TY - JOUR AU - Raetz, C. R. H. PY - 1990 DA - 1990// TI - Biochemistry of endotoxins JO - Annual Review of Biochemistry VL - 59 UR - https://doi.org/10.1146/annurev.bi.59.070190.001021 DO - 10.1146/annurev.bi.59.070190.001021 ID - Raetz1990 ER - TY - JOUR AU - Raetz, C. R. H. AU - Whitfield, C. PY - 2002 DA - 2002// TI - Lipopolysaccharide endotoxins JO - Annual Review of Biochemistry VL - 71 UR - https://doi.org/10.1146/annurev.biochem.71.110601.135414 DO - 10.1146/annurev.biochem.71.110601.135414 ID - Raetz2002 ER - TY - JOUR AU - Bartholomew, J. W. AU - Mittwer, T. PY - 1952 DA - 1952// TI - The Gram stain JO - Bacteriological reviews VL - 16 ID - Bartholomew1952 ER - TY - JOUR AU - Woese, C. R. AU - Fox, G. E. PY - 1977 DA - 1977// TI - Phylogenetic structure of the prokaryotic domain: the primary kingdoms JO - Proceedings of the National Academy of Sciences, USA VL - 74 UR - https://doi.org/10.1073/pnas.74.11.5088 DO - 10.1073/pnas.74.11.5088 ID - Woese1977 ER - TY - CHAP AU - Ludwig, W. AU - Klenk, H. P. ED - Boon, D. R. ED - Castenholz, R. W. PY - 2001 DA - 2001// TI - Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematics BT - Bergey's Manual of Systematic Bacteriology PB - Springer CY - New York, NY UR - https://doi.org/10.1007/978-0-387-21609-6_8 DO - 10.1007/978-0-387-21609-6_8 ID - Ludwig2001 ER - TY - JOUR AU - Rappé, M. S. AU - Giovannoni, S. J. PY - 2003 DA - 2003// TI - The uncultured microbial majority JO - Annu Rev Microbiol VL - 57 UR - https://doi.org/10.1146/annurev.micro.57.030502.090759 DO - 10.1146/annurev.micro.57.030502.090759 ID - Rappé2003 ER - TY - STD TI - Garrity GM, Brenner DJ, Krieg NR, Staley JR, (eds.): Bergey's Manual of Systematic Bacteriology. The Proteobacteria. 2005, New York, NY: Springer, 2 ID - ref7 ER - TY - JOUR AU - Barb, A. W. AU - McClerren, A. L. AU - Snehelatha, K. AU - Reynolds, C. M. AU - Zhou, P. AU - Raetz, C. R. PY - 2007 DA - 2007// TI - Inhibition of lipid A biosynthesis as the primary mechanism of CHIR-090 antibiotic activity in Escherichia coli JO - Biochemistry VL - 46 UR - https://doi.org/10.1021/bi6025165 DO - 10.1021/bi6025165 ID - Barb2007 ER - TY - JOUR AU - Onishi, H. R. AU - Pelak, B. A. AU - Gerckens, L. S. AU - Silver, L. L. AU - Kahan, F. M. AU - Chen, M. H. AU - Patchett, A. A. AU - Galloway, S. M. AU - Hyland, S. A. AU - Anderson, M. S. PY - 1996 DA - 1996// TI - Antibacterial agents that inhibit lipid A biosynthesis JO - Science VL - 274 UR - https://doi.org/10.1126/science.274.5289.980 DO - 10.1126/science.274.5289.980 ID - Onishi1996 ER - TY - JOUR AU - Williams, A. H. AU - Raetz, C. R. H. PY - 2007 DA - 2007// TI - Structural basis for the acyl chain selectivity and mechanism of UDP-N-acetylglucosamine acyltransferase JO - Proceedings of the National Academy of Sciences, USA VL - 104 UR - https://doi.org/10.1073/pnas.0705833104 DO - 10.1073/pnas.0705833104 ID - Williams2007 ER - TY - JOUR AU - Bartling, C. M. AU - Raetz, C. R. H. PY - 2009 DA - 2009// TI - Crystal structure and acyl chain selectivity of Escherichia coli LpxD, the