GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Hormone_recep - Ligand-binding domain of nuclear hormone receptor
Pfam: PF00104 (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. )
Length: 203
Sequences: 2231
Seq/Len: 10.99
HH_delta: 0.138 (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
120_D162_Y0.343532.918
119_L179_L0.302422.569
123_E175_R0.273332.322
43_F51_K0.25782.190
43_F46_L0.236252.007
50_D140_L0.23131.965
99_I103_F0.215881.834
143_E146_E0.207991.767
37_A132_L0.207551.763
52_I56_K0.206721.756
34_V38_K0.187841.595
192_K196_N0.187381.592
133_F148_V0.172711.467
165_Q168_G0.170011.444
177_G181_L0.168771.433
61_E187_R0.168441.431
37_A43_F0.165731.408
99_I102_E0.164871.400
141_S145_R0.162441.380
126_L155_I0.161691.373
137_Y141_S0.160021.359
141_S144_T0.159251.353
168_G171_D0.154871.315
30_L36_W0.154341.311
129_A155_I0.152461.295
87_I92_F0.151821.290
181_L184_P0.151671.288
161_S165_Q0.149151.267
22_L25_I0.14821.259
148_V152_R0.148141.258
130_L155_I0.148051.257
191_E195_E0.147321.251
50_D54_L0.147281.251
146_E149_E0.147261.251
38_K51_K0.145491.236
36_W128_K0.14541.235
30_L59_W0.144581.228
182_L185_S0.144111.224
107_M110_V0.143541.219
140_L144_T0.14291.214
176_F180_L0.141331.200
134_N137_Y0.139531.185
146_E150_E0.139321.183
65_L186_L0.138731.178
75_N78_Q0.138621.177
170_E173_A0.138461.176
66_E128_K0.136821.162
180_L184_P0.136231.157
91_S94_D0.135241.149
119_L123_E0.133841.137
136_D141_S0.13361.135
132_L153_D0.13351.134
31_R38_K0.133391.133
27_R31_R0.131951.121
124_F128_K0.130871.112
18_T21_D0.129541.100
82_P86_F0.129441.099
41_P50_D0.128891.095
65_L127_L0.128821.094
123_E128_K0.128521.092
122_E125_A0.128181.089
159_L176_F0.127961.087
46_L50_D0.127741.085
165_Q170_E0.126841.077
99_I105_Q0.126671.076
79_L82_P0.12611.071
61_E131_I0.126061.071
38_K48_M0.124561.058
89_K95_F0.124321.056
35_D38_K0.124291.056
183_L187_R0.124221.055
23_C63_F0.124031.053
75_N79_L0.123471.049
19_F23_C0.123111.046
77_D89_K0.122081.037
190_S193_H0.121691.034
130_L176_F0.121281.030
80_M86_F0.121211.030
58_S132_L0.120421.023
35_D39_S0.120411.023
36_W129_A0.120241.021
163_Y175_R0.120071.020
48_M51_K0.11981.018
51_K61_E0.119621.016
58_S148_V0.119551.015
112_R116_R0.11951.015
140_L143_E0.119031.011
99_I104_I0.118461.006
153_D178_K0.118261.004
81_F85_T0.117620.999
187_R190_S0.117290.996
120_D130_L0.116680.991
69_Y121_E0.116390.989
84_G87_I0.116320.988
54_L140_L0.115820.984
54_L148_V0.115530.981
69_Y124_F0.11550.981
101_S104_I0.114770.975
59_W128_K0.114530.973
168_G180_L0.114390.972
162_Y168_G0.114030.969
50_D144_T0.114020.968
81_F87_I0.113550.964
30_L35_D0.113370.963
82_P151_L0.113340.963
47_S144_T0.113240.962
59_W62_L0.113090.961
160_H182_L0.113060.960
152_R155_I0.112890.959
24_E27_R0.112620.957
101_S105_Q0.111480.947
28_R36_W0.111260.945
140_L148_V0.111260.945
122_E162_Y0.111060.943
137_Y140_L0.110860.942
54_L62_L0.110640.940
88_D91_S0.110150.936
49_E94_D0.10990.933
137_Y145_R0.109540.930
114_F121_E0.109270.928
39_S158_A0.108950.925
156_I160_H0.108830.924
47_S143_E0.108760.924
34_V55_L0.10870.923
125_A128_K0.10850.922
59_W126_L0.108320.920
42_E45_E0.10830.920
105_Q109_E0.108230.919
