Published in Trends Biochem Sci on April 01, 1998
Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev (2001) 4.75
'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res (2004) 3.50
Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucleic Acids Res (2004) 2.62
A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase. Biophys J (2002) 2.26
Modulatory and catalytic modes of ATP binding by the calcium pump. EMBO J (2006) 1.89
LEPS2, a phosphorus starvation-induced novel acid phosphatase from tomato. Plant Physiol (2001) 1.70
BeF(3)(-) acts as a phosphate analog in proteins phosphorylated on aspartate: structure of a BeF(3)(-) complex with phosphoserine phosphatase. Proc Natl Acad Sci U S A (2001) 1.62
Structure- and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum. J Biol Chem (2003) 1.41
Markers of fitness in a successful enzyme superfamily. Curr Opin Struct Biol (2009) 1.31
Evolution of sucrose synthesis. Plant Physiol (2002) 1.17
Purification, molecular cloning, and sequence analysis of sucrose-6F-phosphate phosphohydrolase from plants. Proc Natl Acad Sci U S A (2000) 1.15
What the structure of a calcium pump tells us about its mechanism. Biochem J (2001) 1.13
The structure of a cyanobacterial sucrose-phosphatase reveals the sugar tongs that release free sucrose in the cell. Plant Cell (2005) 1.11
High residual activity of PMM2 in patients' fibroblasts: possible pitfall in the diagnosis of CDG-Ia (phosphomannomutase deficiency). Am J Hum Genet (2001) 1.06
The acid phosphatase-encoding gene GmACP1 contributes to soybean tolerance to low-phosphorus stress. PLoS Genet (2014) 1.05
Identification of the Mg2+-binding site in the P-type ATPase and phosphatase members of the HAD (haloacid dehalogenase) superfamily by structural similarity to the response regulator protein CheY. Biochem J (1999) 1.04
Investigation of two evolutionarily unrelated halocarboxylic acid dehalogenase gene families. J Bacteriol (1999) 1.04
Crystal structure of the probable haloacid dehalogenase PH0459 from Pyrococcus horikoshii OT3. Protein Sci (2005) 0.94
Identification of the dimerization domain of dehalogenase IVa of Burkholderia cepacia MBA4. Appl Environ Microbiol (2000) 0.93
Diversification of function in the haloacid dehalogenase enzyme superfamily: The role of the cap domain in hydrolytic phosphoruscarbon bond cleavage. Bioorg Chem (2006) 0.91
Structural Studies of Medicago truncatula Histidinol Phosphate Phosphatase from Inositol Monophosphatase Superfamily Reveal Details of Penultimate Step of Histidine Biosynthesis in Plants. J Biol Chem (2016) 0.90
A new family of phosphotransferases related to P-type ATPases. Trends Biochem Sci (1998) 0.90
Modeling a dehalogenase fold into the 8-A density map for Ca(2+)-ATPase defines a new domain structure. Biophys J (2000) 0.89
Farnesyl phosphatase, a Corpora allata enzyme involved in juvenile hormone biosynthesis in Aedes aegypti. PLoS One (2013) 0.87
The complex ATP-Fe(2+) serves as a specific affinity cleavage reagent in ATP-Mg(2+) sites of Na,K-ATPase: altered ligation of Fe(2+) (Mg(2+)) ions accompanies the E(1)-->E(2) conformational change. Proc Natl Acad Sci U S A (2000) 0.85
Recent advances in structure and function of cytosolic IMP-GMP specific 5'-nucleotidase II (cN-II). Purinergic Signal (2006) 0.84
Crystal structures of the novel cytosolic 5'-nucleotidase IIIB explain its preference for m7GMP. PLoS One (2014) 0.84
Substrate ambiguous enzymes within the Escherichia coli proteome offer different evolutionary solutions to the same problem. Mol Biol Evol (2013) 0.83
Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level. BMC Evol Biol (2006) 0.82
Structural organization and energy transduction mechanism of Na+,K+-ATPase studied with transition metal-catalyzed oxidative cleavage. J Bioenerg Biomembr (2001) 0.81
Probing the mechanism of enzymatic phosphoryl transfer with a chemical trick. Proc Natl Acad Sci U S A (2001) 0.81
Characterization and regulation of a bacterial sugar phosphatase of the haloalkanoate dehalogenase superfamily, AraL, from Bacillus subtilis. FEBS J (2011) 0.81
Sucrose phosphate phosphatase in the green alga Klebsormidium flaccidum (Streptophyta) lacks an extensive C-terminal domain and differs from that of land plants. Planta (2011) 0.81
Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS. J Biol Chem (2015) 0.80
Sucrose phosphate synthase and sucrose phosphate phosphatase interact in planta and promote plant growth and biomass accumulation. J Exp Bot (2015) 0.78
Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer. Biochemistry (2016) 0.77
J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4. J Biomol NMR (2014) 0.77
Evolutionary history and functional diversification of phosphomannomutase genes. J Mol Evol (2010) 0.76
Purification, crystallization and preliminary crystallographic analysis of SMU.1108c protein from Streptococcus mutans. Acta Crystallogr Sect F Struct Biol Cryst Commun (2010) 0.75
Stability and Conformation of a Chemoreceptor HAMP Domain Chimera Correlates with Signaling Properties. Biophys J (2017) 0.75
Characterization of the Sucrose Phosphate Phosphatase (SPP) Isoforms from Arabidopsis thaliana and Role of the S6PPc Domain in Dimerization. PLoS One (2016) 0.75
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
A genomic perspective on protein families. Science (1997) 50.51
The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res (2000) 49.22
The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res (2001) 43.17
Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res (1998) 23.87
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res (2001) 22.33
Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc Natl Acad Sci U S A (1994) 18.46
A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins. FASEB J (1997) 15.10
Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science (1998) 13.64
BRCA1 protein products ... Functional motifs... Nat Genet (1996) 11.50
AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res (1999) 11.30
Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science (2000) 10.82
Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res (1989) 10.03
Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol Microbiol (1997) 8.69
Novel domains of the prokaryotic two-component signal transduction systems. FEMS Microbiol Lett (2001) 8.45
Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases. Trends Biochem Sci (1998) 8.01
Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect (2012) 7.97
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics (1999) 6.91
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs). Genome Biol (2000) 6.50
Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol (2001) 6.46
A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci U S A (1996) 6.38
Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science (1998) 6.28
Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol (1998) 6.22
Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J Mol Biol (1999) 5.90
Using the COG database to improve gene recognition in complete genomes. Genetica (2000) 5.80
Cleavage of cohesin by the CD clan protease separin triggers anaphase in yeast. Cell (2000) 5.69
Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr Biol (1996) 5.50
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res (2001) 5.37
Beyond complete genomes: from sequence to structure and function. Curr Opin Struct Biol (1998) 5.16
Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res (1999) 4.80
Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev (2001) 4.75
Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol (2001) 4.59
Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs. Proc Natl Acad Sci U S A (1997) 4.40
The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. Genome Biol (2001) 4.39
Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res (1992) 4.39
Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases. A distinct protein superfamily with a common structural fold. FEBS Lett (1989) 4.29
Common origin of four diverse families of large eukaryotic DNA viruses. J Virol (2001) 4.28
N-terminal domains of putative helicases of flavi- and pestiviruses may be serine proteases. Nucleic Acids Res (1989) 4.27
Identification of paracaspases and metacaspases: two ancient families of caspase-like proteins, one of which plays a key role in MALT lymphoma. Mol Cell (2000) 4.19
The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem Sci (1998) 4.11
SAP - a putative DNA-binding motif involved in chromosomal organization. Trends Biochem Sci (2000) 4.10
Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet (1998) 4.10
The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase. Virology (1991) 4.07
Who's your neighbor? New computational approaches for functional genomics. Nat Biotechnol (2000) 4.04
Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol (2000) 3.99
