GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cas_Cas4 - Domain of unknown function DUF83
Pfam: PF01930 (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: CL0236
Length: 162
Sequences: 1741
Seq/Len: 10.75
HH_delta: 0.389 (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
94_E123_R0.474613.478
102_R115_R0.451213.307
151_C154_C0.352152.581
55_G92_L0.310812.278
51_V57_I0.299122.192
154_C160_C0.289972.125
12_P132_E0.289642.123
120_E124_R0.263381.930
73_K85_Q0.256871.883
8_Y133_I0.250381.835
8_Y12_P0.245951.802
28_T31_M0.245861.802
14_R155_S0.230861.692
86_L103_G0.230571.690
151_C160_C0.229061.679
68_I104_Y0.225681.654
15_A133_I0.224581.646
58_D73_K0.22341.637
102_R117_E0.219731.610
76_R110_D0.217191.592
11_C151_C0.214531.572
71_E89_Y0.212571.558
38_H85_Q0.212091.554
11_C154_C0.211251.548
7_E18_E0.208051.525
37_L74_S0.206991.517
55_G89_Y0.204991.502
14_R18_E0.203111.489
82_H107_Y0.202431.484
48_E56_K0.200381.469
34_G73_K0.19711.444
38_H48_E0.196241.438
149_K152_R0.194071.422
87_A118_I0.193861.421
83_R114_V0.187761.376
34_G58_D0.179531.316
16_Y20_V0.179091.312
10_Y14_R0.178861.311
69_P103_G0.175061.283
124_R128_K0.173381.271
131_E135_K0.17221.262
71_E85_Q0.172171.262
13_R17_L0.17161.258
69_P93_L0.171161.254
4_M19_R0.169611.243
10_Y150_K0.167091.225
6_N14_R0.166951.224
15_A136_I0.165921.216
31_M36_E0.165831.215
2_G92_L0.165121.210
38_H72_I0.163611.199
125_K128_K0.162531.191
34_G38_H0.162011.187
132_E135_K0.161911.187
104_Y115_R0.160841.179
4_M15_A0.16031.175
34_G71_E0.158961.165
58_D71_E0.158361.161
128_K132_E0.158061.158
87_A122_L0.156831.149
13_R16_Y0.156451.147
49_V57_I0.155811.142
80_E125_K0.15461.133
55_G88_A0.151681.112
99_P127_E0.150841.105
7_E14_R0.150491.103
9_V84_M0.148161.086
127_E131_E0.148071.085
68_I102_R0.147521.081
57_I69_P0.14571.068
120_E157_R0.14561.067
85_Q89_Y0.145491.066
38_H89_Y0.144471.059
13_R161_W0.143611.052
58_D85_Q0.142631.045
3_S7_E0.141051.034
49_V60_V0.140711.031
17_L156_Y0.140231.028
49_V112_K0.139661.024
11_C160_C0.139111.019
103_G116_V0.138521.015
94_E100_V0.13771.009
124_R138_E0.135890.996
30_S74_S0.134780.988
124_R127_E0.13470.987
125_K129_L0.133460.978
5_V9_V0.133440.978
2_G88_A0.133190.976
31_M35_R0.132580.972
59_I108_I0.132260.969
77_K110_D0.13220.969
50_P56_K0.131820.966
11_C14_R0.130610.957
130_I133_I0.12930.948
38_H55_G0.128970.945
2_G89_Y0.128590.942
38_H71_E0.128560.942
34_G85_Q0.128470.942
86_L105_I0.127630.935
147_N150_K0.127620.935
83_R87_A0.12660.928
38_H73_K0.126450.927
119_T122_L0.126010.923
129_L133_I0.125710.921
141_S146_E0.125260.918
129_L132_E0.124660.914
66_E101_K0.124420.912
75_G107_Y0.122730.899
75_G108_I0.122180.895
2_G71_E0.122080.895
152_R157_R0.121730.892
9_V53_E0.121170.888
67_I98_I0.12050.883
15_A19_R0.120490.883
61_E68_I0.120360.882
4_M133_I0.120350.882
9_V125_K0.120150.881
14_R156_Y0.119850.878
103_G118_I0.119290.874
59_I72_I0.119220.874
90_A103_G0.119150.873
