GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GMC_oxred_N - GMC oxidoreductase
Pfam: PF00732 (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: CL0063
Length: 296
Sequences: 9181
Seq/Len: 31.02
HH_delta: 0.13 (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
218_R232_E1.11593.817
220_I232_E1.044973.575
219_I228_A0.986293.374
112_S115_D0.953353.261
261_R265_R0.922823.157
220_I230_G0.849782.907
34_P213_N0.845422.892
125_T137_D0.786072.689
211_L214_A0.745752.551
156_L247_A0.695042.378
217_T232_E0.684882.343
233_Y244_I0.684342.341
5_I16_A0.673542.304
217_T234_V0.67212.299
4_I28_L0.648832.219
3_Y25_K0.62092.124
96_P114_D0.611382.091
103_A112_S0.607052.077
17_S21_E0.599652.051
214_A233_Y0.588992.015
5_I15_V0.586312.006
59_Y258_G0.574641.966
178_G211_L0.553471.893
158_D161_E0.553361.893
93_R124_E0.55131.886
258_G261_R0.550231.882
20_S205_R0.542961.857
28_L211_L0.540511.849
221_F268_I0.538161.841
119_Y122_K0.534451.828
228_A250_V0.531211.817
30_L118_P0.523581.791
22_A25_K0.519951.779
157_M161_E0.507031.734
154_Q176_P0.495021.693
94_P99_F0.490581.678
13_S29_V0.490341.677
220_I229_T0.47141.613
30_L214_A0.470491.609
221_F226_G0.466281.595
200_P204_K0.462171.581
216_V262_L0.461251.578
8_S13_S0.458971.570
222_D229_T0.452291.547
3_Y19_L0.450621.541
30_L233_Y0.449311.537
161_E167_V0.442431.513
125_T141_P0.436961.495
35_R203_L0.431531.476
230_G246_A0.428791.467
30_L211_L0.426141.458
231_V250_V0.415941.423
61_S74_W0.413621.415
221_F229_T0.408521.397
100_D103_A0.407781.395
214_A235_D0.401741.374
29_V208_L0.40031.369
232_E243_R0.397061.358
8_S29_V0.395411.353
4_I30_L0.391921.341
165_I179_F0.390921.337
96_P100_D0.390651.336
18_R21_E0.38951.332
263_L266_S0.387921.327
203_L210_L0.385181.318
15_V124_E0.383871.313
105_E117_E0.383211.311
232_E244_I0.380121.300
176_P209_T0.377251.290
117_E121_D0.375721.285
219_I250_V0.371291.270
74_W257_I0.369351.263
134_H218_R0.366521.254
12_G16_A0.362971.242
4_I244_I0.36081.234
202_A205_R0.35761.223
230_G250_V0.357261.222
192_S196_T0.3571.221
235_D238_G0.353361.209
201_P204_K0.348491.192
5_I12_G0.346841.186
200_P203_L0.341991.170
37_P40_D0.341911.170
157_M160_A0.335451.147
41_S44_P0.332291.137
16_A29_V0.331231.133
211_L235_D0.3281.122
222_D225_G0.32741.120
221_F225_G0.327171.119
215_R234_V0.326791.118
262_L266_S0.326771.118
32_A215_R0.326281.116
201_P205_R0.325041.112
220_I244_I0.324541.110
17_S202_A0.324351.110
222_D227_R0.321691.100
99_F120_Y0.321021.098
26_K247_A0.320461.096
171_F180_C0.319281.092
16_A27_V0.31811.088
261_R264_L0.314261.075
15_V19_L0.313561.073
119_Y123_A0.311291.065
256_A260_P0.310621.063
17_S20_S0.304541.042
262_L265_R0.304081.040
94_P120_Y0.303571.038
141_P192_S0.300631.028
60_Y71_T0.300251.027
154_Q158_D0.299911.026
160_A179_F0.294611.008
254_A258_G0.292831.002
52_D56_D0.288980.989
94_P116_L0.288180.986
