GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AAA_12 - AAA domain
Pfam: PF13087 (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: 200
Sequences: 4751
Seq/Len: 23.75
HH_delta: 0.11 (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
34_S187_S0.993543.875
114_S158_D0.928183.620
158_D190_K0.828023.230
116_G157_A0.781893.050
158_D191_S0.759642.963
150_D181_R0.745992.910
119_T125_V0.649982.535
93_E131_A0.638432.490
162_V185_A0.574392.240
159_I192_G0.569562.222
145_K155_Q0.56812.216
116_G160_V0.561692.191
95_I161_I0.548032.138
95_I196_I0.540622.109
23_Q26_M0.538922.102
98_L161_I0.536922.094
100_R135_R0.535142.087
69_F197_G0.516282.014
92_A131_A0.505521.972
161_I196_I0.49841.944
31_A45_S0.480451.874
87_Y127_L0.475111.853
145_K157_A0.470841.837
92_A127_L0.466831.821
32_D36_R0.456921.782
21_T44_V0.425451.659
91_E163_S0.418171.631
99_V117_I0.411621.606
92_A96_V0.411191.604
28_P32_D0.40821.592
19_M42_K0.402931.572
94_F97_E0.401941.568
125_V129_R0.396721.547
157_A160_V0.392091.529
102_L159_I0.383441.496
153_Q183_N0.380991.486
33_F37_L0.377971.474
149_V185_A0.373581.457
26_M31_A0.366151.428
96_V131_A0.365831.427
21_T42_K0.365291.425
98_L196_I0.356941.392
128_I163_S0.351321.370
159_I194_I0.350831.368
23_Q31_A0.348411.359
95_I99_V0.346351.351
127_L131_A0.345521.348
100_R104_D0.341.326
118_I149_V0.338811.322
166_R174_G0.338281.319
27_H66_P0.337131.315
98_L194_I0.333571.301
26_M34_S0.33211.295
116_G152_F0.331051.291
184_V188_R0.330081.287
95_I163_S0.328851.283
152_F157_A0.319581.247
148_T151_S0.318751.243
147_S152_F0.315461.230
118_I152_F0.312961.221
127_L130_K0.312281.218
98_L101_D0.311311.214
90_D93_E0.301321.175
125_V146_V0.299721.169
18_V22_E0.294021.147
92_A128_I0.291571.137
164_L195_I0.289861.131
91_E124_Q0.287931.123
30_I189_A0.28721.120
36_R41_G0.284041.108
99_V132_L0.283521.106
152_F160_V0.280791.095
147_S151_S0.279691.091
131_A135_R0.278071.085
72_V94_F0.276511.079
25_R154_G0.275241.074
6_F9_L0.274031.069
31_A35_S0.268181.046
120_P178_D0.268061.046
99_V115_I0.264861.033
181_R184_V0.262431.024
132_L146_V0.260651.017
99_V103_L0.25711.003
122_R148_T0.256931.002
29_E66_P0.256040.999
22_E46_G0.25590.998
167_T198_N0.255720.997
101_D105_N0.254970.995
96_V100_R0.254610.993
26_M30_I0.252320.984
161_I194_I0.250830.978
162_V193_L0.249320.972
20_L25_R0.249210.972
88_N91_E0.247870.967
128_I146_V0.246560.962
124_Q165_V0.244540.954
117_I146_V0.242790.947
10_I17_V0.241880.943
89_P131_A0.240710.939
99_V144_I0.240530.938
131_A134_S0.240360.938
31_A34_S0.237110.925
118_I160_V0.236160.921
77_S80_E0.235340.918
153_Q184_V0.234290.914
76_E79_S0.233340.910
89_P93_E0.232550.907
184_V187_S0.231410.903
120_P181_R0.230930.901
124_Q163_S0.23090.901
30_I67_I0.227920.889
186_L193_L0.226710.884
7_E11_K0.224080.874
120_P149_V0.222210.867
96_V135_R0.220860.861
70_I194_I0.219150.855
119_T128_I0.218880.854
108_D114_S0.218370.852
115_I159_I0.217750.849
77_S89_P0.215550.841
25_R156_E0.214230.836
39_Y153_Q0.212580.829
24_Y116_G0.210530.821
34_S183_N0.210050.819
49_V52_R0.209090.816
165_V195_I0.2090.815
22_E44_V0.208720.814
113_S158_D0.207160.808
27_H189_A0.206750.806
121_Y175_F0.206580.806
93_E97_E0.204830.799
