GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peripla_BP_1 - Periplasmic binding proteins and sugar binding domain of LacI family
Pfam: PF00532 (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: CL0144
Length: 279
Sequences: 16970
Seq/Len: 60.82
HH_delta: 0.009 (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
103_Y143_D2.293943.566
206_K209_E2.052033.190
118_H182_D1.956443.041
59_G255_L1.766932.747
109_A219_V1.718092.671
138_L142_R1.673132.601
118_H217_S1.664392.587
223_N241_Q1.624372.525
26_E29_E1.467192.281
107_Y147_E1.464252.276
111_E115_K1.439052.237
22_G248_G1.43272.227
250_Q253_E1.430372.224
26_E253_E1.401022.178
168_Y201_E1.377312.141
199_L211_I1.371922.133
96_P258_R1.368132.127
26_E249_R1.320512.053
107_Y143_D1.317492.048
25_Q245_Y1.312852.041
106_G110_T1.268471.972
27_A252_A1.264561.966
107_Y144_A1.259361.958
104_E108_E1.24481.935
105_A221_F1.241711.930
111_E144_A1.220341.897
114_I148_A1.213921.887
113_L183_A1.19131.852
172_R202_R1.182421.838
111_E148_A1.15521.796
107_Y111_E1.153881.794
176_E202_R1.148791.786
112_Y116_K1.145611.781
167_G194_G1.132621.761
172_R198_A1.126381.751
103_Y139_Q1.102861.714
171_A184_I1.09981.710
106_G185_F1.08431.686
243_P246_E1.077921.676
241_Q274_E1.076311.673
104_E107_Y1.075951.673
206_K210_D1.06841.661
246_E249_R1.051151.634
110_T141_Y1.048551.630
168_Y198_A1.033711.607
5_G57_V1.033671.607
85_I251_A1.032591.605
110_T114_I1.022591.590
139_Q143_D1.020111.586
200_R234_Q1.015261.578
114_I144_A1.004761.562
101_D104_E1.000311.555
30_H256_L0.994731.546
186_C195_A0.985081.531
26_E252_A0.96831.505
171_A195_A0.963921.498
205_L210_D0.95981.492
4_I27_A0.955051.485
108_E273_V0.953081.482
124_F187_A0.950411.477
112_Y115_K0.948561.475
22_G245_Y0.947391.473
140_G144_A0.937371.457
123_A181_I0.918451.428
198_A202_R0.918361.428
219_V238_T0.916331.425
253_E257_E0.909491.414
198_A201_E0.904041.405
106_G140_G0.899221.398
26_E30_H0.898341.397
125_I195_A0.886151.378
142_R146_K0.882711.372
246_E250_Q0.880291.368
5_G52_L0.880111.368
144_A147_E0.874721.360
23_I61_I0.869621.352
6_V23_I0.868571.350
73_R77_K0.864321.344
153_D156_W0.855691.330
123_A174_L0.855371.330
110_T144_A0.852821.326
136_E139_Q0.845871.315
118_H183_A0.843121.311
27_A34_L0.835811.299
172_R201_E0.835051.298
189_D239_T0.829031.289
37_C52_L0.828291.288
196_I218_V0.824851.282
110_T140_G0.817631.271
111_E147_E0.815081.267
120_R153_D0.813341.264
199_L205_L0.812691.263
37_C48_Y0.812241.263
168_Y172_R0.811191.261
168_Y197_R0.806211.253
171_A199_L0.805751.253
108_E111_E0.796391.238
105_A273_V0.781691.215
161_D166_S0.778021.210
257_E262_N0.772381.201
165_E169_E0.768441.195
194_G198_A0.767461.193
24_E28_R0.757561.178
103_Y107_Y0.75051.167
178_H181_I0.746951.161
141_Y145_L0.733281.140
122_I145_L0.730351.135
6_V34_L0.728291.132
30_H253_E0.722161.123
103_Y140_G0.71911.118
23_I252_A0.718811.117
61_I251_A0.717931.116
114_I150_L0.716281.114
141_Y185_F0.708981.102
186_C192_A0.707851.100
245_Y249_R0.707431.100
143_D147_E0.706341.098
124_F138_L0.699621.088
158_F173_E0.698021.085
110_T145_L0.693431.078
120_R180_D0.689441.072
109_A185_F0.68761.069
32_Y256_L0.686771.068