20_S27_V0.287550.984
192_S197_T0.287240.983
15_V251_I0.286750.981
235_D239_G0.286230.979
53_S56_D0.28620.979
230_G244_I0.28510.975
100_D104_R0.285020.975
101_E105_E0.284060.972
8_S31_E0.283040.968
160_A188_N0.281760.964
194_A197_T0.281640.963
32_A57_W0.279060.955
166_P175_D0.278830.954
28_L244_I0.278470.953
14_V17_S0.277540.949
221_F228_A0.277260.948
3_Y249_E0.274950.941
47_F50_D0.274760.940
158_D162_E0.274580.939
154_Q246_A0.274510.939
260_P264_L0.273920.937
156_L180_C0.27310.934
130_S259_T0.268270.918
234_V239_G0.267180.914
130_S261_R0.266990.913
160_A163_L0.266640.912
29_V199_L0.26640.911
3_Y251_I0.265970.910
20_S208_L0.26290.899
17_S201_P0.262840.899
92_F171_F0.262240.897
219_I231_V0.262140.897
19_L25_K0.260480.891
254_A262_L0.259370.887
14_V198_Y0.258960.886
180_C186_C0.258660.885
229_T245_V0.257830.882
30_L231_V0.257370.880
211_L233_Y0.25570.875
46_S49_Q0.254670.871
6_V254_A0.254430.870
5_I27_V0.254350.870
222_D245_V0.254140.869
43_P46_S0.253510.867
6_V125_T0.25260.864
233_Y245_V0.251850.862
153_N157_M0.250760.858
183_G186_C0.249930.855
40_D43_P0.249740.854
20_S25_K0.249480.853
157_M167_V0.249390.853
60_Y73_N0.248530.850
197_T201_P0.248170.849
128_G145_S0.248110.849
125_T139_P0.248050.849
229_T232_E0.246580.843
141_P144_S0.244090.835
123_A198_Y0.244090.835
139_P198_Y0.243860.834
32_A95_S0.243020.831
96_P113_W0.242880.831
247_A250_V0.242870.831
61_S64_Q0.242480.829
13_S194_A0.241880.827
124_E134_H0.241530.826
160_A165_I0.241320.826
67_L72_I0.241270.825
91_Y123_A0.239980.821
14_V18_R0.239740.820
193_S196_T0.239640.820
4_I231_V0.239520.819
43_P47_F0.238260.815
100_D112_S0.237480.812
21_E205_R0.236040.807
209_T212_T0.234870.803
44_P47_F0.234160.801
45_S48_Y0.233630.799
155_A175_D0.231440.792
227_R230_G0.229520.785
19_L27_V0.229170.784
217_T265_R0.228450.781
155_A159_A0.227910.780
229_T246_A0.227620.779
196_T200_P0.226890.776
3_Y22_A0.226730.776
62_G65_P0.22450.768
156_L160_A0.223020.763
67_L70_R0.222350.761
216_V231_V0.222250.760
30_L96_P0.221240.757
121_D135_G0.219480.751
217_T220_I0.219230.750
150_S153_N0.219050.749
140_L197_T0.218130.746
157_M179_F0.217540.744
159_A163_L0.216710.741
156_L231_V0.216420.740
6_V262_L0.216370.740
115_D118_P0.214950.735
98_D111_W0.214540.734
101_E104_R0.214460.734
217_T239_G0.214270.733
246_A249_E0.213360.730
25_K248_K0.213020.729
236_N239_G0.212970.729
6_V219_I0.212670.727
93_R117_E0.212560.727
140_L144_S0.210820.721
211_L243_R0.210640.721
168_P171_F0.210580.720
176_P179_F0.209460.717
12_G27_V0.207850.711
18_R122_K0.207030.708
113_W117_E0.206990.708
120_Y123_A0.20690.708
214_A243_R0.206890.708
154_Q248_K0.204880.701
126_F129_P0.204550.700
17_S205_R0.20420.699
145_S183_G0.203730.697
130_S257_I0.203270.695
161_E166_P0.20190.691
186_C213_N0.201840.690
155_A158_D0.200280.685
99_F102_W0.200090.684
58_G73_N0.199080.681
125_T136_V0.198950.681
