthbertson, L., and Nodwell, J. R. (2012). Genome context as a predictive tool for identifying regulatory targets of the TetR family transcriptional regulators. PLoS ONE 7:e50562. doi: 10.1371/journal.pone.0050562
-
(2012)
PLoS ONE
, vol.7
-
-
Ahn, S.K.1
Cuthbertson, L.2
Nodwell, J.R.3
-
2
-
-
84870613442
-
Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile
-
doi:10.1093/nar/gks864
-
Antunes, A., Camiade, E., Monot, M., Courtois, E., Barbut, F., Sernova, N. V., et al. (2012). Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile. Nucleic Acids Res. 40, 10701-10718. doi: 10.1093/nar/gks864
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 10701-10718
-
-
Antunes, A.1
Camiade, E.2
Monot, M.3
Courtois, E.4
Barbut, F.5
Sernova, N.V.6
-
3
-
-
0030790119
-
Allosteric mechanism of induction of CytR-regulated gene expression,Cytr repressor-cytidine interaction
-
doi:10.1074/jbc.272.27.16962
-
Barbier, C. S., Short, S. A., and Senear, D. F. (1997). Allosteric mechanism of induction of CytR-regulated gene expression. Cytr repressor-cytidine interaction. J. Biol. Chem. 272, 16962-16971. doi: 10.1074/jbc.272.27.16962
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 16962-16971
-
-
Barbier, C.S.1
Short, S.A.2
Senear, D.F.3
-
4
-
-
78649667351
-
Local gene regulation details a recognition code within the LacI transcriptional factor family
-
doi:10.1371/journal.pcbi.1000989
-
Camas, F. M., Alm, E. J., and Poyatos, J. F. (2010). Local gene regulation details a recognition code within the LacI transcriptional factor family. PLoS Comput. Biol. 6:e1000989. doi: 10.1371/journal.pcbi.1000989
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Camas, F.M.1
Alm, E.J.2
Poyatos, J.F.3
-
5
-
-
80052615116
-
The PurR regulon in Escherichia coli K-12 MG1655
-
doi:10.1093/nar/gkr307
-
Cho, B. K., Federowicz, S. A., Embree, M., Park, Y. S., Kim, D., and Palsson, B. O. (2011). The PurR regulon in Escherichia coli K-12 MG1655. Nucleic Acids Res. 39, 6456-6464. doi: 10.1093/nar/gkr307
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 6456-6464
-
-
Cho, B.K.1
Federowicz, S.A.2
Embree, M.3
Park, Y.S.4
Kim, D.5
Palsson, B.O.6
-
6
-
-
84875521674
-
RegTransBase-a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes
-
doi:10.1186/1471-2164-14-213
-
Cipriano, M. J., Novichkov, P. N., Kazakov, A. E., Rodionov, D. A., Arkin, A. P., Gelfand, M. S., et al. (2013). RegTransBase-a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. BMC Genomics 14:213. doi: 10.1186/1471-2164-14-213
-
(2013)
BMC Genomics
, vol.14
, pp. 213
-
-
Cipriano, M.J.1
Novichkov, P.N.2
Kazakov, A.E.3
Rodionov, D.A.4
Arkin, A.P.5
Gelfand, M.S.6
-
7
-
-
32044434639
-
Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes
-
doi:10.1128/AEM.71.11.7442-7452.2005
-
Conlan, S., Lawrence, C., and McCue, L. A. (2005). Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes. Appl. Environ. Microbiol. 71, 7442-7452. doi: 10.1128/AEM.71.11.7442-7452.2005
-
(2005)
Appl. Environ. Microbiol.
, vol.71
, pp. 7442-7452
-
-
Conlan, S.1
Lawrence, C.2
McCue, L.A.3
-
8
-
-
2142738304
-
WebLogo: a sequence logo generator
-
doi:10.1101/gr.849004
-
Crooks, G. E., Hon, G., Chandonia, J. M., and Brenner, S. E. (2004). WebLogo: a sequence logo generator. Genome Res. 14, 1188-1190. doi: 10.1101/gr.849004
-
(2004)
Genome Res.
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
9
-
-
75549088819
-
MicrobesOnline: an integrated portal for comparative and functional genomics
-
doi:10.1093/nar/gkp919
-
Dehal, P. S., Joachimiak, M. P., Price, M. N., Bates, J. T., Baumohl, J. K., Chivian, D., et al. (2010). MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res. 38, D396-D400. doi: 10.1093/nar/gkp919
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Dehal, P.S.1
Joachimiak, M.P.2
Price, M.N.3
Bates, J.T.4
Baumohl, J.K.5
Chivian, D.6
-
10
-
-
65849228838
-
Engineering transcription factors with novel DNA-binding specificity using comparative genomics
-
doi:10.1093/nar/gkp079
-
Desai, T. A., Rodionov, D. A., Gelfand, M. S., Alm, E. J., and Rao, C. V. (2009). Engineering transcription factors with novel DNA-binding specificity using comparative genomics. Nucleic Acids Res. 37, 2493-2503. doi: 10.1093/nar/gkp079
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 2493-2503
-
-
Desai, T.A.1
Rodionov, D.A.2
Gelfand, M.S.3
Alm, E.J.4
Rao, C.V.5
-
11
-
-
77953347739
-
Accessing the SEED genome databases via Web services API: tools for programmers
-
doi:10.1186/1471-2105-11-319
-
Disz, T., Akhter, S., Cuevas, D., Olson, R., Overbeek, R., Vonstein, V., et al. (2010). Accessing the SEED genome databases via Web services API: tools for programmers. BMC Bioinformatics 11:319. doi: 10.1186/1471-2105-11-319
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 319
-
-
Disz, T.1
Akhter, S.2
Cuevas, D.3
Olson, R.4
Overbeek, R.5
Vonstein, V.6
-
12
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
doi:10.1093/nar/gkh340
-
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797. doi: 10.1093/nar/gkh340
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
13
-
-
84891782659
-
Pfam: the protein families database
-
doi:10.1093/nar/gkt1223
-
Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., et al. (2014). Pfam: the protein families database. Nucleic Acids Res. 42, D222-D230. doi: 10.1093/nar/gkt1223
-
(2014)
Nucleic Acids Res.
