GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Lyase_1 - Lyase
Pfam: PF00206 (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. )
Length: 312
Sequences: 5411
Seq/Len: 17.34
HH_delta: 0.113 (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
49_A104_W1.07433.678
40_A50_A1.040343.562
41_E217_R0.87733.004
139_I180_A0.853972.924
256_A310_V0.842792.886
136_K183_L0.83892.872
132_L183_L0.817662.799
192_R247_E0.801042.743
127_L248_L0.780752.673
132_L187_E0.752682.577
136_K187_E0.731322.504
37_K58_E0.710162.431
145_L148_E0.709082.428
144_E148_E0.706862.420
41_E221_E0.698322.391
40_A47_K0.688652.358
257_G311_I0.685152.346
124_R194_N0.668742.290
37_K221_E0.662162.267
183_L187_E0.63092.160
263_A303_I0.627992.150
196_S219_A0.619712.122
139_I183_L0.615042.106
217_R221_E0.609542.087
188_E192_R0.608382.083
129_E190_R0.603542.066
59_E90_V0.593052.030
37_K54_V0.589582.019
46_P49_A0.588622.015
188_E191_K0.584542.001
143_A180_A0.582581.995
47_K51_D0.57591.972
51_D55_K0.560311.918
259_L303_I0.554551.899
149_H152_T0.549841.883
181_R243_D0.53331.826
185_R247_E0.529571.813
217_R220_E0.52151.786
33_A58_E0.51521.764
181_R237_D0.512431.754
232_A238_A0.511561.751
182_D258_T0.507531.738
143_A147_E0.506381.734
200_G238_A0.505381.730
135_L255_L0.494841.694
50_A54_V0.484921.660
198_L218_V0.483581.656
16_D19_R0.482121.651
139_I176_A0.476811.632
58_E62_E0.461741.581
250_S254_L0.460271.576
145_L149_H0.448541.536
62_E65_D0.435721.492
189_A251_A0.433161.483
146_A176_A0.428961.469
168_F172_L0.428471.467
33_A61_L0.425511.457
141_A144_E0.418661.433
139_I179_L0.417241.429
246_A254_L0.414271.418
194_N226_T0.413951.417
147_E150_K0.404861.386
32_E114_I0.40361.382
172_L175_W0.402391.378
33_A54_V0.40231.377
173_A234_N0.398051.363
136_K140_D0.397141.360
184_E191_K0.396191.356
34_A222_L0.394131.349
184_E192_R0.393491.347
123_L248_L0.391681.341
36_A45_I0.390151.336
266_L300_L0.389691.334
87_L91_L0.389481.333
150_K169_G0.388521.330
251_A255_L0.387441.327
52_A55_K0.386911.325
134_R137_A0.382441.309
42_A217_R0.381921.308
17_R21_D0.381571.306
32_E35_L0.378121.295
162_P273_E0.377781.293
213_E217_R0.37641.289
157_R162_P0.375651.286
175_W262_I0.370351.268
58_E61_L0.366681.255
44_I107_Y0.366331.254
151_D169_G0.365391.251
260_S304_R0.362911.243
194_N223_G0.362281.240
88_N102_G0.360011.233
132_L190_R0.358991.229
219_A231_P0.357761.225
184_E188_E0.352421.207
127_L190_R0.35231.206
132_L136_K0.351961.205
34_A225_F0.350081.199
76_E82_A0.349851.198
177_D181_R0.348281.192
166_T204_A0.34821.192
51_D54_V0.346971.188
119_L245_L0.344021.178
143_A176_A0.341211.168
186_L255_L0.340251.165
162_P272_T0.338471.159
10_M66_L0.338311.158
307_A311_I0.338181.158
38_A225_F0.337531.156
100_E103_G0.337521.156
54_V58_E0.337351.155
55_K59_E0.336081.151
33_A87_L0.33451.145
142_L262_I0.330631.132
135_L179_L0.33011.130
138_L179_L0.328061.123
159_H301_E0.325141.113
135_L183_L0.324751.112
117_T196_S0.324551.111
52_A101_A0.320971.099
145_L172_L0.320371.097
11_Y16_D0.319321.093
150_K167_T0.319221.093
141_A145_L0.314861.078
76_E85_A0.313311.073
160_G268_L0.312321.069
157_R273_E0.311561.067
39_L42_A0.309951.061
108_G210_I0.309451.059
268_L274_I0.309371.059
171_K269_L0.306261.049
40_A45_I0.303391.039
32_E87_L0.303371.039
191_K226_T0.302781.037
176_A180_A0.299651.026
47_K50_A0.299061.024
48_E52_A0.298851.023
253_A257_G0.298321.021
