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. 2013 Jan;79(2):559–568. doi: 10.1128/AEM.02407-12

Table 2.

Bioinformatics analysis of selected CSP random mutants: predicted signal sequence properties and translational attributes

Mutant Amino acid sequencea D scoreb Cleavage siteb Net charge of N domainc Net hydrophobicity of H domaind Relative translation rate prediction (AU)e Minimum free energy (kcal mol−1)f
CSP mkkkllalallallfngaqam 0.875 AQA-MA +3 9.11 1.00 –29.84
S2 .yrnk.v...c...l..p... 0.804 AMA-HP +2 8.67 0.53 –31.40
S7 .qe..cq...i.......e.. 0.520 AMA-HP* 0 7.19 2.57 –28.80
S15 .rs...s.gv.li.a..gk.. 0.682 AMA-HP +2 8.38 1.09 –28.60
S38 ..r.................. 0.877 AQA-MA +3 9.11 1.00 –29.84
S43 ..s..f..em.v......... 0.678 AMA-HP +2 7.92 0.99 –24.24
S46 ..rs..s....e......... 0.671 AMA-HP +2 6.95 0.14 –26.50
S47 ..rtf.d.....s..s..... 0.689 AMA-HP +2 6.95 0.58 –27.20
S48 ..r...v.....v....eh.. 0.725 AMA-HP +3 9.59 0.33 –27.94
S49 ..r....i...rvsly..... 0.707 AMA-HP +3 5.97 0.33 –28.64
S54 ..r.ff.vt.i.gfgi..... 0.615 AMA-HP +3 9.91 1.64 –25.80
S60 .qq..ssr...pv.lys.... 0.666 AMA-HP +1 4.18 0.87 –26.10
S61 .......v............. 0.884 AQA-MA +3 9.13 1.00 –29.74
a

Periods (.) indicate that the amino acid is identical to the one in CSP at this position.

b

Calculated by SignalP 4.0 (38). S7 did not meet the cutoff criteria. *, the reported cleavage site gave the best score.

c

Calculated for the first five residues, with amino acids D and E defined as −1, R and K defined as +1 and any other amino acid as 0.

d

Calculated as the sum of hydrophobicity for the hydrophobic region (residues 6 to 17), based on the normalized consensus hydrophobicity scale (47).

e

Calculated by the RBS calculator v1.1, reverse engineering mode (39). AU, arbitrary unit(s).

f

Minimum free energy predicted by RNAfold (40) for the optimal secondary structure of the region surrounding the translation initiation site. The analyzed sequence included 32 bp of the nontranslated region, the signal sequence, and 36 bp of the mature bla coding sequence.