GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AAA_28 - AAA domain
Pfam: PF13521 (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: CL0023
Length: 163
Sequences: 15744
Seq/Len: 96.59
HH_delta: 0.416 (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
48_W91_F2.022793.589
83_L86_L1.717173.046
76_V81_G1.70753.029
108_R150_I1.550112.750
143_E147_R1.273472.259
75_V84_D1.248252.215
24_Y30_Y1.245622.210
75_V80_R1.228182.179
4_I15_L1.193792.118
64_L67_E1.035791.838
140_L143_E1.006421.785
81_G84_D1.000581.775
77_I143_E0.983381.745
37_E93_F0.899721.596
86_L90_E0.893771.586
16_I155_V0.870561.544
87_A90_E0.845451.500
4_I153_I0.845431.500
88_Y99_E0.840761.492
142_K146_E0.834031.480
110_D150_I0.826291.466
45_T48_W0.825991.465
36_E39_G0.810871.439
73_S77_I0.802321.423
111_L151_P0.798161.416
56_Q103_E0.787371.397
144_L150_I0.776841.378
113_F153_I0.773441.372
70_A73_S0.760971.350
145_L152_Y0.75781.344
142_K145_L0.756841.343
70_A108_R0.750921.332
136_R139_E0.743711.319
135_E139_E0.740991.315
75_V81_G0.731421.298
63_Q67_E0.711271.262
15_L18_A0.709811.259
18_A25_P0.700691.243
75_V79_D0.692611.229
20_A113_F0.684271.214
25_P28_P0.683831.213
114_L152_Y0.680991.208
134_R159_S0.676791.201
139_E142_K0.67631.200
38_G41_R0.671191.191
79_D84_D0.670511.190
134_R138_D0.668741.186
63_Q66_A0.665431.181
78_C81_G0.664521.179
113_F155_V0.653071.159
66_A69_S0.643131.141
51_D54_A0.642091.139
60_L107_S0.637861.132
133_E136_R0.632931.123
35_I38_G0.629231.116
52_L88_Y0.62691.112
44_D48_W0.625691.110
72_S84_D0.624251.107
132_E136_R0.622751.105
65_E69_S0.620461.101
72_S81_G0.619761.100
114_L141_L0.618471.097
73_S76_V0.605151.074
47_P51_D0.604591.073
91_F95_D0.602091.068
55_F59_I0.5971.059
69_S73_S0.593531.053
141_L152_Y0.59271.052
116_P142_K0.590531.048
97_P100_L0.586111.040
57_E106_L0.58591.039
37_E41_R0.583781.036
118_D137_I0.581951.032
52_L56_Q0.578991.027
91_F140_L0.569041.010
132_E135_E0.567271.006
53_L106_L0.566721.005
142_K154_I0.566681.005
80_R143_E0.557270.989
139_E143_E0.55640.987
25_P74_D0.555310.985
72_S76_V0.553690.982
154_I157_S0.552070.979
8_P133_E0.548990.974
143_E146_E0.546550.970
66_A70_A0.543580.964
114_L154_I0.543320.964
75_V78_C0.538080.955
95_D98_E0.529740.940
3_V154_I0.528770.938
4_I155_V0.52760.936
112_V152_Y0.526780.935
68_A71_K0.525570.932
10_T117_P0.524940.931
100_L103_E0.524580.931
73_S108_R0.522810.928
16_I113_F0.517350.918
39_G42_D0.51520.914
118_D138_D0.511840.908
56_Q59_I0.511730.908
80_R83_L0.510480.906
76_V80_R0.510450.906
8_P98_E0.509930.905
97_P119_P0.509550.904
57_E60_L0.508610.902
37_E42_D0.507080.900
80_R84_D0.505480.897
19_L113_F0.502830.892
37_E40_R0.501860.890
52_L103_E0.500060.887
