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Select item 5216471.

Comparative genomics of the FtsK–HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging

Lakshminarayan M. Iyer, Kira S. Makarova, Eugene V. Koonin, L. Aravind

Nucleic Acids Res. 2004; 32(17): 5260–5279. Published online 2004 Oct 5. doi: 10.1093/nar/gkh828

PMCID:: PMC521647

Abstract Article PDF–4.6M

Select item 5209012.

PCR-Based Identification of Hyperthermophilic Archaea of the Family Thermococcaceae

Galina B. Slobodkina, Nikolai A. Chernyh, Alexander I. Slobodkin, Irina V. Subbotina, Elizaveta A. Bonch-Osmolovskaya, Alexander V. Lebedinsky

Appl Environ Microbiol. 2004 Sep; 70(9): 5701–5703. doi: 10.1128/AEM.70.9.5701-5703.2004

PMCID:: PMC520901

Abstract Article PDF–81K

Select item 5165903.

Modified Pathway To Synthesize Ribulose 1,5-Bisphosphate in Methanogenic Archaea

Michael W. Finn, F. Robert Tabita

J Bacteriol. 2004 Oct; 186(19): 6360–6366. doi: 10.1128/JB.186.19.6360-6366.2004

PMCID:: PMC516590

Abstract Article PDF–157K

Select item 5164844.

Identification and characterization of phosphoseryl-tRNA^[Ser]Sec kinase

Bradley A. Carlson, Xue-Ming Xu, Gregory V. Kryukov, Mahadev Rao, Marla J. Berry, Vadim N. Gladyshev, Dolph L. Hatfield

Proc Natl Acad Sci U S A. 2004 Aug 31; 101(35): 12848–12853. Published online 2004 Aug 18. doi: 10.1073/pnas.0402636101

PMCID:: PMC516484

Abstract Article PDF–551K

Select item 5144505.

Thermophilic ATP synthase has a decamer c-ring: Indication of noninteger 10:3 H⁺/ATP ratio and permissive elastic coupling

Noriyo Mitome, Toshiharu Suzuki, Shigehiko Hayashi, Masasuke Yoshida

Proc Natl Acad Sci U S A. 2004 Aug 17; 101(33): 12159–12164. Published online 2004 Aug 9. doi: 10.1073/pnas.0403545101

PMCID:: PMC514450

Abstract Article PDF–618K

Select item 4908716.

Isoleucine Biosynthesis in Leptospira interrogans Serotype lai Strain 56601 Proceeds via a Threonine-Independent Pathway

Hai Xu, Yuzhen Zhang, Xiaokui Guo, Shuangxi Ren, Andreas A. Staempfli, Juishen Chiao, Weihong Jiang, Guoping Zhao

J Bacteriol. 2004 Aug; 186(16): 5400–5409. doi: 10.1128/JB.186.16.5400-5409.2004

PMCID:: PMC490871

Abstract Article PDF–212K

Select item 4516287.

The Phosphoenolpyruvate Carboxylase from Methanothermobacter thermautotrophicus Has a Novel Structure

Hiten M. Patel, Jessica L. Kraszewski, Biswarup Mukhopadhyay

J Bacteriol. 2004 Aug; 186(15): 5129–5137. doi: 10.1128/JB.186.15.5129-5137.2004

PMCID:: PMC451628

Abstract Article PDF–2.0M

Select item 4216278.

Presence of a Novel Phosphopentomutase and a 2-Deoxyribose 5-Phosphate Aldolase Reveals a Metabolic Link between Pentoses and Central Carbon Metabolism in the Hyperthermophilic Archaeon Thermococcus kodakaraensis

Naeem Rashid, Hiroyuki Imanaka, Toshiaki Fukui, Haruyuki Atomi, Tadayuki Imanaka

J Bacteriol. 2004 Jul; 186(13): 4185–4191. doi: 10.1128/JB.186.13.4185-4191.2004

PMCID:: PMC421627

Abstract Article PDF–121K

Select item 4037639.

Functionality of System Components: Conservation of Protein Function in Protein Feature Space

Lars Juhl Jensen, David W. Ussery, Søren Brunak

Genome Res. 2003 Nov; 13(11): 2444–2449. doi: 10.1101/gr.1190803

PMCID:: PMC403763

Abstract Article PDF–400K

Select item 40375410.

Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii

Neil F.W. Saunders, Torsten Thomas, Paul M.G. Curmi, John S. Mattick, Elizabeth Kuczek, Rob Slade, John Davis, Peter D. Franzmann, David Boone, Karl Rusterholtz, Robert Feldman, Chris Gates, Shellie Bench, Kevin Sowers, Kristen Kadner, Andrea Aerts, Paramvir Dehal, Chris Detter, Tijana Glavina, Susan Lucas, Paul Richardson, Frank Larimer, Loren Hauser, Miriam Land, Ricardo Cavicchioli

Genome Res. 2003 Jul; 13(7): 1580–1588. doi: 10.1101/gr.1180903

PMCID:: PMC403754

Abstract Article PDF–241K

Select item 39590511.

