GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
7tm_2 - 7 transmembrane receptor (Secretin family)
Pfam: PF00002 (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: CL0192
Length: 242
Sequences: 29128
Seq/Len: 120.36
HH_delta: 0.197 (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
41_N120_W1.603643.372
14_S50_N1.483243.118
144_W147_N1.231542.589
158_P162_I1.131482.379
168_V172_L1.123432.362
72_C143_C0.963622.026
162_I166_N0.959292.017
144_W155_F0.946051.989
166_N170_F0.934971.966
144_W151_F0.924421.944
65_S68_N0.92241.939
144_W150_G0.907631.908
170_F173_V0.866451.822
110_R114_W0.856661.801
144_W148_D0.853391.794
128_V132_A0.84231.771
98_Y103_K0.829821.745
92_V119_G0.813471.710
81_Y124_A0.787911.657
48_L82_F0.775431.630
41_N89_W0.775221.630
98_Y102_V0.768541.616
25_Y40_L0.747741.572
171_I175_R0.732091.539
26_L40_L0.726651.528
11_C51_L0.723611.521
148_D151_F0.711711.496
151_F155_F0.711591.496
31_L36_N0.704811.482
151_F154_A0.700391.473
68_N71_L0.694561.460
146_S151_F0.686191.443
69_H73_R0.671021.411
147_N151_F0.667681.404
66_T69_H0.660641.389
172_L175_R0.656151.380
57_I60_T0.651441.370
70_C74_A0.651411.370
166_N169_I0.647911.362
114_W118_I0.640711.347
45_S85_A0.634531.334
100_L104_V0.632371.330
166_N173_V0.631361.327
22_I40_L0.630891.326
158_P166_N0.629481.323
96_Y100_L0.628451.321
42_L46_L0.625471.315
77_I81_Y0.625181.314
147_N150_G0.625061.314
92_V115_Y0.618071.299
40_L44_L0.616651.296
166_N174_L0.604681.271
62_S65_S0.602321.266
145_L150_G0.600451.262
59_Q65_S0.596061.253
44_L48_L0.593461.248
169_I173_V0.581011.222
172_L176_V0.58091.221
56_G59_Q0.577091.213
150_G154_A0.57581.211
175_R179_R0.573711.206
99_R106_N0.573361.205
150_G153_W0.568931.196
19_L23_I0.554781.166
149_W153_W0.554431.166
62_S66_T0.550981.158
200_S203_L0.550741.158
41_N116_Y0.549931.156
196_I199_A0.538831.133
45_S86_S0.537991.131
59_Q62_S0.537811.131
60_T68_N0.536041.127
113_W117_L0.534831.124
130_S133_V0.534231.123
148_D155_F0.532041.119
60_T63_P0.530521.115
145_L148_D0.530421.115
23_I27_L0.530141.115
54_L57_I0.529211.113
38_I93_E0.525791.105
108_S111_R0.525751.105
129_I132_A0.524761.103
152_I155_F0.524291.102
37_K116_Y0.519431.092
199_A203_L0.518751.091
85_A123_P0.51471.082
59_Q64_I0.514061.081
89_W116_Y0.513141.079
63_P68_N0.511681.076
20_L24_T0.502761.057
150_G155_F0.498921.049
146_S155_F0.491731.034
58_S62_S0.491711.034
80_H127_V0.491681.034
145_L151_F0.489521.029
153_W156_V0.482661.015
19_L47_L0.479381.008
115_Y119_G0.479121.007
97_L100_L0.478191.005
57_I61_F0.477111.003
63_P66_T0.475461.000
15_I47_L0.474750.998
87_F91_L0.473450.995
201_L205_P0.468980.986
203_L207_L0.468670.985
159_V162_I0.468640.985
165_I169_I0.466570.981
60_T67_T0.466150.980
96_Y107_S0.463960.975
190_K193_R0.46110.969
98_Y172_L0.458960.965
43_C46_L0.457830.963
148_D152_I0.456280.959
59_Q67_T0.455710.958
70_C73_R0.454410.955
16_I19_L0.451990.950
197_L203_L0.451710.950
58_S66_T0.451640.950
170_F174_L0.451430.949
67_T71_L0.449680.945
46_L86_S0.449010.944
173_V177_L0.447730.941
122_I126_I0.446270.938
110_R113_W0.445320.936
33_S36_N0.444040.934
176_V180_K0.440750.927
59_Q71_L0.440450.926
123_P127_V0.437460.920
114_W117_L0.437010.919
77_I131_V0.436280.917
87_F162_I0.434610.914
81_Y127_V0.43440.913
208_G212_L0.434370.913
103_K106_N0.434270.913
77_I124_A0.433610.912
167_I171_I0.433090.911
37_K41_N0.431060.906
88_F122_I0.430940.906
117_L121_G0.426080.896
151_F156_V0.426010.896
61_F64_I0.424130.892
67_T70_C0.424050.892
163_L167_I0.42190.887
57_I63_P0.418890.881
59_Q66_T0.41620.875
202_I211_W0.414510.871
144_W156_V0.413730.870
147_N156_V0.413660.870
