GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
7tm_1 - 7 transmembrane receptor (rhodopsin family)
Pfam: PF00001 (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: 257
Sequences: 29544
Seq/Len: 114.96
HH_delta: -0.063 (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
25_N109_W1.445954.072
166_I170_R1.084413.054
57_C136_C0.866692.441
99_R103_I0.854692.407
127_F130_D0.851512.398
88_H91_R0.821292.313
55_F59_I0.786252.214
126_Y130_D0.752312.119
169_I173_R0.746762.103
77_A108_I0.73732.076
25_N74_S0.736942.075
83_Y87_C0.717182.020
66_F113_F0.708311.995
32_L67_S0.703341.981
54_S58_R0.698571.967
126_Y129_S0.6951.957
228_S231_S0.689571.942
170_R173_R0.64841.826
83_Y88_H0.648291.826
15_L20_N0.647071.822
9_I24_L0.645571.818
117_L121_F0.642621.810
163_I167_C0.621211.749
40_F44_S0.615871.734
6_I24_L0.596151.679
170_R174_K0.593321.671
50_W53_S0.591361.665
220_I224_L0.589521.660
62_F66_F0.58511.648
77_A104_I0.58361.643
29_A70_S0.578981.630
97_T100_R0.561281.581
103_I107_L0.551381.553
168_Y171_I0.545421.536
83_Y167_C0.535381.508
102_R106_I0.529551.491
25_N105_I0.528821.489
53_S56_L0.527441.485
28_V32_L0.525031.478
81_D85_A0.524691.478
10_L24_L0.521271.468
29_A71_S0.52121.468
39_P42_I0.510881.439
3_I7_L0.510771.438
3_I31_L0.502171.414
83_Y170_R0.500041.408
87_C174_K0.498661.404
21_I105_I0.496731.399
70_S112_S0.496011.397
7_L11_R0.494451.392
91_R95_I0.488411.375
30_D71_S0.48821.375
24_L28_V0.483411.361
253_N257_Y0.482461.359
81_D96_R0.48231.358
17_T20_N0.481191.355
91_R94_R0.478881.349
173_R177_R0.476321.341
55_F58_R0.475821.340
197_E201_A0.473231.333
200_A203_T0.472681.331
215_W246_A0.472571.331
73_F160_P0.469331.322
165_L169_I0.465481.311
172_L176_R0.46411.307
84_L95_I0.457761.289
4_L8_V0.446841.258
27_A30_D0.446091.256
72_I160_P0.445821.255
66_F116_S0.442591.246
74_S105_I0.440881.242
112_S116_S0.436131.228
128_V131_G0.433351.220
58_R124_W0.427131.203
104_I108_I0.421011.186
103_I106_I0.419791.182
147_I151_Y0.419021.180
106_I110_I0.417861.177
62_F120_L0.415541.170
119_P122_F0.415111.169
30_D253_N0.413041.163
22_L78_I0.411871.160
118_P121_F0.411651.159
6_I27_A0.410851.157
62_F113_F0.410281.155
69_F156_F0.407991.149
75_L164_I0.405671.142
13_K16_R0.403051.135
203_T206_I0.402151.132
76_V163_I0.401391.130
151_Y155_V0.400591.128
36_F67_S0.399221.124
227_F230_S0.398081.121
231_S236_S0.396881.118
29_A67_S0.393921.109
74_S109_W0.392831.106
224_L238_L0.392611.106
80_I167_C0.389051.096
92_Y96_R0.387591.091
36_F39_P0.384851.084
76_V160_P0.381831.075
205_L209_L0.378191.065
85_A89_P0.375541.058
99_R102_R0.37481.055
38_I247_F0.373711.052
80_I84_L0.373291.051
210_V256_I0.372451.049
73_F108_I0.372221.048
156_F160_P0.369841.041
40_F56_L0.369081.039
149_F153_F0.368531.038
12_S15_L0.367611.035
79_S168_Y0.367321.034
216_L220_I0.366431.032
72_I76_V0.366171.031
37_C64_F0.36191.019