162_V195_I0.204250.797
124_Q127_L0.20160.786
150_D184_V0.201520.786
97_E100_R0.200740.783
28_P50_K0.199260.777
95_I117_I0.199080.777
106_G109_S0.19660.767
28_P45_S0.196550.767
135_R138_S0.19650.766
94_F196_I0.196010.765
151_S156_E0.195450.762
50_K53_P0.194810.760
65_N68_V0.193580.755
123_A126_A0.190940.745
97_E101_D0.190870.744
117_I128_I0.190780.744
25_R188_R0.190350.742
189_A193_L0.189610.740
74_G79_S0.188780.736
94_F98_L0.188680.736
121_Y150_D0.187790.732
74_G90_D0.1870.729
44_V50_K0.185980.725
30_I116_G0.185530.724
121_Y124_Q0.185310.723
88_N166_R0.184360.719
85_S88_N0.184130.718
91_E95_I0.183650.716
128_I132_L0.183240.715
156_E188_R0.182270.711
105_N108_D0.180550.704
18_V21_T0.179850.702
185_A188_R0.179790.701
164_L183_N0.178830.698
68_V192_G0.178680.697
119_T163_S0.178580.697
101_D104_D0.17820.695
75_S79_S0.178180.695
39_Y43_L0.177520.692
153_Q187_S0.175710.685
103_L109_S0.175390.684
171_S174_G0.175050.683
39_Y183_N0.174140.679
153_Q164_L0.17390.678
93_E96_V0.173380.676
27_H191_S0.172060.671
179_P182_L0.170720.666
133_R137_P0.170450.665
96_V99_V0.170040.663
46_G50_K0.169020.659
173_I176_L0.168810.658
75_S78_S0.168440.657
102_L194_I0.168330.657
64_Q192_G0.167730.654
178_D186_L0.167620.654
89_P127_L0.167460.653
150_D153_Q0.167460.653
175_F178_D0.166550.650
33_F186_L0.165560.646
51_N54_A0.16510.644
99_V161_I0.164880.643
93_E135_R0.16370.639
122_R151_S0.163670.638
70_I97_E0.163580.638
74_G77_S0.163310.637
149_V153_Q0.163180.636
70_I196_I0.163040.636
75_S90_D0.162920.635
175_F181_R0.162330.633
118_I157_A0.162240.633
153_Q181_R0.161810.631
152_F183_N0.161710.631
168_N171_S0.161620.630
70_I98_L0.160460.626
72_V90_D0.159990.624
170_S174_G0.159620.623
67_I193_L0.159530.622
25_R184_V0.158930.620
97_E135_R0.158690.619
38_F179_P0.157240.613
51_N55_P0.155430.606
64_Q67_I0.154350.602
103_L106_G0.153730.600
7_E10_I0.152860.596
122_R126_A0.152770.596
90_D94_F0.152620.595
43_L184_V0.152140.593
85_S175_F0.151840.592
52_R55_P0.15170.592
23_Q45_S0.151210.590
155_Q183_N0.150640.588
26_M150_D0.150610.587
183_N187_S0.150590.587
193_L197_G0.150530.587
87_Y92_A0.150490.587
116_G155_Q0.150420.587
154_G188_R0.149520.583
86_Y166_R0.149190.582
72_V78_S0.148980.581
8_R12_N0.148290.578
39_Y124_Q0.148030.577
35_S43_L0.148010.577
87_Y123_A0.147070.574
89_P92_A0.147070.574
73_S198_N0.146990.573
182_L186_L0.14580.569
24_Y31_A0.145610.568
72_V75_S0.14550.568
119_T165_V0.145440.567
120_P162_V0.145390.567
94_F101_D0.145370.567
126_A129_R0.144990.566
130_K134_S0.144050.562
187_S191_S0.144010.562
102_L106_G0.14380.561
125_V151_S0.143690.560
40_N43_L0.143450.560
23_Q153_Q0.142850.557
23_Q150_D0.14280.557
122_R125_V0.142320.555
132_L137_P0.14230.555
166_R175_F0.141990.554
84_T87_Y0.141840.553
48_S51_N0.140950.550
117_I144_I0.140050.546
100_R136_Y0.139670.545
117_I161_I0.139570.544
109_S113_S0.139480.544
7_E180_N0.13940.544
92_A124_Q0.139120.543
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
2wjyA0.9751000.11
2xzlA0.9751000.114
2gk6A0.9751000.126
4b3fX0.961000.183
3dmnA0.7399.80.464
1pjrA0.8899.70.508
3lfuA0.8899.70.518
1uaaA0.8899.60.536
3u4qA199.50.566
3upuA0.899.50.575

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