GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Iso_dh - Isocitrateisopropylmalate dehydrogenase
Pfam: PF00180 (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: CL0270
Length: 348
Sequences: 3641
Seq/Len: 10.46
HH_delta: 0.003 (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
174_R210_D1.09014.634
167_R207_E1.059254.503
166_A200_F0.785433.339
54_D58_E0.74133.151
167_R171_E0.716013.044
17_A345_G0.684592.910
20_R346_D0.666522.833
220_A224_Q0.657072.793
159_R163_E0.653332.777
23_E35_F0.564462.399
163_E202_E0.550382.340
307_L310_A0.550262.339
302_E312_D0.543972.312
15_M293_M0.536362.280
302_E315_E0.535452.276
58_E62_R0.525922.236
182_T214_E0.521512.217
17_A20_R0.518992.206
50_E54_D0.51412.185
61_K92_L0.49972.124
4_V19_L0.496952.113
326_I347_A0.49562.107
312_D316_K0.492722.095
163_E199_V0.488912.078
316_K320_K0.487832.074
294_I348_V0.483072.053
291_I348_V0.481562.047
12_P16_P0.464491.975
3_A59_A0.464161.973
19_L37_E0.463631.971
167_R208_Y0.463381.970
171_E208_Y0.462211.965
286_G342_E0.461871.963
44_A53_P0.457031.943
200_F213_V0.444011.887
340_S343_E0.442361.880
286_G340_S0.43831.863
124_V172_Y0.438231.863
60_I66_I0.433061.841
39_D47_K0.433031.841
166_A236_V0.430911.832
298_A315_E0.419261.782
184_V221_A0.417541.775
180_K214_E0.416951.772
38_F59_A0.413741.759
61_K91_E0.408691.737
201_Q205_K0.406961.730
203_V207_E0.406191.727
295_L318_V0.403471.715
183_V200_F0.403371.715
228_N231_Q0.40131.706
159_R202_E0.395871.683
199_V202_E0.390511.660
44_A52_L0.386591.643
36_E62_R0.381221.621
22_L33_F0.379031.611
57_L91_E0.378921.611
58_E61_K0.378871.611
10_I288_A0.369751.572
308_P312_D0.368331.566
171_E175_K0.368031.564
155_K238_P0.366071.556
201_Q215_H0.365011.552
5_I40_I0.362471.541
36_E63_A0.360141.531
98_V124_V0.35681.517
3_A63_A0.355331.510
166_A203_V0.352141.497
226_V248_L0.351021.492
39_D48_T0.350351.489
44_A47_K0.348251.480
180_K212_E0.345231.468
163_E167_R0.344471.464
321_V347_A0.344471.464
195_L199_V0.340331.447
87_K91_E0.338821.440
178_R233_D0.337581.435
43_E47_K0.336811.432
302_E311_A0.33631.430
202_E205_K0.33211.412
286_G341_T0.327541.392
52_L57_L0.325481.384
31_L307_L0.324931.381
18_A297_A0.318261.353
17_A286_G0.314741.338
343_E346_D0.313881.334
3_A60_I0.309561.316
198_E202_E0.309071.314
179_K233_D0.308441.311
291_I322_L0.308181.310
51_P55_E0.306781.304
159_R199_V0.304541.295
31_L310_A0.303761.291
126_V168_F0.30351.290
120_G230_E0.302891.288
125_I246_S0.301771.283
170_F208_Y0.300541.278
18_A293_M0.300321.277
160_E163_E0.298431.269
162_I166_A0.297661.265
181_V213_V0.296721.261
167_R203_V0.295191.255
282_I288_A0.293211.246
187_A197_R0.292691.244
183_V215_H0.29251.243
216_M220_A0.292071.242
3_A38_F0.291761.240
78_G81_S0.290131.233
40_I88_L0.289521.231
35_F297_A0.28951.231
171_E174_R0.287421.222
55_E58_E0.28721.221
19_L23_E0.283671.206
98_V126_V0.282851.202
163_E203_V0.282551.201
