GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Me-amine-dh_H - Methylamine dehydrogenase heavy chain (MADH)
Pfam: PF06433 (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: CL0186
Length: 342
Sequences: 26770
Seq/Len: 78.27
HH_delta: 0.108 (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
36_G40_N1.252422.834
51_Y102_L1.178082.666
51_Y71_I1.177422.664
73_D76_T1.103112.496
275_D278_T1.062252.403
99_M112_Q1.060032.398
52_V72_W1.05582.389
110_Y122_V1.035232.342
23_D26_S1.014842.296
253_Y296_V0.991262.243
111_V123_V0.975612.207
70_E79_P0.959422.171
124_D127_A0.938052.122
42_A101_A0.937062.120
69_V111_V0.913492.067
120_V152_M0.912022.064
20_Y29_L0.879851.991
121_T133_E0.877381.985
272_W281_R0.866711.961
121_T130_V0.849791.923
20_Y32_M0.847491.918
254_V274_Y0.832461.884
272_W284_R0.822891.862
297_S301_K0.820281.856
152_M162_V0.815251.845
19_V52_V0.802261.815
211_D214_G0.799951.810
49_T71_I0.790341.788
293_S308_S0.783111.772
111_V115_T0.780511.766
51_Y109_L0.764141.729
44_S102_L0.751381.700
151_S161_T0.748891.694
200_F210_A0.746051.688
253_Y273_V0.744941.685
54_E66_T0.734631.662
36_G52_V0.726241.643
274_Y281_R0.720031.629
144_P147_N0.689791.561
297_S300_D0.675831.529
244_A295_A0.671921.520
199_Y209_S0.667061.509
29_L32_M0.665591.506
200_F204_E0.656171.485
246_H250_G0.635531.438
113_N119_S0.635311.437
130_V133_E0.634241.435
52_V70_E0.63121.428
281_R284_R0.630421.426
108_F122_V0.625521.415
42_A100_F0.618451.399
244_A294_I0.613391.388
44_S48_K0.61121.383
307_L317_Y0.608821.378
182_D186_F0.59781.353
23_D30_L0.594141.344
251_R254_V0.593371.343
297_S303_L0.591831.339
270_E284_R0.59171.339
246_H296_V0.591411.338
98_N114_F0.58971.334
311_D315_D0.585571.325
51_Y100_F0.5851.324
103_S110_Y0.575391.302
159_L200_F0.574941.301
49_T80_T0.573661.298
103_S107_K0.572881.296
308_S311_D0.569361.288
42_A102_L0.567571.284
192_S195_G0.555491.257
45_P106_G0.551011.247
163_T167_D0.550961.247
253_Y294_I0.548491.241
288_E309_A0.546761.237
271_V307_L0.541771.226
73_D80_T0.540181.222
22_I29_L0.538921.219
251_R273_V0.538351.218
19_V41_V0.538161.218
269_T273_V0.530371.200
110_Y150_F0.529171.197
247_A296_V0.523611.185
288_E307_L0.52091.179
103_S106_G0.518131.172
44_S49_T0.514181.163
45_P102_L0.512651.160
154_C157_G0.506251.145
186_F189_P0.505991.145
137_P152_M0.50551.144
140_W153_L0.504211.141
73_D78_S0.502491.137
143_Y147_N0.501521.135
71_I102_L0.501351.134
159_L163_T0.501191.134
119_S133_E0.498071.127
194_D197_R0.498041.127
69_V100_F0.496281.123
103_S108_F0.496121.123
53_A100_F0.49541.121
266_D269_T0.49541.121
251_R282_V0.491461.112
44_S47_G0.491171.111
266_D270_E0.490851.111
48_K75_Q0.488241.105
303_L306_A0.485281.098
49_T52_V0.484711.097
43_L50_I0.481031.088
123_V130_V0.479211.084
50_I74_T0.475841.077
188_H201_V0.475711.076
97_K100_F0.475571.076
198_L201_V0.471381.067
107_K126_A0.471311.066
268_G272_W0.471051.066
309_A313_T0.470851.065
153_L156_D0.470011.063
177_V181_D0.468631.060
292_D310_G0.46791.059
72_W79_P0.467821.058
48_K73_D0.467291.057
24_A27_G0.466511.056
100_F111_V0.465581.053
