GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AAA_30 - AAA domain
Pfam: PF13604 (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: CL0023
Length: 196
Sequences: 9166
Seq/Len: 46.77
HH_delta: 0.225 (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
48_R95_D0.974043.310
35_L127_V0.617812.100
37_A40_E0.59682.028
158_I161_Q0.588642.001
10_V34_L0.573851.950
52_L76_F0.562891.913
129_D132_Q0.552121.876
96_V125_I0.545241.853
53_A56_N0.524411.782
102_A105_V0.510071.734
50_I94_K0.508021.727
164_P168_E0.50041.701
102_A126_L0.48751.657
163_D166_L0.47761.623
94_K97_L0.470321.598
156_T160_R0.466221.584
21_S153_V0.466151.584
23_L127_V0.461241.568
26_P29_T0.460491.565
169_A172_A0.456451.551
47_K95_D0.452371.537
12_A21_S0.445621.514
12_A153_V0.438471.490
53_A58_A0.437081.485
27_A131_N0.436881.485
72_T75_S0.43511.479
56_N59_A0.416591.416
111_A115_R0.413761.406
141_P144_D0.412431.402
165_E169_A0.408581.389
166_L170_A0.404921.376
168_E172_A0.398371.354
157_E161_Q0.397751.352
35_L98_I0.397581.351
114_L118_K0.396111.346
53_A59_A0.384651.307
61_E65_K0.38361.304
38_L42_L0.382211.299
25_G29_T0.379391.289
110_L114_L0.378961.288
42_L96_V0.378321.286
71_Q75_S0.377651.283
147_E150_G0.371781.264
118_K122_A0.367571.249
105_V110_L0.36381.236
131_N174_R0.360741.226
74_H81_P0.360011.224
152_T156_T0.353681.202
72_T76_F0.353221.200
99_V126_L0.344471.171
99_V105_V0.344381.170
142_F146_Q0.342991.166
32_T101_E0.342361.164
128_G132_Q0.339631.154
38_L41_A0.338621.151
57_K61_E0.336631.144
115_R118_K0.335861.141
13_I38_L0.331941.128
41_A44_A0.330361.123
157_E160_R0.330041.122
134_P137_G0.329761.121
38_L125_I0.329341.119
61_E64_E0.328581.117
155_L159_R0.327811.114
50_I97_L0.327411.113
170_A174_R0.322861.097
38_L96_V0.321671.093
32_T100_D0.321631.093
24_Q154_E0.32161.093
153_V156_T0.32021.088
33_T36_K0.319951.087
60_K63_R0.315241.071
135_P138_A0.313851.067
23_L34_L0.31271.063
146_Q149_G0.312591.062
28_G31_K0.312121.061
139_G146_Q0.311931.060
33_T37_A0.311561.059
71_Q76_F0.30531.038
71_Q74_H0.3031.030
144_D148_S0.302461.028
165_E168_E0.297191.010
77_L80_I0.29421.000
82_N85_D0.293420.997
101_E104_M0.292930.996
73_I80_I0.291460.991
156_T164_P0.291410.990
163_D167_R0.289690.985
54_P104_M0.289280.983
80_I84_D0.285650.971
165_E172_A0.28520.969
22_V152_T0.28510.969
37_A41_A0.282780.961
77_L81_P0.282470.960
153_V157_E0.281350.956
140_S144_D0.281120.955
36_K40_E0.280550.953
51_G62_L0.279790.951
33_T159_R0.279440.950
23_L125_I0.278930.948
153_V160_R0.276270.939
143_A146_Q0.27590.938
170_A173_I0.275510.936
35_L51_G0.274670.933
76_F80_I0.272740.927
31_K100_D0.271430.922
54_P57_K0.270310.919
102_A110_L0.269960.917
39_A43_E0.269630.916
59_A75_S0.269630.916
39_A51_G0.268560.913
24_Q130_P0.267370.909
55_T58_A0.267180.908
171_K175_E0.266720.906
74_H77_L0.265470.902
56_N60_K0.26540.902
106_D109_Q0.264830.900
114_L117_A0.264530.899
111_A114_L0.262660.893