131_P135_E0.499010.885
74_D78_C0.497610.883
98_E133_E0.496990.882
138_D142_K0.495870.880
98_E102_R0.492980.875
77_I81_G0.492620.874
69_S72_S0.491610.872
58_G61_E0.489930.869
121_W137_I0.489230.868
2_I153_I0.488630.867
116_P138_D0.487440.865
93_F138_D0.485860.862
48_W99_E0.484030.859
36_E40_R0.481040.853
15_L19_L0.480270.852
104_A112_V0.47340.840
112_V150_I0.472650.839
77_I80_R0.471710.837
96_Y100_L0.470670.835
54_A71_K0.46770.830
130_D158_G0.462010.820
93_F119_P0.461010.818
64_L68_A0.457180.811
75_V83_L0.456080.809
5_T160_I0.45560.808
28_P31_A0.447880.795
42_D110_D0.443840.787
83_L95_D0.443120.786
54_A58_G0.442110.784
45_T89_S0.4420.784
34_I39_G0.441910.784
8_P158_G0.439620.780
54_A68_A0.438870.779
101_E137_I0.438150.777
111_L153_I0.434220.770
79_D136_R0.434150.770
13_T17_E0.433880.770
57_E61_E0.432560.767
57_E62_Q0.432230.767
74_D77_I0.430150.763
54_A67_E0.428120.760
131_P160_I0.428080.759
51_D55_F0.427950.759
47_P52_L0.426660.757
72_S75_V0.424620.753
35_I48_W0.420870.747
36_E41_R0.414880.736
155_V159_S0.413260.733
34_I37_E0.412640.732
53_L56_Q0.412040.731
6_G11_G0.409460.726
93_F97_P0.404770.718
37_E48_W0.401730.713
74_D102_R0.401370.712
84_D87_A0.398270.707
76_V79_D0.397130.705
47_P87_A0.397070.704
56_Q60_L0.395270.701
62_Q67_E0.393640.698
48_W95_D0.393120.697
55_F58_G0.393090.697
44_D96_Y0.392520.696
58_G62_Q0.388540.689
135_E138_D0.385430.684
19_L25_P0.383370.680
71_K80_R0.382560.679
8_P134_R0.382290.678
35_I40_R0.380750.675
63_Q68_A0.377320.669
41_R44_D0.376420.668
98_E130_D0.375240.666
118_D121_W0.374990.665
67_E70_A0.374730.665
3_V157_S0.37440.664
52_L55_F0.37440.664
117_P121_W0.374050.664
80_R99_E0.372390.661
71_K74_D0.370650.658
145_L151_P0.370450.657
77_I147_R0.370130.657
16_I153_I0.367910.653
78_C83_L0.367740.652
4_I115_L0.367160.651
26_V30_Y0.365910.649
118_D157_S0.365590.649
92_Y95_D0.364090.646
138_D154_I0.363720.645
54_A57_E0.363190.644
52_L59_I0.362550.643
26_V29_E0.361540.641
71_K75_V0.360290.639
2_I151_P0.358680.636
51_D57_E0.35470.629
44_D47_P0.353050.626
52_L57_E0.351870.624
102_R105_R0.351470.624
4_I16_I0.350640.622
74_D80_R0.347770.617
138_D157_S0.34770.617
35_I101_E0.347270.616
114_L138_D0.345240.612
106_L109_Y0.344440.611
16_I77_I0.344130.611
136_R140_L0.343990.610
30_Y33_E0.343540.609
102_R106_L0.342810.608
38_G45_T0.342320.607
7_G134_R0.337160.598
59_I62_Q0.334730.594
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
4hlcA0.993999.70.416
3hjnA0.993999.60.43
3tmkA0.993999.60.436
3ld9A0.993999.60.441
3v9pA0.987799.60.462
4edhA199.50.468
3lv8A0.993999.50.47
4tmkA0.993999.50.471
4eaqA0.993999.50.497
1p6xA199.40.526

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