, vol.42
-
-
Finn, R.D.1
Bateman, A.2
Clements, J.3
Coggill, P.4
Eberhardt, R.Y.5
Eddy, S.R.6
-
14
-
-
42449147860
-
A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1
-
doi:10.1186/1471-2164-9-145
-
Francke, C., Kerkhoven, R., Wels, M., and Siezen, R. J. (2008). A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1. BMC Genomics 9:145. doi: 10.1186/1471-2164-9-145
-
(2008)
BMC Genomics
, vol.9
, pp. 145
-
-
Francke, C.1
Kerkhoven, R.2
Wels, M.3
Siezen, R.J.4
-
15
-
-
33646003235
-
Functional domains of the Bacillus subtilis transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector binding
-
doi:10.1128/JB.188.8.3024-3036.2006
-
Franco, I. S., Mota, L. J., Soares, C. M., and De Sa-Nogueira, I. (2006). Functional domains of the Bacillus subtilis transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector binding. J. Bacteriol. 188, 3024-3036. doi: 10.1128/JB.188.8.3024-3036.2006
-
(2006)
J. Bacteriol.
, vol.188
, pp. 3024-3036
-
-
Franco, I.S.1
Mota, L.J.2
Soares, C.M.3
De Sa-Nogueira, I.4
-
16
-
-
65249173472
-
Carbon catabolite control of the metabolic network in Bacillus subtilis
-
doi:10.1271/bbb.80479
-
Fujita, Y. (2009). Carbon catabolite control of the metabolic network in Bacillus subtilis. Biosci. Biotechnol. Biochem. 73, 245-259. doi: 10.1271/bbb.80479
-
(2009)
Biosci. Biotechnol. Biochem.
, vol.73
, pp. 245-259
-
-
Fujita, Y.1
-
17
-
-
0037329109
-
Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins
-
doi:10.1093/molbev/msg038
-
Fukami-Kobayashi, K., Tateno, Y., and Nishikawa, K. (2003). Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins. Mol. Biol. Evol. 20, 267-277. doi: 10.1093/molbev/msg038
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 267-277
-
-
Fukami-Kobayashi, K.1
Tateno, Y.2
Nishikawa, K.3
-
18
-
-
33744780700
-
Evolution of transcriptional regulatory networks in microbial genomes
-
doi:10.1016/j.sbi.2006.04.001
-
Gelfand, M. S. (2006). Evolution of transcriptional regulatory networks in microbial genomes. Curr. Opin. Struct. Biol. 16, 420-429. doi: 10.1016/j.sbi.2006.04.001
-
(2006)
Curr. Opin. Struct. Biol.
, vol.16
, pp. 420-429
-
-
Gelfand, M.S.1
-
19
-
-
38849104227
-
Comparative genomics and functional annotation of bacterial transporters
-
doi:10.1016/j.plrev.2007.10.003
-
Gelfand, M. S., and Rodionov, D. A. (2008). Comparative genomics and functional annotation of bacterial transporters. Phys. Life Rev. 5, 22-49. doi: 10.1016/j.plrev.2007.10.003
-
(2008)
Phys. Life Rev.
, vol.5
, pp. 22-49
-
-
Gelfand, M.S.1
Rodionov, D.A.2
-
20
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
-
doi:10.1093/sysbio/syq010
-
Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., and Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321. doi: 10.1093/sysbio/syq010
-
(2010)
Syst. Biol.
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
21
-
-
0027243123
-
Regulation of Escherichia coli glnB, prsA, and speA by the purine repressor
-
He, B., Choi, K. Y., and Zalkin, H. (1993). Regulation of Escherichia coli glnB, prsA, and speA by the purine repressor. J. Bacteriol. 175, 3598-3606.
-
(1993)
J. Bacteriol.
, vol.175
, pp. 3598-3606
-
-
He, B.1
Choi, K.Y.2
Zalkin, H.3
-
22
-
-
0026436191
-
Escherichia coli purB gene: cloning, nucleotide sequence, and regulation by purR
-
He, B., Smith, J. M., and Zalkin, H. (1992). Escherichia coli purB gene: cloning, nucleotide sequence, and regulation by purR. J. Bacteriol. 174, 130-136.
-
(1992)
J. Bacteriol.
, vol.174
, pp. 130-136
-
-
He, B.1
Smith, J.M.2
Zalkin, H.3
-
23
-
-
1342325451
-
Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media
-
doi:10.1128/JB.186.5.1448-1461.2004
-
Hottes, A. K., Meewan, M., Yang, D., Arana, N., Romero, P., McAdams, H. H., et al. (2004). Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media. J. Bacteriol. 186, 1448-1461. doi: 10.1128/JB.186.5.1448-1461.2004
-
(2004)
J. Bacteriol.
, vol.186
, pp. 1448-1461
-
-
Hottes, A.K.1
Meewan, M.2
Yang, D.3
Arana, N.4
Romero, P.5
McAdams, H.H.6
-
24
-
-
67649986228
-
Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism
-
doi:10.1016/j.str.2009.05.012
-
Huang, N., De Ingeniis, J., Galeazzi, L., Mancini, C., Korostelev, Y. D., Rakhmaninova, A. B., et al. (2009). Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism. Structure 17, 939-951. doi: 10.1016/j.str.2009.05.012
-
(2009)
Structure
, vol.17
, pp. 939-951
-
-
Huang, N.1
De Ingeniis, J.2
Galeazzi, L.3
Mancini, C.4
Korostelev, Y.D.5
Rakhmaninova, A.B.6
-
25
-
-
38649092410
-
Dendroscope: an interactive viewer for large phylogenetic trees
-
doi:10.1186/1471-2105-8-460
-
Huson, D. H., Richter, D. C., Rausch, C., Dezulian, T., Franz, M., and Rupp, R. (2007). Dendroscope: an interactive viewer for large phylogenetic trees. BMC Bioinformatics 8:460. doi: 10.1186/1471-2105-8-460
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 460
-
-
Huson, D.H.1
Richter, D.C.2
Rausch, C.3
Dezulian, T.4
Franz, M.5
Rupp, R.6
-
26
-
-
4043075391
-
Genes of structure and genes of regulation in the biosynthesis of proteins
-
Jacob, F., and Monod, J. (1959). Genes of structure and genes of regulation in the biosynthesis of proteins. C. R. Hebd. Seances Acad. Sci. 249, 1282-1284.