248_L252_L0.359751.013
85_A92_Y0.357841.008
111_I115_I0.357771.007
70_S109_W0.357481.007
176_R179_R0.356291.003
22_L101_A0.355181.000
239_F244_F0.354620.999
73_F111_I0.353760.996
76_V167_C0.353750.996
108_I112_S0.352090.991
19_S23_L0.351260.989
34_G38_I0.351020.988
70_S74_S0.348090.980
172_L175_L0.346030.974
226_V229_P0.342760.965
127_F131_G0.342710.965
174_K177_R0.342320.964
7_L10_L0.341650.962
21_I102_R0.34150.962
157_F219_F0.341110.961
238_L242_S0.341050.960
70_S108_I0.339960.957
17_T21_I0.33930.955
40_F43_Y0.338580.953
82_R85_A0.338510.953
30_D249_N0.338250.953
96_R104_I0.337710.951
115_I152_F0.337140.949
88_H95_I0.336520.948
237_I241_I0.336170.947
250_S254_P0.335110.944
9_I15_L0.33490.943
125_V128_V0.334010.941
227_F231_S0.333510.939
38_I41_Y0.332660.937
195_R198_R0.332230.936
150_I154_I0.332160.935
6_I10_L0.332050.935
201_A207_I0.331990.935
6_I31_L0.330060.929
9_I16_R0.329890.929
207_I211_F0.325790.917
149_F152_F0.324380.913
21_I25_N0.324360.913
114_L118_P0.322350.908
125_V129_S0.322180.907
81_D92_Y0.321090.904
173_R176_R0.319640.900
5_V9_I0.318610.897
120_L124_W0.31790.895
198_R202_R0.317170.893
65_Y116_S0.315970.890
80_I163_I0.315960.890
5_V8_V0.315420.888
41_Y45_L0.314980.887
1_G251_C0.314440.885
98_R102_R0.314210.885
164_I168_Y0.314060.884
20_N23_L0.312780.881
137_F140_F0.312210.879
59_I63_L0.311170.876
33_V250_S0.310550.875
78_I204_L0.310270.874
36_F40_F0.310070.873
199_R203_T0.30950.872
26_L30_D0.309190.871
214_C217_P0.30910.870
79_S167_C0.309060.870
37_C41_Y0.308020.867
78_I81_D0.307660.866
16_R20_N0.305570.860
71_S214_C0.305080.859
152_F156_F0.303810.856
86_I90_L0.303410.854
203_T207_I0.303220.854
172_L201_A0.303140.854
157_F216_L0.300740.847
175_L200_A0.300590.846
6_I28_V0.300060.845
69_F112_S0.298770.841
138_I145_S0.297950.839
125_V130_D0.297570.838
92_Y95_I0.297550.838
162_I166_I0.297040.836
204_L208_V0.292840.825
207_I210_V0.292110.823
155_V159_L0.292030.822
22_L81_D0.291490.821
52_F56_L0.290150.817
135_F138_I0.289690.816
72_I211_F0.289490.815
5_V27_A0.289340.815
226_V230_S0.288720.813
100_R103_I0.286830.808
64_F68_S0.286250.806
34_G250_S0.28580.805
6_I9_I0.285240.803
119_P123_S0.285130.803
65_Y68_S0.285110.803
1_G255_I0.284650.802
22_L105_I0.284610.801
224_L229_P0.284230.800
95_I100_R0.284080.800
19_S22_L0.283740.799
149_F154_I0.283040.797
201_A205_L0.282740.796
61_G64_F0.280690.790
113_F117_L0.279820.788
248_L251_C0.279620.787
85_A90_L0.27960.787
243_Y247_F0.278650.785
79_S171_I0.278440.784
86_I89_P0.278080.783
117_L120_L0.277010.780
69_F115_I0.275440.776
219_F223_L0.27260.768
174_K178_Q0.272230.767
218_Y221_L0.270410.761
217_P242_S0.270030.760
161_L212_L0.269610.759
75_L82_R0.269530.759
84_L88_H0.269060.758
199_R204_L0.268740.757
43_Y47_F0.267560.753
8_V12_S0.266850.751
157_F218_Y0.266260.750
84_L87_C0.266110.749
154_I160_P0.265410.747
117_L124_W0.265260.747
