GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Thioredoxin_4 - Thioredoxin
Pfam: PF13462 (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: CL0172
Length: 162
Sequences: 5681
Seq/Len: 35.07
HH_delta: 0.1 (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
70_C112_C1.393063.973
15_T48_K0.991412.827
17_T52_R0.909792.594
40_K157_K0.905582.582
15_T50_V0.875912.498
17_T50_V0.812372.317
105_S108_Q0.778472.220
106_N110_N0.704322.008
120_A124_A0.69381.978
127_Q131_Q0.683121.948
77_Y80_F0.66391.893
36_K153_I0.65061.855
26_H29_K0.64861.850
96_K110_N0.636731.816
30_F140_F0.631321.800
79_W83_E0.613081.748
152_T155_E0.602181.717
16_V47_V0.598031.705
24_C27_C0.594051.694
100_A106_N0.579111.651
54_V129_A0.558941.594
22_F68_A0.555271.583
18_E140_F0.539031.537
19_F128_L0.531921.517
153_I157_K0.52541.498
36_K40_K0.500331.427
36_K39_K0.497391.418
55_P126_S0.494631.411
141_F146_Y0.493311.407
110_N114_N0.488391.393
127_Q130_R0.487561.390
52_R128_L0.484451.381
108_Q112_C0.478421.364
119_K123_E0.466971.332
40_K153_I0.464151.324
22_F82_H0.456151.301
107_E111_K0.45551.299
53_P69_E0.437831.249
78_F82_H0.435561.242
66_M119_K0.431311.230
21_D61_S0.429381.224
128_L132_L0.426921.217
155_E158_E0.42531.213
20_F51_F0.423941.209
96_K106_N0.421681.202
128_L131_Q0.420371.199
140_F156_L0.420161.198
27_C137_T0.414921.183
123_E126_S0.411831.174
62_L66_M0.410341.170
19_F129_A0.409621.168
67_A109_F0.402541.148
31_H35_E0.402481.148
16_V142_I0.399071.138
151_Y155_E0.398451.136
22_F65_A0.389541.111
71_V75_G0.388921.109
108_Q111_K0.383711.094
69_E121_Q0.382421.091
126_S130_R0.381621.088
52_R125_D0.375611.071
22_F53_P0.372031.061
123_E127_Q0.3681.049
120_A123_E0.367321.047
37_L41_Y0.36671.046
28_A32_E0.364661.040
139_T146_Y0.363621.037
116_D120_A0.36361.037
19_F52_R0.36131.030
29_K33_E0.360421.028
115_S118_I0.359911.026
117_E120_A0.357141.018
69_E125_D0.356251.016
124_A127_Q0.354931.012
53_P125_D0.353591.008
129_A134_I0.351411.002
73_D118_I0.350771.000
66_M69_E0.348970.995
24_C137_T0.348150.993
124_A128_L0.348140.993
18_E49_F0.345530.985
73_D117_E0.344320.982
107_E110_N0.336160.959
23_Q61_S0.335210.956
17_T141_F0.334290.953
155_E159_L0.328210.936
57_D60_S0.325990.930
41_Y44_P0.325050.927
97_D101_N0.324960.927
83_E87_S0.32430.925
18_E31_H0.322210.919
65_A69_E0.321120.916
70_C74_Q0.32060.914
96_K99_A0.319510.911
99_A103_G0.318830.909
80_F84_L0.318660.909
68_A71_V0.315680.900
80_F83_E0.314080.896
31_H82_H0.31340.894
26_H136_G0.313190.893
34_L49_F0.31220.890
121_Q125_D0.311340.888
14_I143_N0.309940.884
30_F34_L0.307420.877
156_L159_L0.306270.873
83_E88_Q0.30270.863
71_V74_Q0.301150.859
20_F27_C0.300870.858
68_A78_F0.299050.853
77_Y81_F0.29650.846
74_Q112_C0.292250.833
69_E73_D0.290770.829
154_E157_K0.288540.823
142_I159_L0.287630.820
84_L101_N0.287350.819
21_D56_L0.285840.815
84_L98_I0.285590.814
136_G139_T0.282810.806
21_D24_C0.281490.803
33_E36_K0.280520.800
118_I121_Q0.27970.798
134_I139_T0.279530.797
90_E97_D0.279290.796
54_V57_D0.278970.796
148_V151_Y0.278260.794
33_E153_I0.278050.793
154_E158_E0.274590.783
35_E39_K0.273770.781
37_L153_I0.273640.780
62_L123_E0.273640.780
98_I102_A0.273310.779
145_K159_L0.271160.773
86_F89_Q0.271090.773
73_D112_C0.27040.771
79_W82_H0.269370.768
81_F84_L0.268610.766
116_D119_K0.26830.765
97_D100_A0.26810.765
71_V104_G0.266010.759
74_Q108_Q0.265590.757
41_Y157_K0.264160.753
31_H51_F0.26280.749
121_Q124_A0.262290.748
19_F132_L0.262240.748
27_C135_T0.261460.746
111_K115_S0.261420.745
81_F85_L0.260270.742
68_A72_A0.259840.741
91_N94_N0.259630.740
55_P58_K0.258070.736
25_P137_T0.257950.736
151_Y156_L0.257940.736
17_T128_L0.256610.732
69_E72_A0.256610.732
74_Q106_N0.25660.732
70_C73_D0.254810.727
112_C118_I0.253020.722
33_E152_T0.250360.714
32_E35_E0.249580.712
88_Q92_F0.248350.708
136_G148_V0.248250.708
54_V137_T0.247140.705
66_M122_L0.24640.703
25_P29_K0.244590.697
147_V159_L0.244380.697
96_K100_A0.24410.696
57_D61_S0.241890.690
126_S129_A0.240520.686
68_A81_F0.237930.678
35_E38_L0.237820.678
38_L41_Y0.237030.676
71_V81_F0.236190.674
56_L136_G0.235530.672
63_R66_M0.235190.671
14_I142_I0.234990.670
35_E83_E0.232720.664
140_F150_P0.231880.661
56_L59_H0.231790.661
71_V109_F0.229370.654
84_L88_Q0.228750.652
66_M116_D0.227760.649
14_I47_V0.22680.647
55_P61_S0.225740.644
69_E122_L0.225170.642
100_A110_N0.224820.641
20_F78_F0.22480.641
139_T148_V0.223220.637
19_F141_F0.222680.635
65_A82_H0.221980.633
29_K150_P0.221220.631
134_I141_F0.218360.623
92_F95_K0.217870.621
27_C31_H0.21770.621
149_G152_T0.21740.620
62_L119_K0.217340.620
86_F92_F0.216930.619
67_A71_V0.213980.610
25_P56_L0.213770.610
82_H87_S0.213550.609
147_V151_Y0.21320.608
23_Q59_H0.213160.608
73_D121_Q0.21310.608
122_L125_D0.213050.608
18_E30_F0.212410.606
46_K50_V0.20980.598
61_S65_A0.209230.597
17_T132_L0.206920.590
55_P129_A0.206050.588
18_E34_L0.205620.586
109_F113_L0.205430.586
16_V34_L0.205020.585
20_F82_H0.204660.584
80_F88_Q0.204110.582
23_Q57_D0.202890.579
67_A81_F0.201660.575
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
3f4sA0.987799.90.1
3ghaA199.90.103
3gmfA0.981599.90.118
3bciA0.993899.90.146
3gykA0.975399.90.188
3gn3A0.956899.90.212
4dvcA0.981599.90.233
2remA0.975399.90.239
2znmA0.975399.90.249
3h93A0.975399.90.249

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