Figure 3

A multiple alignment of the PRC-barrel was constructed using T-Coffee [38] and realigning the sequences by parsing high-scoring pairs from PSI-BLAST search results. The secondary structure assigned by PHD [22] is shown above the alignment, with E representing a β-strand, and H an α-helix. The 85% 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); small (s, ACDGNPSTV, green) and polar (p, CDEHKNQRST, blue). A 'G' denotes the conserved G of the tiny subset of the small class. Columns of residues that are peculiar to a particular category of PRC-barrels (see text) are colored red. The limits of the domains are indicated by the residue positions on each side. The numbers within the alignment are non-conserved inserts that have not been shown. The different families are shown on the right. The sequences are denoted by their gene name followed by the species abbreviation and GenBank identifier (gi). The species abbreviations are: Archaea: Af, Archaeoglobus fulgidus; Hsp, Halobacterium sp. NRC-1; Mac, Methanosarcina acetivorans; Mta, Methanobacterium thermoautotrophicum; Mj, Methanococcus jannaschii; Ph, Pyrococcus horikoshii; Tac, Thermoplasma acidophilum; Bacteria: Atu, Agrobacterium tumefaciens; Aae, Aquifex aeolicus; Ana, Anabaena sp.; Bs, Bacillus subtilis; Bb, Borrelia burgdorferi; Bmel, Brucella melitensis; Cac, Clostridium acetobutylicum; Ccr, Caulobacter crescentus; Cj, Campylobacter jejuni; Des, Desulfitobacterium hafniense; Drad, Deinococcus radiodurans; Ec, Escherichia coli; Hi, Haemophilus influenzae; Hp, Helicobacter pylori; Mlo, Mesorhizobium loti; Mtu, Mycobacterium tuberculosis; Nm, Neisseria meningitidis; Pae, Pseudomonas aeruginosa; Pmar, Prochlorococcus marinus; Rcap, Rhodobacter capsulatus; Rp, Rickettsia prowazekii; Rsp, Rhodobacter sphaeroides; Rvi, Rhodopseudomonas viridis; Sli, Streptomyces lividans; Sme, Sinorhizobium meliloti; Scoe, Streptomyces coelicolor A3; Syco, Synechococcus sp.; Ssp, Synechocystis sp.; Tm, Thermotoga maritima; Tp, Treponema pallidum; Ter, Trichodesmium erythraeum; Tsyn, Thermosynechococcus elongatus; Ttep, Thermochromatium tepidum; Xf, Xylella fastidiosa; Plants: At, Arabidopsis thaliana.