40_A51_D0.295571.012
52_A56_A0.293891.006
41_E47_K0.293841.006
124_R190_R0.292281.001
48_E51_D0.289720.992
127_L186_L0.288990.989
272_T275_G0.288230.987
108_G211_D0.288060.986
6_P9_E0.287250.983
156_G166_T0.287030.983
248_L252_L0.28620.980
143_A146_A0.284410.974
35_L109_R0.281950.965
285_Q298_V0.281380.963
125_D129_E0.281310.963
190_R194_N0.281150.963
146_A173_A0.281090.962
16_D20_F0.280270.960
91_L105_V0.279780.958
140_D144_E0.279670.958
188_E247_E0.278750.954
139_I143_A0.277640.951
126_A130_L0.277470.950
42_A211_D0.277350.950
21_D25_A0.27530.943
241_S258_T0.273810.937
170_H235_W0.272090.932
31_V118_A0.271180.928
147_E151_D0.271150.928
264_E304_R0.269230.922
243_D258_T0.268170.918
263_A300_L0.267930.917
46_P104_W0.267920.917
181_R195_V0.267620.916
59_E66_L0.26670.913
280_P283_E0.265930.910
231_P235_W0.265010.907
24_L302_N0.264230.905
34_A125_D0.264190.905
36_A105_V0.264080.904
142_L176_A0.264060.904
149_H168_F0.263810.903
140_D143_A0.263360.902
34_A37_K0.26280.900
152_T167_T0.261030.894
195_V227_G0.260870.893
142_L172_L0.259190.887
174_A261_K0.258420.885
184_E187_E0.256890.880
237_D243_D0.256260.877
60_I90_V0.254860.873
271_S274_I0.25460.872
35_L114_I0.254270.871
16_D73_D0.253610.868
61_L65_D0.252140.863
135_L186_L0.250540.858
33_A37_K0.250040.856
191_K194_N0.248920.852
60_I67_D0.248470.851
130_L134_R0.248230.850
142_L179_L0.248150.850
177_D233_P0.247620.848
149_H169_G0.24740.847
179_L182_D0.247140.846
123_L193_L0.246870.845
187_E191_K0.246310.843
71_E74_E0.245740.841
154_M269_L0.244740.838
39_L43_G0.244730.838
185_R192_R0.24350.834
178_E258_T0.242770.831
59_E65_D0.242480.830
40_A48_E0.242440.830
221_E225_F0.242250.829
185_R243_D0.241940.828
55_K58_E0.241430.827
137_A141_A0.240470.823
80_G282_P0.240290.823
11_Y299_I0.239960.822
131_L252_L0.239020.818
218_V221_E0.238560.817
76_E81_H0.234080.801
72_L79_I0.232590.796
178_E241_S0.231440.792
196_S231_P0.23050.789
186_L251_A0.230140.788
166_T236_H0.229660.786
41_E220_E0.228640.783
62_E66_L0.225760.773
136_K180_A0.224980.770
270_S279_E0.224780.770
155_P274_I0.224680.769
18_A125_D0.222920.763
195_V244_R0.222880.763
44_I211_D0.222690.762
36_A50_A0.222450.762
127_L189_A0.222250.761
247_E250_S0.222140.761
111_S197_P0.221990.760
144_E147_E0.221250.758
191_K231_P0.221180.757
18_A22_F0.220740.756
237_D258_T0.220720.756
14_F126_A0.22030.754
219_A223_G0.219950.753
260_S264_E0.219350.751
31_V114_I0.218640.749
177_D180_A0.218630.749
213_E220_E0.217910.746
266_L279_E0.215860.739
127_L193_L0.215290.737
121_L222_L0.215030.736
266_L270_S0.214950.736
191_K195_V0.214540.735
49_A53_I0.214440.734
40_A54_V0.214040.733
252_L255_L0.212030.726
82_A85_A0.211940.726
227_G231_P0.211730.725
138_L141_A0.211510.724
53_I91_L0.211430.724
252_L310_V0.211080.723
154_M171_K0.210950.722
218_V231_P0.210280.720
288_S291_M0.210140.719
160_G271_S0.209460.717
19_R23_W0.209430.717
9_E12_A0.207780.711
180_A184_E0.207720.711
49_A101_A0.207580.711
85_A89_E0.207140.709
154_M166_T0.206810.708
22_F285_Q0.205690.704
177_D234_N0.203850.698
101_A104_W0.203260.696
246_A257_G0.203220.696
25_A61_L0.202960.695
304_R308_R0.202270.693
181_R192_R0.201860.691
35_L218_V0.201110.689
195_V232_A0.200510.687
45_I107_Y0.200150.685
182_D185_R0.199310.682
13_I18_A0.199240.682
136_K139_I0.199110.682
263_A304_R0.198520.680
189_A247_E0.198160.678
