GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
E1_dh - Dehydrogenase E1 component
Pfam: PF00676 (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: CL0254
Length: 300
Sequences: 3650
Seq/Len: 12.17
HH_delta: 0.192 (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
269_T272_E0.877554.246
270_E274_D0.692543.351
141_H185_Y0.632573.061
275_A279_E0.559052.705
209_E213_A0.556652.694
190_I206_E0.546892.646
155_I211_A0.532772.578
190_I203_A0.506192.449
133_G164_A0.501972.429
210_Y218_V0.485012.347
208_V212_R0.480982.327
282_A286_E0.476512.306
260_R264_E0.47042.276
263_I270_E0.470362.276
196_D199_A0.455712.205
130_F158_V0.45522.203
67_E290_F0.453182.193
39_A129_F0.437392.116
117_I126_V0.427972.071
191_R223_V0.426852.065
151_K174_A0.421132.038
274_D278_A0.42062.035
50_F113_V0.412541.996
259_R277_E0.411891.993
268_L273_L0.407141.970
82_G85_H0.406621.968
289_E293_A0.405921.964
111_A143_A0.40171.944
259_R263_I0.400631.939
140_F144_L0.400451.938
259_R273_L0.388521.880
210_Y215_K0.379221.835
111_A156_F0.376181.820
107_V140_F0.375821.819
182_A189_G0.37251.802
81_G85_H0.370351.792
272_E275_A0.366591.774
263_I273_L0.36581.770
80_H83_G0.362241.753
192_V203_A0.358381.734
261_Y265_E0.355731.721
286_E290_F0.355681.721
125_V208_V0.353141.709
190_I218_V0.345681.673
81_G84_R0.339511.643
44_R123_D0.336911.630
39_A204_A0.331841.606
204_A220_I0.329171.593
160_N221_E0.32841.589
256_K260_R0.326081.578
271_E274_D0.323741.567
271_E275_A0.322461.560
46_G124_G0.322251.559
67_E286_E0.320031.549
283_E287_A0.311061.505
78_K82_G0.30791.490
157_V222_A0.303031.466
85_H88_H0.301261.458
278_A282_A0.301181.457
67_E287_A0.299831.451
290_F294_S0.297781.441
111_A154_V0.296031.432
180_D183_K0.295551.430
78_K83_G0.294741.426
211_A218_V0.292981.418
195_N227_L0.292941.418
138_G142_E0.292811.417
207_A218_V0.289911.403
83_G88_H0.28951.401
158_V178_I0.287211.390
107_V143_A0.285731.383
177_D180_D0.285311.381
247_E251_K0.285151.380
5_L283_E0.281821.364
130_F134_A0.277671.344
31_G159_E0.27731.342
289_E292_E0.276461.338
205_K209_E0.274841.330
285_E289_E0.272831.320
206_E209_E0.272741.320
157_V204_A0.271791.315
195_N224_T0.271051.312
279_E283_E0.270861.311
117_I124_G0.269791.305
81_G88_H0.268511.299
246_E250_K0.268461.299
194_G224_T0.268411.299
80_H84_R0.267241.293
188_P210_Y0.26581.286
188_P216_G0.26521.283
203_A220_I0.264371.279
198_E258_F0.263571.275
39_A127_V0.262891.272
158_V219_L0.262871.272
21_G292_E0.262381.270
117_I122_K0.261891.267
192_V199_A0.259161.254
127_V155_I0.256911.243
259_R270_E0.256641.242
287_A291_A0.255441.236
242_P246_E0.254331.231
114_A154_V0.2541.229
114_A126_V0.252771.223
102_P105_A0.252151.220
201_Y205_K0.250571.212
260_R263_I0.25051.212
35_I157_V0.247221.196
127_V204_A0.245691.189
35_I222_A0.245271.187
283_E286_E0.244271.182
258_F262_L0.238781.155
38_A197_V0.238291.153
59_A96_I0.237631.150
78_K84_R0.236051.142
200_V222_A0.23521.138
268_L272_E0.23391.132
189_G219_L0.232051.123
80_H85_H0.23161.121
158_V179_A0.231141.118
84_R88_H0.23081.117
91_D94_L0.227421.100
125_V211_A0.226961.098
162_Q223_V0.226751.097
231_S234_D0.225861.093
39_A157_V0.22361.082
243_E247_E0.223241.080
130_F135_T0.219411.062
144_L187_I0.218761.059
48_W117_I0.218671.058
11_D30_A0.218341.057
182_A187_I0.217781.054
146_L150_W0.217011.050
82_G88_H0.215691.044
263_I269_T0.215481.043
110_A126_V0.213551.033
143_A156_F0.213141.031
78_K81_G0.21291.030
100_S105_A0.212881.030
230_H234_D0.212791.030
