M Y Galperin

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint House cleaning, a part of good housekeeping
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Mol Microbiol 59:5-19. 2006
  2. pmc The Molecular Biology Database Collection: 2008 update
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MA 20894, USA
    Nucleic Acids Res 36:D2-4. 2008
  3. pmc Characterization of the N-ATPase, a distinct, laterally transferred Na+-translocating form of the bacterial F-type membrane ATPase
    Daria V Dibrova
    School of Physics, University of Osnabruck, D 49069 Osnabruck, Germany
    Bioinformatics 26:1473-6. 2010
  4. pmc The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:D1-8. 2012
  5. pmc Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 14:2870-90. 2012
  6. pmc Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1
    Jimmy H Saw
    Department of Microbiology, University of Hawai i, 2538 The Mall, Honolulu, HI 96822, USA
    Genome Biol 9:R161. 2008
  7. pmc Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia
    Shaobin Hou
    Advance Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, University of Hawaii, Keller Hall 319, Honolulu, Hawaii, 96822, USA
    Biol Direct 3:26. 2008
  8. pmc Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution
    Marina V Omelchenko
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Biol Direct 5:31. 2010
  9. pmc Evolutionary primacy of sodium bioenergetics
    Armen Y Mulkidjanian
    School of Physics, University of Osnabruck, D 49069 Osnabruck, Germany
    Biol Direct 3:13. 2008
  10. pmc On the origin of life in the zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth
    Armen Y Mulkidjanian
    School of Physics, Universitat Osnabruck, D 49069 Osnabruck, Germany
    Biol Direct 4:27. 2009

Collaborators

Detail Information

Publications93

  1. ncbi request reprint House cleaning, a part of good housekeeping
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Mol Microbiol 59:5-19. 2006
    ..We discuss the structural diversity of these enzymes, their phylogenetic distribution, substrate specificity and the problem of identifying their true substrates...
  2. pmc The Molecular Biology Database Collection: 2008 update
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MA 20894, USA
    Nucleic Acids Res 36:D2-4. 2008
    ..The complete database list and summaries are available online at the Nucleic Acids Research web site, http://nar.oxfordjournals.org/...
  3. pmc Characterization of the N-ATPase, a distinct, laterally transferred Na+-translocating form of the bacterial F-type membrane ATPase
    Daria V Dibrova
    School of Physics, University of Osnabruck, D 49069 Osnabruck, Germany
    Bioinformatics 26:1473-6. 2010
    ..We argue that N-ATPases are an early-diverging branch of membrane ATPases that, similarly to the eukaryotic V-type ATPases, do not synthesize ATP...
  4. pmc The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:D1-8. 2012
    ..org/biodbcore web site. The full content of the Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/)...
  5. pmc Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 14:2870-90. 2012
    ..These profiles should help further experimental studies of uncharacterized widespread sporulation genes, which would ultimately allow delineation of the minimal set(s) of sporulation-specific genes in Bacilli and Clostridia...
  6. pmc Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1
    Jimmy H Saw
    Department of Microbiology, University of Hawai i, 2538 The Mall, Honolulu, HI 96822, USA
    Genome Biol 9:R161. 2008
    ..The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life...
  7. pmc Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia
    Shaobin Hou
    Advance Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, University of Hawaii, Keller Hall 319, Honolulu, Hawaii, 96822, USA
    Biol Direct 3:26. 2008
    ..Similar organisms were independently isolated from geothermal systems in Italy and Russia...
  8. pmc Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution
    Marina V Omelchenko
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Biol Direct 5:31. 2010
    ..In addition, efforts in structural genomics resulted in a vastly improved structural coverage of proteomes, providing for definitive assessment of (non)homologous relationships between proteins...
  9. pmc Evolutionary primacy of sodium bioenergetics
    Armen Y Mulkidjanian
    School of Physics, University of Osnabruck, D 49069 Osnabruck, Germany
    Biol Direct 3:13. 2008
    ..The prevalent proton-dependent ATPases are generally viewed as the primary form of the enzyme whereas the sodium-translocating ATPases of some prokaryotes are usually construed as an exotic adaptation to survival in extreme environments...
