GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AAA_11 - AAA domain
Pfam: PF13086 (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: 236
Sequences: 5654
Seq/Len: 23.96
HH_delta: 0.243 (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
55_K194_D0.934533.873
7_R11_Q0.832923.452
2_L10_I0.666292.761
38_I58_V0.640022.652
5_S8_E0.582292.413
168_L176_T0.519042.151
155_E159_I0.511492.120
176_T179_S0.507592.103
60_S65_A0.49982.071
57_L193_F0.49732.061
32_T36_S0.48272.000
41_L195_V0.479121.985
68_N72_R0.467071.935
183_S186_L0.451981.873
57_L196_V0.440691.826
186_L190_K0.440451.825
52_R55_K0.436841.810
9_A22_I0.416391.725
37_I221_V0.398941.653
157_E160_R0.396361.642
34_L223_V0.395851.640
209_A213_L0.394521.635
92_G95_E0.39161.623
211_I215_R0.391381.622
201_A222_L0.387181.604
156_L160_R0.381791.582
23_Q26_P0.380131.575
21_L24_G0.379311.572
58_V69_I0.378961.570
93_S168_L0.377151.563
4_E8_E0.371551.540
36_S39_A0.369821.532
10_I33_T0.369361.531
67_D70_L0.366731.520
21_L25_P0.366631.519
160_R163_L0.366391.518
210_L213_L0.363461.506
4_E7_R0.362761.503
225_D228_Q0.360061.492
154_K158_K0.355451.473
20_T221_V0.350541.453
34_L197_I0.350491.452
12_S20_T0.347061.438
153_R160_R0.339391.406
139_K142_K0.338211.402
159_I163_L0.33561.391
60_S66_V0.334871.388
23_Q226_P0.332881.379
37_I197_I0.327161.356
82_K85_K0.322091.335
181_A186_L0.31961.324
134_R137_E0.311711.292
195_V219_R0.311191.290
85_K177_T0.309561.283
22_I221_V0.307391.274
11_Q40_Q0.305891.268
224_G228_Q0.305711.267
25_P28_T0.301831.251
62_S65_A0.300731.246
36_S40_Q0.30051.245
84_Y88_I0.299991.243
71_E75_K0.295981.227
125_Q128_E0.295671.225
41_L51_D0.288751.197
174_I207_P0.286681.188
92_G188_N0.284871.180
200_E228_Q0.282781.172
64_A68_N0.282331.170
143_K146_K0.281941.168
2_L36_S0.28141.166
67_D71_E0.28051.162
13_A37_I0.280231.161
187_S191_E0.279251.157
61_P203_Q0.277841.151
118_K122_L0.277081.148
127_E131_Q0.275941.143
211_I214_S0.275881.143
38_I56_I0.274721.138
120_K124_E0.272871.131
173_V177_T0.271091.123
148_S151_R0.271081.123
152_L156_L0.269861.118
124_E127_E0.268471.113
210_L215_R0.267871.110
138_L142_K0.266361.104
122_L126_L0.260731.080
3_N6_Q0.260311.079
197_I221_V0.258521.071
137_E141_E0.258361.071
155_E158_K0.257941.069
134_R138_L0.253961.052
182_A185_F0.253831.052
8_E11_Q0.253351.050
125_Q129_L0.252881.048
37_I219_R0.251481.042
151_R155_E0.249231.033
158_K162_E0.242961.007
174_I177_T0.242431.005
32_T72_R0.241941.003
183_S187_S0.241551.001
153_R156_L0.24131.000
81_G89_I0.240920.998
21_L26_P0.238820.990
124_E131_Q0.23870.989
159_I162_E0.238690.989
135_L138_L0.238670.989
101_D105_F0.237640.985
21_L222_L0.237340.984
110_K113_Q0.236940.982
37_I41_L0.235310.975
90_R95_E0.235120.974
153_R157_E0.23510.974
169_K172_D0.235080.974
35_A65_A0.234330.971
14_L195_V0.233120.966
61_P202_S0.232480.963
95_E182_A0.232470.963
122_L133_I0.232330.963
109_S113_Q0.230570.955
151_R154_K0.230280.954
82_K89_I0.229950.953
63_N67_D0.229330.950
139_K143_K0.226740.940
81_G85_K0.225780.936
3_N9_A0.22540.934
147_K151_R0.224860.932
138_L141_E0.22450.930
170_E173_V0.224250.929
110_K115_F0.223480.926
119_L124_E0.222880.924
155_E162_E0.2220.920
38_I73_L0.220280.913
196_V216_A0.219670.910
98_I101_D0.217730.902
54_K194_D0.215580.893
15_S219_R0.214460.889
130_Q133_I0.214320.888
169_K173_V0.213820.886
37_I195_V0.213730.886
90_R93_S0.213430.884
58_V65_A0.212560.881
148_S152_L0.211480.876
198_V222_L0.211040.875
202_S205_T0.211010.874
203_Q208_E0.210820.874
60_S69_I0.209390.868
118_K126_L0.206770.857
178_L211_I0.20660.856
101_D104_K0.206390.855
124_E129_L0.206140.854
66_V199_D0.205830.853
98_I176_T0.204590.848
70_L74_K0.204490.847
65_A68_N0.203840.845
66_V175_F0.203760.844
38_I197_I0.203190.842
167_I170_E0.202840.841
152_L160_R0.202770.840