72_T77_L0.260560.886
10_V37_A0.259270.881
40_E44_A0.259110.881
97_L122_A0.258470.878
133_L136_V0.258360.878
139_G144_D0.257980.877
166_L174_R0.255850.870
97_L124_L0.255240.867
140_S143_A0.253990.863
165_E170_A0.253430.861
27_A132_Q0.25330.861
79_R83_G0.252550.858
74_H109_Q0.2520.856
112_R116_L0.251710.855
74_H80_I0.250610.852
74_H78_Y0.249740.849
58_A61_E0.248940.846
110_L126_L0.247590.841
133_L137_G0.246750.839
10_V13_I0.246670.838
22_V126_L0.246290.837
83_G86_E0.245070.833
96_V123_K0.24380.829
168_E171_K0.243790.829
167_R171_K0.241770.822
52_L56_N0.239610.814
54_P136_V0.238310.810
28_G101_E0.238130.809
70_A73_I0.236320.803
139_G142_F0.235560.801
46_G49_V0.234570.797
115_R119_K0.234310.796
27_A101_E0.234240.796
70_A74_H0.2340.795
107_S111_A0.233880.795
26_P158_I0.233470.793
167_R170_A0.232540.790
51_G56_N0.2320.788
144_D147_E0.231820.788
60_K64_E0.230510.783
153_V159_R0.230450.783
27_A129_D0.23020.782
132_Q160_R0.230040.782
138_A141_P0.229730.781
75_S79_R0.229450.780
54_P58_A0.229380.780
66_T70_A0.229280.779
13_I23_L0.229140.779
141_P149_G0.229080.779
25_G31_K0.228380.776
28_G32_T0.227560.773
63_R67_G0.227120.772
152_T171_K0.226420.770
27_A128_G0.225390.766
143_A147_E0.221820.754
22_V145_L0.221340.752
121_G126_L0.220650.750
59_A63_R0.220450.749
101_E129_D0.220010.748
81_P84_D0.21910.745
169_A174_R0.219040.744
121_G127_V0.218760.743
79_R85_D0.218690.743
39_A49_V0.218520.743
13_I125_I0.217360.739
99_V113_L0.216930.737
40_E43_E0.216350.735
108_R111_A0.215140.731
86_E157_E0.214940.730
33_T65_K0.214210.728
22_V102_A0.21380.727
51_G58_A0.212910.724
121_G124_L0.212850.723
26_P171_K0.212620.723
108_R112_R0.211290.718
73_I109_Q0.210930.717
146_Q151_I0.210070.714
55_T61_E0.209820.713
164_P172_A0.209270.711
138_A144_D0.208960.710
73_I105_V0.208940.710
94_K122_A0.208530.709
41_A45_A0.208150.707
55_T59_A0.206710.703
91_L94_K0.206450.702
105_V109_Q0.206330.701
103_S132_Q0.206210.701
73_I76_F0.205630.699
140_S146_Q0.203180.691
27_A103_S0.203030.690
49_V53_A0.201980.686
62_L79_R0.201710.686
141_P147_E0.20170.685
69_E73_I0.201070.683
146_Q152_T0.200890.683
154_E157_E0.200430.681
111_A118_K0.200030.680
171_K174_R0.199830.679
78_Y81_P0.199450.678
111_A119_K0.199110.677
104_M132_Q0.198310.674
122_A127_V0.19660.668
161_Q167_R0.196590.668
127_V130_P0.196290.667
34_L108_R0.196180.667
32_T65_K0.195710.665
55_T103_S0.195420.664
114_L126_L0.195030.663
116_L119_K0.194960.663
112_R115_R0.194790.662
71_Q77_L0.194190.660
118_K121_G0.193450.657
139_G145_L0.193190.657
11_R156_T0.192820.655
103_S129_D0.192540.654
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
3e1sA0.964399.90.225
3upuA0.984799.90.283
1w36D0.984799.90.296
4b3fX0.974599.80.362
2xzlA0.969499.80.382
2wjyA0.974599.80.391
2gk6A0.969499.80.397
3lfuA0.969499.70.43
1uaaA0.969499.60.475
1pjrA0.969499.60.48

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