125_T187_P0.198520.679
141_P187_P0.197680.676
62_G71_T0.197430.675
41_S46_S0.196410.672
53_S58_G0.196180.671
93_R111_W0.196110.671
202_A208_L0.195880.670
100_D114_D0.194960.667
4_I250_V0.194810.666
126_F183_G0.194530.665
44_P49_Q0.194410.665
155_A171_F0.193140.661
41_S196_T0.192910.660
61_S65_P0.192650.659
197_T200_P0.192530.659
13_S199_L0.19160.655
42_T45_S0.191180.654
200_P210_L0.191070.654
202_A206_P0.190890.653
260_P263_L0.190330.651
263_L268_I0.190050.650
97_S101_E0.189580.649
174_C180_C0.188790.646
178_G209_T0.188160.644
63_P67_L0.18780.642
16_A20_S0.187080.640
26_K207_N0.187070.640
187_P192_S0.186890.639
134_H170_D0.186750.639
4_I245_V0.186560.638
20_S207_N0.186530.638
127_L141_P0.186280.637
130_S136_V0.186130.637
174_C186_C0.185840.636
42_T51_F0.185550.635
105_E111_W0.185010.633
36_Y41_S0.184620.632
133_L174_C0.184240.630
156_L159_A0.183760.629
99_F266_S0.183560.628
258_G262_L0.183550.628
216_V254_A0.183320.627
3_Y124_E0.182480.624
131_S135_G0.182220.623
133_L173_G0.182180.623
52_D58_G0.181810.622
4_I247_A0.181090.619
97_S100_D0.180810.619
8_S16_A0.18040.617
154_Q178_G0.180360.617
219_I252_L0.180340.617
95_S176_P0.179510.614
159_A164_G0.179190.613
5_I17_S0.179160.613
4_I118_P0.178880.612
222_D226_G0.178870.612
172_N208_L0.178640.611
171_F182_T0.178190.610
42_T46_S0.178060.609
41_S47_F0.177940.609
216_V252_L0.177930.609
8_S212_T0.17740.607
204_K209_T0.177130.606
91_Y94_P0.176720.605
5_I20_S0.176220.603
254_A259_T0.175990.602
99_F116_L0.175540.600
149_P152_M0.175320.600
161_E168_P0.174680.598
246_A250_V0.174250.596
13_S17_S0.173890.595
101_E268_I0.173530.594
203_L208_L0.173530.594
211_L237_D0.173160.592
257_I261_R0.173040.592
112_S118_P0.17290.591
228_A231_V0.172540.590
172_N176_P0.172330.590
135_G139_P0.172110.589
149_P153_N0.171470.587
159_A162_E0.17070.584
7_G12_G0.170440.583
169_Q173_G0.170270.582
20_S23_G0.170180.582
54_E58_G0.170140.582
10_A14_V0.16990.581
35_R38_P0.169610.580
186_C190_A0.16960.580
244_I247_A0.169540.580
103_A117_E0.169490.580
93_R120_Y0.169460.580
47_F51_F0.1690.578
91_Y116_L0.168940.578
113_W116_L0.168560.577
28_L33_G0.168320.576
221_F227_R0.168290.576
14_V21_E0.168250.576
20_S202_A0.168140.575
133_L136_V0.167130.572
220_I245_V0.166610.570
154_Q181_M0.166470.569
114_D117_E0.166460.569
215_R236_N0.166360.569
209_T243_R0.166350.569
182_T215_R0.166340.569
259_T263_L0.166210.569
4_I7_G0.164750.564
22_A207_N0.164670.563
239_G243_R0.163870.561
12_G31_E0.163690.560
123_A126_F0.16320.558
48_Y51_F0.162650.556
42_T47_F0.162550.556
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
3fimB0.99321000.13
3qvpA0.98991000.151
3t37A0.98311000.177
1gpeA0.98311000.19
4ha6A0.9731000.194
3q9tA0.96281000.21
2jbvA0.97641000.22
1ju2A0.89191000.311
1n4wA0.91551000.324
1kdgA0.93241000.348

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