Figure 2

Multiple alignment of ThiS/MoaD-like ubiquitin domain containing proteins. Proteins are listed by gene name, species abbreviation and gi number, separated by underscores. Amino acid residues are colored according to side chain properties and the extent of conservation in the multiple alignment. Coloring is indicative of 70% consensus, which is shown on the last line of the alignment. Consensus similarity designations and coloring scheme are as follows: h, hydrophobic residues (ACFILMVWY), shaded yellow; s, small residues (AGSVCDN), colored green; o, alcohol group containing residues (ST), colored blue; and b, big residues (EFHIKLMQRWY), colored purple and shaded in light gray. Secondary structure assignments are shown above the alignment, where E represents a strand and H represents a helix. The families of the ubiquitin-related domains are shown to the right. Also shown to the right are the row numbers in Table 1, which describe a particular family. Species abbreviations are as follows: Aaeo, Aquifex aeolicus; Adeh, Anaeromyxobacter dehalogenans; Aehr, Alkalilimnicola ehrlichei; Aful, Archaeoglobus fulgidus; Amac, Alteromonas macleodii; Amet, Alkaliphilus metalliredigenes; Asp., Arthrobacter sp.; Azsp, Azoarcus sp.; Atha, Arabidopsis thaliana; Avar, Anabaena variabilis; BJK0, Bacteriophage JK06; Bbro, Bordetella bronchiseptica; Bcen, Burkholderia cenocepacia; Bcep, Burkholderia cepacia; Bcer, Bacillus cereus; Bcla, Bacillus clausii; Blic, Bacillus licheniformis, Bphi, Bacteriophage phiE125; Bsp., Bradyrhizobium sp.; Bsub, Bacillus subtilis; Bthe, Bacteroides thetaiotaomicron; Bthu, Bacillus thuringiensis; Bvie, Burkholderia vietnamiensis; Cace, Clostridium acetobutylicum; Caur, Chloroflexus aurantiacus; Ccol, Campylobacter coli; Cele, Caenorhabditis elegans; Cinc, Chlamydomonas incerta; Cjej, Campylobacter jejuni; Cnec, Cupriavidus necator; Cper, Clostridium perfringens; Cpha, Chlorobium phaeobacteroides; Csac, Caldicellulosiruptor saccharolyticus; Ctet, Clostridium tetani; Dace, Desulfuromonas acetoxidans; Daro, Dechloromonas aromatica; Dhaf, Desulfitobacterium hafniense; Dmel, Drosophila melanogaster; Dpsy, Desulfotalea psychrophila; Drad, Deinococcus radiodurans; Dvul, Desulfovibrio vulgaris; Ecol, Escherichia coli; Elit, Erythrobacter litoralis; Epha, Enterobacteria phage; Fsp., Frankia sp.; Glam, Giardia lamblia; Gmet, Geobacter metallireducens; Goxy, Gluconobacter oxydans; Gsul, Geobacter sulfurreducens; Gura, Geobacter uraniumreducens; Hsap, Homo sapiens; Hsp., Halobacterium sp.; Mace, Methanosarcina acetivorans; Maqu, Marinobacter aquaeolei; Mdeg, Microbulbifer degradans; Mfla, Mycobacterium flavescens, Mgry, Magnetospirillum gryphiswaldense; Mjan, Methanocaldococcus jannaschii; Mlot, Mesorhizobium loti; Mmag, Magnetospirillum magnetotacticum; Mmus, Mus musculus; Msp., Magnetococcus sp.; Mtub, Mycobacterium tuberculosis; Neur, Nitrosomonas europaea; Nfar, Nocardia farcinica; Nham, Nitrobacter hamburgensis; Nisp, Nitrobacter sp.; Nmen, Neisseria meningitidis; Nmul, Nitrosospira multiformis; Noce, Nitrosococcus oceani; Nosp, Nocardioides sp.; Nsp., Nostoc sp.; Nwin, Nitrobacter winogradskyi; Obat, Oceanicola batsensis; PBP-, Phage BP-4795; Paby, Pyrococcus abyssi; Paer, Pseudomonas aeruginosa; Parc, Psychrobacter arcticus; Pber, Parvularcula bermudensis; Pcar, Pelobacter carbinolicus; Pflu, Pseudomonas fluorescens; Pfur, Pyrococcus furiosus; Phor, Pyrococcus horikoshii; Pmen, Pseudomonas mendocina; Pnap, Polaromonas naphthalenivorans; Posp, Polaromonas sp.; Ppro, Pelobacter propionicus; Pput, Pseudomonas putida; Psp., Pseudomonas sp.; Psyr, Pseudomonas syringae; Retl, Rhizobium etli; Reut, Ralstonia eutropha; Rfer, Rhodoferax ferrireducens; Rmet, Ralstonia metallidurans; Rosp, Roseovarius sp.; Rpal, Rhodopseudomonas palustris; Rsol, Ralstonia solanacearum; RhNGR234a, Rhizobium sp. NGR234a plasmid; Rsp, Rhizobium sp. NGR234; Rsph, Rhodobacter sphaeroides; Rusp, Ruegeria sp.; Rxyl, Rubrobacter xylanophilus; Saci, Syntrophus aciditrophicus; Save, Streptomyces avermitilis; Scer, Saccharomyces cerevisiae; Scoe, Streptomyces coelicolor; Sdis, Spisula solidissima; Sepi, Staphylococcus epidermidis; Spom, Schizosaccharomyces pombe; Spur, Strongylocentrotus purpuratus; Srub, Salinibacter ruber; Ssol, Sulfolobus solfataricus; Ssp., Synechocystis sp.; Swsp, Shewanella sp.; Tfus, Thermobifida fusca; Tmar, Thermotoga maritima; Tpar, Theileria parva; Vcho, Vibrio cholerae; Vfis, Vibrio fischeri; Vpar, Vibrio parahaemolyticus; Vsp., Vibrio sp.; Wsuc, Wolinella succinogenes; Xaxo, Xanthomonas axonopodis; Xcam, Xanthomonas campestris; Ymol, Yersinia mollaretii; Ypes, Yersinia pestis.