91_L127_E0.119040.872
71_E90_A0.118810.871
59_I70_V0.11820.866
106_Y157_R0.118070.865
5_V88_A0.118040.865
121_E131_E0.117590.862
9_V129_L0.116820.856
89_Y92_L0.115950.850
135_K139_G0.115410.846
48_E89_Y0.113950.835
51_V92_L0.113020.828
133_I136_I0.111680.818
88_A130_I0.111540.817
84_M126_V0.111230.815
5_V15_A0.110570.810
7_E19_R0.11040.809
4_M7_E0.110170.807
55_G70_V0.109650.804
119_T124_R0.10950.802
13_R143_P0.109380.802
60_V67_I0.109070.799
87_A116_V0.108860.798
29_E32_E0.108070.792
47_R72_I0.10750.788
43_E46_K0.107070.785
27_P33_L0.106980.784
40_E79_R0.106190.778
117_E121_E0.106170.778
8_Y136_I0.105810.775
7_E155_S0.105110.770
27_P82_H0.105070.770
3_S14_R0.104920.769
90_A123_R0.104130.763
16_Y71_E0.104070.763
55_G95_E0.103830.761
59_I106_Y0.10370.760
64_G124_R0.102950.754
55_G96_F0.10280.753
93_L96_F0.102560.752
135_K138_E0.102070.748
55_G72_I0.102060.748
26_E155_S0.101990.747
17_L159_F0.101920.747
104_Y113_R0.101740.746
134_R138_E0.101510.744
62_K69_P0.101390.743
20_V72_I0.101270.742
104_Y117_E0.100650.738
5_V130_I0.10060.737
128_K131_E0.100530.737
17_L21_G0.100430.736
72_I91_L0.10030.735
106_Y113_R0.100060.733
44_R47_R0.099860.732
16_Y19_R0.099670.730
70_V106_Y0.099640.730
146_E149_K0.099430.729
66_E102_R0.09940.728
57_I157_R0.099320.728
121_E132_E0.099180.727
60_V135_K0.098580.722
69_P150_K0.098450.722
37_L108_I0.098350.721
138_E141_S0.098050.719
40_E147_N0.097820.717
121_E124_R0.097730.716
38_H58_D0.09710.712
117_E139_G0.096690.709
10_Y71_E0.096280.706
27_P104_Y0.096110.704
153_R158_E0.095960.703
17_L24_P0.095730.702
41_R111_R0.095520.700
90_A102_R0.095480.700
50_P79_R0.095390.699
48_E57_I0.094610.693
93_L103_G0.094570.693
14_R160_C0.094280.691
130_I134_R0.094230.691
91_L126_V0.093740.687
8_Y137_L0.093630.686
149_K153_R0.093240.683
87_A126_V0.093120.682
63_G128_K0.093050.682
8_Y15_A0.092930.681
130_I138_E0.092650.679
46_K80_E0.09250.678
70_V107_Y0.092490.678
6_N84_M0.092490.678
126_V133_I0.092470.678
65_G101_K0.09220.676
95_E136_I0.092010.674
9_V136_I0.091890.673
26_E35_R0.091880.673
124_R131_E0.091410.670
119_T123_R0.091280.669
122_L126_V0.091120.668
72_I107_Y0.090740.665
124_R144_P0.090590.664
29_E131_E0.090320.662
4_M10_Y0.090320.662
30_S157_R0.090230.661
6_N31_M0.090050.660
53_E153_R0.089860.659
25_E29_E0.089850.658
131_E144_P0.089830.658
28_T32_E0.089650.657
50_P60_V0.089460.656
115_R130_I0.089440.655
55_G85_Q0.088950.652
65_G130_I0.088890.651
60_V94_E0.088740.650
149_K161_W0.088450.648
77_K107_Y0.088220.647
7_E15_A0.088070.645
14_R154_C0.087880.644
41_R121_E0.08780.643
6_N10_Y0.087780.643
34_G89_Y0.087330.640
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
4ic1A0.938399.80.389
3u4qB199.40.55
3l0aA0.925999.30.581
3h4rA0.913698.90.661
3u4qA0.685298.60.699
1w36B0.85897.40.789
1w36C0.956896.50.818
3k93A0.870493.80.85
3sm4A0.876591.60.86
2vldA0.85887.90.871

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