GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Oxidored_FMN - NADHflavin oxidoreductase NADH oxidase family
Pfam: PF00724 (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: CL0036
Length: 341
Sequences: 6067
Seq/Len: 17.79
HH_delta: 0.063 (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
141_E190_E1.354463.996
97_I165_G1.079913.186
207_E248_L0.975862.879
61_S150_D0.970762.864
194_S197_N0.950062.803
89_V96_I0.932432.751
7_K12_T0.918642.710
139_M147_I0.889362.624
36_D84_K0.879772.596
18_V317_L0.872522.574
139_M143_E0.851062.511
76_D157_R0.832952.458
156_R212_A0.829142.446
152_A208_A0.821642.424
137_R143_E0.817222.411
117_V139_M0.788742.327
244_L247_E0.763012.251
332_N336_E0.754972.228
176_L201_F0.753722.224
308_K312_E0.739112.181
6_L317_L0.735012.169
176_L202_L0.709512.093
220_G252_F0.708462.090
50_A324_L0.706942.086
197_N200_R0.705082.080
3_F335_R0.703972.077
307_E311_E0.70262.073
295_I319_A0.699542.064
284_E314_K0.698682.061
87_D91_A0.692012.042
202_L221_V0.690022.036
83_K87_D0.680542.008
43_E92_H0.679912.006
10_N216_D0.67591.994
287_K316_D0.666741.967
90_H164_D0.646611.908
327_D333_K0.643351.898
246_E291_K0.641161.892
153_Q157_R0.633641.870
146_E150_D0.628941.856
149_E153_Q0.62511.844
156_R160_E0.623661.840
159_K213_V0.617821.823
141_E144_I0.614121.812
191_Y204_E0.608911.797
152_A212_A0.606061.788
58_T98_A0.602791.779
170_A221_V0.594971.755
243_K289_A0.594881.755
234_T237_E0.593341.751
43_E88_A0.579311.709
280_L309_A0.566781.672
141_E191_Y0.556881.643
109_P134_Y0.554721.637
140_T143_E0.55151.627
141_E145_E0.549121.620
86_A163_F0.549081.620
330_L334_A0.543121.602
199_A244_L0.536781.584
79_I160_E0.533441.574
145_E190_E0.527361.556
176_L205_I0.520681.536
63_E146_E0.519741.533
22_M321_G0.518731.531
18_V295_I0.515231.520
240_E244_L0.506041.493
284_E288_K0.504791.489
145_E204_E0.502371.482
239_I289_A0.495451.462
159_K214_G0.490151.446
155_A209_I0.487991.440
76_D160_E0.487481.438
39_I84_K0.481261.420
208_A211_E0.480021.416
100_L154_A0.479721.415
14_K95_K0.473241.396
195_L199_A0.46731.379
73_I98_A0.4671.378
306_A320_M0.464161.369
207_E211_E0.464121.369
213_V217_F0.462271.364
159_K217_F0.458311.352
79_I157_R0.457851.351
55_T96_I0.452291.334
202_L241_I0.451971.334
297_V319_A0.45071.330
40_A43_E0.450211.328
153_Q156_R0.448261.323
82_L163_F0.445621.315
39_I88_A0.445271.314
19_M45_R0.445041.313
332_N335_R0.443121.307
170_A176_L0.440461.300
66_G103_A0.439591.297
300_I309_A0.437151.290
149_E208_A0.436961.289
19_M53_I0.435541.285
6_L293_P0.429181.266
149_E152_A0.428481.264
203_L207_E0.427861.262
143_E146_E0.422981.248
44_R329_D0.420771.241
152_A211_E0.419531.238
138_E188_T0.417971.233
13_L52_L0.415291.225
307_E310_L0.414011.222
200_R204_E0.412361.217
152_A156_R0.410331.211
246_E292_I0.410151.210
90_H96_I0.40771.203