202_E206_E0.211191.022
79_G82_G0.210151.017
151_K215_K0.209951.016
141_H184_G0.209591.014
210_Y216_G0.208661.010
65_D68_E0.208311.008
78_K85_H0.207111.002
6_I57_G0.206871.001
125_V212_R0.206420.999
28_L224_T0.206250.998
4_M8_R0.2060.997
115_L119_Y0.205830.996
275_A278_A0.205380.994
282_A285_E0.205210.993
3_M7_R0.204370.989
110_A128_C0.204180.988
7_R10_E0.203510.985
125_V155_I0.203490.985
7_R57_G0.203080.983
83_G87_L0.202380.979
179_A191_R0.201560.975
43_L208_V0.200660.971
136_S181_R0.200240.969
243_E246_E0.199580.966
196_D261_Y0.196810.952
38_A200_V0.196790.952
34_A38_A0.194470.941
207_A220_I0.193520.936
14_A18_Q0.192390.931
118_K151_K0.192380.931
29_S57_G0.192230.930
199_A202_E0.191060.925
192_V222_A0.190580.922
136_S172_Q0.189580.917
41_A201_Y0.189130.915
257_R261_Y0.188810.914
103_V134_A0.188090.910
215_K218_V0.187580.908
151_K216_G0.186760.904
42_A201_Y0.186710.903
43_L49_V0.186440.902
81_G87_L0.185680.898
177_D191_R0.185190.896
7_R253_D0.185180.896
240_R244_E0.183810.889
148_A186_G0.183670.889
107_V130_F0.182320.882
190_I220_I0.182280.882
273_L277_E0.181720.879
61_A69_I0.181690.879
3_M10_E0.180450.873
187_I219_L0.180370.873
78_K88_H0.180020.871
8_R11_D0.179910.871
12_E16_K0.179680.869
227_L253_D0.17960.869
82_G87_L0.179290.868
114_A153_P0.179280.868
240_R245_Y0.179140.867
4_M255_I0.178820.865
111_A152_L0.178560.864
207_A211_A0.178120.862
163_Y244_E0.176840.856
255_I273_L0.175970.851
268_L276_I0.17580.851
43_L127_V0.17560.850
280_I284_V0.175160.848
31_G129_F0.175020.847
107_V128_C0.174710.845
279_E282_A0.174180.843
84_R87_L0.172560.835
247_E250_K0.172530.835
98_G101_S0.172520.835
274_D277_E0.172140.833
242_P245_Y0.171440.830
53_Y106_Q0.170640.826
203_A207_A0.170430.825
248_W252_R0.170380.824
79_G83_G0.170260.824
12_E285_E0.168920.817
5_L280_I0.168090.813
135_T178_I0.168040.813
101_S104_G0.167950.813
58_H129_F0.167170.809
29_S36_Q0.166090.804
129_F157_V0.165860.803
104_G134_A0.165850.803
148_A187_I0.165770.802
105_A109_I0.165730.802
25_F231_S0.165510.801
113_V126_V0.165410.800
159_E224_T0.165410.800
290_F293_A0.165150.799
175_S181_R0.164930.798
42_A205_K0.16470.797
32_Q159_E0.164590.796
27_H56_H0.164280.795
34_A204_A0.164170.794
155_I207_A0.163670.792
48_W97_L0.163030.789
213_A216_G0.162780.788
202_E205_K0.162590.787
128_C156_F0.162530.786
144_L219_L0.162340.786
210_Y214_G0.16190.783
228_R232_E0.161650.782
137_Q142_E0.161420.781
278_A281_K0.161320.781
287_A290_F0.160860.778
194_G222_A0.159810.773
38_A204_A0.159770.773
38_A155_I0.158280.766
204_A208_V0.158060.765
276_I280_I0.15740.762
12_E288_V0.157210.761
229_G236_P0.156520.757
182_A219_L0.156190.756
64_I96_I0.155910.754
207_A210_Y0.155380.752
140_F219_L0.155060.750
195_N225_Y0.154750.749
147_A154_V0.154680.748
66_L283_E0.15460.748
262_L268_L0.154420.747
175_S184_G0.154170.746
53_Y231_S0.154080.746
252_R257_R0.153280.742
262_L267_V0.153030.740
173_T178_I0.152890.740
41_A209_E0.152790.739
53_Y232_E0.152310.737
29_S56_H0.151960.735
46_G62_R0.151720.734
164_A172_Q0.151520.733
71_A76_K0.151410.733
25_F232_E0.150940.730
5_L66_L0.150690.729
144_L185_Y0.150440.728
59_A64_I0.150310.727
12_E15_R0.150110.726
198_E261_Y0.150.726
175_S180_D0.149090.721
13_R73_L0.148970.721
196_D257_R0.14850.719
42_A208_V0.148470.718
44_R124_G0.148230.717
165_I231_S0.148080.717
181_R184_G0.147970.716
34_A200_V0.147880.716
103_V106_Q0.147870.716
246_E260_R0.147830.715
97_L100_S0.14750.714
27_H101_S0.147390.713
98_G104_G0.147090.712