Viral proteins containing the purine NTP-binding sequence pattern. Nucleic Acids Res (1989) 3.96
Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science (1998) 3.83
Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res (1999) 3.62
SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res (2000) 3.56
Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res (1999) 3.44
Coronavirus genome: prediction of putative functional domains in the non-structural polyprotein by comparative amino acid sequence analysis. Nucleic Acids Res (1989) 3.38
DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history. Nucleic Acids Res (1999) 3.32
A new superfamily of putative NTP-binding domains encoded by genomes of small DNA and RNA viruses. FEBS Lett (1990) 3.30
Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. J Mol Biol (1999) 3.28
Lineage-specific loss and divergence of functionally linked genes in eukaryotes. Proc Natl Acad Sci U S A (2000) 3.27
Non-orthologous gene displacement. Trends Genet (1996) 3.12
Lineage-specific gene expansions in bacterial and archaeal genomes. Genome Res (2001) 3.10
A novel superfamily of nucleoside triphosphate-binding motif containing proteins which are probably involved in duplex unwinding in DNA and RNA replication and recombination. FEBS Lett (1988) 3.09
An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication. J Mol Evol (1989) 3.00
A conserved NTP-motif in putative helicases. Nature (1988) 2.94
Novel families of putative protein kinases in bacteria and archaea: evolution of the "eukaryotic" protein kinase superfamily. Genome Res (1998) 2.91
Detection of new genes in a bacterial genome using Markov models for three gene classes. Nucleic Acids Res (1995) 2.89
Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange. Trends Genet (1999) 2.87
Predicting functions from protein sequences--where are the bottlenecks? Nat Genet (1998) 2.86
Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Nucleic Acids Res (1998) 2.82
SEALS: a system for easy analysis of lots of sequences. Proc Int Conf Intell Syst Mol Biol (1997) 2.80
Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. Nucleic Acids Res (2000) 2.80
RNA sequence of astrovirus: distinctive genomic organization and a putative retrovirus-like ribosomal frameshifting signal that directs the viral replicase synthesis. Proc Natl Acad Sci U S A (1993) 2.77
Role of CED-4 in the activation of CED-3. Nature (1997) 2.76
The U box is a modified RING finger - a common domain in ubiquitination. Curr Biol (2000) 2.73
Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. J Mol Biol (2001) 2.68
Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily. Proteins (2001) 2.65
Phosphoesterase domains associated with DNA polymerases of diverse origins. Nucleic Acids Res (1998) 2.61
The NACHT family - a new group of predicted NTPases implicated in apoptosis and MHC transcription activation. Trends Biochem Sci (2000) 2.58
The genome of molluscum contagiosum virus: analysis and comparison with other poxviruses. Virology (1997) 2.58
The domains of death: evolution of the apoptosis machinery. Trends Biochem Sci (1999) 2.56
DNA-binding proteins and evolution of transcription regulation in the archaea. Nucleic Acids Res (1999) 2.53
A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity. Protein Sci (1997) 2.47
Gene order is not conserved in bacterial evolution. Trends Genet (1996) 2.44
Did DNA replication evolve twice independently? Nucleic Acids Res (1999) 2.44
Hedgehog patterning activity: role of a lipophilic modification mediated by the carboxy-terminal autoprocessing domain. Cell (1996) 2.39
The bacterial replicative helicase DnaB evolved from a RecA duplication. Genome Res (2000) 2.39
Fold prediction and evolutionary analysis of the POZ domain: structural and evolutionary relationship with the potassium channel tetramerization domain. J Mol Biol (1999) 2.37
Superfamily of UvrA-related NTP-binding proteins. Implications for rational classification of recombination/repair systems. J Mol Biol (1990) 2.34
A novel family of predicted phosphoesterases includes Drosophila prune protein and bacterial RecJ exonuclease. Trends Biochem Sci (1998) 2.33
Genome sequence comparison and scenarios for gene rearrangements: a test case. Genomics (1995) 2.32
Searching for drug targets in microbial genomes. Curr Opin Biotechnol (1999) 2.29
Distribution of protein folds in the three superkingdoms of life. Genome Res (1999) 2.29
Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. Nucleic Acids Res (1999) 2.28