N-acyltransferase of lipid A biosynthesis JO - Biochemistry VL - 48 UR - https://doi.org/10.1021/bi901025v DO - 10.1021/bi901025v ID - Bartling2009 ER - TY - JOUR AU - Babinski, K. J. AU - Ribeiro, A. A. AU - Raetz, C. R. H. PY - 2002 DA - 2002// TI - The Escherichia coli gene encoding the UDP-2,3-diacylglucosamine pyrophosphatase of lipid A biosynthesis JO - Journal of Biological Chemistry VL - 277 UR - https://doi.org/10.1074/jbc.M204067200 DO - 10.1074/jbc.M204067200 ID - Babinski2002 ER - TY - JOUR AU - Babinski, K. J. AU - Kanjilal, S. J. AU - Raetz, C. R. H. PY - 2002 DA - 2002// TI - Accumulation of the lipid A precursor UDP-2,3-diacylglucosamine in an Escherichia coli mutant lacking the lpxH gene JO - Journal of Biological Chemistry VL - 277 UR - https://doi.org/10.1074/jbc.M204068200 DO - 10.1074/jbc.M204068200 ID - Babinski2002 ER - TY - CHAP AU - Finn, R. D. AU - Mistry, J. AU - Tate, J. AU - Coggill, P. AU - Heger, A. AU - Pollington, J. E. AU - Gavin, O. L. AU - Gunasekaran, P. AU - Ceric, G. AU - Forslund, K. PY - 2009 DA - 2009// TI - The Pfam protein families database BT - Nucleic Acids Res ID - Finn2009 ER - TY - JOUR AU - Zhuo, S. AU - Clemens, J. C. AU - Stone, R. L. AU - Dixon, J. E. PY - 1994 DA - 1994// TI - Mutational analysis of a Ser/Thr phosphatase JO - Journal of Biological Chemistry VL - 269 ID - Zhuo1994 ER - TY - JOUR AU - Tyagi, R. AU - Shenoy, A. R. AU - Visweswariah, S. S. PY - 2009 DA - 2009// TI - Characterization of an evolutionarily conserved metallophosphoesterase that is expressed in the fetal brain and associated with the WAGR syndrome JO - Journal of Biological Chemistry VL - 284 UR - https://doi.org/10.1074/jbc.M805996200 DO - 10.1074/jbc.M805996200 ID - Tyagi2009 ER - TY - JOUR AU - Miller, D. J. AU - Shuvalova, L. AU - Evdokimova, E. AU - Savchenko, A. AU - Yakunin, A. F. AU - Anderson, W. F. PY - 2007 DA - 2007// TI - Structural and biochemical characterization of a novel Mn2+-dependent phosphodiesterase encoded by the yfcE gene JO - Protein Science VL - 16 UR - https://doi.org/10.1110/ps.072764907 DO - 10.1110/ps.072764907 ID - Miller2007 ER - TY - JOUR AU - Shenoy, A. R. AU - Capuder, M. AU - Draškovič, P. AU - Lamba, D. AU - Visweswariah, S. S. AU - Podobnik, M. PY - 2007 DA - 2007// TI - Structural and biochemical analysis of the Rv0805 cyclic nucleotide phosphodiesterase from Mycobacterium tuberculosis JO - Journal of Molecular Biology VL - 365 UR - https://doi.org/10.1016/j.jmb.2006.10.005 DO - 10.1016/j.jmb.2006.10.005 ID - Shenoy2007 ER - TY - JOUR AU - Metzger, L. E. AU - Raetz, C. R. PY - 2010 DA - 2010// TI - An alternative route for UDP-diacylglucosamine hydrolysis in bacterial lipid A biosynthesis JO - Biochemistry VL - 49 UR - https://doi.org/10.1021/bi1008744 DO - 10.1021/bi1008744 ID - Metzger2010 ER - TY - JOUR AU - Geurtsen, J. AU - Angevaare, E. AU - Janssen, M. AU - Hamstra, H. J. AU - ten Hove, J. AU - de Haan, A. AU - Kuipers, B. AU - Tommassen, J. AU - van der Ley, P. PY - 2007 DA - 2007// TI - A novel secondary acyl chain in the lipopolysaccharide of