15_N51_G0.406591.200
81_G84_K0.404261.193
240_E243_K0.403591.191
285_A289_A0.401361.184
199_A203_L0.400711.182
295_I317_L0.400021.180
17_I331_P0.397321.172
43_E91_A0.394041.163
177_S181_S0.393551.161
309_A315_A0.391661.156
13_L18_V0.39061.152
285_A288_K0.38611.139
87_D90_H0.386021.139
73_I154_A0.384281.134
303_P337_G0.381891.127
24_T37_R0.379071.118
117_V120_S0.378151.116
296_G315_A0.376821.112
117_V137_R0.37541.108
39_I85_L0.374071.104
203_L248_L0.370441.093
180_L202_L0.36931.090
170_A202_L0.367561.084
59_A70_Q0.366861.082
7_K10_N0.366371.081
145_E191_Y0.365161.077
76_D80_P0.364641.076
168_I205_I0.362531.070
304_E308_K0.362391.069
13_L317_L0.36121.066
34_P82_L0.360871.065
175_L201_F0.359961.062
148_I152_A0.359311.060
148_I204_E0.357381.054
148_I208_A0.356641.052
208_A212_A0.356641.052
183_L231_G0.352851.041
47_K92_H0.352031.039
55_T163_F0.349331.031
148_I191_Y0.347981.027
36_D40_A0.347491.025
83_K160_E0.347471.025
13_L51_G0.347151.024
150_D153_Q0.34711.024
72_G78_Q0.347081.024
71_P82_L0.346831.023
86_A96_I0.345181.018
203_L244_L0.345161.018
33_V78_Q0.343251.013
300_I318_V0.340811.006
86_A161_A0.340371.004
39_I43_E0.33810.998
315_A318_V0.338090.998
98_A158_A0.337820.997
75_D78_Q0.336530.993
140_T145_E0.336010.991
96_I164_D0.335230.989
324_L331_P0.334630.987
155_A213_V0.332880.982
253_L292_I0.331960.979
11_L95_K0.331130.977
2_L306_A0.329630.973
33_V81_G0.324030.956
60_V151_F0.323410.954
9_G220_G0.322990.953
96_I163_F0.321090.947
8_I13_L0.31990.944
138_E186_R0.319750.943
235_L285_A0.31950.943
19_M22_M0.318420.939
206_I245_L0.317610.937
35_T38_L0.316440.934
168_I209_I0.316440.934
221_V250_V0.316380.933
95_K164_D0.315370.930
199_A202_L0.315120.930
243_K247_E0.315030.929
210_R251_D0.314730.929
19_M50_A0.313320.924
79_I161_A0.312670.923
103_A107_A0.311910.920
172_H256_S0.311040.918
195_L240_E0.310850.917
105_R184_T0.310560.916
79_I86_A0.310490.916
137_R140_T0.307760.908
20_A321_G0.307410.907
74_W78_Q0.306970.906
21_P222_R0.306170.903
190_E200_R0.304230.898
148_I205_I0.302930.894
191_Y207_E0.302620.893
14_K94_A0.302380.892
73_I78_Q0.302010.891
210_R219_V0.301810.890
302_T305_Q0.301160.889
193_G198_R0.300920.888
48_G332_N0.300640.887
43_E47_K0.300170.886
206_I248_L0.298460.881
223_L238_T0.297470.878
209_I219_V0.297390.877
144_I148_I0.297330.877
119_P184_T0.296760.876
52_L97_I0.295980.873
165_G220_G0.293820.867
252_F295_I0.293410.866
80_P87_D0.291740.861
242_A290_V0.291170.859
9_G251_D0.289220.853
90_H95_K0.288250.850
280_L296_G0.287820.849
221_V245_L0.284950.841
145_E148_I0.284620.840
206_I250_V0.282780.834
139_M144_I0.282260.833
144_I191_Y0.2820.832
199_A240_E0.281420.830
236_E239_I0.281140.829
41_Y45_R0.280820.829
182_P235_L0.280590.828
17_I50_A0.280210.827
213_V219_V0.279450.825
169_H174_Y0.279420.824
159_K216_D0.277970.820
55_T82_L0.277910.820
