D-Net

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Kovach, M.E., Elzer, P.H., Hill, D.S., Robertson, G.T., Farris, M.A., Roop, R.M., Peterson, K.M.. Four new derivatives of the broad-host range cloning vector pBBR1MCS, carrying different antibiotic resistance cassettes. Gene. 1995; 166: 175-176", "destinationDocumentId": "dedupedId", "externalDestinationDocumentIds": {"pmid": "8529885" }}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Keen, N.T., Tamaki, S., Kobayashi, D., Trollinger, D.. Improved broad-host range plasmids for DNA cloning in gram-negative bacteria. Gene. 1988; 70: 191-197", "destinationDocumentId": "50|od_______908::4b612aa8b8300b343ace510627710d44", "externalDestinationDocumentIds": {"pmid": "2853689" }}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Huerta, M.A., Collado-Vides, J.. Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J. Mol. Biol.. 2003; 333: 261-278", "externalDestinationDocumentIds": {"pmid": "14529615" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Taté, R., Riccio, A., Iaccarino, M., Patriarca, E.J.. Cloning and transcriptional análisis of the lipA (lipoic acid synthetase) gene from Rhizobium etli. FEMS Microbiol. Lett.. 1997; 149: 165-172", "externalDestinationDocumentIds": {"pmid": "9141657" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Ramírez-Romero, M.A., Téllez-Sosa, J., Barrios, H., Pérez-Oseguera, A., Rosas, V., Cevallos, M.A.. RepA negatively autoregulates the transcription of the repABC operon of the Rhizobium etli symbiotic plasmid basic replicon. Mol. Microbiol.. 2001; 42: 195-204", "externalDestinationDocumentIds": {"pmid": "11679078" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Campbell, E.A., Muzzin, O., Chlenov, M., Sun, J.L., Olson, C.A., Weinman, O., Trester-Zedlitz, M.L., Darst, S.A.. Structure of the bacterial RNA polymerase promoter especificity sigma subunit. Mol. Cell.. 2002; 9: 527-539", "externalDestinationDocumentIds": {"pmid": "11931761" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Studier, F.W., Rosenberg, A.H., Dunn, J.J., Dubendorff, J.W.. Use of T7 RNA polymerase to direct expression of cloned genes. Meth. Enzymol.. 1990; 185: 60-89", "externalDestinationDocumentIds": {"pmid": "2199796" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Miranda-Rios, J., Morera, C., Taboada, H., Dávalos, A., Encarnación, S., Mora, J., Soberón, M.. Expressión of thiamin biosynthetic genes (thiCOGE) and production of symbiotic terminal oxidase cbb3 in Rhizobium etli. J. Bacteriol.. 1997; 179: 6887-6893", "externalDestinationDocumentIds": {"pmid": "9371431" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Kumar, A., Malloch, R.A., Fujita, N., Smillie, D.A., Ishihama, A., Hayward, R.S.. The minus 35-recognition region of Escherichia coli sigma 70 is inessential for initiation of transcription at an \u2018Extended minus 10\u2019 promoter. J. Mol. Biol.. 1993; 232: 406-418", "externalDestinationDocumentIds": {"pmid": "8345519" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Cullen, P.J., Kaufman, C.K., Bowman, W.C., Kranz, R.G.. Characterization of the Rhodobacter capsulatus housekeeping RNA polymerase. In vitro transcripcion of photosynthesis and other genes. J. Biol. Chem.. 1997; 272: 27266-27273", "externalDestinationDocumentIds": {"pmid": "9341173" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Harley, C.B., Reynolds, R.P.. Analysis of E.coli promoter sequences. Nucleic Acids Res.. 1987; 15: 2343-2361", "externalDestinationDocumentIds": {"pmid": "3550697" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Lisser, S., Margalit, H.. Compilation of E.coli mRNA promoter sequences. Nucleic Acids Res.. 1993; 21: 1507-1516", "externalDestinationDocumentIds": {"pmid": "8479900" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Paget, M.S., Helmann, J.D.. The sigma70 family of sigma factors. Genome Biol.. 2003; 4: 203.1-203.6", "externalDestinationDocumentIds": {"pmid": "12540296" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Tang, H., Severinov, K., Goldfarb, A., Ebright, H.. Rapid RNA polymerase genetics: one-day, no column preparation of reconstituted recombinant Escherichia coli RNA polymerase. Proc. Natl Acad. Sci. USA. 1995; 92: 4902-4906", "externalDestinationDocumentIds": {"pmid": "7761421" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Corpet, F.. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res.. 1988; 16: 10881-10890", "externalDestinationDocumentIds": {"pmid": "2849754" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Hanahan, D.. