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Figure 1 | Genome Biology

Figure 1

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

Figure 1

Multiple alignment of the RelE/ParE superfamily. Multiple sequence alignments of the different families of RelE/ParE were constructed using T-Coffee [20] and PCMA [50] after parsing high-scoring pairs from PSI-BLAST search results. The PHD-secondary structure [21] is shown above the alignment with E representing a β strand, and H an α-helix. The consensus of the individual families and the entire superfamily is shown, and the names of each family are shown on the right. The 90% (or 80%) consensus shown below the alignment was derived using the following amino acid classes: hydrophobic (h: ALICVMYFW, yellow shading); the aliphatic subset of the hydrophobic class (l: ALIVMC, yellow shading); aromatic (a: FHWY, yellow shading); small (s: ACDGNPSTV, green); the tiny subset of the small class (u: GAS, green shading); polar (p: CDEHKNQRST, blue); alcohol subset of polar (o: ST, blue); charged subset of polar (c: DEHKR, pink); positive subset of polar (+: HKR, pink); and negative subset of polar (-: DE, pink). An amino acid in capitals like 'G', or 'E' shows the completely conserved amino acid in that group. The operon information (op) and/or the domain architecture information are shown on the right for each family. The limits of the domains are indicated by the residue positions, in bold, on each side. The numbers within the alignment are non-conserved inserts that have not been shown. The sequences are denoted by their gene name followed by the species abbreviation and GenBank Identifier. The phylogenetic relationship between the families is shown as a tree to the right. The species abbreviations are: Af, Archaeoglobus fulgidus; Ape, Aeropyrum pernix; Hsp, Halobacterium sp.; Mace, Methanosarcina acetivorans; Mjan, Methanocaldococcus jannaschii; Phor, Pyrococcus horikoshii; Stok, Sulfolobus tokodaii; Ana, Anabaena sp.; Atum, Agrobacterium tumefaciens; Avin, Azotobacter vinelandii; Bthe, Bacteroides thetaiotaomicron; Ccre, Caulobacter crescentus; Ceff, Corynebacterium efficiens; Cglu, Corynebacterium glutamicum; Chut, Cytophaga hutchinsonii; Ec, Escherichia coli; Fnuc, Fusobacterium nucleatum; Mlot, Mesorhizobium loti; Mmag, Magnetospirillum magnetotacticum; Msp, Magnetococcus sp.; Mtu, Mycobacterium tuberculosis; Neur, Nitrosomonas europaea; Nm, Neisseria meningitidis; Paer, Pseudomonas aeruginosa; Pflu, Pseudomonas fluorescens; Pput, Pseudomonas putida; Psyr, Pseudomonas syringae; Rcon, Rickettsia conorii; Saur, Staphylococcus aureus; Scoe, Streptomyces coelicolor; Smel, Sinorhizobium meliloti; Ssp, Synechocystis sp.; Syn, Synechococcus sp.; Tery, Trichodesmium erythraeum; Tfus, Thermobifida fusca; Tten, Thermoanaerobacter tengcongensis; Vcho, Vibrio cholerae; Xaxo, Xanthomonas axonopodis; Xcam, Xanthomonas campestris; Xf, Xylella fastidiosa.

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