21_T25_Y0.413260.869
85_A89_W0.413160.869
200_S204_L0.41270.868
162_I170_F0.411180.864
60_T66_T0.41070.863
58_S61_F0.410560.863
60_T69_H0.409410.861
144_W154_A0.408030.858
85_A120_W0.407970.858
61_F65_S0.407430.857
18_L97_L0.405920.853
89_W120_W0.405360.852
155_F158_P0.405330.852
21_T43_C0.40370.849
197_L200_S0.403020.847
65_S70_C0.402980.847
53_F79_L0.402220.846
119_G123_P0.402150.846
88_F119_G0.401780.845
58_S68_N0.401230.844
125_L129_I0.401050.843
174_L178_V0.400370.842
202_I207_L0.399490.840
25_Y31_L0.396120.833
196_I200_S0.395560.832
200_S207_L0.394110.829
66_T70_C0.394080.829
150_G162_I0.390330.821
99_R102_V0.389050.818
95_F169_I0.388060.816
99_R103_K0.387730.815
50_N54_L0.386970.814
145_L155_F0.386740.813
11_C50_N0.386220.812
45_S82_F0.386150.812
147_N155_F0.384770.809
93_E96_Y0.383610.807
149_W152_I0.382190.804
105_F108_S0.382150.803
61_F68_N0.381980.803
203_L211_W0.3810.801
23_I26_L0.380880.801
144_W152_I0.380610.800
148_D156_V0.379070.797
79_L83_F0.377890.795
80_H83_F0.377260.793
59_Q68_N0.375960.790
52_S82_F0.375030.788
203_L206_L0.374480.787
145_L152_I0.373050.784
46_L97_L0.372570.783
32_R36_N0.371870.782
91_L165_I0.371850.782
98_Y169_I0.370930.780
35_R39_H0.370890.780
58_S67_T0.370410.779
62_S69_H0.370120.778
22_I43_C0.369940.778
197_L201_L0.369710.777
126_I130_S0.365710.769
174_L177_L0.364020.765
162_I169_I0.363230.764
91_L162_I0.361890.761
84_L158_P0.361270.760
109_R113_W0.361110.759
25_Y32_R0.360940.759
146_S150_G0.359640.756
60_T65_S0.359250.755
74_A78_L0.359070.755
84_L126_I0.358640.754
193_R197_L0.358340.753
84_L123_P0.357790.752
169_I174_L0.357710.752
45_S120_W0.356680.750
199_A202_I0.355830.748
113_W116_Y0.355630.748
196_I203_L0.355280.747
53_F56_G0.354850.746
130_S134_N0.353910.744
95_F99_R0.353360.743
124_A128_V0.352950.742
153_W157_G0.35090.738
62_S67_T0.349550.735
159_V163_L0.349050.734
52_S56_G0.348190.732
89_W119_G0.346870.729
17_C43_C0.346150.728
144_W153_W0.344870.725
198_R202_I0.344240.724
207_L210_T0.343590.722
164_L168_V0.342840.721
59_Q63_P0.342320.720
21_T24_T0.341690.718
146_S152_I0.341660.718
59_Q69_H0.341210.717
93_E97_L0.34120.717
58_S64_I0.339720.714
39_H93_E0.339140.713
176_V179_R0.338140.711
173_V178_V0.335750.706
93_E200_S0.333750.702
17_C42_L0.332350.699
193_R200_S0.331930.698
76_A79_L0.331710.697
76_A134_N0.331130.696
152_I156_V0.331110.696
9_V13_L0.33060.695
166_N172_L0.330410.695
155_F160_L0.330270.694
178_V181_S0.330130.694
60_T71_L0.330.694
149_W155_F0.329610.693
86_S210_T0.32910.692
170_F177_L0.329080.692
154_A158_P0.328970.692
126_I129_I0.327570.689
15_I50_N0.322910.679
76_A80_H0.322790.679
203_L210_T0.32210.677
118_I122_I0.320460.674
97_L104_V0.319560.672
175_R178_V0.319420.672
199_A207_L0.319270.671
148_D153_W0.319250.671
95_F165_I0.319190.671
65_S71_L0.317960.669
63_P67_T0.31740.667
146_S154_A0.31650.665
47_L51_L0.316180.665
62_S68_N0.315380.663
147_N152_I0.315050.662
163_L166_N0.314970.662
205_P208_G0.314590.661
144_W149_W0.314510.661
107_S115_Y0.314290.661
66_T71_L0.313770.660
156_V159_V0.313680.660
12_S16_I0.312620.657
38_I96_Y0.312110.656
107_S111_R0.312050.656
162_I165_I0.311120.654
64_I68_N0.310920.654
18_L46_L0.310250.652
202_I205_P0.310050.652
73_R134_N0.30990.652
57_I62_S0.30990.652
55_I75_I0.309260.650
29_R32_R0.308540.649
60_T70_C0.30850.649
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
3vw7A199.90.197
3v2yA0.995999.90.206
3pblA199.90.208
4grvA199.90.209
4dklA199.90.219
2rh1A199.90.225
3oduA0.995999.90.229
3rzeA199.90.235
3uonA199.90.235
4ea3A199.90.235

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