Table 2

A selected set of 10 proteins from P. aerophilum predicted by the Triangle Method to have disulfide bonds, contrasted with homologs from E. coli that do not have disulfide bonds

PA IDE. coli IDPA/EC E valuePDB matchPA/PDB E valueEC/PDB E value
pag5_1383ecoli-17862207.00E-243hdha00
pag5_2460ecoli-17868092.00E-241qdla00
pag5_2582ecoli-17888692.00E-10 1rhd 01.43E-08
pag5_2887ecoli-17903985.00E-401aosa00
pag5_3221ecoli-17862369.00E-27 1yub 7.89E-101.33E-08
pag5_3343ecoli-17881841.00E-291bs2a00
pag5_3383ecoli-17903831.00E-10 1dik 2.59E-140
pag5_3453ecoli-17902885.00E-101e5ka04.16E-09
pag5_3596ecoli-17898253.00E-181qmhb00
pag5_63ecoli-17863191.00E-221g2915.97E-140
  • The first two columns give the identification numbers (ID) for the genome sequences. The third column gives the blast E values between the two sequences, showing high similarities (low scores). Columns 5 and 6 give the blast E values between the P. aerophilum (PA) and E. coli (EC) sequences, respectively, and the sequence of the protein of known structure identified in column 4. Again, the E values are small, indicating structural similarity among all three proteins. In each case, the P. aerophilum protein contains at least one pair of cysteine residues whose Cα atoms lie in proximity when mapped onto the Protein Data Bank (PDB) structure. This suggests that each P. aerophilum protein may form a disulfide bond in an oxidizing environment. The corresponding E. coli proteins cannot form disulfide bonds, because they lack spatially proximal cysteine residues.