21_D83_N0.108150.919
114_F119_L0.108090.918
47_S174_Q0.107910.917
35_D56_K0.10770.915
191_E194_I0.10760.914
127_L180_L0.107260.911
27_R63_F0.106850.908
40_F129_A0.106720.906
21_D113_P0.106380.904
36_W184_P0.106160.902
90_D93_D0.106080.901
100_F103_F0.105830.899
36_W59_W0.10580.899
65_L70_R0.105520.896
88_D94_D0.105150.893
156_I182_L0.10510.893
152_R168_G0.104860.891
188_K192_K0.104820.890
32_L47_S0.104320.886
43_F117_L0.10420.885
175_R179_L0.103950.883
55_L59_W0.103820.882
105_Q185_S0.103520.879
33_I139_G0.103510.879
94_D167_K0.103480.879
42_E150_E0.102840.873
145_R151_L0.102680.872
79_L84_G0.102540.871
64_I127_L0.102450.870
36_W125_A0.102440.870
40_F66_E0.102390.870
53_A139_G0.102220.868
82_P88_D0.10180.865
87_I90_D0.101280.860
29_E63_F0.101220.860
163_Y173_A0.100960.858
157_Q179_L0.100780.856
37_A46_L0.100680.855
60_F119_L0.10030.852
79_L83_N0.100250.851
38_K43_F0.099850.848
32_L58_S0.099040.841
58_S61_E0.098930.840
136_D140_L0.098750.839
20_E34_V0.098740.839
55_L133_F0.098540.837
38_K55_L0.098170.834
26_W34_V0.097970.832
156_I177_G0.097660.829
56_K59_W0.097640.829
133_F151_L0.097470.828
166_S195_E0.09730.826
43_F186_L0.097180.825
30_L43_F0.097150.825
187_R191_E0.096790.822
58_S62_L0.096590.820
78_Q86_F0.096590.820
167_K173_A0.096370.819
84_G88_D0.096350.818
192_K195_E0.096340.818
62_L194_I0.096290.818
67_L107_M0.095760.813
63_F70_R0.095730.813
50_D158_A0.095640.812
30_L47_S0.095530.811
25_I83_N0.095420.810
76_Q81_F0.095140.808
83_N86_F0.095080.808
186_L189_I0.094990.807
67_L71_S0.094960.807
38_K63_F0.094670.804
113_P116_R0.094620.804
50_D55_L0.094530.803
162_Y175_R0.094440.802
33_I62_L0.094260.801
18_T22_L0.093890.797
25_I29_E0.093770.796
163_Y176_F0.093520.794
174_Q178_K0.093410.793
109_E189_I0.093220.792
155_I160_H0.093170.791
77_D112_R0.092970.790
62_L128_K0.092920.789
33_I43_F0.09270.787
156_I181_L0.092650.787
72_Y115_R0.092480.785
29_E114_F0.092440.785
22_L59_W0.092310.784
81_F84_G0.092260.784
59_W132_L0.09170.779
153_D157_Q0.091590.778
89_K105_Q0.091420.776
75_N81_F0.091230.775
129_A148_V0.091210.775
66_E70_R0.091190.775
179_L182_L0.091070.774
136_D182_L0.090990.773
48_M52_I0.09090.772
136_D189_I0.09090.772
18_T90_D0.090880.772
83_N90_D0.090880.772
110_V189_I0.090870.772
66_E72_Y0.09070.770
145_R150_E0.090690.770
152_R159_L0.090690.770
138_P141_S0.090620.770
131_I183_L0.09060.770
44_S177_G0.090140.766
128_K134_N0.090080.765
115_R119_L0.090030.765
36_W43_F0.089990.764
22_L55_L0.089940.764
122_E126_L0.089880.763
72_Y101_S0.089810.763
153_D177_G0.08970.762
23_C27_R0.08960.761
65_L169_P0.089440.760
66_E124_F0.089290.758
157_Q170_E0.089230.758
22_L29_E0.089110.757
34_V50_D0.089070.757
24_E120_D0.088890.755
153_D188_K0.088790.754
49_E53_A0.088630.753
42_E133_F0.088590.752
23_C26_W0.088370.751
90_D94_D0.088370.751
153_D156_I0.088330.750
168_G173_A0.088160.749
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
3k6pA0.96551000.138
3ltxA0.96551000.142
3tx7B0.98031000.158
3plzA0.97541000.162
2e2rA0.96061000.165
1g2nA0.96551000.169
3ipqA0.96551000.17
3vhvA0.97041000.17
2ocfA0.98521000.171
3p0uA0.98031000.173

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