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol.. 1983; 166: 557-580", "externalDestinationDocumentIds": {"pmid": "6345791" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Vlahovicek, K., Kaján, L., Pongor, S.. DNA analysis servers: plot.it, bend.it, model.it and IS. Nucleic Acids Res.. 2003; 31: 3686-3687", "externalDestinationDocumentIds": {"pmid": "12824394" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Metcalf, W.W., Wanner, B.L.. Construction of new β-glucuronidase cassettes for making transcriptional fusions and their use with new methods for allele replacement. Gene. 1993; 129: 17-25", "externalDestinationDocumentIds": {"pmid": "8335256" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Tapias, A., Fernández de Henestrosa, A.R., Barbé, J.. Characterization of the promoter of the Rhizobium etli recA gene. J. Bacteriol.. 1997; 179: 1573-1579", "externalDestinationDocumentIds": {"pmid": "9045815" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Higgins, D., Thompson, J., Gibson,Thompson, J.D., Higgins, D.G., Gibson, T.J.. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res.. 1994; 22: 4673-4680", "externalDestinationDocumentIds": {"pmid": "7984417" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Ornstein, R.L., Rein, R., Breen, D.L., MacElroy, R.D.. An optimized potential function for the calculation of nucleic acid interaction energies I. Base stacking. Biopolymers. 1978; 17: 2341-2360", "externalDestinationDocumentIds": { }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "González, . The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons. Proc. Natl Acad. Sci. USA. 2005; 103: 3834-3839", "externalDestinationDocumentIds": { }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Wilson, K.J., Huges, S.G., Jefferson, R.A., Gallagher, S.R.. The Escherichia coli gus operon, induction and expression of the gus operon in E.coli and the occurrence and use of GUS in other bacteria. Gus Protocols, Using the Gus Gene as a Reporter of Gene Expression. 1992; Vol. 1: 7-23", "externalDestinationDocumentIds": { }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Corvera, A., Promé, D., Promé, J.C., Martínez-Romero, E., Romero, D.. The nolL gene from Rhizobium etli determines nodulation efficiency by mediating the acetylation of the fucosyl residue in the nodulation factor. Mol. Plant\u2013Microbe Interact.. 1999; 12: 236-246", "externalDestinationDocumentIds": { }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Sambrook, J., Fritsch, E.F., Maniatis, T.. Molecular Cloning. A Laboratory Manual. 1989", "externalDestinationDocumentIds": { }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Ozoline, O.N., Deev, A.A., Arkhipova, M.V.. Non-canonical sequence elements in the promoter structure. Cluster analysis of promoters recognized by Escherichia coli RNA polymerase. Nucleic Acids Res.. 1997; 25: 4703-4709", "externalDestinationDocumentIds": {"pmid": "9365247" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Luka, S., Patriarca, E.J., Riccio, A., Iaccarino, M., Defez, R.. Cloning of the rpoD analog from Rhizobium etli: sigA of R.etli is growth phase regulated. J. Bacteriol.. 1996; 178: 7138-7143", "externalDestinationDocumentIds": {"pmid": "8955394" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Bravo, A., Mora, J.. Ammonium assimilation in Rhizobium phaseoli by the glutamine synthetase-glutamate synthase pathway. J. Bacteriol.. 1988; 170: 980-984", "externalDestinationDocumentIds": {"pmid": "2892829" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Venkova-Canova, T., Soberón, N.E., Ramírez-Romero, M.A., Cevallos, Miguel A.. Two discrete elements are required for the replication of repABC plasmid: an antisense RNA and a stem\u2013loop structure. Mol. Microbiol.. 2004; 54: 1431-1444", "externalDestinationDocumentIds": {"pmid": "15554980" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Hertz, G.Z., Stormo, G.D.. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics. 1999; 15: 563-577", "externalDestinationDocumentIds": {"pmid": "10487864" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Sugimoto, N., Nakano, S., Yoneyama, M., Honda, K.. Improved thermodynamic parameters and helix initiation factors to predict stability of DNA duplexes. Nucleic Acids Res.. 1996; 24: 4501-4505", "externalDestinationDocumentIds": {"pmid": "8948641" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Peck, M.C., Gaal, T., Fisher, R.F., Gourse, R.L., Long, S.R.. The RNA polymerase alpha subunit from Shinorhizobium meliloti can assemble with RNA polymerase subunits from Escherichia coli and function in basal and activated transcription both in vivo and in vitro. J. Bacteriol.. 2002; 184: 3808-3814", "externalDestinationDocumentIds": {"pmid": "12081950" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Wosten, M.M.S.M.. Eubacterial sigma-factors. FEMS Microbiol. Rev.. 1998; 22: 127-150", "externalDestinationDocumentIds": {"pmid": "9818380" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Lonetto, M., Gribskov, M., Gross, C.A.. The σ70 family: sequence conservation and evolutionary relationships. J. Bacteriol.. 