  10. pmc On the origin of life in the zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth
    Armen Y Mulkidjanian
    School of Physics, Universitat Osnabruck, D 49069 Osnabruck, Germany
    Biol Direct 4:27. 2009
    ..The hypothesis suggests that life emerged within compartmentalized, photosynthesizing ZnS formations of hydrothermal origin (the Zn world), assembled in sub-aerial settings on the surface of the primeval Earth...
  11. pmc Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes
    Boris G Mirkin
    School of Information Systems and Computer Science, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK
    BMC Evol Biol 3:2. 2003
    ..This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task...
  12. pmc Survival of the fittest before the beginning of life: selection of the first oligonucleotide-like polymers by UV light
    Armen Y Mulkidjanian
    Division of Biophysics, Department of Biology and Chemistry, Universitat Osnabruck, D 49069 Osnabruck, Germany
    BMC Evol Biol 3:12. 2003
    ..However, so far there has been no explanation of how the first RNA-like biopolymers could originate and survive on the primordial Earth...
  13. pmc Structural classification of bacterial response regulators: diversity of output domains and domain combinations
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Bacteriol 188:4169-82. 2006
    ..The complete list of response regulators encoded in each of the 200 analyzed genomes is available online at http://www.ncbi.nlm.nih.gov/Complete_Genomes/RRcensus.html...
  14. ncbi request reprint A square archaeon, the smallest eukaryote and the largest bacteria
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 8:1683-7. 2006
  15. ncbi request reprint The fuzzy border between a cell and an organelle
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 8:2062-7. 2006
  16. ncbi request reprint Genomes to aid in bioremediation of dry cleaning solvents, mothballs and more
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 8:949-55. 2006
  17. ncbi request reprint The minimal genome keeps growing
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 8:569-73. 2006
  18. ncbi request reprint Sampling of microbial diversity by complete genomes
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 8:1313-7. 2006
  19. ncbi request reprint Protecting sausages with bacteria instead of salt
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 8:185-92. 2006
  20. ncbi request reprint To finish or not to finish?
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 7:1061-4. 2005
  21. pmc A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Microbiol 5:35. 2005
    ....
  22. pmc The Molecular Biology Database Collection: 2006 update
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:D3-5. 2006
    ..The complete database list and summaries are available online at the Nucleic Acids Research website http://nar.oxfordjournals.org/...
  23. ncbi request reprint More cool news from marine bacteria
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 7:1864-7. 2005
  24. ncbi request reprint The secret of being cool
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 7:1499-504. 2005
  25. pmc The Molecular Biology Database Collection: 2007 update
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 35:D3-4. 2007
    ..The complete database list and summaries are available online on the Nucleic Acids Research web site http://nar.oxfordjournals.org/...
  26. ncbi request reprint Using archaeal genomics to fight global warming and clostridia to fight cancer
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 9:279-86. 2007
  27. ncbi request reprint Mycobacterial genomes for all tastes: from BCG to biodegradation of naphtalene and pyrene
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 9:839-45. 2007
  28. pmc From complete genome sequence to 'complete' understanding?
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Biotechnol 28:398-406. 2010
    ..We also discuss problems in understanding the functions of the remaining 'conserved hypothetical' genes...
  29. pmc Interplay of heritage and habitat in the distribution of bacterial signal transduction systems
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
    Mol Biosyst 6:721-8. 2010
    ..Thus, they reflect evolutionary relationships between organisms as well as individual adaptations of each organism to its specific ecological niche...
  30. pmc Diversity of structure and function of response regulator output domains
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Opin Microbiol 13:150-9. 2010
    ..Patterns of the distribution of various RR families are generally conserved within key microbial lineages and can be used to trace adaptations of various species to their unique ecological niches...
  31. ncbi request reprint Novel domains of the prokaryotic two-component signal transduction systems
    M Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    FEMS Microbiol Lett 203:11-21. 2001
    ..It appears that the real picture of the complexity of phosphorelay signal transduction in prokaryotes is only beginning to unfold...
  32. pmc The quest for biofuels fuels genome sequencing
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 10:2471-5. 2008
  33. pmc Genomes of model organisms: know thy tools
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 10:1383-91. 2008
  34. pmc The dawn of synthetic genomics
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 10:821-5. 2008
  35. pmc Social bacteria and asocial eukaryotes
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 10:281-8. 2008
  36. pmc Some bacteria degrade explosives, others prefer boiling methanol
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Environ Microbiol 9:2905-10. 2007
  37. pmc Dark matter in a deep-sea vent and in human mouth
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 9:2385-91. 2007
  38. pmc Genomics against flatulence
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 9:1869-77. 2007
  39. pmc Linear chromosomes in bacteria: no straight edge advantage?
