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  • 1
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    tRNA reorientation defines Dus enzyme specificity [Biochemistry] (2015)
    National Academy of Sciences
    Details
    Publication Date: 2015-05-13
    Description: The reduction of specific uridines to dihydrouridine is one of the most common modifications in tRNA. Increased levels of the dihydrouridine modification are associated with cancer. Dihydrouridine synthases (Dus) from different subfamilies selectively reduce distinct uridines, located at spatially unique positions of folded tRNA, into dihydrouridine. Because the catalytic center...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-10-23
    Description: Analysis of the 1,042,519-base pair Chlamydia trachomatis genome revealed unexpected features related to the complex biology of chlamydiae. Although chlamydiae lack many biosynthetic capabilities, they retain functions for performing key steps and interconversions of metabolites obtained from their mammalian host cells. Numerous potential virulence-associated proteins also were characterized. Several eukaryotic chromatin-associated domain proteins were identified, suggesting a eukaryotic-like mechanism for chlamydial nucleoid condensation and decondensation. The phylogenetic mosaic of chlamydial genes, including a large number of genes with phylogenetic origins from eukaryotes, implies a complex evolution for adaptation to obligate intracellular parasitism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stephens, R S -- Kalman, S -- Lammel, C -- Fan, J -- Marathe, R -- Aravind, L -- Mitchell, W -- Olinger, L -- Tatusov, R L -- Zhao, Q -- Koonin, E V -- Davis, R W -- AI 39258/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1998 Oct 23;282(5389):754-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Infectious Diseases, University of California, Berkeley, CA 94720, USA. ctgenome@socrates.berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9784136" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Amino Acid Sequence ; Amino Acids/biosynthesis ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Proteins/chemistry/genetics ; Biological Evolution ; Chlamydia trachomatis/classification/*genetics/metabolism/physiology ; DNA Repair ; Energy Metabolism ; Enzymes/chemistry/genetics ; *Genome, Bacterial ; Humans ; Lipids/biosynthesis ; Molecular Sequence Data ; Peptidoglycan/biosynthesis/genetics ; Phylogeny ; Protein Biosynthesis ; Recombination, Genetic ; *Sequence Analysis, DNA ; Transcription, Genetic ; Transformation, Bacterial ; Virulence
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Bacterial rhodopsin: evidence for a new type of phototrophy in the sea (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-09-16
    Description: Extremely halophilic archaea contain retinal-binding integral membrane proteins called bacteriorhodopsins that function as light-driven proton pumps. So far, bacteriorhodopsins capable of generating a chemiosmotic membrane potential in response to light have been demonstrated only in halophilic archaea. We describe here a type of rhodopsin derived from bacteria that was discovered through genomic analyses of naturally occuring marine bacterioplankton. The bacterial rhodopsin was encoded in the genome of an uncultivated gamma-proteobacterium and shared highest amino acid sequence similarity with archaeal rhodopsins. The protein was functionally expressed in Escherichia coli and bound retinal to form an active, light-driven proton pump. The new rhodopsin exhibited a photochemical reaction cycle with intermediates and kinetics characteristic of archaeal proton-pumping rhodopsins. Our results demonstrate that archaeal-like rhodopsins are broadly distributed among different taxa, including members of the domain Bacteria. Our data also indicate that a previously unsuspected mode of bacterially mediated light-driven energy generation may commonly occur in oceanic surface waters worldwide.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beja, O -- Aravind, L -- Koonin, E V -- Suzuki, M T -- Hadd, A -- Nguyen, L P -- Jovanovich, S B -- Gates, C M -- Feldman, R A -- Spudich, J L -- Spudich, E N -- DeLong, E F -- HG01775-02S1/HG/NHGRI NIH HHS/ -- R01GM27750/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Sep 15;289(5486):1902-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039-0628, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10988064" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Amino Acid Sequence ; Archaea/classification/physiology ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; Cloning, Molecular ; Escherichia coli ; Gammaproteobacteria/classification/genetics/*physiology ; Molecular Sequence Data ; Oceans and Seas ; Photochemistry ; Photosynthesis ; Phylogeny ; Phytoplankton/genetics/physiology ; Protein Binding ; Proton Pumps/physiology ; Retinaldehyde/metabolism ; Rhodopsin/*physiology ; Rhodopsins, Microbial ; *Water Microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-11-06
