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Figure 3 | Genome Biology

Figure 3

From: New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system

Figure 3

Contextual information and an ordered graph of gene neighborhood and domain architectures of the PSK network. The top panel shows the gene neighborhoods (predicted operons) for some of the PSK systems and other relevant gene clusters. The arrows indicate the direction of transcription. For each gene neighborhood, representative gene names are given below the depicted operon and the phyletic distribution of the operons is provided in brackets. The organisms are abbreviated as Figures 1 and 2. If an organism has more than one representative of a given PSK system, that number is appended before the organism's abbreviation. If one of the organisms has additional functionally relevant genes in the neighborhood, then these neighborhoods are shown separately, and linked to the core conserved gene neighborhood with an arrow. The lower right panel shows the ordered graph for the contextual information contained in conserved gene neighborhoods and domain fusions. The red edge in the graph denotes a neighboring gene, while the black edge denotes domain fusion. The direction of the edge denotes the order of the genes or the order of the fusion of domain in the polypeptide. Members of the vast assemblage of DNA-binding domains that share common structural features, namely the HTH (helix-turn-helix) and the RHH (ribbon-helix-helix) folds, have been colored blue. The triangles indicate toxins and the stars indicate anti-toxins/transcription factors. Domain architectures of a select set of proteins discussed in the text are shown in the lower left panel. The domain abbreviations are: abhydr, alpha/beta hydrolase; eif2G, translation initiation factor eIF-2, gamma subunit; FF, protein-protein interaction domain from human hypa/fbp11; Frpts, tetratricopeptide repeats; HTH Psq, HTH of the pipsqueak variety; LRR, leucine rich repeats; N, amino-terminal alpha-helical domain found in MloA-like proteins; RpoE1, DNA-directed RNA polymerase subunit E9; RpoE2, DNA-directed RNA polymerase subunit E99; S6E, ribosomal protein S6E; S24E, 30S ribosomal protein S24E; S27AE, 30S ribosomal protein S27AE; Sag, Yersinia/Haemophilus virulence surface antigen; TPR, tetratricopeptide repeats; YjeFKin, YjeF-like ribokinase. The species abbreviations are as shown in Figures 1, 2 and additionally: Pab, Pyrococcus abyssi; Pfu, Pyrococcus furiosus; Pyae, Pyrobaculum aerophilum; Hsom, Haemophilus somnus; Pmul, Pasteurella multocida; Spne, Streptococcus pneumoniae; Styp, Salmonella typhimurium; Ypes, Yersinia pestis.

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