GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
eIF2A - Eukaryotic translation initiation factor eIF2A
Pfam: PF08662 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0186
Length: 194
Sequences: 29266
Seq/Len: 150.86
HH_delta: 0.155 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
39_F43_Y2.645494.130
68_S108_W1.793512.800
21_L67_W1.516322.367
116_V151_W1.468222.292
66_A107_S1.442992.252
107_S150_E1.387672.166
14_Q67_W1.368052.135
116_V129_F1.342232.095
12_H66_A1.31782.057
105_T118_A1.279391.997
128_E137_K1.260541.968
39_F42_F1.224841.912
109_S151_W1.209371.888
117_L130_W1.181311.844
86_T97_S1.174161.833
159_A175_I1.150791.796
131_D134_K1.066961.665
85_V117_L1.066171.664
148_D161_A1.056511.649
94_K97_S1.002411.565
130_W137_K0.976141.524
127_L160_T0.973061.519
63_H81_M0.961561.501
160_T176_W0.954011.489
128_E140_T0.943881.473
86_T94_K0.93761.464
107_S149_V0.936741.462
107_S151_W0.896621.400
157_Y175_I0.875311.366
84_K97_S0.865571.351
104_N120_F0.858631.340
152_S156_R0.855721.336
12_H65_V0.85221.330
21_L65_V0.845861.320
66_A106_I0.840891.313
119_G128_E0.82571.289
147_T163_T0.822281.284
68_S73_E0.821521.282
114_F129_F0.796921.244
109_S114_F0.787911.230
109_S113_R0.777761.214
162_T174_K0.775251.210
152_S155_G0.770151.202
73_E76_V0.764871.194
110_P151_W0.762021.189
45_N48_N0.759951.186
162_T170_D0.755521.179
64_D79_G0.753131.176
152_S157_Y0.750921.172
137_K140_T0.750621.172
114_F117_L0.749411.170
66_A108_W0.744451.162
113_R133_R0.742321.159
14_Q18_D0.740281.156
108_W132_V0.73531.148
69_P108_W0.732561.144
157_Y160_T0.72721.135
110_P155_G0.722821.128
70_N73_E0.719511.123
162_T172_G0.719231.123
19_Y22_V0.704691.100
19_Y43_Y0.703561.098
87_L108_W0.69461.084
14_Q17_G0.692761.081
64_D106_I0.689061.076
16_S19_Y0.687471.073
116_V158_L0.683021.066
68_S72_N0.67671.056
152_S159_A0.676441.056
15_P67_W0.676141.055
170_D174_K0.672381.050
87_L96_F0.670851.047
23_K65_V0.670691.047
19_Y23_K0.668271.043
40_E53_S0.667631.042
111_D114_F0.663511.036
68_S71_G0.663081.035
69_P112_G0.660271.031
103_R106_I0.651921.018
76_V88_Y0.65161.017
43_Y46_E0.650451.015
115_L132_V0.648581.012
154_D157_Y0.643551.005
123_L128_E0.641991.002
24_V40_E0.640851.000
12_H67_W0.639110.998
21_L41_L0.633480.989
129_F151_W0.633390.989
23_K62_I0.626490.978
146_A149_V0.623540.973
92_G96_F0.622110.971
96_F135_K0.611630.955
67_W90_V0.609590.952
105_T149_V0.606130.946
73_E87_L0.60350.942
116_V149_V0.601410.939
22_V42_F0.599860.936
11_L22_V0.594620.928
73_E89_D0.593120.926
51_V54_I0.589930.921
39_F44_L0.588120.918
62_I65_V0.566780.885
39_F46_E0.558270.871
114_F138_I0.555990.868
20_L23_K0.552620.863
160_T174_K0.551630.861
14_Q19_Y0.550170.859
64_D105_T0.548720.857
55_E58_K0.548290.856
15_P71_G0.546740.853
105_T148_D0.546690.853