-
(1959)
C. R. Hebd. Seances Acad. Sci.
, vol.249
, pp. 1282-1284
-
-
Jacob, F.1
Monod, J.2
-
27
-
-
54249116230
-
Genetic regulatory mechanisms in the synthesis of proteins
-
doi:10.1016/S0022-2836(61)80072-7
-
Jacob, F., and Monod, J. (1961). Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318-356. doi: 10.1016/S0022-2836(61)80072-7
-
(1961)
J. Mol. Biol.
, vol.3
, pp. 318-356
-
-
Jacob, F.1
Monod, J.2
-
28
-
-
1642452921
-
Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families
-
doi:10.1110/ps.03191704
-
Kalinina, O. V., Mironov, A. A., Gelfand, M. S., and Rakhmaninova, A. B. (2004). Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. Protein Sci. 13, 443-456. doi: 10.1110/ps.03191704
-
(2004)
Protein Sci.
, vol.13
, pp. 443-456
-
-
Kalinina, O.V.1
Mironov, A.A.2
Gelfand, M.S.3
Rakhmaninova, A.B.4
-
29
-
-
0037124326
-
Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain
-
doi:10.1093/emboj/cdf318
-
Kalodimos, C. G., Bonvin, A. M., Salinas, R. K., Wechselberger, R., Boelens, R., and Kaptein, R. (2002). Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain. EMBO J. 21, 2866-2876. doi: 10.1093/emboj/cdf318
-
(2002)
EMBO J.
, vol.21
, pp. 2866-2876
-
-
Kalodimos, C.G.1
Bonvin, A.M.2
Salinas, R.K.3
Wechselberger, R.4
Boelens, R.5
Kaptein, R.6
-
30
-
-
84858983547
-
KEGG for integration and interpretation of large-scale molecular data sets
-
doi:10.1093/nar/gkr988
-
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., and Tanabe, M. (2012). KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 40, D109-D114. doi: 10.1093/nar/gkr988
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
Furumichi, M.4
Tanabe, M.5
-
31
-
-
58149479236
-
Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria
-
doi:10.1128/JB.01175-08
-
Kazakov, A. E., Rodionov, D. A., Alm, E., Arkin, A. P., Dubchak, I., and Gelfand, M. S. (2009). Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. J. Bacteriol. 191, 52-64. doi: 10.1128/JB.01175-08
-
(2009)
J. Bacteriol.
, vol.191
, pp. 52-64
-
-
Kazakov, A.E.1
Rodionov, D.A.2
Alm, E.3
Arkin, A.P.4
Dubchak, I.5
Gelfand, M.S.6
-
32
-
-
84872011384
-
Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes
-
doi:10.1128/JB.01977-12
-
Kazakov, A. E., Rodionov, D. A., Price, M. N., Arkin, A. P., Dubchak, I., and Novichkov, P. S. (2013). Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes. J. Bacteriol. 195, 29-38. doi: 10.1128/JB.01977-12
-
(2013)
J. Bacteriol.
, vol.195
, pp. 29-38
-
-
Kazakov, A.E.1
Rodionov, D.A.2
Price, M.N.3
Arkin, A.P.4
Dubchak, I.5
Novichkov, P.S.6
-
33
-
-
84875463123
-
Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum
-
doi:10.1093/nar/gks1184
-
Kazanov, M. D., Li, X., Gelfand, M. S., Osterman, A. L., and Rodionov, D. A. (2013). Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum. Nucleic Acids Res. 41, 790-803. doi: 10.1093/nar/gks1184
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 790-803
-
-
Kazanov, M.D.1
Li, X.2
Gelfand, M.S.3
Osterman, A.L.4
Rodionov, D.A.5
-
34
-
-
79960004119
-
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
-
doi:10.1093/nar/gkr201
-
Letunic, I., and Bork, P. (2011). Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 39, W475-W478. doi: 10.1093/nar/gkr201
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Letunic, I.1
Bork, P.2
-
35
-
-
20444411150
-
The lac repressor
-
doi:10.1016/j.crvi.2005.04.004
-
Lewis, M. (2005). The lac repressor. C. R. Biol. 328, 521-548. doi: 10.1016/j.crvi.2005.04.004
-
(2005)
C. R. Biol.
, vol.328
, pp. 521-548
-
-
Lewis, M.1
-
36
-
-
84877989943
-
Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis
-
doi:10.1128/JB.00140-13
-
Leyn, S. A., Kazanov, M. D., Sernova, N. V., Ermakova, E. O., Novichkov, P. S., and Rodionov, D. A. (2013). Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis. J. Bacteriol. 195, 2463-2473. doi: 10.1128/JB.00140-13
-
(2013)
