GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
OprF - OprF membrane domain
Pfam: PF05736 (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: CL0193
Length: 184
Sequences: 2741
Seq/Len: 14.9
HH_delta: 0.288 (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
31_E58_G0.649383.818
154_R175_G0.605423.559
113_S140_G0.572973.369
35_F54_G0.506682.979
33_E56_S0.454772.674
147_F153_A0.452992.663
151_F178_V0.406892.392
108_L145_Y0.405852.386
107_A145_Y0.404082.376
148_T151_F0.397842.339
157_V170_W0.393982.316
152_Y177_G0.377332.218
111_Y142_G0.375112.205
30_V57_I0.348122.047
151_F176_L0.337691.985
71_Y91_S0.323831.904
108_L143_A0.318761.874
37_K52_L0.317961.869
68_N96_D0.314751.851
30_V59_Y0.311151.829
96_D138_N0.281781.657
117_A136_F0.275271.618
118_H133_Q0.273291.607
61_L67_L0.268821.580
54_G72_G0.265091.559
64_D99_Y0.256311.507
65_V97_A0.2391.405
111_Y154_R0.2371.393
118_H135_T0.234631.379
111_Y156_G0.233751.374
106_D110_P0.22751.338
145_Y155_A0.222881.310
66_S100_H0.222321.307
31_E68_N0.218691.286
144_K154_R0.211961.246
119_Q136_F0.20651.214
48_E85_N0.202581.191
139_V159_A0.202541.191
29_A59_Y0.202091.188
60_F66_S0.201731.186
66_S98_Q0.201591.185
159_A168_T0.201141.183
58_G98_Q0.196181.153
52_L175_G0.189021.111
56_S68_N0.188121.106
156_G173_S0.187811.104
159_A170_W0.186441.096
90_G119_Q0.186431.096
33_E37_K0.185691.092
113_S156_G0.185131.088
116_F135_T0.185121.088
146_Y179_N0.184341.084
113_S158_E0.182131.071
111_Y140_G0.179491.055
115_G138_N0.179241.054
144_K152_Y0.175711.033
71_Y93_T0.174621.027
152_Y179_N0.173711.021
140_G156_G0.173161.018
58_G100_H0.172641.015
96_D100_H0.171371.008
94_S138_N0.170611.003
87_K132_D0.166130.977
105_G108_L0.164160.965
155_A174_V0.163620.962
32_V57_I0.163450.961
109_R112_V0.162790.957
141_A157_V0.162570.956
78_R165_N0.1610.947
33_E177_G0.160460.943
146_Y152_Y0.159990.941
35_F72_G0.158350.931
98_Q113_S0.157690.927
85_N88_I0.156890.922
101_F110_P0.154570.909
61_L95_L0.153870.905
68_N156_G0.15310.900
54_G158_E0.153040.900
70_S94_S0.152740.898
46_D87_K0.152550.897
60_F100_H0.152460.896
53_P73_E0.151710.892
152_Y175_G0.15130.890
90_G94_S0.150920.887
93_T120_S0.149530.879
56_S177_G0.149020.876
150_N178_V0.148560.873
68_N158_E0.146160.859
96_D158_E0.144290.848
100_H144_K0.144120.847
137_A161_Y0.143930.846
132_D163_I0.143290.842
66_S140_G0.143060.841
32_V129_G0.142950.840
45_R57_I0.142560.838
34_G57_I0.141250.830
55_A152_Y0.140860.828
86_K119_Q0.140370.825
58_G70_S0.140110.824
78_R130_G0.139760.822
110_P143_A0.13960.821
39_Y74_Y0.137850.810
110_P114_G0.137760.810
38_K49_N0.137540.809
109_R144_K0.136420.802
98_Q144_K0.136280.801
62_T65_V0.136080.800
164_D167_D0.135230.795
68_N111_Y0.13470.792
58_G92_N0.134690.792
115_G119_Q0.134570.791
143_A157_V0.134360.790
140_G158_E0.13420.789
46_D80_N0.13410.788
147_F175_G0.133990.788
145_Y148_T0.133720.786
35_F56_S0.133260.783
154_R177_G0.131270.772
98_Q101_F0.131160.771
94_S136_F0.130920.770
65_V99_Y0.13090.770
53_P71_Y0.130860.769
48_E133_Q0.12960.762
132_D139_V0.129590.762
36_Y40_F0.129410.761
99_Y110_P0.129310.760
36_Y51_N0.129230.760
56_S113_S0.12860.756
112_V141_A0.128590.756
93_T122_G0.128510.756
34_G178_V0.127950.752
64_D174_V0.127770.751
91_S120_S0.127690.751
96_D115_G0.12740.749
157_V172_A0.127360.749
98_Q156_G0.126240.742
33_E70_S0.126130.742
58_G68_N0.125960.741
108_L113_S0.125930.740
106_D109_R0.125570.738
177_G180_F0.125440.738
43_S87_K0.124320.731
98_Q109_R0.12350.726
108_L151_F0.122190.718
70_S73_E0.121910.717
120_S153_A0.121660.715
143_A176_L0.121410.714
123_N129_G0.120260.707
84_G87_K0.120090.706
133_Q136_F0.11930.701
40_F49_N0.119290.701
150_N180_F0.119050.700
48_E167_D0.118930.699
52_L55_A0.118820.699
120_S123_N0.11880.698
79_S90_G0.118310.696
95_L116_F0.118220.695
68_N154_R0.118190.695
64_D100_H0.11710.688
71_Y122_G0.116910.687
68_N100_H0.116780.687
98_Q154_R0.116740.686
117_A137_A0.116520.685
143_A155_A0.116270.684
33_E95_L0.116180.683
111_Y115_G0.116130.683
159_A163_I0.116090.683
50_G105_G0.116030.682
56_S154_R0.115960.682
69_L93_T0.115730.680
144_K177_G0.115460.679
154_R171_A0.115280.678
60_F142_G0.114420.673
60_F109_R0.114320.672
139_V178_V0.114220.672
122_G131_R0.114030.670
42_D161_Y0.114020.670
147_F152_Y0.113880.670
88_I121_I0.113810.669
50_G53_P0.113310.666
138_N160_D0.113170.665
29_A61_L0.113070.665
68_N157_V0.112370.661
97_A129_G0.111920.658
106_D148_T0.111910.658
117_A135_T0.111850.658
99_Y136_F0.111240.654
65_V80_N0.111170.654
109_R146_Y0.111130.653
45_R61_L0.110770.651
68_N120_S0.110590.650
96_D111_Y0.110590.650
73_E91_S0.110490.650
49_N132_D0.110450.649
70_S173_S0.110390.649
54_G94_S0.110320.649
139_V157_V0.110110.647
113_S119_Q0.109920.646
37_K171_A0.109870.646
93_T117_A0.109850.646
90_G156_G0.109670.645
56_S60_F0.109580.644
52_L173_S0.109420.643
49_N131_R0.109230.642
136_F139_V0.109120.642
159_A162_N0.109090.641
49_N58_G0.108480.638
120_S133_Q0.108230.636
166_G174_V0.108180.636
70_S138_N0.10810.636
34_G157_V0.108040.635
101_F162_N0.107910.634
38_K158_E0.107710.633
42_D162_N0.106850.628
41_T48_E0.10680.628
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
3nb3A0.983799.90.288
2k0lA0.923999.80.391
2x27X0.880499.70.416
1qjpA0.853399.70.45
2f1vA0.869699.60.483
1p4tA0.815299.60.486
2jmmA0.793599.60.489
3qraA0.815299.50.521
2lhfA0.798999.40.541
1ormA0.793599.30.567

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