243_P271_I0.685091.065
171_A175_L0.6851.065
163_D166_S0.682761.061
145_L150_L0.67811.054
112_Y238_T0.677681.054
139_Q142_R0.677561.053
248_G252_A0.675491.050
184_I195_A0.675081.049
61_I255_L0.671631.044
169_E173_E0.666671.036
103_Y136_E0.664681.033
200_R235_P0.662831.030
20_I24_E0.660891.027
25_Q29_E0.659561.025
166_S169_E0.658341.023
249_R253_E0.657361.022
120_R182_D0.656751.021
196_I207_I0.651151.012
135_R139_Q0.64421.001
122_I183_A0.643941.001
220_G239_T0.638680.993
250_Q254_M0.636230.989
29_E249_R0.633360.985
109_A240_I0.62890.978
144_A148_A0.627920.976
250_Q269_I0.626230.974
167_G171_A0.625230.972
127_G162_F0.623860.970
25_Q249_R0.620790.965
189_D220_G0.619270.963
186_C191_M0.616790.959
23_I248_G0.614020.955
189_D192_A0.611230.950
223_N276_I0.598560.931
3_T33_Q0.597660.929
116_K217_S0.59530.925
21_R24_E0.593210.922
21_R25_Q0.591230.919
23_I34_L0.589040.916
255_L259_I0.587330.913
143_D146_K0.586150.911
6_V20_I0.579770.901
166_S170_A0.578710.900
160_G191_M0.575180.894
115_K148_A0.572350.890
196_I233_E0.570230.886
3_T35_L0.569880.886
100_I242_Q0.564560.878
222_D242_Q0.562780.875
164_Y197_R0.559680.870
59_G259_I0.559180.869
73_R76_I0.557170.866
169_E172_R0.554830.863
15_F244_A0.554160.861
53_L80_I0.545560.848
108_E240_I0.544850.847
123_A184_I0.544510.846
50_E54_Q0.54230.843
100_I243_P0.542290.843
173_E177_S0.541980.843
101_D272_P0.540650.840
223_N230_S0.537570.836
59_G83_V0.537220.835
170_A173_E0.537190.835
124_F185_F0.537010.835
207_I210_D0.53380.830
113_L219_V0.5330.829
160_G166_S0.531780.827
98_V254_M0.531610.826
175_L202_R0.529630.823
189_D223_N0.528690.822
4_I61_I0.528650.822
199_L218_V0.527870.821
42_D45_K0.526460.818
129_E159_E0.523820.814
119_R182_D0.523730.814
177_S181_I0.523560.814
202_R205_L0.519520.808
3_T55_R0.51920.807
125_I186_C0.518490.806
40_G45_K0.51050.794
132_S136_E0.509140.792
114_I119_R0.503250.782
250_Q271_I0.502540.781
22_G249_R0.501920.780
205_L211_I0.501630.780
158_F170_A0.501140.779
167_G170_A0.500290.778
19_I244_A0.499450.776
142_R152_I0.4990.776
172_R176_E0.498740.775
83_V258_R0.497660.774
107_Y140_G0.497090.773
254_M257_E0.496340.772
175_L198_A0.494610.769
232_L235_P0.49180.765
184_I211_I0.491530.764
45_K48_Y0.490070.762
100_I273_V0.489110.760
241_Q276_I0.488630.760
142_R154_E0.48670.757
52_L57_V0.483410.752
4_I32_Y0.483280.751
122_I141_Y0.481560.749
130_D135_R0.479520.745
104_E272_P0.479390.745
50_E74_R0.478530.744
177_S180_D0.477110.742
171_A198_A0.475710.740
185_F219_V0.475340.739
5_G60_I0.473210.736
199_L202_R0.471480.733
252_A256_L0.471370.733
188_N191_M0.471160.732
136_E140_G0.469950.731
35_L57_V0.468950.729
245_Y248_G0.467560.727
7_I48_Y0.467530.727
182_D217_S0.466830.726
145_L152_I0.466570.725
28_R45_K0.466180.725
35_L55_R0.465890.724
231_T234_Q0.465030.723
197_R200_R0.460990.717
262_N265_E0.460910.717
193_I233_E0.45910.714
238_T275_L0.458490.713
112_Y275_L0.455890.709
119_R150_L0.45450.707
231_T236_P0.453170.704
243_P274_E0.453010.704
19_I85_I0.451780.702
162_F187_A0.451550.702
105_A108_E0.450930.701
13_N190_M0.450160.700
165_E168_Y0.449940.699
152_I157_I0.44970.699
44_E47_E0.448570.697
18_E245_Y0.446650.694
47_E50_E0.446460.694
