The tRNAScanSE tool [40] was used to find tRNA genes, whereas ribosomal RNAs were found selleckchem by using RNAmmer [41] and BLASTn against the GenBank database. Lipoprotein signal peptides and numbers of transmembrane helices were predicted using SignalP [42] and TMHMM [43] respectively. ORFans were identified if their BLASTP E-value was lower than 1e-03 for alignment length greater than 80 amino acids. If alignment lengths were smaller than 80 amino acids, we used an E-value of 1e-05. Such parameter thresholds have already been used in previous works to define ORFans. To estimate the mean level of nucleotide sequence similarity at the genome level between N. massiliensis and three other members of the family Staphylococcaceae (Table 6), we used the Average Genomic Identity of Orthologous gene Sequences (AGIOS) home-made software.
Briefly, this software combines the Proteinortho software (version 1.4) [44] for detecting orthologous proteins between genomes compared two by two, then retrieves the corresponding genes and determines the mean percentage of nucleotide sequence identity among orthologous ORFs using the Needleman-Wunsch global alignment algorithm. Nosocomiicoccus massiliensis strain NP2T was compared to Macrococcus caseolyticus strain JCSC5402 (GenBank accession number “type”:”entrez-nucleotide”,”attrs”:”text”:”NC_011999″,”term_id”:”222150250″,”term_text”:”NC_011999″NC_011999), Staphylococcus pseudointermedius strain ED 99 (“type”:”entrez-nucleotide”,”attrs”:”text”:”NC_017568″,”term_id”:”386318029″,”term_text”:”NC_017568″NC_017568), and Salinicoccus albus strain DSM 19776 (“type”:”entrez-nucleotide”,”attrs”:”text”:”ARQJ00000000″,”term_id”:”482965635″,”term_text”:”ARQJ00000000″ARQJ00000000).
Artemis [45] was used for data management and DNA Plotter [46] was used for visualization of genomic features. The Mauve alignment tool was used for multiple genomic sequence alignment and visualization [47]. Table 6 The numbers of orthologous protein shared between genomes Genome properties The genome of N. massiliensis strain NP2T is 1,6452,44 bp long (1 chromosome, but no plasmid) with a 36.40% G + C content of (Figure 6 and Table 4). Of the 1,783 predicted genes, 1,738 were protein-coding genes, and 45 were RNAs. Three rRNA genes (one 16S rRNA, one 23S rRNA and one 5S rRNA) and 42 predicted tRNA genes were identified in the genome.
A total of 1,350 genes (75.71%) were assigned a putative function. Two hundred forty-six genes were identified as ORFans (13.79%). The remaining genes were annotated as hypothetical proteins. The properties and the statistics of the genome are summarized in Table 4 and Table 5. The distribution of genes into COGs functional categories is presented in Table 5. Figure 6 Graphical circular map of the Carfilzomib chromosome.
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