1992; 174: 3843-3849", "externalDestinationDocumentIds": {"pmid": "1597408" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Patriarca, E.J., Riccio, A., Taté, R., Colonna-Romano, S., Iaccarino, M., Defez, R.. The ntrBC genes of Rhizobium leguminosarum are part of a complex operon subject to negative regulation. Mol Microbiol.. 1993; 9: 569-577", "externalDestinationDocumentIds": {"pmid": "8412703" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Richard, C.L., Tandon, A., Kranz, R.G.. Rhodobacter capsulatus nifA1 promoter: High-GC−10 regions in high-GC bacteria and basis for their transcription. J. Bacteriol.. 2004; 186: 740-749", "externalDestinationDocumentIds": {"pmid": "14729700" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Malakooti, J., Wang, S.P., Ely, B.. A consensus promoter sequence for Caulobacter crescentus genes involved in biosynthetic and housekeeping functions. J. Bacteriol.. 1995; 177: 4372-4376", "externalDestinationDocumentIds": {"pmid": "7543475" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Murakami, K.S., Masuda, S., Darst, S.A.. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution. Science. 2002; 296: 1280-1284", "externalDestinationDocumentIds": {"pmid": "12016306" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Wu, J., Ohta, N., Benson, A.K., Ninfa, A.J., Newton, A.. Purification, characterization, and reconstitution of DNA-dependent RNA polymerases from Caulobacter crescentus. J. Biol. Chem.. 1997; 272: 21558-21564", "externalDestinationDocumentIds": {"pmid": "9261176" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Maeda, H., Fujita, N., Ishihama, A.. Competition among seven Escherichia coli sigma subunits: relative binding affinities to the core RNA polymerase. Nucleic Acids Res.. 2000; 28: 3497-3503", "externalDestinationDocumentIds": {"pmid": "10982868" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Lisser, S., Margalit, H.. Determination of common structural features in Escherichia coli promoters by computer analysis. Eur. J. Biochem.. 1994; 223: 823-830", "externalDestinationDocumentIds": {"pmid": "8055959" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Helmann, J.D.. Compilation and analysis of Bacillus subtilis σA-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res.. 1995; 23: 2351-2360", "externalDestinationDocumentIds": {"pmid": "7630711" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Mitchell, J.E., Zheng, D., Busby, S.J., Minchin, S.D.. Identification and analysis of \u2018extended \u201310\u2019 promoters in Escherichia coli. Nucleic Acids Res.. 2003; 31: 4689-4695", "externalDestinationDocumentIds": {"pmid": "12907708" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Noel, K.D., Sánchez, A., Fernández, L., Leemans, J., Cevallos, M.A.. Rhizobium phaseoli symbiotic mutants with transposon Tn5 insertions. J. Bacteriol.. 1984; 158: 148-155", "externalDestinationDocumentIds": {"pmid": "6325385" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Morrison, D.A., Jaurin, B.. Sttreptococcus pneumoniae possesses canonical Escherichia coli (sigma 70) promoters. Mol. Microbiol.. 1990; 4: 1143-1152", "externalDestinationDocumentIds": {"pmid": "2233251" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Vogel, J., Axmann, I.M., Herzel, H., Hess, W.R.. Experimental and computer analysis of transcriptional start sites in the cyanobacterium Prochlorococcus MED4. Nucleic Acids Res.. 2003; 31: 2890-2899", "externalDestinationDocumentIds": {"pmid": "12771216" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Mittenhuber, G.. An inventory of genes encoding RNA polymerase sigma factors in 31 completely sequenced eubacterial genomes. J. Mol. Microbiol. Biotechnol.. 2002; 4: 77-91", "externalDestinationDocumentIds": {"pmid": "11763973" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Burr, T., Mitchell, J., Kolb, A., Minchin, S., Busby, S.. DNA sequence elements located immediately upstream of the −10 hexamer in Escherichia coli promoters: a systematic study. Nucleic Acids Res.. 2000; 28: 1864-1870", "externalDestinationDocumentIds": {"pmid": "10756184" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Pedersen, A.G., Jensen, L.J., Brunak, S., Staerfeldt, H.H., Ussery, D.W.. A DNA structural atlas for Escherichia coli. J. Mol. Biol.. 2000; 299: 907-930", "externalDestinationDocumentIds": {"pmid": "10843847" }, "destinationDocumentId": null}

{"sourceDocumentId": "50|od_______908::e2dc735fdbbeec38013f265ee187af06", "rawText": "Barne, K.A., Bown, J., Busby, S.J., Minchin, S.D.. Region 2.5 of the Escherichia coli RNA polymerase sigma70 subunit is responsible for the recognition of the \u2018extended-10\u2019 motif at promoters. EMBO J.. 1997; 16: 4034-4040", "externalDestinationDocumentIds": {"pmid": "9233812" }, "destinationDocumentId": null}