J. Bacteriol.
, vol.195
, pp. 2463-2473
-
-
Leyn, S.A.1
Kazanov, M.D.2
Sernova, N.V.3
Ermakova, E.O.4
Novichkov, P.S.5
Rodionov, D.A.6
-
37
-
-
80053915498
-
Control of Proteobacterial central carbon metabolism by the HexR transcriptional regulator,A case study in Shewanella oneidensis
-
doi:10.1074/jbc.M111.267963
-
Leyn, S. A., Li, X., Zheng, Q., Novichkov, P. S., Reed, S., Romine, M. F., et al. (2011). Control of Proteobacterial central carbon metabolism by the HexR transcriptional regulator. A case study in Shewanella oneidensis. J. Biol. Chem. 286, 35782-35794. doi: 10.1074/jbc.M111.267963
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 35782-35794
-
-
Leyn, S.A.1
Li, X.2
Zheng, Q.3
Novichkov, P.S.4
Reed, S.5
Romine, M.F.6
-
38
-
-
52649145421
-
The cis-regulatory map of Shewanella genomes
-
doi:10.1093/nar/gkn515
-
Liu, J., Xu, X., and Stormo, G. D. (2008). The cis-regulatory map of Shewanella genomes. Nucleic Acids Res. 36, 5376-5390. doi: 10.1093/nar/gkn515
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 5376-5390
-
-
Liu, J.1
Xu, X.2
Stormo, G.D.3
-
39
-
-
79960976768
-
UniProt Knowledgebase: a hub of integrated protein data
-
bar009. doi:10.1093/database/bar009
-
Magrane, M., and Consortium, U. (2011). UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011:bar009. doi: 10.1093/database/bar009
-
(2011)
Database (Oxford)
, vol.2011
-
-
Magrane, M.1
Consortium, U.2
-
40
-
-
0033986506
-
Carbon catabolite repression in Lactobacillus pentosus: analysis of the ccpA region
-
doi:10.1128/AEM.66.1.277-283.2000
-
Mahr, K., Hillen, W., and Titgemeyer, F. (2000). Carbon catabolite repression in Lactobacillus pentosus: analysis of the ccpA region. Appl. Environ. Microbiol. 66, 277-283. doi: 10.1128/AEM.66.1.277-283.2000
-
(2000)
Appl. Environ. Microbiol.
, vol.66
, pp. 277-283
-
-
Mahr, K.1
Hillen, W.2
Titgemeyer, F.3
-
41
-
-
0034669669
-
Predicting regulons and their cis-regulatory motifs by comparative genomics
-
doi:10.1093/nar/28.22.4523
-
Manson McGuire, A., and Church, G. M. (2000). Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucleic Acids Res. 28, 4523-4530. doi: 10.1093/nar/28.22.4523
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 4523-4530
-
-
Manson McGuire, A.1
Church, G.M.2
-
42
-
-
0027050193
-
Structural homology between rbs repressor and ribose binding protein implies functional similarity
-
doi:10.1002/pro.5560010702
-
Mauzy, C. A., and Hermodson, M. A. (1992). Structural homology between rbs repressor and ribose binding protein implies functional similarity. Protein Sci. 1, 843-849. doi: 10.1002/pro.5560010702
-
(1992)
Protein Sci.
, vol.1
, pp. 843-849
-
-
Mauzy, C.A.1
Hermodson, M.A.2
-
43
-
-
0035253676
-
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
-
doi:10.1093/nar/29.3.774
-
McCue, L., Thompson, W., Carmack, C., Ryan, M. P., Liu, J. S., Derbyshire, V., et al. (2001). Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res. 29, 774-782. doi: 10.1093/nar/29.3.774
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 774-782
-
-
McCue, L.1
Thompson, W.2
Carmack, C.3
Ryan, M.P.4
Liu, J.S.5
Derbyshire, V.6
-
44
-
-
58149292217
-
Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: bioinformatics-based predictions generate true positives and false negatives
-
doi:10.1002/prot.22121
-
Meinhardt, S., and Swint-Kruse, L. (2008). Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: bioinformatics-based predictions generate true positives and false negatives. Proteins 73, 941-957. doi: 10.1002/prot.22121
-
(2008)
Proteins
, vol.73
, pp. 941-957
-
-
Meinhardt, S.1
Swint-Kruse, L.2
-
45
-
-
77952738827
-
Functional rules for lac repressor-operator associations and implications for protein-DNA interactions
-
doi:10.1002/pro.389
-
Milk, L., Daber, R., and Lewis, M. (2010). Functional rules for lac repressor-operator associations and implications for protein-DNA interactions. Protein Sci. 19, 1162-1172. doi: 10.1002/pro.389
-
(2010)
Protein Sci.
, vol.19
, pp. 1162-1172
-
-
Milk, L.1
Daber, R.2
Lewis, M.3
-
46
-
-
18144444203
-
Using orthologous and paralogous proteins to identify specificity determining residues
-
PREPRINT0002. doi:10.1186/gb-2002-3-3-preprint0002
-
Mirny, L. A., and Gelfand, M. S. (2002). Using orthologous and paralogous proteins to identify specificity determining residues. Genome Biol. 3:PREPRINT0002. doi: 10.1186/gb-2002-3-3-preprint0002
-
(2002)
Genome Biol.
, vol.3
-
-
Mirny, L.A.1
Gelfand, M.S.2
-
47
-
-
0034153918
-
Software for analyzing bacterial genomes
-
Mironov, A. A., Vinokurova, N. P., and Gel'fand, M. S. (2000). Software for analyzing bacterial genomes. Mol. Biol. 34, 253-262.
-
(2000)
Mol. Biol.
, vol.34
, pp. 253-262
-
-
Mironov, A.A.1
Vinokurova, N.P.2
Gel'fand, M.S.3
-
48
-
-
0029609722
-
Phylogenetic, structural and functional analyses of the LacI-GalR family of bacterial transcription factors
-
doi:10.1016/0014-5793(95)01344-X
-
Nguyen, C. C., and Saier, M. H. Jr. (1995). Phylogenetic, structural and functional analyses of the LacI-GalR family of bacterial transcription factors. FEBS Lett. 377, 98-102. doi: 10.1016/0014-5793(95)01344-X
-
(1995)
FEBS Lett.