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 9:1357-62. 2007
  40. pmc The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:D1-6. 2011
    ..oxfordjournals.org/nar/database/a/, now lists 1330 carefully selected molecular biology databases. The full content of the Database Issue is freely available online at the Nucleic Acids Research web site (http://nar.oxfordjournals.org/)...
  41. pmc A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity
    M Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Protein Sci 6:2639-43. 1997
    ....
  42. ncbi request reprint Looking at big brothers for clues
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 6:767-8. 2004
  43. pmc The Molecular Biology Database Collection: 2004 update
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 32:D3-22. 2004
    ..Each database in the list comes with a recently updated brief description. The database list and the database descriptions can be accessed online at the Nucleic Acids Research web site http://nar. oupjournals.org/...
  44. pmc Bacterial signal transduction network in a genomic perspective
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Environ Microbiol 6:552-67. 2004
    ..Experimental characterization of the novel domains and domain combinations would be needed for achieving a better understanding of the mechanisms of signalling response and the intracellular hierarchy of different signalling pathways...
  45. ncbi request reprint Metagenomics: from acid mine to shining sea
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 6:543-5. 2004
  46. ncbi request reprint All bugs, big and small
    Michael Y Galperin
    National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 6:435-7. 2004
  47. ncbi request reprint Searching for drug targets in microbial genomes
    M Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Opin Biotechnol 10:571-8. 1999
    ..Species-specific genes, on the other hand, may offer the possibility to design drugs against a particular, narrow group of pathogens...
  48. ncbi request reprint Conserved core structure and active site residues in alkaline phosphatase superfamily enzymes
    M Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 45:318-24. 2001
    ..We predict that catalytical cycles of all the enzymes of AlkP superfamily include phosphoenzyme (or sulfoenzyme) intermediates...
  49. ncbi request reprint MHYT, a new integral membrane sensor domain
    M Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    FEMS Microbiol Lett 205:17-23. 2001
    ..A model of the membrane topology of the MHYT domain indicates that its conserved residues could coordinate one or two copper ions, suggesting a role in sensing oxygen, CO, or NO...
  50. ncbi request reprint Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption
    M Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    In Silico Biol 1:55-67. 1998
    ..e. involvement of structurally unrelated proteins in the same function. These observations suggest that case by case validation of functional annotation by expert biologists remains crucial for productive genome analysis...
  51. ncbi request reprint The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase
    M Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 41:238-47. 2000
    ..These results should help in understanding the enzymology of cobalamin biosynthesis and in resolving the role of phosphotransacetylase in regulation of the carbon flow to and from acetate...
  52. ncbi request reprint Aldolases of the DhnA family: a possible solution to the problem of pentose and hexose biosynthesis in archaea
    M Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    FEMS Microbiol Lett 183:259-64. 2000
    ..The DhnA-family enzymes are predicted to possess an aldolase activity and to play a critical role in sugar biosynthesis in archaea...
  53. pmc A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases
    M Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Protein Sci 7:1829-35. 1998
    ..Mutational changes in the vicinity of these residues in several sulfatases cause mucopolysaccharidosis (Hunter, Maroteaux-Lamy, Morquio, and Sanfilippo syndromes) and metachromatic leucodystrophy...
  54. ncbi request reprint The bugs that came in from the cold
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 6:1001-4. 2004
  55. ncbi request reprint The vibrio that sheds light
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 7:757-60. 2005
  56. ncbi request reprint Life is not defined just in base pairs
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 7:149-52. 2005
  57. ncbi request reprint Genomes back-to-back: when sequencing race is a good thing
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 6:1205-9. 2004
  58. ncbi request reprint On the bottom of the deep blue sea
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 7:453-8. 2005
  59. pmc The Molecular Biology Database Collection: 2005 update
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 33:D5-24. 2005
    ..The database list and summaries are available online at the Nucleic Acids Research web site, http://nar.oupjournals.org/...
