GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
K_oxygenase - L-lysine 6-monooxygenase (NADPH-requiring)
Pfam: PF13434 (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: 341
Sequences: 4885
Seq/Len: 14.33
HH_delta: 0.221 (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
194_A330_V1.08714.815
217_K295_R0.730353.235
6_I134_V0.673382.983
194_A315_L0.662392.934
6_I32_L0.661282.929
148_A151_V0.621832.754
314_R329_E0.621552.753
17_L152_V0.618412.739
3_Y30_L0.614742.723
6_I146_Y0.612472.713
192_R217_K0.598982.653
4_D149_R0.571492.531
6_I148_A0.560732.484
304_S316_T0.556932.467
219_T297_L0.540282.393
306_E314_R0.525182.326
192_R331_D0.510152.260
34_R117_E0.507052.246
301_E318_R0.48292.139
312_G329_E0.477982.117
5_L21_L0.473492.097
194_A221_I0.472892.095
203_A220_W0.467082.069
4_D28_K0.451011.998
133_R145_T0.441361.955
133_R147_R0.421991.869
135_T145_T0.420341.862
308_D314_R0.417431.849
316_T327_T0.416631.845
135_T143_G0.413411.831
32_L146_Y0.41111.821
306_E316_T0.407641.806
191_K217_K0.405471.796
303_T318_R0.404371.791
308_D312_G0.394711.748
219_T330_V0.394071.745
309_G312_G0.390261.729
3_Y122_E0.386791.713
93_S96_E0.37991.683
225_P299_N0.379821.682
314_R327_T0.375491.663
192_R219_T0.372931.652
189_A216_A0.360881.598
96_E99_D0.360221.595
136_T146_Y0.360211.595
36_P115_G0.345711.531
223_R301_E0.342941.519
6_I30_L0.341721.514
297_L326_E0.338431.499
221_I317_L0.324971.439
161_I335_L0.324911.439
194_A333_V0.311451.379
193_V209_L0.308571.367
5_L27_L0.308031.364
99_D103_W0.307861.364
317_L328_L0.306131.356
3_Y6_I0.305641.354
98_N102_R0.299471.326
175_F183_R0.298971.324
32_L136_T0.297871.319
4_D30_L0.296331.312
116_S136_T0.293841.301
8_I153_L0.293631.301
47_P50_R0.290121.285
191_K331_D0.289311.281
173_R332_A0.287891.275
297_L300_T0.287251.272
176_H179_E0.287141.272
172_P307_Q0.285941.266
37_S102_R0.285171.263
305_A313_V0.2831.253
318_R325_E0.279041.236
189_A212_R0.278061.232
34_R127_G0.277221.228
192_R329_E0.277121.227
30_L124_D0.276781.226
46_L50_R0.274371.215
5_L152_V0.270611.199
213_G218_V0.269421.193
7_G14_N0.268261.188
260_L290_G0.267631.185
303_T316_T0.266911.182
317_L326_E0.265531.176
173_R313_V0.265411.176
124_D133_R0.265331.175
159_P176_H0.264561.172
19_A23_E0.262791.164
308_D329_E0.261581.159
3_Y28_K0.260421.153
180_Y208_D0.260221.153
175_F332_A0.258761.146
316_T325_E0.255221.130
30_L146_Y0.251481.114
121_I151_V0.249561.105
194_A328_L0.24661.092
44_M48_G0.245721.088
174_V335_L0.244161.081
219_T295_R0.243441.078
4_D27_L0.237061.050
159_P178_S0.23611.046
30_L113_R0.235261.042
192_R330_V0.233611.035
192_R216_A0.231621.026
10_F14_N0.230751.022
134_V151_V0.229331.016
300_T317_L0.228441.012
122_E133_R0.226471.003
22_E29_A0.225721.000
206_F220_W0.224470.994
27_L149_R0.224370.994
21_L29_A0.224070.992
192_R312_G0.223970.992
196_V333_V0.221360.980