147_I150_D0.276980.817
301_R305_Q0.276770.817
59_A65_R0.276570.816
42_Y53_I0.276440.816
73_I158_A0.275770.814
242_A286_I0.275620.813
239_I243_K0.275570.813
50_A331_P0.274580.810
40_A44_R0.274160.809
180_L199_A0.274150.809
225_P255_V0.273540.807
196_E244_L0.273180.806
59_A74_W0.273140.806
153_Q212_A0.272830.805
300_I306_A0.272660.804
223_L255_V0.272020.803
113_G116_P0.270730.799
142_E145_E0.270590.798
303_P334_A0.270050.797
255_V286_I0.269740.796
237_E240_E0.269670.796
329_D333_K0.266460.786
124_A138_E0.266330.786
57_A101_W0.265370.783
244_L248_L0.263910.779
235_L239_I0.26320.777
195_L244_L0.262340.774
97_I220_G0.261990.773
106_Q230_E0.261910.773
117_V143_E0.261740.772
183_L229_V0.26160.772
18_V52_L0.260730.769
144_I202_L0.260550.769
20_A319_A0.260390.768
84_K87_D0.259780.766
54_I97_I0.258140.762
18_V54_I0.257780.761
88_A92_H0.257770.761
73_I157_R0.257330.759
19_M324_L0.256830.758
159_K212_A0.256570.757
283_A294_V0.255880.755
199_A241_I0.255820.755
55_T98_A0.25580.755
245_L250_V0.255490.754
75_D79_I0.254230.750
190_E197_N0.254230.750
167_E254_D0.252640.745
320_M330_L0.251710.743
145_E208_A0.250820.740
6_L9_G0.250020.738
60_V150_D0.249680.737
169_H172_H0.249380.736
306_A334_A0.24920.735
80_P84_K0.248050.732
277_G305_Q0.247540.730
118_G184_T0.246260.727
64_G102_H0.245470.724
210_R213_V0.244730.722
296_G318_V0.244640.722
19_M42_Y0.24440.721
66_G70_Q0.244150.720
60_V101_W0.244120.720
287_K294_V0.243720.719
61_S147_I0.24340.718
222_R254_D0.242410.715
140_T147_I0.242320.715
152_A209_I0.241950.714
46_A89_V0.241350.712
36_D39_I0.241070.711
157_R160_E0.240920.711
239_I285_A0.239650.707
88_A91_A0.238960.705
238_T286_I0.238250.703
192_G198_R0.238180.703
82_L158_A0.238120.703
54_I165_G0.238060.702
34_P81_G0.237920.702
201_F205_I0.237730.701
44_R47_K0.236960.699
89_V94_A0.236840.699
98_A163_F0.236470.698
168_I206_I0.23570.695
224_S227_D0.235650.695
204_E207_E0.235540.695
242_A253_L0.233940.690
105_R136_P0.233630.689
12_T95_K0.23310.688
105_R178_Q0.232980.687
18_V319_A0.232720.687
309_A314_K0.231830.684
83_K86_A0.231750.684
148_I201_F0.231570.683
8_I293_P0.231020.682
276_P305_Q0.229920.678
210_R214_G0.229180.676
115_P137_R0.229080.676
146_E153_Q0.228980.676
332_N338_R0.227430.671
320_M324_L0.227310.671
20_A254_D0.227130.670
17_I330_L0.226830.669
11_L97_I0.226820.669
296_G309_A0.226740.669
156_R159_K0.225110.664
152_A205_I0.225030.664
286_I290_V0.223530.660
57_A60_V0.222760.657
149_E211_E0.222530.657
41_Y56_E0.221890.655
84_K88_A0.221560.654
233_I241_I0.221420.653
210_R215_P0.221360.653
220_G295_I0.220570.651
308_K311_E0.220430.650
195_L241_I0.220380.650
120_S139_M0.219430.647
286_I294_V0.21790.643
254_D319_A0.217710.642
53_I96_I0.217660.642
38_L85_L0.217180.641
49_G332_N0.217080.640
70_Q103_A0.216470.639
227_D232_G0.216420.639
