Orthologs, paralogs, and evolutionary genomics

EV Koonin - Annu. Rev. Genet., 2005 - annualreviews.org
Orthologs and paralogs are two fundamentally different types of homologous genes that
evolved, respectively, by vertical descent from a single ancestral gene and by duplication …

The TetR family of transcriptional repressors

JL Ramos, M Martínez-Bueno… - Microbiology and …, 2005 - Am Soc Microbiol
We have developed a general profile for the proteins of the TetR family of repressors. The
stretch that best defines the profile of this family is made up of 47 amino acid residues that …

VFDB: a reference database for bacterial virulence factors

L Chen, J Yang, J Yu, Z Yao, L Sun… - Nucleic acids …, 2005 - academic.oup.com
Bacterial pathogens continue to impose a major threat to public health worldwide in the 21st
century. Intensified studies on bacterial pathogenesis have greatly expanded our knowledge …

Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM

E Altermann, WM Russell… - Proceedings of the …, 2005 - National Acad Sciences
Lactobacillus acidophilus NCFM is a probiotic bacterium that has been produced
commercially since 1972. The complete genome is 1,993,564 nt and devoid of plasmids …

Protein length in eukaryotic and prokaryotic proteomes

L Brocchieri, S Karlin - Nucleic acids research, 2005 - academic.oup.com
We analyzed length differences of eukaryotic, bacterial and archaeal proteins in relation to
function, conservation and environmental factors. Comparing Eukaryotes and Prokaryotes …

A novel method for accurate operon predictions in all sequenced prokaryotes

MN Price, KH Huang, EJ Alm, AP Arkin - Nucleic acids research, 2005 - academic.oup.com
We combine comparative genomic measures and the distance separating adjacent genes to
predict operons in 124 completely sequenced prokaryotic genomes. Our method …

Whole-Genome Transcriptional Analysis of Heavy Metal Stresses in Caulobacter crescentus

P Hu, EL Brodie, Y Suzuki, HH McAdams… - Journal of …, 2005 - Am Soc Microbiol
The bacterium Caulobacter crescentus and related stalk bacterial species are known for
their distinctive ability to live in low-nutrient environments, a characteristic of most heavy …

The Genome of Sulfolobus acidocaldarius, a Model Organism of the Crenarchaeota

L Chen, K Brügger, M Skovgaard… - Journal of …, 2005 - Am Soc Microbiol
Sulfolobus acidocaldarius is an aerobic thermoacidophilic crenarchaeon which grows
optimally at 80° C and pH 2 in terrestrial solfataric springs. Here, we describe the genome …

[HTML][HTML] Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks

DA Rodionov, IL Dubchak, AP Arkin… - PLoS computational …, 2005 - journals.plos.org
Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory
intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides …

Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection

M Kuroda, A Yamashita, H Hirakawa… - Proceedings of the …, 2005 - National Acad Sciences
Staphylococcus saprophyticus is a uropathogenic Staphylococcus frequently isolated from
young female outpatients presenting with uncomplicated urinary tract infections. We …