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. 2015 Feb 3;35(5):899–911. doi: 10.1128/MCB.01020-14

TABLE 2.

Amino acid representation within the libraries

Amino acid(s) ND prion formation librarya
 ORD prion formation libraryb
 Prion maintenance libraryc
Frequency of amino acid in:
 Odds ratiod Frequency of amino acid in:
 Odds ratiod Frequency of amino acid in:
 Odds ratioe
Selected [PSI+] library Unselected naive library Selected [PSI+] library Unselected naive library White [PSI+] colonies Red [psi−] colonies
Individual amino acids
    Alanine 0.053 0.055 0.96 0.095 0.068 1.40 0.089 0.069 1.32
    Arginine 0.024 0.095 0.26*** 0.044 0.107 0.41** 0.054 0.121 0.41****
    Asparagine 0.061 0.031 1.95 0.047 0.021 2.24 0.038 0.032 1.20
    Aspartic acid 0.028 0.046 0.60 0.033 0.058 0.57 0.054 0.064 0.83
    Cysteine 0.065 0.071 0.91 0.084 0.062 1.35 0.072 0.047 1.58*
    Glutamic acid 0.003 0.008 0.42 0.006 0.012 0.53 0.015 0.006 2.70
    Glutamine 0.007 0.016 0.41 0.003 0.003 0.94 0.008 0.007 1.12
    Glycine 0.13 0.213 0.61* 0.144 0.151 0.95 0.114 0.109 1.05
    Histidine 0.031 0.029 1.08 0.047 0.038 1.26 0.04 0.043 0.94
    Isoleucine 0.088 0.055 1.60 0.04 0.058 0.69 0.025 0.043 0.57
    Leucine 0.065 0.071 0.91 0.058 0.06 0.96 0.04 0.063 0.62*
    Lysine 0 0 N/A 0.016 0.009 0.31 0 0.003 0.00
    Methionine 0.014 0.014 0.96 0.088 0.06 1.89 0.002 0.009 0.17
    Phenylalanine 0.121 0.042 2.88*** 0.037 0.053 1.45 0.068 0.049 1.40
    Proline 0.017 0.035 0.48 0.123 0.113 0.70 0.048 0.045 1.07
    Serine 0.109 0.125 0.87 0.04 0.038 1.09 0.12 0.102 1.20
    Threonine 0.061 0.042 1.45 0.016 0.016 1.07 0.037 0.039 0.94
    Tryptophan 0.014 0.021 0.67 0.076 0.055 1.04 0.018 0.005 4.07*
    Tyrosine 0.069 0.042 1.63 0.076 0.086 1.40 0.074 0.028 2.81****
    Valine 0.125 0.078 1.60 0.095 0.068 0.89 0.085 0.116 0.70*
Groups of amino acids
    Charged (D, E, K, R) 0.054 0.139 0.35*** 0.129 0.210 0.43*** 0.123 0.194 0.58***
    Nonaromatic hydrophobic (I, L, M, V) 0.267 0.206 1.41 0.181 0.200 0.88 0.151 0.231 0.59****
    Prion-promoting nonaromatic hydrophobic (I, M, V) 0.206 0.139 1.61* 0.126 0.143 0.86 0.111 0.168 0.62**
    Aromatic (F, W, Y) 0.186 0.101 2.04** 0.168 0.124 1.42 0.160 0.082 2.14***
    Polar (N, Q, S, T) 0.220 0.198 1.14 0.197 0.162 1.27 0.203 0.180 1.16
a

The ND library consists of 37 selected [PSI+] sequences (296 amino acids) and 62 unselected sequences (496 amino acids).

b

The ORD prion formation library consists of 31 selected [PSI+] sequences (310 amino acids) and 58 unselected sequences (580 amino acids).

c

The prion maintenance library consists of 65 white [PSI+] sequences (650 amino acids) and 87 red [psi−] sequences (870 amino acids).

d

Odds ratios reflect the degree of overrepresentation or underrepresentation of each amino acid among the prion-forming isolates, as calculated according to equation 1. Values above 1 indicate overrepresentation among prion-forming isolates. Statistical significance of the over- or underrepresentation is indicated: *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.

e

Odds ratios reflect the degree of overrepresentation or underrepresentation of each amino acid among the white (prion-propagating) isolates, as calculated using equation 3.