    Description: Chromosome 2 of Plasmodium falciparum was sequenced; this sequence contains 947,103 base pairs and encodes 210 predicted genes. In comparison with the Saccharomyces cerevisiae genome, chromosome 2 has a lower gene density, introns are more frequent, and proteins are markedly enriched in nonglobular domains. A family of surface proteins, rifins, that may play a role in antigenic variation was identified. The complete sequencing of chromosome 2 has shown that sequencing of the A+T-rich P. falciparum genome is technically feasible.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gardner, M J -- Tettelin, H -- Carucci, D J -- Cummings, L M -- Aravind, L -- Koonin, E V -- Shallom, S -- Mason, T -- Yu, K -- Fujii, C -- Pederson, J -- Shen, K -- Jing, J -- Aston, C -- Lai, Z -- Schwartz, D C -- Pertea, M -- Salzberg, S -- Zhou, L -- Sutton, G G -- Clayton, R -- White, O -- Smith, H O -- Fraser, C M -- Adams, M D -- Venter, J C -- Hoffman, S L -- R01 AI40125-01/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1998 Nov 6;282(5391):1126-32.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9804551" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antigens, Protozoan/chemistry/genetics ; Base Composition ; Chromosomes/*genetics ; Evolution, Molecular ; *Genes, Protozoan ; Genome, Protozoan ; Introns ; Membrane Proteins/chemistry/genetics ; Molecular Sequence Data ; Multigene Family ; Physical Chromosome Mapping ; Plasmodium falciparum/*genetics ; Protozoan Proteins/chemistry/*genetics ; RNA, Protozoan/genetics ; RNA, Transfer, Glu/genetics ; Repetitive Sequences, Nucleic Acid ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; *Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Comparison of the complete protein sets of worm and yeast: orthology and divergence (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-12-16
    Description: Comparative analysis of predicted protein sequences encoded by the genomes of Caenorhabditis elegans and Saccharomyces cerevisiae suggests that most of the core biological functions are carried out by orthologous proteins (proteins of different species that can be traced back to a common ancestor) that occur in comparable numbers. The specialized processes of signal transduction and regulatory control that are unique to the multicellular worm appear to use novel proteins, many of which re-use conserved domains. Major expansion of the number of some of these domains seen in the worm may have contributed to the advent of multicellularity. The proteins conserved in yeast and worm are likely to have orthologs throughout eukaryotes; in contrast, the proteins unique to the worm may well define metazoans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057080/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057080/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chervitz, S A -- Aravind, L -- Sherlock, G -- Ball, C A -- Koonin, E V -- Dwight, S S -- Harris, M A -- Dolinski, K -- Mohr, S -- Smith, T -- Weng, S -- Cherry, J M -- Botstein, D -- HG 00044/HG/NHGRI NIH HHS/ -- HG01315/HG/NHGRI NIH HHS/ -- P41 HG001315/HG/NHGRI NIH HHS/ -- P41 HG001315-16/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 1998 Dec 11;282(5396):2022-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9851918" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caenorhabditis elegans/*chemistry/genetics/physiology ; Evolution, Molecular ; Fungal Proteins/*chemistry/genetics/physiology ; Gene Expression Regulation ; Genes, Fungal ; Genes, Helminth ; Helminth Proteins/*chemistry/genetics/physiology ; Saccharomyces cerevisiae/*chemistry/genetics/physiology ; Sequence Homology, Amino Acid ; Signal Transduction
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-22
    Description: A comparison of the proteins encoded in the recently (nearly) completed human genome to those from the fly and nematode genomes reveals a major increase in the complexity of the apoptotic molecular machinery in vertebrates, in terms of both the number of proteins involved and their domain architecture. Several components of the apoptotic system are shared by humans and flies, to the exclusion of nematodes, which seems to support the existence of a coelomate clade in animal evolution. A considerable repertoire of apoptotic protein domains was detected in Actinomycetes and Cyanobacteria, which suggests a major contribution of horizontal gene transfer to the early evolution of apoptosis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aravind, L -- Dixit, V M -- Koonin, E V -- New York, N.Y. -- Science. 2001 Feb 16;291(5507):1279-84.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11181990" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; *Apoptosis/genetics ; Caenorhabditis elegans/genetics ; Conserved Sequence ; Drosophila melanogaster/genetics ; *Evolution, Molecular ; *Genome ; *Genome, Human ; Helminth Proteins/chemistry/genetics/physiology ; Humans ; Insect Proteins/chemistry/genetics/physiology ; Protein Structure, Tertiary ; Proteins/*chemistry/*genetics/physiology ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-08-17