206_I210_V0.265030.746
87_C171_I0.264670.745
157_F161_L0.264490.745
30_D33_V0.263780.743
236_S239_F0.26280.740
218_Y222_S0.26160.737
84_L96_R0.260730.734
15_L18_P0.259990.732
122_F125_V0.259440.731
200_A204_L0.259380.730
153_F157_F0.25910.730
219_F222_S0.258880.729
73_F156_F0.257880.726
242_S246_A0.256910.723
126_Y131_G0.256760.723
245_L249_N0.255310.719
198_R205_L0.255080.718
29_A109_W0.254530.717
121_F124_W0.254490.717
72_I215_W0.254010.715
102_R105_I0.253210.713
119_P145_S0.252550.711
114_L117_L0.251880.709
115_I118_P0.251810.709
212_L216_L0.250610.706
116_S120_L0.250540.706
105_I109_W0.25040.705
153_F158_I0.250320.705
181_R195_R0.250210.705
206_I256_I0.250180.705
222_S225_S0.250170.704
83_Y166_I0.24940.702
118_P122_F0.249040.701
115_I119_P0.248580.700
110_I113_F0.248570.700
171_I175_L0.248420.700
155_V160_P0.247440.697
60_F64_F0.247220.696
178_Q196_R0.247170.696
226_V231_S0.247060.696
9_I20_N0.247030.696
53_S57_C0.246950.695
44_S49_D0.246790.695
160_P163_I0.245740.692
251_C254_P0.245460.691
31_L35_L0.244940.690
243_Y246_A0.244880.690
171_I204_L0.244860.690
229_P236_S0.243920.687
2_N6_I0.243470.686
214_C245_L0.243160.685
74_S108_I0.241810.681
7_L12_S0.24180.681
18_P101_A0.241310.680
153_F223_L0.2410.679
73_F77_A0.240680.678
197_E200_A0.240450.677
21_I101_A0.240090.676
247_F253_N0.239890.676
148_Y152_F0.23980.675
42_I46_L0.239580.675
237_I240_Y0.23850.672
90_L96_R0.238110.671
33_V67_S0.237770.670
14_R17_T0.237670.669
231_S237_I0.237670.669
82_R207_I0.237530.669
149_F156_F0.237380.668
43_Y46_L0.237330.668
69_F73_F0.237210.668
34_G78_I0.237120.668
242_S245_L0.236990.667
49_D52_F0.23680.667
69_F116_S0.236670.666
206_I211_F0.236020.665
32_L63_L0.235960.664
39_P43_Y0.235770.664
5_V253_N0.234890.661
138_I149_F0.234260.660
48_D51_I0.234250.660
116_S149_F0.233480.657
62_F117_L0.233380.657
139_D142_S0.233340.657
146_Q150_I0.233330.657
224_L230_S0.232830.656
119_P149_F0.23240.654
164_I208_V0.23220.654
57_C62_F0.232010.653
73_F112_S0.231850.653
64_F243_Y0.231130.651
37_C40_F0.231090.651
88_H170_R0.230840.650
39_P60_F0.230680.650
29_A32_L0.229650.647
223_L227_F0.229470.646
236_S240_Y0.229430.646
175_L179_R0.228890.645
43_Y51_I0.22810.642
54_S124_W0.228010.642
11_R16_R0.227610.641
25_N28_V0.227470.641
168_Y175_L0.227460.641
177_R181_R0.226640.638
145_S149_F0.226450.638
75_L81_D0.226410.638
66_F112_S0.225730.636
107_L111_I0.224290.632
175_L178_Q0.22370.630
44_S50_W0.223170.628
119_P124_W0.222960.628
30_D82_R0.222760.627
221_L224_L0.222460.626
38_I42_I0.221780.625
63_L67_S0.220960.622
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
4grvA1100-0.063
2rh1A0.9844100-0.041
3vw7A1100-0.029
3uonA0.9844100-0.021
3rzeA0.9844100-0.006
3sn6R0.98831000.001
3v2yA0.96891000.005
4dklA0.98831000.007
3emlA0.99221000.011
4ib4A0.99221000.011

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