GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cu-oxidase - Multicopper oxidase
Pfam: PF00394 (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: CL0026
Length: 159
Sequences: 2446
Seq/Len: 15.38
HH_delta: 0.155 (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
96_A119_D0.864983.924
69_R121_L0.632222.868
41_I152_A0.619982.813
74_L85_F0.560152.541
91_P106_K0.558082.532
6_M77_A0.547112.482
69_R123_T0.522632.371
72_L120_V0.484622.199
91_P108_D0.469992.132
65_K68_E0.456822.072
64_V124_A0.444672.017
74_L120_V0.444382.016
133_I154_L0.436181.979
61_V155_R0.431081.956
67_G124_A0.428771.945
88_D134_R0.420591.908
74_L110_L0.420331.907
92_M120_V0.39221.779
71_R119_D0.382671.736
97_A118_Y0.366721.664
85_F110_L0.364771.655
85_F133_I0.362741.646
87_I122_V0.358841.628
112_L118_Y0.358171.625
84_N111_V0.35561.613
5_I74_L0.351541.595
93_T106_K0.344511.563
87_I92_M0.334711.518
87_I133_I0.325231.475
63_K155_R0.311921.415
13_D17_D0.311561.413
39_I150_A0.30961.405
71_R95_I0.305851.388
11_Y18_L0.303471.377
39_I83_F0.302061.370
5_I133_I0.298591.355
90_H131_Y0.289331.313
92_M122_V0.288831.310
132_W153_I0.288131.307
102_V105_Y0.286031.298
82_S113_A0.285791.297
62_I152_A0.278941.265
78_G83_F0.277031.257
14_D17_D0.27481.247
128_P131_Y0.269911.224
64_V154_L0.267281.213
78_G114_P0.264931.202
20_Q24_A0.263641.196
44_K60_P0.250731.137
7_L83_F0.249081.130
82_S111_V0.247161.121
90_H156_Y0.245761.115
8_S77_A0.245271.113
130_N155_R0.241291.095
79_A115_G0.240021.089
110_L118_Y0.238331.081
33_P36_P0.238011.080
145_P148_G0.236521.073
41_I135_A0.23571.069
70_Y124_A0.23191.052
86_S108_D0.231191.049
90_H125_D0.230431.045
86_S134_R0.2221.007
40_L43_G0.216520.982
43_G71_R0.216240.981
73_R119_D0.216230.981
89_G126_Q0.216030.980
126_Q131_Y0.215770.979
11_Y36_P0.214190.972
4_V75_I0.210260.954
59_P153_I0.209840.952
96_A101_P0.209190.949
83_F135_A0.208770.947
64_V122_V0.206570.937
19_L33_P0.204980.930
72_L87_I0.202390.918
8_S40_L0.200240.908
94_V107_V0.199640.906
131_Y156_Y0.194790.884
39_I135_A0.19430.881
66_P128_P0.193580.878
66_P125_D0.193480.878
13_D21_Q0.193250.877
110_L120_V0.192760.874
125_D131_Y0.190340.863
97_A102_V0.189930.862
67_G123_T0.185630.842
91_P125_D0.183980.835
60_P152_A0.181440.823
94_V120_V0.181440.823
130_N153_I0.181430.823
33_P80_S0.181150.822
11_Y77_A0.180860.820
21_Q24_A0.18030.818
3_Y62_I0.179550.815
11_Y116_Q0.179050.812
16_D20_Q0.178010.808
90_H124_A0.177520.805
12_H38_S0.174320.791
122_V154_L0.17430.791
44_K57_G0.172150.781
17_D21_Q0.1680.762
39_I89_G0.167660.761
86_S109_T0.166340.755
3_Y72_L0.166260.754
62_I133_I0.166110.754
105_Y108_D0.164990.748
86_S136_S0.163970.744
80_S114_P0.163880.743
74_L133_I0.163830.743
74_L112_L0.162530.737
87_I154_L0.161820.734
75_I117_R0.160650.729
101_P113_A0.160540.728
39_I151_L0.160150.727
59_P132_W0.159870.725
39_I148_G0.159640.724
4_V69_R0.159620.724
146_Q149_N0.159430.723
102_V116_Q0.15910.722
124_A156_Y0.158990.721
65_K106_K0.158650.720
34_P78_G0.156760.711
95_I117_R0.156670.711
113_A116_Q0.156590.710
68_E121_L0.15570.706
125_D128_P0.155660.706
64_V70_Y0.155260.704
64_V72_L0.15380.698
78_G111_V0.152930.694
83_F148_G0.151930.689
36_P81_T0.150380.682
84_N134_R0.149490.678
5_I85_F0.147820.671
144_D147_N0.146820.666
90_H94_V0.146710.666
7_L85_F0.145120.658
111_V134_R0.144560.656
11_Y15_S0.14390.653
64_V156_Y0.141980.644
98_D117_R0.141030.640
24_A130_N0.14050.637
39_I145_P0.140310.637
66_P123_T0.139810.634
74_L104_P0.139670.634
34_P116_Q0.139440.633
39_I81_T0.139130.631
40_L44_K0.13890.630
5_I62_I0.137990.626
58_E122_V0.137760.625
66_P126_Q0.137720.625
94_V102_V0.13750.624
92_M110_L0.137440.624
96_A102_V0.137360.623
18_L21_Q0.137240.623
143_N147_N0.137020.622
126_Q129_G0.136480.619
13_D35_I0.135410.614
70_Y95_I0.135270.614
19_L102_V0.134470.610
18_L34_P0.134440.610
98_D119_D0.134240.609
17_D24_A0.13420.609
44_K128_P0.133510.606
134_R149_N0.133330.605
19_L57_G0.132920.603
59_P136_S0.132820.603
89_G129_G0.132610.602
7_L41_I0.132590.602
3_Y124_A0.131870.598
24_A150_A0.131850.598
7_L74_L0.130890.594
44_K112_L0.130490.592
15_S74_L0.130440.592
36_P71_R0.130350.591
94_V105_Y0.129930.589
20_Q23_F0.129880.589
97_A116_Q0.129630.588
15_S118_Y0.129480.587
93_T123_T0.129220.586
81_T114_P0.129040.585
8_S11_Y0.128430.583
21_Q149_N0.128290.582
63_K66_P0.127510.578
34_P136_S0.126330.573
89_G128_P0.126220.573
100_V116_Q0.125680.570
16_D33_P0.124750.566
7_L146_Q0.124620.565
144_D149_N0.124390.564
34_P100_V0.124370.564
91_P94_V0.124340.564
66_P124_A0.124330.564
25_P58_E0.124330.564
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
3sqrA0.96231000.155
3t6vA0.91191000.201
3pxlA0.89941000.205
1aozA0.96231000.217
1v10A0.93081000.242
1hfuA0.89941000.244
2q9oA0.93081000.246
1zpuA0.91191000.249
2uxtA0.867999.90.348
2xu9A0.874299.90.352

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