, vol.377
, pp. 98-102
-
-
Nguyen, C.C.1
Saier Jr., M.H.2
-
49
-
-
84886739636
-
RegPrecise 3.0 - A resource for genome-scale exploration of transcriptional regulation in bacteria
-
doi:10.1186/1471-2164-14-745
-
Novichkov, P. S., Kazakov, A. E., Ravcheev, D. A., Leyn, S. A., Kovaleva, G. Y., Sutormin, R. A., et al. (2013). RegPrecise 3.0 - A resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics 14:745. doi: 10.1186/1471-2164-14-745
-
(2013)
BMC Genomics
, vol.14
, pp. 745
-
-
Novichkov, P.S.1
Kazakov, A.E.2
Ravcheev, D.A.3
Leyn, S.A.4
Kovaleva, G.Y.5
Sutormin, R.A.6
-
50
-
-
77954254495
-
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach
-
doi:10.1093/nar/gkq531
-
Novichkov, P. S., Rodionov, D. A., Stavrovskaya, E. D., Novichkova, E. S., Kazakov, A. E., Gelfand, M. S., et al. (2010). RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res. 38, W299-W307. doi: 10.1093/nar/gkq531
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Novichkov, P.S.1
Rodionov, D.A.2
Stavrovskaya, E.D.3
Novichkova, E.S.4
Kazakov, A.E.5
Gelfand, M.S.6
-
51
-
-
0037398732
-
Missing genes in metabolic pathways: a comparative genomics approach
-
doi:10.1016/S1367-5931(03)00027-9
-
Osterman, A., and Overbeek, R. (2003). Missing genes in metabolic pathways: a comparative genomics approach. Curr. Opin. Chem. Biol. 7, 238-251. doi: 10.1016/S1367-5931(03)00027-9
-
(2003)
Curr. Opin. Chem. Biol.
, vol.7
, pp. 238-251
-
-
Osterman, A.1
Overbeek, R.2
-
52
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
doi:10.1093/nar/gki866
-
Overbeek, R., Begley, T., Butler, R. M., Choudhuri, J. V., Chuang, H. Y., Cohoon, M., et al. (2005). The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33, 5691-5702. doi: 10.1093/nar/gki866
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.Y.5
Cohoon, M.6
-
53
-
-
84896714562
-
Multiple co-evolutionary networks are supported by the common tertiary scaffold of the LacI/GalR proteins
-
doi:10.1371/journal.pone.0084398
-
Parente, D. J., and Swint-Kruse, L. (2013). Multiple co-evolutionary networks are supported by the common tertiary scaffold of the LacI/GalR proteins. PLoS ONE 8:e84398. doi: 10.1371/journal.pone.0084398
-
(2013)
PLoS ONE
, vol.8
-
-
Parente, D.J.1
Swint-Kruse, L.2
-
54
-
-
84862195656
-
CoryneRegNet 6.0-Updated database content, new analysis methods and novel features focusing on community demands
-
doi:10.1093/nar/gkr883
-
Pauling, J., Rottger, R., Tauch, A., Azevedo, V., and Baumbach, J. (2012). CoryneRegNet 6.0-Updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Res. 40, D610-D614. doi: 10.1093/nar/gkr883
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Pauling, J.1
Rottger, R.2
Tauch, A.3
Azevedo, V.4
Baumbach, J.5
-
55
-
-
32144442848
-
Prediction of functional specificity determinants from protein sequences using log-likelihood ratios
-
doi:10.1093/bioinformatics/bti766
-
Pei, J., Cai, W., Kinch, L. N., and Grishin, N. V. (2006). Prediction of functional specificity determinants from protein sequences using log-likelihood ratios. Bioinformatics 22, 164-171. doi: 10.1093/bioinformatics/bti766
-
(2006)
Bioinformatics
, vol.22
, pp. 164-171
-
-
Pei, J.1
Cai, W.2
Kinch, L.N.3
Grishin, N.V.4
-
56
-
-
63149115913
-
Transcription factor function and promoter architecture govern the evolution of bacterial regulons
-
doi:10.1073/pnas.0810343106
-
Perez, J. C., and Groisman, E. A. (2009). Transcription factor function and promoter architecture govern the evolution of bacterial regulons. Proc. Natl. Acad. Sci. U.S.A. 106, 4319-4324. doi: 10.1073/pnas.0810343106
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 4319-4324
-
-
Perez, J.C.1
Groisman, E.A.2
-
57
-
-
84873699939
-
Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria
-
doi: 10.1186/1471-2164-14-94
-
Ravcheev, D. A., Best, A. A., Sernova, N. V., Kazanov, M. D., Novichkov, P. S., and Rodionov, D. A. (2013b). Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria. BMC Genomics 14:94. doi: 10.1186/1471-2164-14-94
-
(2013)
BMC Genomics
, vol.14
, pp. 94
-
-
Ravcheev, D.A.1
Best, A.A.2
Sernova, N.V.3
Kazanov, M.D.4
Novichkov, P.S.5
Rodionov, D.A.6
-
58
-
-
84889976808
-
Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks
-
doi:10.1186/1471-2164-14-873
-
Ravcheev, D., Godzik, A., Osterman, A., and Rodionov, D. (2013a). Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks. BMC Genomics 14:873. doi: 10.1186/1471-2164-14-873
-
(2013)
BMC Genomics
, vol.14
, pp. 873
-
-
Ravcheev, D.1
Godzik, A.2
Osterman, A.3
Rodionov, D.4
-
59
-
-
79959363284
-
Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence
-
doi:10.1128/JB.00350-11
-
Ravcheev, D. A., Best, A. A., Tintle, N., Dejongh, M., Osterman, A. L., Novichkov, P. S., et al. (2011). Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence. J. Bacteriol. 193, 3228-3240. doi: 10.1128/JB.00350-11
-
(2011)
J. Bacteriol.
, vol.193
, pp. 3228-3240
-
-
Ravcheev, D.A.1
Best, A.A.2
Tintle, N.3
Dejongh, M.4
Osterman, A.L.5
Novichkov, P.S.6
-
60
-
-
0036716306
-
Purine regulon of gamma-proteobacteria: a detailed description
-
doi:10.1023/A:1020231513079
-
Ravcheev, D. A., Gel'fand, M. S., Mironov, A. A., and Rakhmaninova, A. B. (2002). Purine regulon of gamma-proteobacteria: a detailed description. Genetika 38, 1203-1214. doi: 10.1023/A:1020231513079
-
(2002)
Genetika
, vol.38
, pp. 1203-1214
-
-
Ravcheev, D.A.1
Gel'fand, M.S.2
Mironov, A.A.3
Rakhmaninova, A.B.4
-
61
-
-
33847670273
-
Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae)
-
doi:10.1186/1471-2164-8-54
-
Ravcheev, D. A., Gerasimova, A. V., Mironov, A. A., and Gelfand, M. S. (2007). Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae). BMC Genomics 8:54. doi: 10.1186/1471-2164-8-54
-
(2007)
BMC Genomics
, vol.8
, pp. 54
-
-
Ravcheev, D.A.1
Gerasimova, A.V.2
Mironov, A.A.3
Gelfand, M.S.4
-
62
-
-
84863285072
-
Transcriptional regulation of central carbon and energy metabolism in bacteria by redox responsive repressor Rex
-
doi:10.1128/JB.06412-11
-
Ravcheev, D. A., Li, X., Latif, H., Zengler, K., Leyn, S. A., Korostelev, Y. D., et al. (2012). Transcriptional regulation of central carbon and energy metabolism in bacteria by redox responsive repressor Rex. J. Bacteriol. 194, 1145-1157. doi: 10.1128/JB.06412-11
-
(2012)