167_E220_G0.216250.638
205_I208_A0.216090.638
323_P330_L0.215870.637
308_K314_K0.215720.636
11_L165_G0.21560.636
320_M323_P0.215410.636
86_A90_H0.214090.632
60_V205_I0.213910.631
27_A38_L0.213330.629
181_S232_G0.213260.629
125_L231_G0.212880.628
5_P12_T0.211830.625
281_D284_E0.211680.625
243_K246_E0.211460.624
17_I324_L0.211230.623
52_L165_G0.211030.623
144_I185_N0.2110.623
14_K93_G0.21090.622
221_V253_L0.210850.622
124_A127_S0.210670.622
14_K335_R0.209250.617
3_F17_I0.208840.616
45_R329_D0.207990.614
154_A157_R0.20650.609
196_E240_E0.20580.607
3_F331_P0.205540.606
42_Y56_E0.205380.606
206_I221_V0.20440.603
246_E290_V0.204380.603
80_P83_K0.203470.600
106_Q124_A0.202630.598
214_G217_F0.20240.597
152_A213_V0.201460.594
290_V293_P0.200920.593
34_P85_L0.200550.592
139_M175_L0.200380.591
67_F70_Q0.200150.591
71_P85_L0.199210.588
304_E337_G0.198050.584
145_E149_E0.197080.581
320_M334_A0.196910.581
196_E200_R0.196850.581
120_S186_R0.19660.580
102_H147_I0.196110.579
179_F189_D0.195630.577
144_I176_L0.19550.577
309_A318_V0.19530.576
151_F176_L0.194730.575
58_T73_I0.194450.574
143_E147_I0.19370.572
305_Q309_A0.192730.569
180_L241_I0.192470.568
206_I219_V0.192190.567
209_I212_A0.191890.566
233_I238_T0.191560.565
20_A324_L0.191140.564
22_M325_L0.190840.563
310_L318_V0.190660.563
241_I245_L0.190450.562
79_I153_Q0.189450.559
176_L209_I0.188890.557
46_A92_H0.188770.557
52_L95_K0.188040.555
3_F334_A0.187740.554
24_T41_Y0.187290.553
241_I244_L0.186840.551
144_I201_F0.186670.551
60_V64_G0.186040.549
19_M321_G0.185940.549
302_T330_L0.185560.547
53_I89_V0.185260.547
303_P307_E0.184640.545
140_T146_E0.18430.544
222_R297_V0.18430.544
62_P74_W0.184130.543
118_G136_P0.184070.543
202_L205_I0.183810.542
255_V294_V0.18380.542
195_L233_I0.183590.542
306_A318_V0.183570.542
246_E294_V0.183250.541
272_F275_E0.182670.539
24_T38_L0.182670.539
60_V154_A0.182190.538
254_D297_V0.181790.536
24_T56_E0.18160.536
10_N217_F0.180990.534
235_L238_T0.180940.534
193_G197_N0.18070.533
141_E148_I0.180610.533
182_P237_E0.179850.531
61_S146_E0.179620.530
38_L56_E0.179130.529
115_P124_A0.179120.528
115_P134_Y0.179040.528
75_D157_R0.178440.526
223_L286_I0.178280.526
53_I94_A0.178050.525
190_E204_E0.177520.524
228_F232_G0.177440.524
70_Q101_W0.177350.523
252_F317_L0.176620.521
183_L232_G0.176470.521
239_I286_I0.176320.520
331_P335_R0.176250.520
171_A224_S0.176240.520
177_S227_D0.176170.520
59_A103_A0.175240.517
27_A71_P0.174780.516
155_A175_L0.173480.512
324_L330_L0.173480.512
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
4gbuA0.99411000.063
3l5aA0.96481000.066
3kruA0.95011000.067
3hgjA0.96481000.072
3gr7A0.94721000.073
3l5lA0.96481000.074
3k30A0.96771000.092
4jicA0.95891000.092
4awtA0.95011000.097
4a3uA0.9561000.099

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