216_M224_Q0.281951.199
287_I329_P0.281711.198
176_R233_D0.281071.195
126_V172_Y0.276941.177
6_P37_E0.276311.175
39_D44_A0.275681.172
20_R345_G0.271931.156
222_A245_L0.270941.152
79_I83_N0.270081.148
302_E308_P0.270031.148
102_R319_E0.269361.145
20_R342_E0.268361.141
170_F204_A0.267251.136
102_R122_D0.266081.131
44_A48_T0.266011.131
157_I238_P0.265091.127
133_L155_K0.261981.114
25_A314_I0.261611.112
172_Y176_R0.261061.110
80_R83_N0.26031.107
286_G343_E0.259291.102
291_I344_F0.258021.097
53_P56_T0.256571.091
133_L238_P0.256521.090
265_G269_H0.255571.086
224_Q231_Q0.255481.086
36_E59_A0.255341.085
129_N263_N0.253411.077
18_A67_L0.25241.073
214_E231_Q0.251371.069
153_D192_S0.250471.065
174_R211_I0.250261.064
151_A195_L0.249811.062
300_M305_L0.248971.058
301_L310_A0.248171.055
125_I249_A0.24731.051
282_I329_P0.245441.043
22_L297_A0.243461.035
320_K324_E0.243351.034
298_A302_E0.242551.031
96_A165_I0.241421.026
18_A22_L0.240861.024
78_G82_E0.240781.024
187_A217_L0.239941.020
68_K85_L0.238971.016
184_V218_V0.238881.015
216_M221_A0.238551.014
216_M232_F0.237491.010
170_F211_I0.237181.008
224_Q228_N0.235881.003
170_F181_V0.235311.000
26_A33_F0.234990.999
21_V314_I0.234490.997
123_I225_L0.233010.991
342_E346_D0.232610.989
70_A276_H0.231050.982
155_K192_S0.230680.981
9_G60_I0.230260.979
281_D329_P0.22870.972
48_T55_E0.228540.972
290_P348_V0.22840.971
150_V156_V0.227770.968
76_P81_S0.226890.964
344_F348_V0.226770.964
44_A56_T0.226630.963
14_V293_M0.22640.962
173_A181_V0.22550.959
19_L35_F0.225490.959
79_I82_E0.224360.954
282_I287_I0.222920.948
75_K109_V0.22230.945
76_P83_N0.222220.945
222_A248_L0.221470.941
312_D315_E0.221180.940
297_A300_M0.220570.938
140_E198_E0.220010.935
6_P16_P0.219530.933
78_G83_N0.219220.932
26_A31_L0.218790.930
309_E312_D0.218690.930
200_F236_V0.217270.924
218_V238_P0.216590.921
157_I162_I0.216490.920
317_A321_V0.216490.920
67_L297_A0.21510.914
26_A32_D0.213410.907
23_E27_E0.213180.906
301_L314_I0.213080.906
185_H197_R0.213040.906
274_P293_M0.2130.905
93_D164_R0.21260.904
41_G44_A0.212460.903
57_L61_K0.212370.903
185_H215_H0.211940.901
221_A232_F0.211460.899
150_V158_T0.21130.898
169_A181_V0.211230.898
50_E87_K0.211060.897
175_K306_G0.210940.897
158_T161_G0.210140.893
20_R23_E0.209520.891
225_L235_I0.209020.889
17_A342_E0.208870.888
24_A27_E0.208740.887
295_L315_E0.208340.886
14_V69_G0.207640.883
76_P80_R0.207470.882
17_A346_D0.207060.880
4_V37_E0.206890.879
59_A63_A0.206520.878
181_V234_V0.205580.874
227_K251_G0.205030.872
181_V203_V0.204960.871
76_P82_E0.204110.868
317_A348_V0.203620.866
132_G238_P0.20360.865
96_A168_F0.203550.865
76_P79_I0.203410.865
165_I236_V0.203050.863
169_A236_V0.202510.861
332_G335_A0.201780.858
18_A294_I0.201250.856
126_V169_A0.199960.850
21_V294_I0.198240.843
291_I318_V0.197410.839
281_D288_A0.196260.834
15_M69_G0.195960.833
320_K323_E0.19430.826
4_V15_M0.193980.825