62_L84_L0.441770.687
158_F174_L0.441360.686
192_A220_G0.438840.682
154_E157_I0.438530.682
22_G26_E0.437690.680
21_R245_Y0.435380.677
9_P16_F0.434750.676
101_D270_I0.433130.673
120_R156_W0.432480.672
13_N16_F0.4310.670
27_A32_Y0.430930.670
96_P254_M0.430110.669
102_N137_R0.430090.669
126_G138_L0.429470.668
59_G81_P0.429040.667
124_F141_Y0.42860.666
15_F19_I0.428160.666
156_W177_S0.426950.664
49_I60_I0.425590.662
75_L82_V0.425010.661
171_A174_L0.423960.659
152_I155_E0.42310.658
118_H180_D0.422660.657
233_E236_P0.421990.656
83_V98_V0.421170.655
3_T58_D0.421150.655
39_T48_Y0.42020.653
197_R201_E0.420180.653
83_V255_L0.419420.652
138_L157_I0.418550.651
24_E34_L0.418240.650
4_I252_A0.416930.648
92_P95_V0.416820.648
180_D205_L0.416350.647
84_L89_I0.415680.646
53_L78_S0.415210.645
103_Y106_G0.414680.645
254_M269_I0.413520.643
100_I105_A0.412360.641
173_E176_E0.411050.639
102_N136_E0.410840.639
162_F191_M0.406990.633
57_V60_I0.405430.630
74_R78_S0.405380.630
107_Y110_T0.403270.627
24_E38_N0.401910.625
224_L228_D0.401690.624
242_Q247_M0.400810.623
91_N94_G0.400610.623
106_G141_Y0.399030.620
257_E261_K0.398560.620
5_G37_C0.398380.619
120_R151_P0.397620.618
20_I36_L0.397570.618
74_R77_K0.3950.614
61_I85_I0.391960.609
30_H257_E0.390410.607
32_Y259_I0.390310.607
113_L185_F0.388930.605
230_S235_P0.387820.603
120_R179_P0.386330.601
108_E112_Y0.385080.599
37_C51_L0.383510.596
171_A194_G0.383240.596
166_S191_M0.382910.595
59_G251_A0.382010.594
104_E273_V0.381790.594
32_Y58_D0.380330.591
97_S268_R0.379090.589
99_Y270_I0.378830.589
163_D167_G0.378510.588
230_S239_T0.376950.586
69_D73_R0.376810.586
86_D133_T0.376680.586
228_D231_T0.376140.585
170_A174_L0.375190.583
193_I197_R0.375120.583
186_C220_G0.370360.576
187_A191_M0.369650.575
168_Y171_A0.368960.574
4_I259_I0.368390.573
197_R236_P0.367690.572
49_I53_L0.367370.571
25_Q28_R0.366740.570
71_E75_L0.366430.570
160_G167_G0.364870.567
221_F242_Q0.364710.567
181_I205_L0.363940.566
26_E256_L0.362870.564
114_I145_L0.362560.564
183_A219_V0.361510.562
229_F233_E0.361220.562
51_L55_R0.360270.560
123_A171_A0.358920.558
193_I224_L0.356940.555
211_I217_S0.356430.554
22_G25_Q0.356020.553
102_N242_Q0.355790.553
125_I171_A0.354250.551
16_F63_A0.354130.551
14_P190_M0.354020.550
3_T57_V0.353770.550
18_E21_R0.353580.550
192_A218_V0.353440.549
205_L208_P0.352320.548
99_Y102_N0.351580.547
150_L154_E0.350030.544
257_E267_R0.349510.543
127_G134_S0.349060.543
86_D247_M0.348380.542
23_I251_A0.347910.541
22_G244_A0.34710.540
120_R123_A0.346860.539
208_P217_S0.346250.538
76_I94_G0.346210.538
197_R234_Q0.345570.537
110_T185_F0.345060.536
96_P267_R0.344940.536
118_H122_I0.343570.534
70_E73_R0.34350.534
7_I39_T0.341330.531
100_I247_M0.340370.529
201_E234_Q0.340150.529
39_T46_E0.339980.529
53_L56_R0.338840.527
22_G252_A0.337960.525
18_E244_A0.33690.524
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
3qk7A0.96061000.009
3kkeA0.95341000.023
3kjxA0.96061000.026
3e3mA0.96061000.026
2hsgA0.96061000.031
3dbiA0.9571000.032
3huuA0.94621000.033
3mizA0.9571000.033
3k9cA0.93911000.034
3k4hA0.96421000.037

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