280_I283_E0.147060.712
246_E251_K0.146880.711
60_L69_I0.146580.709
67_E294_S0.146440.709
252_R260_R0.146180.707
135_T140_F0.145490.704
4_M280_I0.145180.703
199_A203_A0.145170.702
110_A154_V0.144440.699
4_M277_E0.144340.698
259_R274_D0.143050.692
192_V200_V0.14260.690
85_H98_G0.141680.686
99_A103_V0.141330.684
175_S185_Y0.141090.683
246_E249_W0.140870.682
195_N257_R0.140760.681
7_R11_D0.140660.681
273_L276_I0.140450.680
98_G103_V0.140020.678
66_L284_V0.139910.677
52_Y106_Q0.13940.675
11_D14_A0.138960.672
99_A102_P0.138780.672
263_I268_L0.138590.671
64_I94_L0.138050.668
3_M6_I0.137010.663
24_G27_H0.136680.661
31_G157_V0.136280.659
9_F281_K0.13620.659
136_S173_T0.135680.657
114_A152_L0.135610.656
229_G232_E0.13560.656
165_I233_S0.135580.656
7_R17_L0.135550.656
166_S232_E0.13550.656
134_A158_V0.135310.655
165_I232_E0.135190.654
136_S139_D0.135150.654
30_A228_R0.13470.652
8_R281_K0.134350.650
101_S105_A0.134270.650
227_L249_W0.134270.650
16_K74_L0.134090.649
169_T173_T0.133960.648
128_C154_V0.133760.647
9_F284_V0.133580.646
71_A290_F0.13310.644
44_R208_V0.1330.644
25_F53_Y0.1330.644
9_F70_F0.132990.644
9_F61_A0.132890.643
107_V144_L0.132190.640
179_A219_L0.132060.639
53_Y165_I0.131680.637
133_G172_Q0.131110.634
148_A174_A0.130980.634
4_M11_D0.13040.631
168_P171_E0.130190.630
155_I204_A0.13010.630
193_D196_D0.129310.626
15_R19_R0.128950.624
31_G34_A0.128950.624
256_K259_R0.128930.624
40_A43_L0.128890.624
41_A205_K0.128840.623
272_E276_I0.128560.622
11_D228_R0.127980.619
41_A278_A0.127710.618
8_R277_E0.127690.618
95_N124_G0.127460.617
226_R266_G0.127290.616
225_Y244_E0.126670.613
16_K22_R0.126570.612
80_H88_H0.126150.610
226_R230_H0.125580.608
32_Q52_Y0.125530.607
213_A270_E0.125180.606
157_V220_I0.1250.605
127_V157_V0.124980.605
49_V96_I0.124890.604
74_L292_E0.124790.604
108_P111_A0.124720.604
139_D143_A0.124420.602
258_F261_Y0.124380.602
162_Q169_T0.124250.601
147_A185_Y0.124150.601
68_E93_G0.123990.600
276_I279_E0.123810.599
40_A129_F0.123730.599
20_Q24_G0.123670.598
29_S58_H0.123370.597
104_G137_Q0.123290.597
177_D223_V0.123210.596
260_R274_D0.123150.596
10_E17_L0.122930.595
10_E27_H0.122830.594
79_G88_H0.122680.594
251_K257_R0.122640.593
70_F288_V0.122560.593
35_I129_F0.122550.593
253_D256_K0.122450.593
4_M7_R0.122140.591
255_I277_E0.12210.591
113_V117_I0.121950.590
269_T275_A0.121870.590
148_A151_K0.121850.590
34_A157_V0.121660.589
116_A120_R0.121660.589
108_P143_A0.121330.587
261_Y275_A0.12130.587
4_M10_E0.121220.587
9_F24_G0.120840.585
242_P249_W0.120790.584
40_A62_R0.12070.584
129_F248_W0.120690.584
225_Y248_W0.120550.583
52_Y55_D0.120520.583
180_D191_R0.120460.583
102_P106_Q0.120370.582
3_M41_A0.120360.582
65_D88_H0.119980.581
98_G102_P0.119680.579
166_S231_S0.119660.579
130_F156_F0.119620.579
193_D199_A0.119550.578
3_M9_F0.119510.578
49_V114_A0.119470.578
152_L217_P0.119190.577
155_I212_R0.118640.574
37_V205_K0.11830.572
226_R234_D0.118280.572
79_G85_H0.11820.572
264_E271_E0.11810.571
10_E56_H0.118030.571
147_A156_F0.117710.570
50_F109_I0.117550.569
155_I218_V0.117510.569
234_D240_R0.11730.568
108_P139_D0.117220.567
35_I224_T0.11720.567
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
2ozlA0.98671000.192
1qs0A0.99331000.202
1w85A0.96671000.217
2bfdA0.99671000.228
2xt6A0.981000.24
2yicA0.981000.245
1umdA0.99331000.268
2jgdA0.98331000.276
2o1sA0.921000.635
1gpuA0.951000.64

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