101_A110_Y0.46551.053
207_V254_V0.462391.046
154_C158_S0.460961.043
144_P148_R0.459911.041
43_L74_T0.459671.040
111_V121_T0.457971.036
246_H249_S0.456781.034
245_Y252_L0.456551.033
108_F131_V0.45511.030
151_S191_Y0.453671.026
269_T272_W0.452721.024
303_L316_V0.451331.021
246_H251_R0.451161.021
247_A300_D0.451061.021
251_R255_L0.450671.020
153_L159_L0.442671.002
74_T77_L0.442361.001
137_P154_C0.441370.999
266_D272_W0.441350.999
21_V43_L0.441130.998
46_D49_T0.440830.997
113_N121_T0.440110.996
296_V319_A0.439340.994
195_G198_L0.438660.993
54_E70_E0.435120.984
53_A97_K0.43420.982
275_D282_V0.432340.978
244_A296_V0.431380.976
23_D28_K0.430960.975
152_M160_L0.429240.971
254_V266_D0.429050.971
287_L317_Y0.428860.970
160_L173_K0.427440.967
199_Y245_Y0.427120.966
102_L109_L0.425410.963
276_L279_H0.424710.961
255_L291_I0.416080.941
252_L276_L0.415210.939
43_L102_L0.414630.938
273_V285_I0.413990.937
49_T73_D0.413640.936
115_T119_S0.412650.934
192_S245_Y0.412130.932
43_L296_V0.411640.931
140_W144_P0.410530.929
97_K111_V0.41020.928
31_G77_L0.406480.920
291_I294_I0.40340.913
108_F111_V0.403140.912
197_R209_S0.401610.909
181_D185_L0.4010.907
109_L125_L0.399460.904
202_S206_N0.398820.902
150_F153_L0.398270.901
148_R165_D0.397890.900
273_V282_V0.39580.896
154_C160_L0.395480.895
156_D160_L0.394480.893
41_V45_P0.393920.891
112_Q115_T0.393120.889
252_L255_L0.393050.889
243_I247_A0.392610.888
290_P310_G0.392430.888
250_G277_K0.391440.886
102_L125_L0.388930.880
105_D108_F0.388490.879
70_E84_E0.385190.872
306_A316_V0.384260.869
275_D280_K0.384250.869
71_I81_G0.384030.869
41_V52_V0.382780.866
140_W143_Y0.381340.863
254_V272_W0.380430.861
122_V132_G0.379630.859
179_D182_D0.378570.857
201_V204_E0.375940.851
36_G66_T0.375740.850
223_W226_L0.374780.848
309_A312_G0.374570.847
21_V30_L0.36950.836
243_I254_V0.369390.836
119_S135_D0.367330.831
170_E173_K0.367280.831
248_A251_R0.366390.829
35_T72_W0.366310.829
301_K318_D0.365520.827
149_G161_T0.365490.827
37_F40_N0.365450.827
107_K124_D0.365120.826
253_Y304_L0.36440.824
101_A142_I0.363960.823
285_I317_Y0.362530.820
102_L296_V0.361710.818
54_E68_V0.360430.816
36_G70_E0.359860.814
245_Y276_L0.357650.809
109_L123_V0.35760.809
21_V33_I0.356590.807
124_D129_K0.354310.802
66_T70_E0.353070.799
120_V134_I0.351710.796
273_V296_V0.351710.796
143_Y146_G0.351240.795
75_Q126_A0.349930.792
125_L128_K0.348450.788
279_H282_V0.348250.788
271_V294_I0.347540.786
174_S178_F0.347470.786
285_I288_E0.345980.783
255_L294_I0.344690.780
44_S51_Y0.344510.779
167_D170_E0.344360.779
97_K113_N0.341780.773
81_G128_K0.341320.772
304_L319_A0.341240.772
288_E291_I0.340410.770
36_G54_E0.34040.770
71_I80_T0.339890.769
134_I137_P0.339640.768
181_D184_P0.339120.767
152_M156_D0.337910.765
194_D198_L0.336790.762
273_V283_A0.335570.759
108_F112_Q0.335540.759
201_V210_A0.334940.758
182_D200_F0.334350.756
307_L315_D0.331820.751
190_A244_A0.330690.748
222_P226_L0.329210.745
41_V50_I0.327320.741
299_D303_L0.325850.737
42_A99_M0.325410.736
49_T108_F0.325170.736
289_H310_G0.325020.735
174_S177_V0.324320.734
