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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 metabolism in bacteria is diverse and involves FNR-like transcription factors HcpR, DNR, and NnrR; two-component systems NarXL and NarQP; NO-responsive activator NorR; and(More)
Analysis of a newly sequenced bacterial genome starts with identification of protein-coding genes. Functional assignment of proteins requires the exact knowledge of protein N-termini. We present a new program ORPHEUS that identifies candidate genes and accurately predicts gene starts. The analysis starts with a database similarity search and identification(More)
BACKGROUND Nickel (Ni) and cobalt (Co) are trace elements required for a variety of biological processes. Ni is directly coordinated by proteins, whereas Co is mainly used as a component of vitamin B12. Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited. (More)
Riboswitches are structures that form in mRNA and regulate gene expression in bacteria. Unlike other known RNA regulatory structures, they are directly bound by small ligands. The mechanism by which gene expression is regulated involves the formation of alternative structures that, in the repressing conformation, cause premature termination of transcription(More)
Alternative splicing has recently emerged as a major mechanism of generating protein diversity in higher eukaryotes. We compared alternative splicing isoforms of 166 pairs of orthologous human and mouse genes. As the mRNA and EST libraries of human and mouse are not complete and thus cannot be compared directly, we instead analyzed whether known cassette(More)
Concepts of orthology and paralogy are become increasingly important as whole-genome comparison allows their identification in complete genomes. Functional specificity of proteins is assumed to be conserved among orthologs and is different among paralogs. We used this assumption to identify residues which determine specificity of protein-DNA and(More)
The RegPrecise database (http://regprecise.lbl.gov) was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. A significant number of high-quality inferences of transcriptional regulatory interactions have been(More)
We used comparative genomics to investigate the distribution of conserved DNA-binding motifs in the regulatory regions of genes involved in iron and manganese homeostasis in alpha-proteobacteria. Combined with other computational approaches, this allowed us to reconstruct the metal regulatory network in more than three dozen species with available genome(More)
Recognition of transcription regulatory sites in bacterial genomes is a notoriously difficult problem. There are no algorithms capable of making reliable predictions even for well-studied sites such as the CRP (cyclic AMP receptor protein) box. However, availability of complete bacterial genomes makes it possible to make reliable predictions with bad rules.(More)
BACKGROUND The arginine repressor ArgR/AhrC is a transcription factor universally conserved in bacterial genomes. Its recognition signal (the ARG box), a weak palindrome, is also conserved between genomes, despite a very low degree of similarity between individual sites within a genome. Thus, the arginine repressor is different from two other universal(More)