A domain for editing by an archaebacterial tRNA synthetase

Kirk Beebe, Eve Merriman, Lluis Ribas de Pouplana, Paul Schimmel

Proc Natl Acad Sci U S A. 2004 Apr 20; 101(16): 5958–5963. Published online 2004 Apr 12. doi: 10.1073/pnas.0401530101

PMCID:: PMC395905

Abstract Article PDF–641K

Select item 39577012.

Visualization of the phylogenetic content of five genomes using dekapentagonal maps

Olga Zhaxybayeva, Lutz Hamel, Jason Raymond, J Peter Gogarten

Genome Biol. 2004; 5(3): R20. Published online 2004 Feb 16. doi: 10.1186/gb-2004-5-3-r20

PMCID:: PMC395770

Abstract Article PDF–544K

Select item 39576713.

Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox

Céline Brochier, Patrick Forterre, Simonetta Gribaldo

Genome Biol. 2004; 5(3): R17. Published online 2004 Feb 26. doi: 10.1186/gb-2004-5-3-r17

PMCID:: PMC395767

Abstract Article PDF–294K

Select item 39575114.

A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

Eugene V Koonin, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Dmitri M Krylov, Kira S Makarova, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Sridhar Rao, Igor B Rogozin, Sergei Smirnov, Alexander V Sorokin, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale

Genome Biol. 2004; 5(2): R7. Published online 2004 Jan 15. doi: 10.1186/gb-2004-5-2-r7

PMCID:: PMC395751

Abstract Article PDF–523K

Select item 39431415.

SIGI: score-based identification of genomic islands

Rainer Merkl

BMC Bioinformatics. 2004; 5: 22. Published online 2004 Mar 3. doi: 10.1186/1471-2105-5-22

PMCID:: PMC394314

Abstract Article PDF–588K

Select item 39027516.

A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea

F. Constantinesco, P. Forterre, E. V. Koonin, L. Aravind, C. Elie

Nucleic Acids Res. 2004; 32(4): 1439–1447. Published online 2004 Feb 27. doi: 10.1093/nar/gkh283

PMCID:: PMC390275

Abstract Article PDF–858K

Select item 38309417.

Spatial Distribution of Marine Crenarchaeota Group I in the Vicinity of Deep-Sea Hydrothermal Systems

Ken Takai, Hanako Oida, Yohey Suzuki, Hisako Hirayama, Satoshi Nakagawa, Takuro Nunoura, Fumio Inagaki, Kenneth H. Nealson, Koki Horikoshi

Appl Environ Microbiol. 2004 Apr; 70(4): 2404–2413. doi: 10.1128/AEM.70.4.2404-2413.2004

PMCID:: PMC383094

Abstract Article PDF–660K

Select item 37439118.

Reconstruction of the Central Carbohydrate Metabolism of Thermoproteus tenax by Use of Genomic and Biochemical Data

Bettina Siebers, Britta Tjaden, Klaus Michalke, Christine Dörr, Hatim Ahmed, Melanie Zaparty, Paul Gordon, Christoph W. Sensen, Arne Zibat, Hans-Peter Klenk, Stephan C. Schuster, Reinhard Hensel

J Bacteriol. 2004 Apr; 186(7): 2179–2194. doi: 10.1128/JB.186.7.2179-2194.2004

PMCID:: PMC374391

Abstract Article PDF–883K

Select item 36832719.

Spatial Heterogeneity of Crenarchaeal Assemblages within Mesophilic Soil Ecosystems as Revealed by PCR-Single-Stranded Conformation Polymorphism Profiling

Marek K. Sliwinski, Robert M. Goodman

Appl Environ Microbiol. 2004 Mar; 70(3): 1811–1820. doi: 10.1128/AEM.70.3.1811-1820.2004

PMCID:: PMC368327

Abstract Article PDF–1.0M

Select item 36210920.

Lessons from the Genome Sequence of Neurospora crassa: Tracing the Path from Genomic Blueprint to Multicellular Organism

Katherine A. Borkovich, Lisa A. Alex, Oded Yarden, Michael Freitag, Gloria E. Turner, Nick D. Read, Stephan Seiler, Deborah Bell-Pedersen, John Paietta, Nora Plesofsky, Michael Plamann, Marta Goodrich-Tanrikulu, Ulrich Schulte, Gertrud Mannhaupt, Frank E. Nargang, Alan Radford, Claude Selitrennikoff, James E. Galagan, Jay C. Dunlap, Jennifer J. Loros, David Catcheside, Hirokazu Inoue, Rodolfo Aramayo, Michael Polymenis, Eric U. Selker, Matthew S. Sachs, George A. Marzluf, Ian Paulsen, Rowland Davis, Daniel J. Ebbole, Alex Zelter, Eric R. Kalkman, Rebecca O'Rourke, Frederick Bowring, Jane Yeadon, Chizu Ishii, Keiichiro Suzuki, Wataru Sakai, Robert Pratt

Microbiol Mol Biol Rev. 2004 Mar; 68(1): 1–108. doi: 10.1128/MMBR.68.1.1-108.2004

PMCID:: PMC362109

Abstract Article PDF–6.4M

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