251_R303_L0.324140.733
270_E286_P0.323370.732
189_P192_S0.32310.731
41_V44_S0.322610.730
151_S189_P0.322010.729
288_E311_D0.321670.728
79_P130_V0.320920.726
219_F222_P0.320670.726
160_L170_E0.318280.720
69_V97_K0.318220.720
200_F208_Y0.318110.720
301_K320_A0.316770.717
135_D138_G0.315730.714
31_G81_G0.315390.714
49_T251_R0.314660.712
143_Y150_F0.314050.711
104_A147_N0.313120.708
42_A51_Y0.312880.708
275_D279_H0.312480.707
110_Y253_Y0.312290.707
306_A317_Y0.310020.701
124_D131_V0.309770.701
109_L112_Q0.309590.700
35_T39_G0.309180.700
211_D215_D0.308970.699
103_S143_Y0.308370.698
113_N118_T0.308180.697
146_G149_G0.307770.696
162_V170_E0.307110.695
168_G171_A0.306730.694
23_D27_G0.305520.691
73_D77_L0.303880.688
177_V180_P0.302810.685
209_S245_Y0.302670.685
163_T171_A0.300120.679
144_P149_G0.299850.678
307_L311_D0.299670.678
222_P225_L0.298650.676
277_K320_A0.298610.676
153_L157_G0.298070.674
214_G217_A0.295270.668
223_W227_T0.295110.668
211_D216_S0.294820.667
108_F124_D0.294250.666
192_S196_G0.29420.666
141_L144_P0.294130.665
68_V84_E0.294060.665
27_G30_L0.292410.662
69_V109_L0.292390.662
46_D106_G0.292220.661
101_A141_L0.291830.660
201_V205_G0.291740.660
267_P290_P0.291640.660
153_L186_F0.289870.656
245_Y296_V0.289160.654
29_L79_P0.288460.653
49_T53_A0.287240.650
246_H253_Y0.287170.650
306_A309_A0.286460.648
25_D75_Q0.286160.647
178_F182_D0.285970.647
207_V211_D0.285560.646
50_I53_A0.284970.645
204_E208_Y0.284590.644
202_S208_Y0.284440.644
249_S255_L0.28390.642
79_P170_E0.283670.642
295_A306_A0.283360.641
296_V304_L0.282980.640
196_G213_S0.282680.640
54_E67_D0.282330.639
164_L319_A0.282240.639
176_K179_D0.28170.637
36_G39_G0.281520.637
134_I138_G0.281520.637
199_Y252_L0.281320.637
195_G199_Y0.281290.636
51_Y125_L0.281130.636
208_Y217_A0.280970.636
29_L170_E0.280670.635
154_C162_V0.280550.635
32_M35_T0.279510.632
300_D303_L0.279010.631
195_G200_F0.278230.630
255_L269_T0.278120.629
197_R200_F0.276770.626
250_G275_D0.276750.626
176_K180_P0.276440.625
148_R151_S0.275840.624
271_V317_Y0.27470.622
288_E315_D0.272910.617
273_V319_A0.272870.617
51_Y69_V0.272340.616
124_D128_K0.271980.615
108_F303_L0.271510.614
178_F181_D0.27040.612
78_S280_K0.270090.611
212_L215_D0.267760.606
78_S129_K0.267660.606
292_D309_A0.266920.604
185_L189_P0.265830.601
28_K78_S0.265070.600
21_V31_G0.265050.600
192_S197_R0.265020.600
161_T191_Y0.264930.599
200_F209_S0.264420.598
186_F191_Y0.26440.598
207_V243_I0.264340.598
161_T164_L0.26380.597
110_Y120_V0.263720.597
50_I72_W0.263530.596
33_I36_G0.262170.593
202_S205_G0.262140.593
278_T281_R0.261440.592
145_S148_R0.260930.590
303_L318_D0.260230.589
113_N123_V0.259890.588
81_G132_G0.259590.587
53_A111_V0.259190.586
180_P185_L0.259180.586
224_S227_T0.258850.586
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
1nr0A0.8831000.108
4jsnD0.86841000.125
4jspD0.86841000.125
1vyhC0.77781000.14
1nr0A0.86551000.141
1erjA0.83921000.176
3vl1A0.85671000.178
3sfzA0.87431000.179
4j87A0.81581000.18
3iz6a0.83921000.18

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