Bordetella pertussis required for efficient infection of human macrophages JO - J Biol Chem VL - 282 UR - https://doi.org/10.1074/jbc.M706391200 DO - 10.1074/jbc.M706391200 ID - Geurtsen2007 ER - TY - JOUR AU - Raetz, C. R. AU - Guan, Z. AU - Ingram, B. O. AU - Six, D. A. AU - Song, F. AU - Wang, X. AU - Zhao, J. PY - 2009 DA - 2009// TI - Discovery of new biosynthetic pathways: the lipid A story JO - J Lipid Res VL - 50 ID - Raetz2009 ER - TY - JOUR AU - Clementz, T. AU - Zhou, Z. AU - Raetz, C. R. H. PY - 1997 DA - 1997// TI - Function of the Escherichia coli msbB gene, a multicopy suppressor of htrB knockouts, in the acylation of lipid A JO - Journal of Biological Chemistry VL - 272 ID - Clementz1997 ER - TY - JOUR AU - Six, D. A. AU - Carty, S. M. AU - Guan, Z. AU - Raetz, C. R. PY - 2008 DA - 2008// TI - Purification and mutagenesis of LpxL, the lauroyltransferase of Escherichia coli lipid A biosynthesis JO - Biochemistry VL - 47 UR - https://doi.org/10.1021/bi800873n DO - 10.1021/bi800873n ID - Six2008 ER - TY - JOUR AU - Karow, M. AU - Georgopoulos, C. PY - 1992 DA - 1992// TI - Isolation and characterization of the Escherichia coli msbB gene, a multicopy suppressor of null mutations in the high-temperature requirement gene htrB JO - Journal of Bacteriology VL - 174 ID - Karow1992 ER - TY - JOUR AU - Karow, M. AU - Fayet, O. AU - Cegielska, A. AU - Ziegelhoffer, T. AU - Georgopoulos, C. PY - 1991 DA - 1991// TI - Isolation and characterization of the Escherichia coli htrB gene, whose product is essential for bacterial viability above 33 degrees C in rich media JO - J Bacteriol VL - 173 ID - Karow1991 ER - TY - JOUR AU - Vorachek-Warren, M. K. AU - Ramirez, S. AU - Cotter, R. J. AU - Raetz, C. R. PY - 2002 DA - 2002// TI - A triple mutant of Escherichia coli lacking secondary acyl chains on lipid A JO - J Biol Chem VL - 277 UR - https://doi.org/10.1074/jbc.M200409200 DO - 10.1074/jbc.M200409200 ID - Vorachek-Warren2002 ER - TY - JOUR AU - Lee, N. G. AU - Sunshine, M. G. AU - Engstrom, J. J. AU - Gibson, B. W. AU - Apicella, M. A. PY - 1995 DA - 1995// TI - Mutation of the htrB locus of Haemophilus influenzae nontypable strain 2019 is associated with modifications of lipid A and phosphorylation of the lipo-oligosaccharide JO - Journal of Biological Chemistry VL - 270 UR - https://doi.org/10.1074/jbc.270.45.27151 DO - 10.1074/jbc.270.45.27151 ID - Lee1995 ER - TY - JOUR AU - Carty, S. M. AU - Sreekumar, K. R. AU - Raetz, C. R. PY - 1999 DA - 1999// TI - Effect of cold shock on lipid A biosynthesis in Escherichia coli. Induction At 12 degrees C of an acyltransferase specific for palmitoleoyl-acyl carrier protein JO - J Biol Chem VL - 274 UR - https://doi.org/10.1074/jbc.274.14.9677 DO - 10.1074/jbc.274.14.9677 ID - Carty1999 ER - TY - JOUR AU - Montminy, S. W. AU - Khan, N. AU - McGrath, S. AU - Walkowicz, M. J. AU - Sharp, F. AU - Conlon, J. E. AU - Fukase, K. AU - Kusumoto, S. AU - Sweet, C. AU - Miyake, K. PY - 2006 DA - 2006// TI - Virulence factors of Yersinia pestis are overcome by a strong lipopolysaccharide