  60. ncbi request reprint C-di-GMP: the dawning of a novel bacterial signalling system
    Ute Romling
    Microbiology and Tumor Biology Center, Karolinska Institutet, Box 280, SE 17177 Stockholm, Sweden
    Mol Microbiol 57:629-39. 2005
    ..The accumulated data clearly indicate that a novel ubiquitous signalling system in bacteria has been discovered...
  61. ncbi request reprint Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Mol Microbiol 25:619-37. 1997
    ..It is likely that the evolution of archaea included at least one major merger between ancestral cells from the bacterial lineage and the lineage leading to the eukaryotic nucleocytoplasm...
  62. pmc The COG database: a tool for genome-scale analysis of protein functions and evolution
    R L Tatusov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 28:33-6. 2000
    ..The COG database is accompanied by the COGNITOR program that is used to fit new proteins into the COGs and can be applied to functional and phylogenetic annotation of newly sequenced genomes...
  63. ncbi request reprint Prokaryotic genomes: the emerging paradigm of genome-based microbiology
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, Maryland 20894, USA
    Curr Opin Genet Dev 7:757-63. 1997
    ....
  64. pmc A novel type of conserved DNA-binding domain in the transcriptional regulators of the AlgR/AgrA/LytR family
    Anastasia N Nikolskaya
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:2453-9. 2002
    ..In addition to response regulators, the LytTR domain is found in combination with MHYT, PAS and other sensor domains...
  65. ncbi request reprint Beyond complete genomes: from sequence to structure and function
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Curr Opin Struct Biol 8:355-63. 1998
    ..Taken together, sequence and structure comparisons provide a powerful methodology that can successfully complement traditional experimental approaches...
  66. pmc Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea
    Igor B Zhulin
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332 0230, USA
    J Bacteriol 185:285-94. 2003
    ..The variety of signaling pathways using the CHASE-type domains indicates that these domains sense some critically important extracellular signals...
  67. ncbi request reprint Identification of sensory and signal-transducing domains in two-component signaling systems
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Methods Enzymol 422:47-74. 2007
    ..These protocols rely on publicly available computational tools and databases and can be utilized by anyone with Internet access...
  68. pmc Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
    Eugene Kolker
    BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
    Nucleic Acids Res 32:2353-61. 2004
    ....
  69. ncbi request reprint PilZ domain is part of the bacterial c-di-GMP binding protein
    Dorit Amikam
    Department of Biotechnology and Environmental Sciences, Tel Hai Academic College Tel Hai, Israel
    Bioinformatics 22:3-6. 2006
    ....
  70. ncbi request reprint Independent evolution of heavy metal-associated domains in copper chaperones and copper-transporting atpases
    I K Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Evol 53:622-33. 2001
    ..Copper chaperone-Cu-ATPase operons appear to have evolved independently in different prokaryotic lineages, probably due to a strong selective pressure for coexpression of these genes...
  71. ncbi request reprint MASE1 and MASE2: two novel integral membrane sensory domains
    Anastsia N Nikolskaya
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Microbiol Biotechnol 5:11-6. 2003
    ....
  72. pmc 'Conserved hypothetical' proteins: prioritization of targets for experimental study
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 32:5452-63. 2004
    ....
  73. ncbi request reprint Sequence analysis and characterization of a novel fibronectin-binding repeat domain from the surface of Streptococcus pneumoniae
    Daniela Bumbaca
    Children s Hospital Oakland Research Institute, Oakland, California 94609, USA
    OMICS 8:341-56. 2004
    ..pneumoniae SP0082 protein and its homologs in other streptococci as fibronectin-binding surface adhesins. The SSURE domain is likely to contain a novel protein fold, which was tentatively modeled using ab initio modeling methods...
  74. pmc Sequence conservation in the chagasin family suggests a common trend in cysteine proteinase binding by unrelated protein inhibitors
    Daniel J Rigden
    National Centre of Genetic Resources and Biotechnology, Cenargen Embrapa, S A I N Parque Rural, Final W5 Norte, 70770 900 Brasília, Brazil
    Protein Sci 11:1971-7. 2002
    ....
  75. pmc Sentra: a database of signal transduction proteins for comparative genome analysis
    Elizabeth M Glass
    Computational Biology Group, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
    Nucleic Acids Res 35:D271-3. 2007
    ..Sentra leverages the PUMA2 system to support interactive analysis and annotation of signal transduction proteins by the users...