37_K225_F0.1980.678
32_E36_A0.197990.678
288_S292_P0.197960.678
13_I130_L0.197840.677
182_D251_A0.19740.676
152_T168_F0.197080.675
32_E83_V0.196910.674
260_S308_R0.196840.674
196_S218_V0.196280.672
157_R274_I0.196210.672
254_L258_T0.195220.668
281_F295_R0.195120.668
243_D247_E0.194290.665
185_R188_E0.194180.665
291_M294_K0.194060.664
268_L271_S0.193460.662
181_R247_E0.192810.660
189_A248_L0.192090.658
127_L132_L0.191680.656
254_L257_G0.191460.656
265_D269_L0.190990.654
49_A52_A0.190910.654
34_A121_L0.190870.653
241_S261_K0.190620.653
161_Q270_S0.190610.653
60_I87_L0.189660.649
87_L118_A0.188630.646
133_E137_A0.188580.646
45_I50_A0.188490.645
173_A176_A0.1880.644
152_T169_G0.187570.642
197_P238_A0.187420.642
53_I101_A0.186120.637
197_P239_V0.18610.637
120_R244_R0.184870.633
8_D12_A0.184660.632
145_L168_F0.184320.631
178_E240_S0.183560.628
179_L255_L0.18320.627
149_H172_L0.182650.625
175_W178_E0.182020.623
247_E254_L0.181680.622
44_I108_G0.18130.621
72_L82_A0.18020.617
9_E13_I0.180190.617
250_S253_A0.179860.616
11_Y15_S0.179850.616
288_S294_K0.179710.615
23_W126_A0.178840.612
46_P50_A0.178570.611
261_K265_D0.178220.610
57_L60_I0.177210.607
34_A217_R0.176630.605
104_W107_Y0.175760.602
40_A46_P0.175620.601
200_G232_A0.175510.601
44_I50_A0.175320.600
119_L242_R0.17450.597
182_D254_L0.174390.597
146_A150_K0.174370.597
41_E211_D0.174360.597
72_L81_H0.17420.596
163_A202_V0.174110.596
44_I225_F0.17410.596
56_A59_E0.173610.594
189_A193_L0.17340.594
15_S299_I0.173330.593
41_E213_E0.173310.593
22_F122_Q0.173130.593
35_L39_L0.173130.593
25_A125_D0.172980.592
243_D246_A0.172950.592
192_R243_D0.172370.590
169_G173_A0.172350.590
186_L248_L0.171980.589
235_W239_V0.171780.588
59_E62_E0.171320.587
146_A169_G0.171290.586
48_E144_E0.171040.586
7_T10_M0.17060.584
40_A49_A0.169660.581
168_F171_K0.169660.581
186_L252_L0.169210.579
186_L194_N0.168940.578
166_T170_H0.168630.577
156_G203_G0.168590.577
256_A307_A0.168440.577
237_D247_E0.167990.575
56_A91_L0.167740.574
38_A42_A0.167470.573
38_A218_V0.167410.573
120_R245_L0.167390.573
270_S281_F0.167320.573
179_L183_L0.166790.571
158_T163_A0.166750.571
42_A45_I0.166650.571
277_V280_P0.166650.571
6_P15_S0.166390.570
137_A144_E0.166260.569
36_A39_L0.166230.569
78_D284_G0.166230.569
259_L263_A0.16620.569
54_V221_E0.166080.569
81_H85_A0.165880.568
181_R233_P0.165810.568
179_L259_L0.165370.566
108_G208_L0.165360.566
37_K61_L0.165270.566
288_S296_N0.164570.563
133_E136_K0.164380.563
253_A311_I0.164340.563
154_M157_R0.164070.562
194_N227_G0.163910.561
171_K265_D0.163510.560
109_R114_I0.163340.559
38_A222_L0.163010.558
192_R195_V0.162810.557
37_K217_R0.161810.554
137_A140_D0.161720.554
120_R193_L0.161280.552
35_L121_L0.161180.552
172_L266_L0.161150.552
306_L309_Q0.160840.551
132_L251_A0.160690.550
22_F125_D0.160610.550
33_A60_I0.160430.549
33_A57_L0.160060.548
20_F72_L0.15980.547
83_V87_L0.159740.547
79_I84_E0.159710.547
117_T198_L0.15970.547
35_L242_R0.159690.547
246_A250_S0.159390.546
132_L139_I0.159020.544
127_L131_L0.158560.543
260_S311_I0.158560.543
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
1tj7A0.94871000.113
1k7wA0.94551000.117
2e9fA0.94551000.121
1q5nA0.92951000.126
4eeiA0.91031000.129
3c8tA0.92311000.134
1furA0.97441000.139
1vdkA0.97761000.139
1jswA0.97441000.14
3r6qA0.97441000.14

Page generated in 0.0311 seconds.