GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HD_4 - HD domain
Pfam: PF13328 (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: CL0237
Length: 153
Sequences: 2119
Seq/Len: 13.85
HH_delta: -0.022 (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
60_E65_E0.995774.626
39_E66_D0.684423.179
26_E119_H0.53972.507
28_A41_I0.524312.436
36_L111_L0.520132.416
31_L44_A0.500772.326
4_F55_T0.478052.221
129_P133_R0.475422.208
70_L112_I0.447542.079
7_E10_A0.415421.930
21_I24_P0.404641.880
73_A109_A0.404111.877
137_R141_D0.386891.797
38_E42_A0.384461.786
50_I59_I0.383021.779
60_E68_A0.376491.749
30_I122_R0.376281.748
43_A70_L0.368491.712
36_L40_T0.366951.705
58_D61_E0.350161.627
129_P132_Q0.348571.619
41_I44_A0.329491.531
69_D105_E0.329051.529
26_E29_E0.320941.491
39_E42_A0.319071.482
6_A10_A0.31261.452
65_E69_D0.311941.449
31_L40_T0.297131.380
8_A55_T0.29711.380
5_A21_I0.294511.368
2_L45_L0.290061.347
15_K127_L0.284411.321
3_A7_E0.28371.318
117_R139_T0.283391.316
8_A58_D0.282841.314
31_L36_L0.281511.308
128_P131_K0.278231.292
3_A6_A0.277751.290
31_L41_I0.273211.269
50_I68_A0.27111.259
6_A21_I0.269371.251
4_F62_R0.267931.245
51_E120_N0.264611.229
124_I135_Y0.264011.226
43_A112_I0.257751.197
59_I68_A0.25741.196
52_D120_N0.255551.187
42_A67_V0.253781.179
2_L6_A0.252731.174
118_L122_R0.250121.162
47_H116_D0.249431.159
57_E61_E0.248591.155
127_L131_K0.246291.144
48_D51_E0.246021.143
88_R134_R0.245591.141
51_E75_T0.242291.126
4_F58_D0.2411.120
48_D120_N0.237531.103
116_D120_N0.23681.100
119_H123_T0.23561.094
10_A13_R0.234241.088
87_E90_E0.234161.088
55_T58_D0.233361.084
58_D62_R0.233171.083
25_L45_L0.233131.083
8_A54_E0.229581.066
27_V44_A0.227981.059
57_E60_E0.224841.044
23_H47_H0.221791.030
1_A5_A0.221261.028
4_F8_A0.220731.025
34_L152_I0.220451.024
113_K117_R0.220011.022
48_D52_D0.219771.021
42_A63_F0.218121.013
121_L139_T0.218091.013
127_L135_Y0.217871.012
50_I72_D0.217331.010
60_E69_D0.214820.998
133_R137_R0.214710.997
23_H120_N0.21390.994
35_G100_L0.213470.992
30_I115_A0.212390.987
74_L113_K0.209890.975
51_E116_D0.208940.971
117_R138_E0.206790.961
99_M103_M0.205390.954
55_T62_R0.200610.932
34_L146_L0.200310.930
42_A45_L0.199780.928
96_L100_L0.199770.928
9_H48_D0.19590.910
3_A10_A0.195580.909
68_A72_D0.193590.899
2_L25_L0.19280.896
121_L124_I0.192460.894
14_R123_T0.191720.891
125_K130_E0.189960.882
88_R91_E0.18950.880
9_H120_N0.188820.877
8_A49_V0.188430.875
39_E67_V0.187570.871
40_T70_L0.186550.867
16_S126_Y0.18610.864
99_M102_A0.184890.859
27_V116_D0.18460.858
31_L74_L0.183650.853
66_D108_R0.183520.852
64_G68_A0.182660.849
132_Q145_P0.182550.848
23_H48_D0.182280.847
94_E97_R0.181870.845
101_L148_H0.181860.845
131_K134_R0.180740.840
