GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MEKHLA - MEKHLA domain
Pfam: PF08670 (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: CL0183
Length: 148
Sequences: 25936
Seq/Len: 175.24
HH_delta: 0.067 (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
42_F143_S3.085893.416
112_S116_R2.346522.597
45_L140_A2.305222.552
61_A64_D2.0642.285
112_S118_F1.922922.129
43_A65_L1.916532.122
38_W57_Y1.849242.047
109_I119_R1.823022.018
31_E35_K1.73481.920
43_A142_F1.710111.893
111_I117_R1.699411.881
63_L70_W1.659431.837
58_A62_A1.612471.785
30_A33_L1.57351.742
48_G54_I1.541511.706
68_T113_S1.536581.701
60_Q64_D1.472141.630
121_E143_S1.463481.620
109_I117_R1.463281.620
35_K39_H1.457441.613
46_S137_G1.453481.609
127_N135_Y1.368221.515
69_T72_E1.36131.507
58_A63_L1.356121.501
122_R142_F1.34771.492
96_Q100_Q1.345911.490
76_L80_L1.340261.484
40_A44_I1.332921.475
39_H60_Q1.322981.464
83_E86_E1.319331.460
46_S139_A1.310861.451
45_L62_A1.280981.418
108_G122_R1.277191.414
129_I135_Y1.276631.413
54_I77_P1.268611.404
105_N121_E1.262331.397
130_D134_N1.240391.373
34_A38_W1.233921.366
45_L55_F1.229141.361
63_L69_T1.198611.327
60_Q63_L1.153851.277
49_T135_Y1.13921.261
32_E36_A1.108331.227
95_A99_Q1.107731.226
50_K54_I1.106481.225
48_G56_I1.092331.209
46_S57_Y1.080211.196
33_L46_S1.065031.179
91_Q95_A1.064741.179
33_L57_Y1.012891.121
47_H140_A1.004111.112
77_P80_L1.002561.110
92_S96_Q0.99211.098
47_H94_L0.991951.098
120_I142_F0.973681.078
72_E113_S0.972951.077
56_I137_G0.971931.076
70_W74_V0.967911.071
118_F144_N0.962151.065
62_A66_F0.960531.063
60_Q70_W0.943161.044
130_D136_C0.941831.043
57_Y70_W0.924561.023
47_H78_S0.924461.023
27_D30_A0.919571.018
79_R91_Q0.900810.997
26_D30_A0.898770.995
68_T72_E0.893610.989
46_S56_I0.892820.988
58_A73_L0.888120.983
86_E109_I0.887950.983
43_A62_A0.885160.980
79_R87_R0.862280.955
66_F110_R0.858740.951
107_S121_E0.839440.929
110_R120_I0.831460.920
45_L142_F0.82710.916
42_F141_M0.824490.913
27_D31_E0.822770.911
29_S33_L0.813880.901
89_E93_L0.803620.890
34_A37_L0.801160.887
62_A73_L0.798190.884
87_R91_Q0.795140.880
25_S29_S0.791180.876
128_L137_G0.779320.863
36_A139_A0.765770.848
89_E92_S0.755310.836
66_F142_F0.750190.830
83_E117_R0.746170.826
38_W44_I0.74540.825
47_H55_F0.725050.803
107_S110_R0.71280.789
67_E114_T0.712730.789
26_D29_S0.708950.785
30_A34_A0.707030.783
24_P27_D0.706410.782
63_L73_L0.703480.779
47_H138_Q0.702080.777
84_E87_R0.698730.773
86_E89_E0.695610.770
43_A61_A0.687230.761
105_N123_A0.685780.759
68_T73_L0.678460.751
42_F61_A0.678270.751
43_A59_N0.677640.750
35_K57_Y0.676810.749
44_I139_A0.672710.745
90_R93_L0.669780.741
119_R145_W0.661120.732
49_T136_C0.660720.731
88_K92_S0.646280.715
31_E34_A0.644030.713
40_A141_M0.639730.708
108_G111_I0.63720.705
123_A143_S0.634190.702
82_A86_E0.630540.698
130_D135_Y0.628580.696
93_L96_Q0.628140.695
128_L139_A0.62550.692
82_A87_R0.625150.692
86_E90_R0.624520.691
49_T134_N0.622230.689
65_L118_F0.620440.687
54_I74_V0.619160.685
44_I141_M0.615420.681
110_R118_F0.614110.680
82_A108_G0.612910.678
82_A85_P0.610550.676
32_E35_K0.609560.675
61_A65_L0.609480.675
38_W59_N0.607180.672
62_A142_F0.602610.667
37_L40_A0.601510.666
119_R146_S0.592610.656
88_K91_Q0.586920.650
68_T81_S0.575630.637
47_H53_P0.57480.636
37_L46_S0.571770.633
59_N62_A0.569440.630
55_F58_A0.569370.630
96_Q99_Q0.568010.629
37_L139_A0.567680.628
44_I59_N0.561220.621
63_L66_F0.557190.617
37_L44_I0.554240.614
41_P143_S0.553940.613
33_L37_L0.551570.611
129_I133_G0.540370.598
78_S82_A0.533960.591
97_V138_Q0.532020.589
83_E111_I0.531160.588
101_G129_I0.521140.577
54_I75_G0.521070.577
41_P61_A0.519730.575
90_R108_G0.517490.573
76_L81_S0.514770.570
128_L136_C0.514210.569
53_P95_A0.51230.567
97_V100_Q0.506110.560
132_D135_Y0.503640.558
83_E87_R0.503630.557
58_A70_W0.499270.553
46_S128_L0.497420.551
95_A98_M0.494460.547
97_V104_D0.49370.547
83_E109_I0.491490.544
93_L97_V0.491190.544
93_L106_Y0.487960.540
67_E116_R0.486590.539
129_I136_C0.48560.538
45_L122_R0.4850.537
97_V101_G0.484810.537
96_Q101_G0.484680.537
98_M102_Y0.484460.536
40_A43_A0.484110.536
112_S115_G0.483870.536
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
3p7nA0.979799.40.067
4ehoA0.97399.40.107
3ewkA0.932499.40.111
2gj3A0.797399.30.124
3ue6A0.979799.30.138
4gczA0.844699.30.14
3f1pA0.763599.30.154
3mr0A0.824399.30.165
3f1pB0.77799.20.173
4hiaA0.824399.20.178

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