J. Bacteriol.
, vol.194
, pp. 1145-1157
-
-
Ravcheev, D.A.1
Li, X.2
Latif, H.3
Zengler, K.4
Leyn, S.A.5
Korostelev, Y.D.6
-
63
-
-
3242674438
-
Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships
-
doi:10.1093/nar/gkh673
-
Rigali, S., Schlicht, M., Hoskisson, P., Nothaft, H., Merzbacher, M., Joris, B., et al. (2004). Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships. Nucleic Acids Res. 32, 3418-3426. doi: 10.1093/nar/gkh673
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 3418-3426
-
-
Rigali, S.1
Schlicht, M.2
Hoskisson, P.3
Nothaft, H.4
Merzbacher, M.5
Joris, B.6
-
64
-
-
34548219522
-
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria
-
doi:10.1021/cr068309+
-
Rodionov, D. A. (2007). Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem. Rev. 107, 3467-3497. doi: 10.1021/cr068309+
-
(2007)
Chem. Rev.
, vol.107
, pp. 3467-3497
-
-
Rodionov, D.A.1
-
65
-
-
20644446065
-
Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling
-
doi:10.1016/j.tig.2005.05.011
-
Rodionov, D. A., and Gelfand, M. S. (2005). Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling. Trends Genet. 21, 385-389. doi: 10.1016/j.tig.2005.05.011
-
(2005)
Trends Genet.
, vol.21
, pp. 385-389
-
-
Rodionov, D.A.1
Gelfand, M.S.2
-
66
-
-
33845971293
-
Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria
-
doi:10.1371/journal.pcbi.0020163
-
Rodionov, D. A., Gelfand, M. S., Todd, J. D., Curson, A. R., and Johnston, A. W. (2006). Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria. PLoS Comput. Biol. 2:e163. doi: 10.1371/journal.pcbi.0020163
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
Rodionov, D.A.1
Gelfand, M.S.2
Todd, J.D.3
Curson, A.R.4
Johnston, A.W.5
-
67
-
-
79958842141
-
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus
-
doi: 10.1186/1471-2164-12-S1-S3
-
Rodionov, D. A., Novichkov, P. S., Stavrovskaya, E. D., Rodionova, I. A., Li, X., Kazanov, M. D., et al. (2011). Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics 12(Suppl. 1):S3. doi: 10.1186/1471-2164-12-S1-S3
-
(2011)
BMC Genomics
, vol.12
, Issue.SUPPL. 1
-
-
Rodionov, D.A.1
Novichkov, P.S.2
Stavrovskaya, E.D.3
Rodionova, I.A.4
Li, X.5
Kazanov, M.D.6
-
68
-
-
84884247784
-
Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima
-
doi:10.3389/fmicb.2013.00244
-
Rodionov, D. A., Rodionova, I. A., Li, X., Ravcheev, D. A., Tarasova, Y., Portnoy, V. A., et al. (2013). Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima. Front. Microbiol. 4:244. doi: 10.3389/fmicb.2013.00244
-
(2013)
Front. Microbiol.
, vol.4
, pp. 244
-
-
Rodionov, D.A.1
Rodionova, I.A.2
Li, X.3
Ravcheev, D.A.4
Tarasova, Y.5
Portnoy, V.A.6
-
69
-
-
77958493458
-
Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes
-
doi:10.1093/bioinformatics/btq501
-
Sahota, G., and Stormo, G. D. (2010). Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes. Bioinformatics 26, 2672-2677. doi: 10.1093/bioinformatics/btq501
-
(2010)
Bioinformatics
, vol.26
, pp. 2672-2677
-
-
Sahota, G.1
Stormo, G.D.2
-
70
-
-
0029941168
-
The catabolite repressor/activator (Cra) protein of enteric bacteria
-
Saier, M. H., and Ramseier, T. M. (1996). The catabolite repressor/activator (Cra) protein of enteric bacteria. J. Bacteriol. 178, 3411-3417.
-
(1996)
J. Bacteriol.
, vol.178
, pp. 3411-3417
-
-
Saier, M.H.1
Ramseier, T.M.2
-
71
-
-
84876543942
-
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
-
doi:10.1093/nar/gks1201
-
Salgado, H., Peralta-Gil, M., Gama-Castro, S., Santos-Zavaleta, A., Muniz-Rascado, L., Garcia-Sotelo, J. S., et al. (2013). RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res. 41, D203-D213. doi: 10.1093/nar/gks1201
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Salgado, H.1
Peralta-Gil, M.2
Gama-Castro, S.3
Santos-Zavaleta, A.4
Muniz-Rascado, L.5
Garcia-Sotelo, J.S.6
-
72
-
-
0028173030
-
Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices
-
doi:10.1126/science.7973627
-
Schumacher, M. A., Choi, K. Y., Zalkin, H., and Brennan, R. G. (1994). Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices. Science 266, 763-770. doi: 10.1126/science.7973627
-
(1994)
Science
, vol.266
, pp. 763-770
-
-
Schumacher, M.A.1
Choi, K.Y.2
Zalkin, H.3
Brennan, R.G.4
-
73
-
-
79954607096
-
Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators
-
doi:10.1093/nar/gkq1177
-
Schumacher, M. A., Sprehe, M., Bartholomae, M., Hillen, W., and Brennan, R. G. (2011). Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators. Nucleic Acids Res. 39, 2931-2942. doi: 10.1093/nar/gkq1177
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 2931-2942
-
-
Schumacher, M.A.1
Sprehe, M.2
Bartholomae, M.3
Hillen, W.4
Brennan, R.G.5
-
74
-
-
67650642124
-
Effect of a glucose impulse on the CcpA regulon in Staphylococcus aureus
-
doi:10.1186/1471-2180-9-95
-
Seidl, K., Muller, S., Francois, P., Kriebitzsch, C., Schrenzel, J., Engelmann, S., et al. (2009). Effect of a glucose impulse on the CcpA regulon in Staphylococcus aureus. BMC Microbiol. 9:95. doi: 10.1186/1471-2180-9-95
-
(2009)
BMC Microbiol.