70_L108_R0.180560.839
72_D98_R0.180290.837
99_M150_L0.180220.837
13_R133_R0.179420.833
82_K91_E0.17940.833
31_L115_A0.178580.830
9_H23_H0.178540.829
6_A13_R0.176780.821
114_L152_I0.173960.808
52_D75_T0.17390.808
46_L63_F0.173630.807
78_K81_S0.172610.802
110_V146_L0.172440.801
71_V75_T0.171920.799
52_D116_D0.171010.794
89_S148_H0.170680.793
23_H51_E0.169930.789
29_E33_E0.169690.788
9_H47_H0.169570.788
80_L89_S0.169090.785
48_D75_T0.167550.778
73_A98_R0.167470.778
113_K138_E0.16740.778
100_L104_S0.167360.777
46_L59_I0.167230.777
49_V55_T0.166470.773
47_H51_E0.16570.770
28_A45_L0.165260.768
23_H52_D0.16470.765
29_E32_A0.164470.764
40_T111_L0.16430.763
48_D53_T0.162760.756
130_E134_R0.160760.747
49_V54_E0.160490.746
124_I132_Q0.15960.741
143_Y146_L0.159070.739
104_S148_H0.158790.738
9_H12_Q0.158770.738
11_G14_R0.158720.737
52_D71_V0.158540.736
44_A112_I0.157750.733
38_E100_L0.157420.731
9_H51_E0.156670.728
43_A71_V0.156640.728
20_Y120_N0.156610.727
9_H52_D0.156370.726
107_V135_Y0.155640.723
47_H120_N0.155230.721
75_T120_N0.154320.717
94_E98_R0.154160.716
55_T88_R0.153440.713
7_E62_R0.153250.712
9_H20_Y0.152830.710
70_L106_D0.152210.707
18_E123_T0.152060.706
50_I75_T0.151960.706
37_D66_D0.151820.705
78_K91_E0.151570.704
11_G19_P0.151410.703
16_S123_T0.150480.699
13_R19_P0.149660.695
47_H75_T0.148450.690
37_D108_R0.147990.687
88_R137_R0.146910.682
121_L132_Q0.146570.681
82_K90_E0.145870.678
35_G38_E0.145680.677
90_E94_E0.145110.674
29_E45_L0.144610.672
120_N123_T0.144560.672
124_I136_A0.144360.671
24_P45_L0.144280.670
26_E35_G0.144040.669
7_E11_G0.143720.668
64_G71_V0.143290.666
99_M149_R0.143250.665
7_E29_E0.142730.663
41_I45_L0.142260.661
137_R140_L0.141820.659
131_K135_Y0.141780.659
49_V53_T0.141110.655
9_H75_T0.140780.654
33_E122_R0.139720.649
106_D149_R0.139680.649
1_A42_A0.139650.649
73_A106_D0.13950.648
67_V71_V0.138650.644
125_K137_R0.138170.642
103_M107_V0.137740.640
74_L77_I0.137510.639
47_H52_D0.137410.638
27_V92_Y0.136350.633
121_L136_A0.135520.630
54_E58_D0.135330.629
24_P49_V0.135140.628
92_Y95_R0.134950.627
28_A44_A0.134580.625
14_R116_D0.133920.622
13_R38_E0.132990.618
3_A94_E0.132740.617
1_A23_H0.132490.615
79_K89_S0.13240.615
50_I60_E0.132310.615
109_A118_L0.132160.614
5_A9_H0.131820.612
75_T116_D0.131460.611
6_A11_G0.131290.610
107_V142_I0.131240.610
95_R98_R0.130950.608
46_L67_V0.130930.608
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
1vj7A0.9804100-0.022
3nr1A0.94121000.273
3nqwA0.94121000.275
3b57A0.888993.20.881
2pq7A0.869392.70.882
2qgsA0.882489.80.89
3gw7A0.908589.60.891
3djbA0.888987.90.894
3dtoA0.869386.80.896
2gz4A0.888981.90.902

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