10_F33_E0.22040.976
231_D235_F0.220220.975
10_F31_F0.219760.973
206_F294_L0.219720.973
47_P53_V0.219290.971
196_V335_L0.21860.968
47_P51_M0.218390.967
102_R106_E0.218310.967
160_R337_T0.217730.964
99_D102_R0.215530.955
46_L49_A0.214820.951
19_A108_L0.213760.947
223_R302_V0.211050.935
161_I176_H0.209710.929
220_W296_L0.209520.928
116_S144_E0.20810.922
193_V216_A0.207260.918
226_G229_P0.20720.918
113_R146_Y0.205220.909
32_L118_V0.20420.904
177_S205_I0.203250.900
43_G48_G0.20310.900
162_P337_T0.202790.898
42_P178_S0.201860.894
113_R116_S0.201080.891
303_T325_E0.200570.888
46_L52_Q0.197430.874
44_M51_M0.196990.873
198_G220_W0.196220.869
94_R100_Y0.195850.867
163_E166_Q0.195630.866
173_R307_Q0.194120.860
58_D61_T0.193950.859
53_V69_F0.191740.849
20_L24_H0.191040.846
319_H326_E0.190130.842
97_F100_Y0.189440.839
124_D127_G0.189270.838
28_K122_E0.188980.837
103_W106_E0.188720.836
221_I328_L0.188420.835
14_N18_A0.188180.833
131_L147_R0.187850.832
114_Y118_V0.18740.830
43_G47_P0.184920.819
116_S121_I0.184310.816
178_S339_Y0.183970.815
3_Y124_D0.182910.810
219_T328_L0.182910.810
136_T144_E0.182270.807
210_L217_K0.182170.807
313_V333_V0.181250.803
10_F112_V0.181240.803
93_S97_F0.181060.802
50_R54_S0.180890.801
196_V337_T0.180660.800
195_V206_F0.179660.796
177_S339_Y0.179380.795
221_I315_L0.178170.789
136_T143_G0.177810.788
211_R292_G0.177570.786
39_S44_M0.177140.785
54_S57_K0.176980.784
183_R332_A0.176840.783
8_I118_V0.175970.779
18_A31_F0.175650.778
319_H325_E0.175110.776
191_K332_A0.1750.775
20_L23_E0.173990.771
228_F259_L0.173770.770
122_E135_T0.173620.769
58_D62_L0.173360.768
50_R57_K0.172990.766
165_F305_A0.172770.765
190_G216_A0.171890.761
175_F179_E0.171480.760
94_R98_N0.171450.759
188_L191_K0.171030.758
92_P97_F0.170840.757
53_V100_Y0.170350.755
44_M47_P0.170170.754
94_R101_L0.170090.753
198_G227_F0.169720.752
305_A315_L0.169470.751
297_L317_L0.16930.750
202_A222_S0.169180.749
53_V57_K0.168990.748
57_K61_T0.168060.744
100_Y104_V0.168010.744
297_L328_L0.166750.739
35_R42_P0.166660.738
177_S201_S0.165470.733
6_I132_F0.165460.733
7_G29_A0.164720.730
6_I151_V0.164530.729
7_G18_A0.164130.727
171_S179_E0.163890.726
202_A223_R0.163610.725
33_E52_Q0.163350.724
43_G49_A0.163190.723
113_R125_D0.162450.720
48_G51_M0.162380.719
93_S100_Y0.162180.718
115_G119_T0.161820.717
202_A220_W0.16170.716
121_I134_V0.160530.711
120_S135_T0.160330.710
207_L211_R0.160280.710
124_D147_R0.160210.710
307_Q312_G0.159970.709
44_M50_R0.159840.708
317_L327_T0.159480.706
31_F123_P0.158810.703
38_F44_M0.158670.703
49_A52_Q0.158530.702
118_V125_D0.158090.700
201_S339_Y0.15750.698
27_L150_N0.157140.696
101_L105_A0.156620.694
46_L53_V0.156610.694
116_S123_P0.156340.692
191_K309_G0.156230.692
206_F218_V0.156230.692
188_L332_A0.155170.687
100_Y132_F0.154290.683