97_N275_V0.193880.824
182_T216_M0.193730.824
101_V123_I0.192990.820
13_E284_G0.192160.817
20_R24_A0.191390.814
9_G66_I0.191080.812
170_F213_V0.190940.812
159_R195_L0.189490.806
174_R179_K0.189380.805
110_P114_K0.188530.801
45_Y51_P0.187490.797
25_A313_A0.187060.795
181_V204_A0.186770.794
46_D73_T0.186390.792
174_R181_V0.186340.792
181_V236_V0.186120.791
33_F297_A0.185970.791
38_F56_T0.185570.789
22_L301_L0.185490.789
122_D233_D0.184040.782
75_K83_N0.183930.782
101_V249_A0.183670.781
25_A297_A0.183580.780
42_G46_D0.182890.777
132_G155_K0.182430.775
162_I199_V0.182220.775
310_A313_A0.181860.773
38_F55_E0.180930.769
66_I271_M0.180540.767
25_A310_A0.17970.764
95_Y267_D0.179470.763
40_I68_K0.179240.762
316_K319_E0.17890.760
35_F67_L0.178440.759
322_L327_R0.178190.757
262_A272_F0.177210.753
130_T135_S0.177030.753
181_V211_I0.176520.750
77_P81_S0.175910.748
23_E26_A0.175430.746
175_K308_P0.175160.745
103_S121_I0.174910.744
133_L240_L0.174910.744
50_E55_E0.174780.743
54_D87_K0.174160.740
55_E59_A0.174010.740
171_E203_V0.173960.739
111_S194_D0.173630.738
218_V222_A0.173540.738
321_V344_F0.173540.738
279_A282_I0.172030.731
176_R179_K0.171680.730
184_V245_L0.17150.729
101_V253_V0.170630.725
260_P292_A0.170450.725
321_V326_I0.170280.724
220_A256_L0.169980.723
108_G323_E0.169840.722
220_A231_Q0.169690.721
183_V213_V0.168540.716
321_V348_V0.167750.713
294_I318_V0.167640.713
203_V208_Y0.167510.712
123_I249_A0.166710.709
2_I33_F0.166540.708
225_L249_A0.166510.708
184_V235_I0.166030.706
288_A329_P0.165510.704
303_H306_G0.165370.703
326_I335_A0.165110.702
157_I161_G0.164960.701
76_P138_E0.164940.701
60_I88_L0.164070.697
67_L293_M0.163920.697
171_E207_E0.163490.695
70_A293_M0.163420.695
218_V244_I0.163420.695
201_Q213_V0.163270.694
204_A213_V0.162840.692
39_D43_E0.162830.692
52_L56_T0.162750.692
194_D241_F0.16270.692
93_D130_T0.162180.689
155_K240_L0.161370.686
260_P295_L0.16040.682
42_G73_T0.160010.680
72_G278_S0.159940.680
38_F63_A0.159890.680
174_R208_Y0.159380.678
243_D247_D0.159190.677
2_I300_M0.1590.676
185_H217_L0.158630.674
25_A30_G0.158350.673
104_F319_E0.158090.672
126_V165_I0.157870.671
155_K194_D0.157750.671
124_V234_V0.156940.667
88_L91_E0.156930.667
260_P299_M0.156360.665
33_F307_L0.156080.663
16_P19_L0.155350.660
221_A245_L0.154720.658
23_E37_E0.154330.656
42_G72_G0.154320.656
311_A315_E0.154140.655
110_P331_L0.153910.654
68_K73_T0.153440.652
59_A62_R0.153360.652
328_T344_F0.153270.652
199_V203_V0.153240.651
121_I229_P0.153050.651
93_D131_E0.152710.649
25_A31_L0.15270.649
197_R201_Q0.152650.649
313_A316_K0.152550.648
317_A320_K0.152430.648
155_K241_F0.15170.645
39_D55_E0.15160.644
77_P194_D0.15120.643
319_E323_E0.150680.641
166_A213_V0.150080.638
264_I270_A0.149570.636
40_I52_L0.148790.632
15_M18_A0.148710.632
56_T66_I0.148680.632
286_G290_P0.148590.632
285_K329_P0.14850.631
124_V176_R0.148240.630
