The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation were performed within the Integrated Microbial Genomes – Expert Review (IMG-ER) platform . Genome properties The genome consists www.selleckchem.com/products/Rapamycin.html of a 1,314,639 bp long chromosome with a G+C content of 53.1% (Table 3 and Figure 3). Of the 1,421 genes predicted, 1,371 were protein-coding genes, and 50 RNAs; 26 pseudogenes were also identified. The majority of the protein-coding genes (65.5%) were assigned with a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.
Table 3 Genome Statistics Figure 3 Graphical circular map of genome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew. Table 4 Number of genes associated with the general COG functional categories Acknowledgements We would like to gratefully acknowledge the help of Olivier D. Ngatchou-Djao (HZI) in preparing the manuscript. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No.
DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2.
A representative genomic 16S rRNA sequence from strain ATCC 11845T was compared using NCBI BLAST under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release Carfilzomib of the Greengenes database  and the relative frequencies, weighted by BLAST scores, of taxa and keywords (reduced to their stem ) were determined. The five most frequent genera were Riemerella (79.2%), Chryseobacterium (17.1%), Bergeyella (2.6%), ��Rosa�� (0.6%; misnomer) and Cloacibacterium (0.5%) (166 hits in total). Regarding the 124 hits to sequences from members of the species, the average identity within HSPs was 99.5%, whereas the average coverage by HSPs was 95.2%. Among all other species, the one yielding the highest score was ��Rosa chinensis��, apparently a severe misannotation, which corresponded to an identity of 99.8% and an HSP coverage of 91.9%.