    Description: The 26S proteasome mediates degradation of ubiquitin-conjugated proteins. Although ubiquitin is recycled from proteasome substrates, the molecular basis of deubiquitination at the proteasome and its relation to substrate degradation remain unknown. The Rpn11 subunit of the proteasome lid subcomplex contains a highly conserved Jab1/MPN domain-associated metalloisopeptidase (JAMM) motif-EX(n)HXHX(10)D. Mutation of the predicted active-site histidines to alanine (rpn11AXA) was lethal and stabilized ubiquitin pathway substrates in yeast. Rpn11(AXA) mutant proteasomes assembled normally but failed to either deubiquitinate or degrade ubiquitinated Sic1 in vitro. Our findings reveal an unexpected coupling between substrate deubiquitination and degradation and suggest a unifying rationale for the presence of the lid in eukaryotic proteasomes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Verma, Rati -- Aravind, L -- Oania, Robert -- McDonald, W Hayes -- Yates, John R 3rd -- Koonin, Eugene V -- Deshaies, Raymond J -- RR11823-05-01/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2002 Oct 18;298(5593):611-5. Epub 2002 Aug 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12183636" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Carbon-Nitrogen Lyases/chemistry/*metabolism ; Cyclin-Dependent Kinase Inhibitor Proteins ; Cysteine Endopeptidases/metabolism ; DNA-Binding Proteins/chemistry ; Endopeptidases/chemistry/*metabolism ; Fungal Proteins/*metabolism ; Metalloendopeptidases/chemistry/*metabolism ; Molecular Sequence Data ; Multienzyme Complexes/metabolism ; Mutation ; Oligopeptides/pharmacology ; Peptide Hydrolases/*metabolism ; Proteasome Endopeptidase Complex ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; Transcription Factors/chemistry ; Ubiquitins/*metabolism ; Yeasts/metabolism ; Zinc/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Photosystem I gene cassettes are present in marine virus genomes (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-08-28
    Description: Cyanobacteria of the Synechococcus and Prochlorococcus genera are important contributors to photosynthetic productivity in the open oceans. Recently, core photosystem II (PSII) genes were identified in cyanophages and proposed to function in photosynthesis and in increasing viral fitness by supplementing the host production of these proteins. Here we show evidence for the presence of photosystem I (PSI) genes in the genomes of viruses that infect these marine cyanobacteria, using pre-existing metagenomic data from the global ocean sampling expedition as well as from viral biomes. The seven cyanobacterial core PSI genes identified in this study, psaA, B, C, D, E, K and a unique J and F fusion, form a cluster in cyanophage genomes, suggestive of selection for a distinct function in the virus life cycle. The existence of this PSI cluster was confirmed with overlapping and long polymerase chain reaction on environmental DNA from the Northern Line Islands. Potentially, the seven proteins encoded by the viral genes are sufficient to form an intact monomeric PSI complex. Projection of viral predicted peptides on the cyanobacterial PSI crystal structure suggested that the viral-PSI components might provide a unique way of funnelling reducing power from respiratory and other electron transfer chains to the PSI.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4605144/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4605144/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sharon, Itai -- Alperovitch, Ariella -- Rohwer, Forest -- Haynes, Matthew -- Glaser, Fabian -- Atamna-Ismaeel, Nof -- Pinter, Ron Y -- Partensky, Frederic -- Koonin, Eugene V -- Wolf, Yuri I -- Nelson, Nathan -- Beja, Oded -- Z99 LM999999/Intramural NIH HHS/ -- England -- Nature. 2009 Sep 10;461(7261):258-62. doi: 10.1038/nature08284. Epub 2009 Aug 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19710652" target="_blank"〉PubMed〈/a〉
    Keywords: Adhesins, Bacterial/chemistry/genetics ; Amino Acid Sequence ; Bacteriophages/*genetics/metabolism ; Biodiversity ; Genes, Bacterial/genetics ; Genes, Viral/*genetics ; Genome, Bacterial/genetics ; Genome, Viral/*genetics ; Geography ; Lipoproteins/chemistry/genetics ; Models, Molecular ; Molecular Sequence Data ; Oceans and Seas ; Open Reading Frames/genetics ; Oxidation-Reduction ; Photosynthesis/genetics ; Photosystem I Protein Complex/chemistry/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Prochlorococcus/*virology ; Protein Conformation ; Seawater/*microbiology ; Synechococcus/*virology ; Viral Proteins/chemistry/genetics/metabolism ; Water Microbiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 9
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    The evolution of eukaryotes (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Martin, William -- Dagan, Tal -- Koonin, Eugene V -- Dipippo, Jonathan L -- Gogarten, J Peter -- Lake, James A -- New York, N.Y. -- Science. 2007 Apr 27;316(5824):542-3; author reply 542-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17463271" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeal Proteins/chemistry ; Bacterial Proteins/chemistry ; *Biological Evolution ; *Eukaryotic Cells ; Evolution, Molecular ; Fungal Proteins/chemistry ; Genomics ; Humans ; Mitochondria ; Phagocytosis ; Prokaryotic Cells ; Proteins/*chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Evidence for a family of archaeal ATPases (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-03-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koonin, E V -- New York, N.Y. -- Science. 1997 Mar 7;275(5305):1489-90.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9045616" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/metabolism ; Amino Acid Sequence ; Archaea/*enzymology ; Bacterial Proteins/*chemistry/metabolism ; Conserved Sequence ; Databases, Factual ; Methanococcus/*enzymology ; Molecular Sequence Data ; Sequence Alignment
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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