3_N63_N0.20230.838
41_L56_I0.201650.836
118_K124_E0.201480.835
32_T35_A0.20060.831
134_R142_K0.200080.829
2_L6_Q0.199380.826
193_F196_V0.199370.826
171_A174_I0.198340.822
34_L199_D0.198130.821
120_K127_E0.197610.819
201_A204_I0.197460.818
128_E131_Q0.197120.817
125_Q132_K0.196750.815
35_A73_L0.196560.815
128_E132_K0.19620.813
87_K172_D0.196180.813
16_S219_R0.195680.811
99_H103_Q0.195290.809
200_E203_Q0.194960.808
30_K200_E0.194860.807
102_L106_S0.194650.807
90_R94_E0.194430.806
88_I181_A0.193270.801
98_I103_Q0.192740.799
32_T68_N0.192190.796
129_L133_I0.192160.796
123_R126_L0.192090.796
86_P90_R0.192040.796
82_K86_P0.191070.792
27_G30_K0.190790.791
156_L163_L0.190260.788
30_K199_D0.189810.787
126_L130_Q0.189460.785
123_R128_E0.189110.784
142_K146_K0.189090.784
51_D55_K0.189050.783
134_R139_K0.18880.782
135_L139_K0.188330.780
110_K114_R0.187750.778
141_E144_K0.187650.778
71_E74_K0.187460.777
12_S16_S0.187430.777
187_S190_K0.187090.775
119_L129_L0.186950.775
65_A72_R0.18630.772
153_R159_I0.186120.771
37_I202_S0.185090.767
99_H166_F0.182390.756
126_L131_Q0.181180.751
13_A195_V0.181170.751
6_Q9_A0.181140.751
178_L212_P0.18110.750
189_F193_F0.180830.749
97_K101_D0.180450.748
170_E180_S0.180140.746
134_R144_K0.180120.746
119_L123_R0.180090.746
199_D203_Q0.180060.746
144_K147_K0.179940.746
178_L181_A0.179690.745
95_E184_P0.179550.744
153_R161_E0.178880.741
206_E210_L0.178770.741
210_L214_S0.178720.741
142_K145_L0.177920.737
123_R127_E0.177810.737
126_L132_K0.177770.737
105_F110_K0.177520.736
157_E161_E0.17730.735
55_K192_K0.176790.733
23_Q223_V0.176640.732
27_G31_T0.17630.731
150_K160_R0.1760.729
198_V204_I0.175970.729
189_F192_K0.175950.729
97_K104_K0.175390.727
10_I37_I0.175040.725
61_P200_E0.175030.725
168_L173_V0.174980.725
24_G28_T0.174880.725
3_N204_I0.174520.723
154_K157_E0.172380.714
106_S110_K0.171830.712
212_P215_R0.171790.712
120_K126_L0.17170.712
68_N223_V0.171580.711
88_I92_G0.171240.710
63_N174_I0.170550.707
4_E11_Q0.170410.706
191_E194_D0.170370.706
103_Q111_L0.169990.704
23_Q28_T0.16960.703
119_L126_L0.169330.702
209_A212_P0.1690.700
97_K103_Q0.168870.700
61_P66_V0.168620.699
66_V69_I0.168620.699
145_L149_I0.168550.698
58_V73_L0.168460.698
177_T181_A0.168050.696
170_E177_T0.167420.694
63_N66_V0.167210.693
61_P208_E0.166990.692
102_L110_K0.166750.691
163_L167_I0.166260.689
171_A177_T0.165920.688
81_G84_Y0.165910.688
111_L115_F0.165710.687
119_L125_Q0.165660.686
91_L95_E0.164810.683
62_S203_Q0.164640.682
108_E112_E0.164510.682
101_D111_L0.164260.681
66_V205_T0.163640.678
65_A200_E0.163560.678
121_R124_E0.163260.677
35_A72_R0.163250.676
88_I93_S0.163170.676
135_L142_K0.162950.675
104_K108_E0.162780.675
65_A228_Q0.162590.674
156_L159_I0.162150.672
61_P72_R0.162080.672
37_I203_Q0.162040.671
118_K121_R0.161810.671
12_S15_S0.161670.670
176_T181_A0.161590.670
92_G189_F0.16140.669
134_R141_E0.161350.669
118_K125_Q0.161090.668
188_N192_K0.16090.667
63_N200_E0.160760.666
31_T66_V0.160490.665
205_T223_V0.160390.665
148_S159_I0.16020.664
136_S139_K0.160180.664
21_L221_V0.160070.663
109_S112_E0.159760.662
103_Q108_E0.159620.661
175_F178_L0.159510.661
141_E150_K0.159470.661
12_S221_V0.158940.659
7_R10_I0.158830.658
138_L146_K0.158310.656
89_I94_E0.15810.655
34_L72_R0.157530.653
122_L127_E0.157410.652
199_D202_S0.157410.652
34_L202_S0.157340.652
91_L188_N0.157080.651
39_A72_R0.15690.650
103_Q109_S0.15660.649
33_T201_A0.156570.649
138_L143_K0.156480.648
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
4b3fX0.92371000.243
2xzlA0.85171000.288
2gk6A0.86021000.288
2wjyA0.86021000.292
3lfuA0.953499.90.412
1pjrA0.949299.90.415
1uaaA0.957699.90.427
3e1sA0.57299.80.486
3u4qA0.970399.80.486
3upuA0.605999.80.49

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