21_L43_Y0.546030.852
106_I117_L0.545480.851
109_S112_G0.544380.850
53_S56_L0.543250.848
50_P53_S0.542860.847
63_H104_N0.540810.844
158_L178_F0.539570.842
46_E49_I0.53380.833
43_Y52_E0.531980.830
22_V44_L0.529970.827
73_E77_I0.527310.823
109_S116_V0.527180.823
118_A149_V0.525710.821
38_E43_Y0.524760.819
114_F131_D0.524140.818
127_L149_V0.523490.817
117_L128_E0.517730.808
149_V160_T0.514880.804
88_Y94_K0.512560.800
150_E159_A0.509940.796
58_K80_S0.5080.793
21_L74_F0.50730.792
141_F144_S0.500720.782
24_V38_E0.499870.780
92_G98_F0.499230.779
93_K98_F0.49650.775
22_V40_E0.496420.775
13_W151_W0.493440.770
74_F77_I0.488180.762
157_Y161_A0.486250.759
102_P120_F0.486230.759
92_G95_I0.483940.755
18_D45_N0.483120.754
64_D77_I0.479830.749
119_G123_L0.477680.746
85_V106_I0.477590.746
157_Y177_S0.475360.742
89_D93_K0.473920.740
58_K62_I0.470750.735
132_V135_K0.469080.732
127_L131_D0.468480.731
13_W20_L0.466570.728
134_K137_K0.459810.718
117_L121_G0.456470.713
78_Y88_Y0.452060.706
72_N91_K0.451930.705
51_V55_E0.450220.703
49_I54_I0.450140.703
95_I98_F0.447760.699
19_Y90_V0.447660.699
12_H21_L0.446880.698
56_L59_E0.44640.697
96_F99_G0.445720.696
98_F130_W0.44570.696
81_M104_N0.445270.695
45_N49_I0.444190.693
82_P86_T0.443010.692
116_V178_F0.442810.691
58_K82_P0.442470.691
144_S160_T0.441140.689
76_V80_S0.44010.687
158_L161_A0.440030.687
156_R177_S0.439650.686
80_S84_K0.433970.677
63_H102_P0.431840.674
118_A146_A0.431250.673
22_V25_Q0.430930.673
113_R131_D0.430930.673
146_A160_T0.429070.670
19_Y67_W0.428310.669
119_G122_N0.425890.665
24_V42_F0.424350.662
89_D92_G0.423250.661
70_N112_G0.423220.661
79_G103_R0.419940.656
173_F177_S0.419330.655
81_M120_F0.419230.654
48_N52_E0.415820.649
115_L118_A0.414590.647
47_K50_P0.41340.645
13_W67_W0.412580.644
38_E53_S0.412350.644
151_W158_L0.411160.642
46_E50_P0.411080.642
134_K138_I0.410870.641
120_F163_T0.410580.641
129_F141_F0.410250.640
110_P153_P0.409830.640
94_K99_G0.409790.640
72_N89_D0.409520.639
139_S142_E0.409450.639
129_F138_I0.408980.638
19_Y45_N0.407550.636
38_E42_F0.407480.636
94_K98_F0.405550.633
156_R159_A0.405550.633
61_P81_M0.404880.632
151_W178_F0.404420.631
52_E56_L0.403370.630
80_S83_A0.402820.629
81_M102_P0.402740.629
129_F139_S0.401310.626
13_W44_L0.396850.619
89_D95_I0.39590.618
103_R117_L0.394580.616
104_N147_T0.393410.614
77_I103_R0.391850.612
144_S170_D0.38760.605
11_L20_L0.385360.602
76_V79_G0.383680.599
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
1nr0A0.896999.80.155
1nr0A0.809399.80.172
2j04A0.922799.80.181
3dm0A0.881499.80.184
2ymuA0.783599.80.185
4h5iA0.886699.80.185
4gqbB0.881499.80.186
1vyhC0.881499.80.186
2ymuA0.871199.80.188
3dwlC0.881499.80.191

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