response JO - Nat Immunol VL - 7 UR - https://doi.org/10.1038/ni1386 DO - 10.1038/ni1386 ID - Montminy2006 ER - TY - JOUR AU - Keleti, G. AU - Sykora, J. L. PY - 1982 DA - 1982// TI - Production and properties of cyanobacterial endotoxins JO - Applied and Environmental Microbiology VL - 43 ID - Keleti1982 ER - TY - JOUR AU - Weckesser, J. AU - Jurgens, U. J. PY - 1988 DA - 1988// TI - Cell walls and external layers JO - Methods in Enzymology VL - 67 UR - https://doi.org/10.1016/0076-6879(88)67018-2 DO - 10.1016/0076-6879(88)67018-2 ID - Weckesser1988 ER - TY - JOUR AU - Trent, S. M. PY - 2004 DA - 2004// TI - Biosynthesis, transport, and modification of lipid A JO - Biochemistry and Cell Biology VL - 82 UR - https://doi.org/10.1139/o03-070 DO - 10.1139/o03-070 ID - Trent2004 ER - TY - JOUR AU - Snyder, S. D. AU - Brahamsha, B. AU - Azadi, P. AU - Palenki, B. PY - 2009 DA - 2009// TI - Structure of compositionally simple lipopolysaccharide from marine Synechococcus JO - Journal of Bacteriology VL - 191 UR - https://doi.org/10.1128/JB.00121-09 DO - 10.1128/JB.00121-09 ID - Snyder2009 ER - TY - JOUR AU - Stewart, I. AU - Schluter, P. J. AU - Shaw, G. R. PY - 2006 DA - 2006// TI - Cyanobacterial lipopolysaccharides and human health - a review JO - Environmental Health VL - 5 UR - https://doi.org/10.1186/1476-069X-5-7 DO - 10.1186/1476-069X-5-7 ID - Stewart2006 ER - TY - JOUR AU - Demerec, M. AU - Ozeki, H. PY - 1959 DA - 1959// TI - Tests for Allelism among Auxotrophs of Salmonella Typhimurium JO - Genetics VL - 44 ID - Demerec1959 ER - TY - JOUR AU - Itoh, T. AU - Takemoto, K. AU - Mori, H. AU - Gojobori, T. PY - 1999 DA - 1999// TI - Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes JO - Mol Biol Evol VL - 16 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026114 DO - 10.1093/oxfordjournals.molbev.a026114 ID - Itoh1999 ER - TY - JOUR AU - Overbeek, R. AU - Fonstein, M. AU - D'Souza, M. AU - Pusch, G. D. AU - Maltsev, N. PY - 1999 DA - 1999// TI - The use of gene clusters to infer functional coupling JO - Proc Natl Acad Sci USA VL - 96 UR - https://doi.org/10.1073/pnas.96.6.2896 DO - 10.1073/pnas.96.6.2896 ID - Overbeek1999 ER - TY - JOUR AU - Mohan, S. AU - Kelly, T. M. AU - Eveland, S. S. AU - Raetz, C. R. AU - Anderson, M. S. PY - 1994 DA - 1994// TI - An Escherichia coli gene (FabZ) encoding (3R)-hydroxymyristoyl acyl carrier protein dehydrase. Relation to fabA and suppression of mutations in lipid A biosynthesis JO - J Biol Chem VL - 269 ID - Mohan1994 ER - TY - JOUR AU - Brochier, C. AU - Bapteste, E. AU - Moreira, D. AU - Philippe, H. PY - 2002 DA - 2002// TI - Eubacterial phylogeny based on translational apparatus proteins JO - Trends in Genetics VL - 18 UR - https://doi.org/10.1016/S0168-9525(01)02522-7 DO - 10.1016/S0168-9525(01)02522-7 ID - Brochier2002 ER - TY - JOUR AU - Ciccarelli, F. D. AU - Doerks, T. AU - Mering, C. v. AU - Creevey, C. J. AU - Snel, B. AU - Bork, P. PY - 2006 DA - 2006// TI - Toward automatic reconstruction of a highly resolved tree of life JO - Science VL - 311 UR - https://doi.org/10.1126/science.1123061 DO - 10.1126/science.1123061 ID - Ciccarelli2006 ER - TY - JOUR AU - Battistuzzi, F. U. AU - Hedges, S. B. PY - 2009 DA - 2009// TI - A major clade of prokaryotes with ancient adaptations to life on land JO - Molecular Biology and Evolution VL - 26 UR - https://doi.org/10.1093/molbev/msn247 DO - 10.1093/molbev/msn247 ID - Battistuzzi2009 ER - TY - JOUR AU - Gao, B. AU - Mohan, R. AU - Gupta, R. S. PY - 2009 DA - 2009// TI - Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria JO - Int J Syst Evol Microbiol VL - 59 UR - https://doi.org/10.1099/ijs.0.002741-0 DO - 10.1099/ijs.0.002741-0 ID - Gao2009 ER - TY - JOUR AU - Lin, M. AU - Rikihisa, Y. PY - 2003 DA - 2003// TI - Ehrlichia chaffeensis and Anaplasma phagocytophilum lack genes for lipid A biosynthesis and incorporate cholesterol for their survival JO - Infect Immun VL - 71 UR - https://doi.org/10.1128/IAI.71.9.5324-5331.2003 DO - 10.1128/IAI.71.9.5324-5331.2003 ID - Lin2003 ER - TY - JOUR AU - Wu, M. AU - Sun, L. V. AU - Vamathevan, J. AU - Riegler, M. AU - Deboy, R. AU - Brownlie, J. C. AU - McGraw, E. A. AU - Martin, W. AU - Esser, C. AU - Ahmadinejad, N. PY - 2004 DA - 2004// TI - Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements JO - PLoS Biol VL - 2 UR - https://doi.org/10.1371/journal.pbio.0020069 DO - 10.1371/journal.pbio.0020069 ID - Wu2004 ER - TY - JOUR AU - Aderem, A. AU - Ulevitch, R. J. PY - 2000 DA - 2000// TI - Toll-like receptors in the induction of the innate immune response JO - Nature VL - 406 UR - https://doi.org/10.1038/35021228 DO - 10.1038/35021228 ID - Aderem2000 ER - TY - JOUR AU - Janssens, S. AU - Beyaert, R. PY - 2003 DA - 2003// TI - Role of Toll-like receptors in pathogen recognition JO - Clin Microbiol Rev VL - 16 UR - https://doi.org/10.1128/CMR.16.4.637-646.2003 DO - 10.1128/CMR.16.4.637-646.2003 ID - Janssens2003 ER - TY - JOUR AU - Beck, G. AU - Habicht, G. S. AU - Benach, J. L. AU - Coleman, J. L. PY - 1985 DA - 1985// TI - Chemical and biologic characterization of a lipopolysaccharide extracted from the Lyme disease spirochete (Borrelia burgdorferi) JO - Journal of Infectious Diseases VL - 152 UR - https://doi.org/10.1093/infdis/152.1.108 DO - 10.1093/infdis/152.1.108 ID - Beck1985 ER - TY - JOUR AU - Takayama, K. AU - Rothenberg, R. J. AU - Barbour, A. G. PY - 1987 DA - 1987// TI - Absence of lipopolysaccharide in the Lyme disease spirochete, Borrelia burgdorferi JO - Infection and Immunity VL - 55 ID - Takayama1987 ER - TY - JOUR AU - Dahle, U. R. AU - Tronstad, L. AU - Olsen, I. PY - 1996 DA - 1996// TI - 3-hydroxy fatty acids in a lipopolysaccharide-like material from Treponema denticola strain FM JO - Endodontics and Dental Traumatology VL - 12 UR - https://doi.org/10.1111/j.1600-9657.1996.tb00515.x DO - 10.1111/j.1600-9657.1996.tb00515.x ID - Dahle1996 ER - TY - JOUR AU - Schultz, C. P. AU - Wolf, V. AU - Lange, R. AU - Mertens, E. AU - Wecke, J. AU - Naumann, D. AU - Zähringer, U. PY - 1998 DA - 1998// TI - Evidence for a new yype of outer membrane lipid in oral spirochete Treponema