31_F116_S0.154270.683
210_L294_L0.153960.682
198_G335_L0.15350.680
113_R144_E0.152910.677
177_S336_A0.152880.677
103_W107_Q0.152720.676
17_L21_L0.152130.674
224_S299_N0.152130.674
50_R53_V0.151960.673
226_G233_S0.150930.668
316_T329_E0.150830.668
132_F151_V0.150570.667
305_A333_V0.150510.667
38_F42_P0.150490.667
48_G54_S0.150460.666
193_V334_I0.150460.666
47_P52_Q0.149360.662
195_V202_A0.149020.660
106_E124_D0.148890.659
47_P54_S0.148380.657
15_L19_A0.148180.656
46_L51_M0.148140.656
7_G31_F0.148090.656
39_S48_G0.148020.656
160_R163_E0.147830.655
16_S19_A0.147090.651
42_P46_L0.146860.650
118_V134_V0.14640.648
92_P96_E0.146190.648
40_W176_H0.146110.647
47_P205_I0.146090.647
96_E100_Y0.145650.645
153_L204_E0.145170.643
44_M49_A0.1450.642
220_W227_F0.144420.640
15_L40_W0.144370.639
68_P71_F0.144320.639
290_G295_R0.144230.639
306_E327_T0.144070.638
39_S46_L0.14390.637
227_F298_P0.143350.635
95_R102_R0.143010.633
189_A209_L0.142910.633
205_I208_D0.142550.631
5_L150_N0.142490.631
223_R333_V0.142440.631
12_P204_E0.142350.630
221_I300_T0.141510.627
198_G298_P0.141060.625
12_P101_L0.140930.624
106_E110_N0.140440.622
19_A104_V0.14030.621
177_S204_E0.140260.621
32_L148_A0.140170.621
94_R103_W0.139420.618
193_V332_A0.138940.615
165_F174_V0.138070.612
95_R99_D0.138010.611
47_P57_K0.137790.610
227_F296_L0.137380.608
195_V205_I0.13690.606
57_K62_L0.136760.606
43_G51_M0.136360.604
38_F339_Y0.136240.603
112_V116_S0.135670.601
18_A29_A0.135560.600
95_R98_N0.135350.599
3_Y144_E0.135320.599
109_D113_R0.135310.599
8_I113_R0.134890.597
223_R337_T0.134840.597
120_S126_D0.134610.596
16_S40_W0.134420.595
196_V221_I0.134010.594
161_I337_T0.1340.594
304_S307_Q0.133150.590
300_T319_H0.133030.589
312_G331_D0.132850.588
13_F154_A0.132780.588
119_T122_E0.132430.587
95_R132_F0.132190.585
305_A337_T0.132190.585
48_G52_Q0.131990.585
43_G46_L0.131950.584
171_S307_Q0.131940.584
202_A206_F0.131890.584
134_V149_R0.131860.584
7_G10_F0.131750.584
133_R143_G0.131560.583
172_P187_S0.131370.582
52_Q69_F0.131330.582
98_N101_L0.131330.582
111_Q114_Y0.131260.581
201_S222_S0.130710.579
12_P174_V0.130680.579
200_Q205_I0.130030.576
179_E183_R0.129840.575
92_P100_Y0.12920.572
61_T71_F0.128830.571
48_G57_K0.128750.570
43_G50_R0.128510.569
208_D212_R0.128070.567
51_M230_M0.127530.565
172_P305_A0.12720.563
111_Q115_G0.126940.562
9_G14_N0.126650.561
11_G199_G0.126520.560
203_A227_F0.126130.559
224_S227_F0.126060.558
126_D142_D0.125950.558
25_G29_A0.12560.556
131_L149_R0.125490.556
3_Y111_Q0.125410.555
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
4b63A0.98831000.221
3s5wA0.99121000.277
3uoxA0.88561000.45
3gwfA0.88861000.451
4ap3A0.88561000.451
1w4xA0.88561000.494
2xveA0.75951000.495
4b1bA0.80651000.505
2gv8A0.73611000.515
3qfaA0.82111000.519

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