Figure 1.

Multiple sequence alignment of the NlpC/P60 superfamily. Multiple sequence alignments of the different families of NlpC/P60 were constructed using T-Coffee [35] after parsing high-scoring pairs from PSI-BLAST search results. The PHD-secondary structure [36] 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 are (l, ALIVMC, yellow shading), small (s, ACDGNPSTV, green) and polar (p, CDEHKNQRST, blue). A 'G', 'D', 'C' or 'N' shows the completely conserved amino acid in that group. The numbers colored light blue show the region where a zinc ribbon domain is inserted in the Arabidopsis LRAT homologs. The catalytic residues are highlighted in red, while the conserved cysteine present in LRAT and related proteins is colored red. Specific columns of residues that are peculiar to a particular category of NlpC/P60 (see text) are colored red. The consensus of the individual families and the entire superfamily are shown, and the subgroups of each family are separated by a space. The limits of the domains are indicated by the residue positions, in bold, on each side, or internally in the case of the permuted versions. A dotted line separates the amino and carboxyl termini of the permuted versions. 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 GeneBank identifier (gi). An alignment covering members of the bacterial P60 family is available in PFAM [78]. The species abbreviations are: Af, Archaeoglobus fulgidus; BPDP1, bacteriophage Dp-1; Ana, Anabaena; Atu, Agrobacterium tumefaciens; Ban, Bacillus anthracis; Bha, Bacillus halodurans; Bs, Bacillus subtilis; Bmel, Brucella melitensis; Cac, Clostridium acetobutylicum; Ccr, Caulobacter crescentus; Cj, Campylobacter jejuni; Ct, Chlamydia trachomatis; Cpn, Chlamydophila pneumoniae; Dr, Deinococcus radiodurans; Ec, Escherichia coli; Hi, Haemophilus influenzae; Hp, Helicobacter pylori; Lla, Lactococcus lactis; Lin, Listeria innocua; Lmo, Listeria monocytogenes; Mle, Mycobacterium leprae; Mlo, Mesorhizobium loti; Mtu, Mycobacterium tuberculosis; Nm, Neisseria meningitidis; Pae, Pseudomonas aeruginosa; Pmu, Pasteurella multocida; Rsol, Ralstonia solanacearum; Rrhi, Rhizobium rhizogenes; St, Salmonella typhimurium; Sme, Sinorhizobium meliloti; Sa, Staphylococcus aureus; Scoe, Streptomyces coelicolor A3; Spn, Streptococcus pneumoniae; Spy, Streptococcus pyogenes; Ssp, Synechocystis sp.; Tm, Thermotoga maritima; Vch, Vibrio cholerae; Xaxo, Xanthomonas axonopodis; Xf, Xylella fastidiosa; Ype, Yersinia pestis; At, Arabidopsis thaliana; Ce, Caenorhabditis elegans; Cfas, Crithidia fasciculata; Hs, Homo sapiens; Mm, Mus musculus; Rn, Rattus norvegicus; Tcr, Trypanosoma cruzi; CV, cowpox virus; FPV, fowlpox virus; MCV, molluscum contagiosum virus; MV, myxoma virus; RFV, rabbit fibroma virus; ShPV, sheeppox virus; SPV, swinepox virus; VV, vaccinia virus; VarV, variola virus; YDV, Yaba-like disease virus; AMV, Amsacta moorei entomopoxvirus; MSV, Melanoplus sanguinipes entomopoxvirus; AiV, Aichi virus; BCV, bovine calicivirus; ChV, Chiba virus; LV, Lordsdale virus; NorV, Norwalk virus; ShV, Southampton virus; Aev, avian encephalomyelitis virus.