denticola. Functioning permeation barrier without lipopolysaccharides JO - Journal of Biological Chemistry VL - 273 UR - https://doi.org/10.1074/jbc.273.25.15661 DO - 10.1074/jbc.273.25.15661 ID - Schultz1998 ER - TY - JOUR AU - Fraser, C. M. AU - Casjens, S. AU - Huang, W. M. AU - Sutton, G. G. AU - Clayton, R. AU - Lathigra, R. AU - White, O. AU - Ketchum, K. A. AU - Dodson, R. AU - Hickey, E. K. PY - 1997 DA - 1997// TI - Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi JO - Nature VL - 390 UR - https://doi.org/10.1038/37551 DO - 10.1038/37551 ID - Fraser1997 ER - TY - JOUR AU - Fraser, C. M. AU - Norris, S. J. AU - Weinstock, G. M. AU - White, O. AU - Sutton, G. G. AU - Dodson, R. AU - Gwinn, M. AU - Hickey, E. K. AU - Clayton, R. AU - Ketchum, K. A. PY - 1998 DA - 1998// TI - Complete genome sequence of Treponema pallidum, the syphilis spirochete JO - Science VL - 281 UR - https://doi.org/10.1126/science.281.5375.375 DO - 10.1126/science.281.5375.375 ID - Fraser1998 ER - TY - JOUR AU - Seshadri, R. AU - Myers, G. S. AU - Tettelin, H. AU - Eisen, J. A. AU - Heidelberg, J. F. AU - Dodson, R. J. AU - Davidsen, T. M. AU - DeBoy, R. T. AU - Fouts, D. E. AU - Haft, D. H. PY - 2004 DA - 2004// TI - Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0307639101 DO - 10.1073/pnas.0307639101 ID - Seshadri2004 ER - TY - JOUR AU - Bellgard, M. I. AU - Wanchanthuek, P. AU - La, T. AU - Ryan, K. AU - Moolhuijzen, P. AU - Albertyn, Z. AU - Shaban, B. AU - Motro, Y. AU - Dunn, D. S. AU - Schibeci, D. PY - 2009 DA - 2009// TI - Genome sequence of the pathogenic intestinal spirochete Brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine JO - PLoS One VL - 4 UR - https://doi.org/10.1371/journal.pone.0004641 DO - 10.1371/journal.pone.0004641 ID - Bellgard2009 ER - TY - JOUR AU - Ren, S. X. AU - Fu, G. AU - Jiang, X. G. AU - Zeng, R. AU - Miao, Y. G. AU - Xu, H. AU - Zhang, Y. X. AU - Xiong, H. AU - Lu, G. AU - Lu, L. F. PY - 2003 DA - 2003// TI - Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing JO - Nature VL - 422 UR - https://doi.org/10.1038/nature01597 DO - 10.1038/nature01597 ID - Ren2003 ER - TY - JOUR AU - Arp, D. J. AU - Stein, L. Y. PY - 2003 DA - 2003// TI - Metabolism of inorganic N compounds by ammonia-oxidizing bacteria JO - Critical Reviews in Biochemistry and Molecular Biology VL - 38 UR - https://doi.org/10.1080/10409230390267446 DO - 10.1080/10409230390267446 ID - Arp2003 ER - TY - JOUR AU - Chain, P. AU - Lamerdin, J. AU - Larimer, F. AU - Regala, W. AU - Lao, V. AU - Land, M. AU - Hauser, L. AU - Hooper, A. AU - Klotz, M. AU - Norton, J. PY - 2003 DA - 2003// TI - Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea JO - J Bacteriol VL - 185 UR - https://doi.org/10.1128/JB.185.9.2759-2773.2003 DO - 10.1128/JB.185.9.2759-2773.2003 ID - Chain2003 ER - TY - JOUR AU - Norton, J. M. AU - Klotz, M. G. AU - Stein, L. Y. AU - Arp, D. J. AU - Bottomley, P. J. AU - Chain, P. S. AU - Hauser, L. J. AU - Land, M. L. AU - Larimer, F. W. AU - Shin, M. W. PY - 2008 DA - 2008// TI - Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment JO - Appl Environ Microbiol VL - 74 UR - https://doi.org/10.1128/AEM.02722-07 DO - 10.1128/AEM.02722-07 ID - Norton2008 ER - TY - JOUR AU - Arp, D. J. AU - Chain, P. S. AU - Klotz, M. G. PY - 2007 DA - 2007// TI - The impact of genome analyses on our understanding of ammonia-oxidizing bacteria JO - Annu Rev Microbiol VL - 61 UR - https://doi.org/10.1146/annurev.micro.61.080706.093449 DO - 10.1146/annurev.micro.61.080706.093449 ID - Arp2007 ER - TY - JOUR AU - Raetz, C. R. AU - Reynolds, C. M. AU - Trent, M. S. AU - Bishop, R. E. PY - 2007 DA - 2007// TI - Lipid A modification systems in gram-negative bacteria JO - Annu Rev Biochem VL - 76 UR - https://doi.org/10.1146/annurev.biochem.76.010307.145803 DO - 10.1146/annurev.biochem.76.010307.145803 ID - Raetz2007 ER - TY - JOUR AU - Armstrong, M. T. AU - Theg, S. M. AU - Braun, N. AU - Wainwright, N. AU - Pardy, R. L. AU - Armstrong, P. B. PY - 2006 DA - 2006// TI - Histochemical evidence for lipid A (endotoxin) in eukaryote chloroplasts JO - FASEB J VL - 20 UR - https://doi.org/10.1096/fj.05-5484fje DO - 10.1096/fj.05-5484fje ID - Armstrong2006 ER - TY - STD TI - National Center for Biotechnology Information. [http://www.ncbi.nlm.nih.gov/] UR - http://www.ncbi.nlm.nih.gov/ ID - ref62 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schäffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Research VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Hughey, R. AU - Krogh, A. PY - 1996 DA - 1996// TI - Hidden Markov models for sequence analysis: extension and analysis of the basic method JO - Computer Applications in the Biosciences VL - 12 ID - Hughey1996 ER - TY - STD TI - Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, et al: InterPro: the integrative protein signature database. Nucleic Acids Res. 2009, D211-215. 10.1093/nar/gkn785. 37 Database ID - ref65 ER - TY - JOUR AU - Katoh, K. AU - Toh, H. PY - 2008 DA - 2008// TI - Recent developments in the MAFFT multiple sequence alignment program JO - Briefings in Bioinformatics VL - 9 UR - https://doi.org/10.1093/bib/bbn013 DO - 10.1093/bib/bbn013 ID - Katoh2008 ER - TY - JOUR AU - Eddy, S. R. PY - 2006 DA - 2006// TI - Computational analysis of RNAs JO - Cold Spring Harbor Symposia on Quantitative Biology VL - 71 UR - https://doi.org/10.1101/sqb.2006.71.003 DO - 10.1101/sqb.2006.71.003 ID - Eddy2006 ER - TY - JOUR AU - Stamatakis, A. PY - 2006 DA - 2006// TI - RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl446 DO - 10.1093/bioinformatics/btl446 ID - Stamatakis2006 ER - TY - JOUR AU - Baldauf, S. L. AU - Palmer, J. D. AU - Doolittle, F. W. PY - 1996 DA - 1996// TI - The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny JO - Proceedings of the National Academy of Sciences, USA VL - 93 UR - https://doi.org/10.1073/pnas.93.15.7749 DO - 10.1073/pnas.93.15.7749 ID - Baldauf1996 ER - TY - JOUR AU - Fitz-Gibbon, S. T. AU - House, C. H. PY - 1999 DA - 1999// TI - Whole genome-based phylogenetic analysis of free-living microorganisms JO - Nucleic Acids Research VL - 27 UR - https://doi.org/10.1093/nar/27.21.4218 DO - 10.1093/nar/27.21.4218 ID - Fitz-Gibbon1999 ER - TY - JOUR AU - Gupta, R. S. PY - 2000 DA - 2000// TI - The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes JO - FEMS Microbiology Reviews VL - 24 UR - https://doi.org/10.1111/j.1574-6976.2000.tb00547.x DO - 10.1111/j.1574-6976.2000.tb00547.x ID - Gupta2000 ER - TY - JOUR AU - Lake, J. A. AU - Skophammer, R. G. AU - Herbold, C. W. AU - Servin, J. A. PY - 2009 DA - 2009// TI - Genome beginnings: rooting the tree of life JO - Philos Trans R Soc Lond B Biol Sci VL - 364 UR - https://doi.org/10.1098/rstb.2009.0035 DO - 10.1098/rstb.2009.0035 ID - Lake2009 ER - TY - JOUR AU - Crooks, G. E. AU - Hon, G. AU - Chandonia, J. M. AU - Brenner, S. E. PY - 2004 DA - 2004// TI - WebLogo: a sequence logo generator JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.849004 DO - 10.1101/gr.849004 ID - Crooks2004 ER - TY - JOUR AU - Schneider, T. D. AU - Stephens, R. M. PY - 1990 DA - 1990// TI - Sequence logos: a new way to display consensus sequences JO - Nucleic Acids Res VL - 18 UR - https://doi.org/10.1093/nar/18.20.6097 DO - 10.1093/nar/18.20.6097 ID - Schneider1990 ER - TY - STD TI - WebLogo Web server. [http://weblogo.berkeley.edu/] UR - http://weblogo.berkeley.edu/ ID - ref75 ER - TY - JOUR AU - Arnold, K. AU - Bordoli, L. AU - Kopp, J. AU - Schwede, T. PY - 2006 DA - 2006// TI - The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/bti770 DO - 10.1093/bioinformatics/bti770 ID - Arnold2006 ER - TY - STD TI - SWISS-MODEL Web server. [http://swissmodel.expasy.org/] UR - http://swissmodel.expasy.org/ ID - ref77 ER - TY - JOUR AU - Berman, H. M. AU - Westbrook, J. AU - Feng, Z. AU - Gilliland, G. AU - Bhat, T. N. AU - Weissig, H. AU - Shindyalov, I. N. AU - Bourne, P. E. PY - 2000 DA - 2000// TI - The Protein Data Bank JO - Nucleic Acids Research VL - 28 UR - https://doi.org/10.1093/nar/28.1.235 DO - 10.1093/nar/28.1.235 ID - Berman2000 ER - TY - CHAP AU - DeLano, W. L. PY - 2002 DA - 2002// BT - The PyMOL Molecular Graphics System PB - DeLano Scientific CY - San Carlos, CA ID - DeLano2002 ER - TY - JOUR AU - Tarbouriech, N. AU - Buisson, M. AU - Seigneurin, J. M. AU - Cusack, S. AU - Burmeister, W. P. PY - 2005 DA - 2005// TI - The monomeric dUTPase from Epstein-Barr virus mimics trimeric dUTPases JO - Structure VL - 13 UR - https://doi.org/10.1016/j.str.2005.06.009 DO - 10.1016/j.str.2005.06.009 ID - Tarbouriech2005 ER - TY - JOUR AU - Homma, K. AU - Moriyama, H. PY - 2009 DA - 2009// TI - Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase JO - Acta Crystallogr Sect F Struct Biol Cryst Commun VL - 65 UR - https://doi.org/10.1107/S1744309109034459 DO - 10.1107/S1744309109034459 ID - Homma2009 ER - TY - JOUR AU - Németh-Pongrácz, V. AU - Barabas, O. AU - Fuxreiter, M. AU - Simon, I. AU - Pichova, I. AU - Rumlova, M. AU - Zabranska, H. AU - Svergun, D. AU - Petoukhov, M. AU - Harmat, V. PY - 2007 DA - 2007// TI - Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkl1074 DO - 10.1093/nar/gkl1074 ID - Németh-Pongrácz2007 ER -