183_V201_Q0.148090.630
262_A299_M0.148050.629
22_L314_I0.147920.629
123_I252_L0.147680.628
204_A211_I0.147520.627
131_E161_G0.146710.624
297_A314_I0.146540.623
16_P20_R0.146150.621
6_P12_P0.144980.616
16_P37_E0.144390.614
69_G293_M0.144230.613
309_E313_A0.142920.608
121_I125_I0.142860.607
182_T212_E0.142780.607
21_V24_A0.142680.607
38_F53_P0.142510.606
10_I14_V0.142480.606
243_D276_H0.142090.604
243_D277_G0.141540.602
90_K136_G0.14140.601
220_A232_F0.141380.601
297_A301_L0.141210.600
263_N273_E0.141080.600
18_A21_V0.140950.599
246_S256_L0.140770.598
255_G292_A0.140750.598
168_F172_Y0.140470.597
67_L311_A0.140430.597
80_R138_E0.140350.597
3_A36_E0.140260.596
98_V262_A0.140210.596
204_A209_P0.139920.595
329_P334_S0.139690.594
77_P80_R0.139560.593
52_L88_L0.139550.593
132_G135_S0.139510.593
144_G158_T0.139220.592
125_I245_L0.139110.591
258_L331_L0.138490.589
165_I246_S0.138440.588
43_E46_D0.138160.587
335_A343_E0.137850.586
247_D277_G0.136940.582
104_F315_E0.136250.579
322_L331_L0.136050.578
301_L311_A0.135960.578
25_A294_I0.135940.578
298_A318_V0.135540.576
272_F303_H0.135220.575
179_K211_I0.135170.575
275_V292_A0.134490.572
162_I238_P0.134250.571
342_E345_G0.133850.569
168_F171_E0.133650.568
287_I341_T0.133640.568
277_G280_P0.133470.567
125_I235_I0.133080.566
64_D268_G0.132950.565
108_G111_S0.132920.565
34_E62_R0.132580.564
326_I344_F0.132360.563
150_V159_R0.132030.561
65_A300_M0.131950.561
152_I156_V0.131940.561
33_F301_L0.131870.561
181_V214_E0.13180.560
99_R247_D0.131760.560
4_V35_F0.131590.559
315_E319_E0.131510.559
6_P19_L0.131170.558
253_V258_L0.130990.557
21_V345_G0.130830.556
75_K194_D0.130760.556
73_T76_P0.130660.555
329_P340_S0.130560.555
162_I196_F0.130460.555
198_E205_K0.130290.554
305_L308_P0.130010.553
75_K111_S0.129620.551
17_A294_I0.129570.551
265_G268_G0.129520.551
60_I63_A0.129220.549
247_D256_L0.129180.549
186_K219_D0.128940.548
224_Q282_I0.128870.548
83_N139_H0.128680.547
37_E47_K0.128340.546
65_A305_L0.128190.545
330_D333_G0.128010.544
104_F295_L0.127960.544
122_D178_R0.127960.544
205_K209_P0.127610.542
98_V168_F0.127430.542
37_E43_E0.127140.540
99_R243_D0.127120.540
238_P241_F0.126860.539
33_F310_A0.126840.539
294_I314_I0.12680.539
134_Y273_E0.126710.539
112_P335_A0.126260.537
83_N138_E0.126250.537
22_L35_F0.126120.536
328_T331_L0.126060.536
93_D160_E0.125970.535
137_I154_T0.125890.535
223_M255_G0.125770.535
153_D190_L0.125620.534
65_A68_K0.125430.533
247_D276_H0.124470.529
12_P15_M0.124010.527
140_E143_D0.123920.527
184_V237_T0.123660.526
229_P343_E0.123320.524
78_G194_D0.12330.524
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
3r8wA0.98851000.003
3u1hA0.9771000.007
3flkA0.97411000.007
3uduA0.96551000.009
3vmkA0.99141000.01
1cnzA0.98281000.022
1vlcA0.95691000.024
2y3zA0.96261000.026
1a05A0.98851000.028
3ty4A0.95111000.03

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