, vol.9
, pp. 95
-
-
Seidl, K.1
Muller, S.2
Francois, P.3
Kriebitzsch, C.4
Schrenzel, J.5
Engelmann, S.6
-
75
-
-
0030917364
-
Phylogenetic footprinting of hypersensitive site 3 of the beta-globin locus control region
-
Shelton, D. A., Stegman, L., Hardison, R., Miller, W., Bock, J. H., Slightom, J. L., et al. (1997). Phylogenetic footprinting of hypersensitive site 3 of the beta-globin locus control region. Blood 89, 3457-3469.
-
(1997)
Blood
, vol.89
, pp. 3457-3469
-
-
Shelton, D.A.1
Stegman, L.2
Hardison, R.3
Miller, W.4
Bock, J.H.5
Slightom, J.L.6
-
76
-
-
38549162091
-
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
-
doi:10.1093/nar/gkm910
-
Sierro, N., Makita, Y., De Hoon, M., and Nakai, K. (2008). DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res. 36, D93-D96. doi: 10.1093/nar/gkm910
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Sierro, N.1
Makita, Y.2
De Hoon, M.3
Nakai, K.4
-
77
-
-
36248971737
-
Control of key metabolic intersections in Bacillus subtilis
-
doi:10.1038/nrmicro1772
-
Sonenshein, A. L. (2007). Control of key metabolic intersections in Bacillus subtilis. Nat. Rev. Microbiol. 5, 917-927. doi: 10.1038/nrmicro1772
-
(2007)
Nat. Rev. Microbiol.
, vol.5
, pp. 917-927
-
-
Sonenshein, A.L.1
-
78
-
-
84864003884
-
Regulation and evolution of the malonate and propionate catabolism in the proteobacteria
-
doi:10.1128/JB.00163-12
-
Suvorova, I. A., Ravcheev, D. A., and Gelfand, M. S. (2012). Regulation and evolution of the malonate and propionate catabolism in the proteobacteria. J. Bacteriol. 194, 3234-3240. doi: 10.1128/JB.00163-12
-
(2012)
J. Bacteriol.
, vol.194
, pp. 3234-3240
-
-
Suvorova, I.A.1
Ravcheev, D.A.2
Gelfand, M.S.3
-
79
-
-
79960392023
-
Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gamma-proteobacteria
-
doi:10.1128/JB.00277-11
-
Suvorova, I. A., Tutukina, M. N., Ravcheev, D. A., Rodionov, D. A., Ozoline, O. N., and Gelfand, M. S. (2011). Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gamma-proteobacteria. J. Bacteriol. 193, 3228-3240. doi: 10.1128/JB.00277-11
-
(2011)
J. Bacteriol.
, vol.193
, pp. 3228-3240
-
-
Suvorova, I.A.1
Tutukina, M.N.2
Ravcheev, D.A.3
Rodionov, D.A.4
Ozoline, O.N.5
Gelfand, M.S.6
-
80
-
-
63749116038
-
Allostery in the LacI/GalR family: variations on a theme
-
doi:10.1016/j.mib.2009.01.009
-
Swint-Kruse, L., and Matthews, K. S. (2009). Allostery in the LacI/GalR family: variations on a theme. Curr. Opin. Microbiol. 12, 129-137. doi: 10.1016/j.mib.2009.01.009
-
(2009)
Curr. Opin. Microbiol.
, vol.12
, pp. 129-137
-
-
Swint-Kruse, L.1
Matthews, K.S.2
-
81
-
-
0035051602
-
A comparative genomics approach to prediction of new members of regulons
-
doi:10.1101/gr.149301
-
Tan, K., Moreno-Hagelsieb, G., Collado-Vides, J., and Stormo, G. D. (2001). A comparative genomics approach to prediction of new members of regulons. Genome Res. 11, 566-584. doi: 10.1101/gr.149301
-
(2001)
Genome Res.
, vol.11
, pp. 566-584
-
-
Tan, K.1
Moreno-Hagelsieb, G.2
Collado-Vides, J.3
Stormo, G.D.4
-
82
-
-
0037337737
-
The activator of GntII genes for gluconate metabolism, GntH, exerts negative control of GntR-regulated GntI genes in Escherichia coli
-
doi:10.1128/JB.185.6.1783-1795.2003
-
Tsunedomi, R., Izu, H., Kawai, T., Matsushita, K., Ferenci, T., and Yamada, M. (2003a). The activator of GntII genes for gluconate metabolism, GntH, exerts negative control of GntR-regulated GntI genes in Escherichia coli. J. Bacteriol. 185, 1783-1795. doi: 10.1128/JB.185.6.1783-1795.2003
-
(2003)
J. Bacteriol.
, vol.185
, pp. 1783-1795
-
-
Tsunedomi, R.1
Izu, H.2
Kawai, T.3
Matsushita, K.4
Ferenci, T.5
Yamada, M.6
-
83
-
-
0345491593
-
Dual control by regulators, GntH and GntR, of the GntII genes for gluconate metabolism in Escherichia coli
-
doi:10.1159/000073407
-
Tsunedomi, R., Izu, H., Kawai, T., and Yamada, M. (2003b). Dual control by regulators, GntH and GntR, of the GntII genes for gluconate metabolism in Escherichia coli. J. Mol. Microbiol. Biotechnol. 6, 41-56. doi: 10.1159/000073407
-
(2003)