  76. ncbi request reprint Phylogenomic analysis of the Giardia intestinalis transcarboxylase reveals multiple instances of domain fusion and fission in the evolution of biotin-dependent enzymes
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Microbiol Biotechnol 5:172-89. 2003
    ....
  77. pmc New metrics for comparative genomics
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Opin Biotechnol 17:440-7. 2006
    ..Several new metrics have recently been used in comparative genome analysis, yet challenges remain in finding an appropriate language for the emerging discipline of systems biology...
  78. ncbi request reprint Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions
    Olga V Moroz
    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
    J Mol Biol 347:243-55. 2005
    ..We outline probable tertiary and quaternary structures of the all-alpha NTP pyrophosphatase superfamily members...
  79. ncbi request reprint The PA14 domain, a conserved all-beta domain in bacterial toxins, enzymes, adhesins and signaling molecules
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
    Trends Biochem Sci 29:335-9. 2004
  80. pmc Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome
    Alexis Dufresne
    Station Biologique, Unité Mixte de Recherche 7127, Centre National de la Recherche Scientifique et Université Paris 6, BP74, 29682 Roscoff Cedex, France
    Proc Natl Acad Sci U S A 100:10020-5. 2003
    ..Because of its remarkable compactness, the genome of P. marinus SS120 might approximate the minimal gene complement of a photosynthetic organism...
  81. ncbi request reprint The crystal structure of a complex of Campylobacter jejuni dUTPase with substrate analogue sheds light on the mechanism and suggests the "basic module" for dimeric d(C/U)TPases
    Olga V Moroz
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
    J Mol Biol 342:1583-97. 2004
    ..These results in concert with a number of conserved residues responsible for interdomain cross-talk provide valuable insight towards rational drug design...
  82. pmc Telling bacteria: do not LytTR
    Michael Y Galperin
    Structure 16:657-9. 2008
  83. ncbi request reprint Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 22:1297-301. 2006
    ....
  84. pmc Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:D1-4. 2009
    ..The complete database list and summaries are available online at the Nucleic Acids Research web site (http://nar.oxfordjournals.org/)...
  85. pmc Sequence analysis of GerM and SpoVS, uncharacterized bacterial 'sporulation' proteins with widespread phylogenetic distribution
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
    Bioinformatics 24:1793-7. 2008
    ..SpoVS is predicted to adopt the AlbA archaeal chromatin protein fold, which suggests that it is a DNA-binding protein, most likely a novel transcriptional regulator...
  86. ncbi request reprint Genome-based identification and characterization of a putative mucin-binding protein from the surface of Streptococcus pneumoniae
    Daniela Bumbaca
    Center for Immunobiology and Vaccine Development, Children s Hospital Oakland Research Institute, Oakland, California 94609, USA
    Proteins 66:547-58. 2007
    ..It appears to be one of the very few unambiguous pneumococcal adhesin molecules known to date. A hypothetical model constructed by ab initio techniques predicts a novel beta-sandwich protein structure...
  87. ncbi request reprint The DxDxDG motif for calcium binding: multiple structural contexts and implications for evolution
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
    J Mol Biol 343:971-84. 2004
    ..The analysis presented here has consequences for the prediction of calcium binding from sequence alone...
  88. pmc Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy
    Shaobin Hou
    Department of Microbiology, University of Hawaii, Snyder Hall 111, 2538 The Mall, Honolulu, HI 96822, USA
    Proc Natl Acad Sci U S A 101:18036-41. 2004
    ..In summary, the I. loihiensis genome reveals an integrated mechanism of metabolic adaptation to the constantly changing deep-sea hydrothermal ecosystem...
  89. ncbi request reprint An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands
    Daniel J Rigden
    National Center of Genetic Resources and Biotechnology, Cenargen Embrapa, Brasilia D F 70770 900, Brazil
    FEMS Microbiol Lett 221:103-10. 2003
    ..This loop is thus more widespread than hitherto recognized and the evolution of EF-hand-like domains is probably more complex than previously appreciated...
  90. ncbi request reprint Purification, cloning, and expression of an apyrase from the bed bug Cimex lectularius. A new type of nucleotide-binding enzyme
    J G Valenzuela
    Medical Entomology Section, Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892 0425, USA
    J Biol Chem 273:30583-90. 1998
    ..elegans and in mouse and human expressed sequence tags from fetal and tumor EST libraries...