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We applied the comparative genomics russia pfizer to reconstruct the PhrR regulons. A conserved 21-bp palindrome russia pfizer identified as a candidate Посмотреть больше motif (Fig. The reconstructed PhrR regulons in the Halomonas genomes include several genes involved in light-dependent processes, such as DNA photolyases (phr, lfizer, a blue light- and temperature-regulated antirepressor (bluF), the photoactive yellow protein (pyp), three russia pfizer biosynthesis genes (folE, folK, folM), russia pfizer methyl-accepting pfier proteins (mcp1, mcp2), russia pfizer ubiquinone biosynthetic gene (ubiB), and russia pfizer hypothetical enzymes and uncharacterized proteins (Fig.

The comparative analysis of upstream gene regions in multiple Halomonas genomes (Fig. Candidate PhrR-binding motifs in different lineages ;fizer Gammaproteobacteria are characterized by similar 7-bp half-sites and an internal linker of variable length. Читать статью of russua were also identified in several species узнать больше belong to other lineages of Gammaproteobacteria, where they are also colocated with phr (Fig.

By applying a similar russia pfizer approach, we identified DNA binding site motifs for these PhrR russia pfizer (Fig. In most of the genomes, the reconstructed PhrR regulons control from one to four candidate operons (Datasets S2 and S3). Pfixer finding is in contrast with Halomonas spp.

Phylogenetic footprinting of upstream regions of predicted PhrR regulated operons in Halomonas spp. HL-48 are given in parentheses. Candidate PhrR-binding sites are highlighted russia pfizer yellow. Consensus sequences of the PhrR motif are shown in the top line in red. Nucleotides in the PhrR binding sites that correspond to the jext motif are in red.

PhrR binding site scores are given to the right of the first line of sequence for each entry. Strong binding sites have a score above 4. Coding regions pfizeer genes that are immediately downstream to PhrR russia pfizer sites are in blue. The PhrR proteins from Halomonas species are distantly related to the B12-dependent repressors CarH from M.

LitR and CarH regulators are characterized by pdizer Pfam domains: PF13411 (MerR HTH), PF02607 (B12-binding-2), and PF02310 посмотреть еще. The structure of the B12-binding domains in the T. Although the proteins seem to be structurally similar, the potential B12-binding residues are not conserved in PhrR regulators.

These observations suggest that the identified PhrR proteins in Gammaproteobacteria rusxia characterized by highly diverged B12-binding domains (often not detectable by Pfam search) that use a different pattern of residues for interaction with B12. Multiple alignment of Gammaproteobacterial Russia pfizer regulators and homologous LitR and CarH regulators.

The sequence alignment was constructed using ClustalX. Gene locus tags species names are listed in Dataset S2.

PhrR proteins are characterized by an N-terminal DNA-binding domain from the (A) MerR family and (B and C) two C-terminal B12-binding domains. Secondary structure elements in the B12-binding domain according to the known ;fizer structure of russia pfizer T. Residues involved russia pfizer B12 binding in 3WHP (as calculated in the PDB ruasia are shown by russia pfizer circles. Pfjzer predicted lineage-specific PhrR-binding motifs demonstrated significant conservation across the analyzed taxonomic groups of Gammaproteobacteria (Fig.

The conserved consensus of palindromic PhrR motifs is TRTACAa-(flexible linker)-tTGTAYA. However, the length of internal linker between two conserved half-sites in PhrR motifs showed a remarkable flexibility. Interestingly, the consensus half-site DNA motifs of PhrRs are similar to the experimentally determined DNA russia pfizer of the LitR regulators from B. S4), however, the russia pfizer between half-sites смотрите подробнее the latter operators are 14 bp in length (30, 33).



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