Comparative analysis of protein expression from full length synthetic genes. Proteins were expressed and purified in parallel from Gene Composer engineered (E) or native (N) genes as described in Materials and Methods (see Additional File 1). Proteins from Brucella melitensis, str. biovar Abortus 2308 were compared in pairs: Pair 1) Lactate/malate dehydrogenase:L-lactate dehydrogenase:TrkA potassium uptake protein (44.8 kDa); Pair 2) CbxX/CfqX superfamily:Disease resistance protein:ATP/GTP-binding site motif A (P-loop):AAA ATPase:AAA ATPase, central region (49.4 kDa); Pair 3) Glyceraldehyde 3-phosphate dehydrogenase:TrkA potassium uptake protein:Glyceraldehyde-3-phosphate dehydrogenase, type I (47.4 kDa); Pair 4) 3' exoribonuclease:Ribonuclease PH (37.0 kDa). Burkholderia pseudomallei, str. 1710b: Pair 5) malate dehydrogenase (46.2 kDa); Pair 6) glutaryl-CoA dehydrogenase (54.3 kDa); Pair 7) glyceraldehyde-3-phosphate dehydrogenase, type I (47.3 kDa); Pair 8) beta-lactamase (44.0 kDa); Rickettsia prowazekii, str. Madrid E: Pair 9) 2,3,4,5-Tetrahydropyridine-2-Carboxylate N-Succinyltransferase (dapD) (41.3 kDa); Pair 10) Holliday junction DNA helicase RuvB (49.6 kDa); Pair 11) DNA polymerase III subunit epsilon (37.2 kDa). Bacillus subtilis, subsp. Subtilis, str. 168; Pair 12) FtsZ (full length, 42.8 kDa). Molecular weight markers are present in lanes 1, 14, 27.