J. Mol. Microbiol. Biotechnol.
, vol.6
, pp. 41-56
-
-
Tsunedomi, R.1
Izu, H.2
Kawai, T.3
Yamada, M.4
-
84
-
-
34249891364
-
Functional consequences of exchanging domains between LacI and PurR are mediated by the intervening linker sequence
-
doi:10.1002/prot.21412
-
Tungtur, S., Egan, S. M., and Swint-Kruse, L. (2007). Functional consequences of exchanging domains between LacI and PurR are mediated by the intervening linker sequence. Proteins 68, 375-388. doi: 10.1002/prot.21412
-
(2007)
Proteins
, vol.68
, pp. 375-388
-
-
Tungtur, S.1
Egan, S.M.2
Swint-Kruse, L.3
-
85
-
-
73849085331
-
Comparing the functional roles of nonconserved sequence positions in homologous transcription repressors: implications for sequence/function analyses
-
doi:10.1016/j.jmb.2009.10.001
-
Tungtur, S., Meinhardt, S., and Swint-Kruse, L. (2010). Comparing the functional roles of nonconserved sequence positions in homologous transcription repressors: implications for sequence/function analyses. J. Mol. Biol. 395, 785-802. doi: 10.1016/j.jmb.2009.10.001
-
(2010)
J. Mol. Biol.
, vol.395
, pp. 785-802
-
-
Tungtur, S.1
Meinhardt, S.2
Swint-Kruse, L.3
-
86
-
-
79954573471
-
Functionally important positions can comprise the majority of a protein's architecture
-
doi:10.1002/prot.22985
-
Tungtur, S., Parente, D. J., and Swint-Kruse, L. (2011). Functionally important positions can comprise the majority of a protein's architecture. Proteins 79, 1589-1608. doi: 10.1002/prot.22985
-
(2011)
Proteins
, vol.79
, pp. 1589-1608
-
-
Tungtur, S.1
Parente, D.J.2
Swint-Kruse, L.3
-
87
-
-
55549139516
-
Analysis of the LacI family regulators of Erwinia chrysanthemi 3937, involvement in the bacterial phytopathogenicity
-
doi:10.1094/MPMI-21-11-1471
-
Van Gijsegem, F., Wlodarczyk, A., Cornu, A., Reverchon, S., and Hugouvieux-Cotte-Pattat, N. (2008). Analysis of the LacI family regulators of Erwinia chrysanthemi 3937, involvement in the bacterial phytopathogenicity. Mol. Plant Microbe Interact. 21, 1471-1481. doi: 10.1094/MPMI-21-11-1471
-
(2008)
Mol. Plant Microbe Interact.
, vol.21
, pp. 1471-1481
-
-
Van Gijsegem, F.1
Wlodarczyk, A.2
Cornu, A.3
Reverchon, S.4
Hugouvieux-Cotte-Pattat, N.5
-
88
-
-
0026724966
-
A family of bacterial regulators homologous to Gal and Lac repressors
-
Weickert, M. J., and Adhya, S. (1992). A family of bacterial regulators homologous to Gal and Lac repressors. J. Biol. Chem. 267, 15869-15874.
-
(1992)
J. Biol. Chem.
, vol.267
, pp. 15869-15874
-
-
Weickert, M.J.1
Adhya, S.2
-
89
-
-
33645832957
-
Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups
-
doi:10.1093/nar/gkl138
-
Wels, M., Francke, C., Kerkhoven, R., Kleerebezem, M., and Siezen, R. J. (2006). Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. Nucleic Acids Res. 34, 1947-1958. doi: 10.1093/nar/gkl138
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 1947-1958
-
-
Wels, M.1
Francke, C.2
Kerkhoven, R.3
Kleerebezem, M.4
Siezen, R.J.5
-
90
-
-
78650856199
-
Catabolite control protein A controls hydrogen peroxide production and cell death in Streptococcus sanguinis
-
doi:10.1128/JB.01131-10
-
Zheng, L., Chen, Z., Itzek, A., Ashby, M., and Kreth, J. (2011). Catabolite control protein A controls hydrogen peroxide production and cell death in Streptococcus sanguinis. J. Bacteriol. 193, 516-526. doi: 10.1128/JB.01131-10
-
(2011)
J. Bacteriol.
, vol.193
, pp. 516-526
-
-
Zheng, L.1
Chen, Z.2
Itzek, A.3
Ashby, M.4
Kreth, J.5
-
91
-
-
84863274870
-
CcpA regulates biofilm formation and competence in Streptococcus gordonii
-
doi:10.1111/j.2041-1014.2011.00633.x
-
Zheng, L., Chen, Z., Itzek, A., Herzberg, M. C., and Kreth, J. (2012). CcpA regulates biofilm formation and competence in Streptococcus gordonii. Mol. Oral Microbiol. 27, 83-94. doi: 10.1111/j.2041-1014.2011.00633.x
-
(2012)
Mol. Oral Microbiol.
, vol.27
, pp. 83-94
-
-
Zheng, L.1
Chen, Z.2
Itzek, A.3
Herzberg, M.C.4
Kreth, J.5
-
92
-
-
84857913423
-
Inactivation of ccpA and aeration affect growth, metabolite production and stress tolerance in Lactobacillus plantarum WCFS1
-
doi:10.1016/j.ijfoodmicro.2012.01.017
-
Zotta, T., Ricciardi, A., Guidone, A., Sacco, M., Muscariello, L., Mazzeo, M. F., et al. (2012). Inactivation of ccpA and aeration affect growth, metabolite production and stress tolerance in Lactobacillus plantarum WCFS1. Int. J. Food Microbiol. 155, 51-59. doi: 10.1016/j.ijfoodmicro.2012.01.017
-
(2012)
Int. J. Food Microbiol.
, vol.155
, pp. 51-59
-
-
Zotta, T.1
Ricciardi, A.2
Guidone, A.3
Sacco, M.4
Muscariello, L.5
Mazzeo, M.F.6
|