GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
OEP - Outer membrane efflux protein
Pfam: PF02321 (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: CL0105
Length: 188
Sequences: 17462
Seq/Len: 92.88
HH_delta: 0.014 (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
29_I92_Y2.044112.457
121_Q176_L1.816832.184
142_E146_E1.752812.107
8_A110_V1.733142.083
128_E169_L1.699072.042
135_K166_Q1.670772.008
131_L166_Q1.561481.877
136_E139_E1.541921.853
120_A179_A1.538041.849
131_L169_L1.524621.832
169_L173_Q1.51081.816
22_I99_L1.468341.765
120_A172_A1.461871.757
124_L173_Q1.449851.743
138_L162_L1.441731.733
135_K162_L1.429291.718
142_E159_Q1.427691.716
19_R99_L1.422231.709
26_E92_Y1.391851.673
22_I96_K1.379841.658
145_Y155_L1.367891.644
151_S154_D1.346681.619
162_L166_Q1.3431.614
20_A23_E1.325271.593
101_Q105_E1.319041.585
135_K139_E1.313721.579
128_E173_Q1.302431.565
145_Y152_E1.296241.558
97_A100_E1.286521.546
29_I89_K1.276621.534
144_R150_I1.272151.529
131_L162_L1.259611.514
138_L142_E1.255641.509
36_Y85_I1.245951.498
176_L180_L1.236111.486
99_L103_K1.231851.481
124_L176_L1.223361.470
91_E94_Q1.222091.469
28_Q31_A1.206031.450
117_L176_L1.190371.431
139_E143_K1.18671.426
124_L169_L1.180731.419
6_E10_Q1.173361.410
138_L159_Q1.1711.407
92_Y96_K1.166571.402
134_A165_A1.118821.345
95_A98_Q1.116781.342
132_E136_E1.109441.333
33_K85_I1.106591.330
150_I154_D1.103651.327
21_Q24_A1.102581.325
131_L135_K1.096291.318
87_A91_E1.092621.313
83_A86_K1.088631.308
122_E125_E1.061551.276
143_K146_E1.060711.275
29_I33_K1.060271.274
124_L128_E1.055571.269
163_L166_Q1.053871.267
9_L107_R1.050651.263
90_A93_E1.047671.259
108_L112_Q1.046071.257
43_S68_G1.041621.252
93_E96_K1.035031.244
29_I85_I1.031731.240
27_A30_K1.022251.229
77_D81_R1.020751.227
100_E103_K1.018291.224
76_F79_G1.017391.223
17_A21_Q1.013051.218
81_R85_I1.012961.218
85_I89_K1.009931.214
129_E132_E0.994641.195
12_N186_L0.988351.188
23_E26_E0.983451.182
120_A123_Q0.97511.172
141_A150_I0.967671.163
7_L11_N0.96721.163
125_E129_E0.963711.158
174_N178_I0.958921.153
117_L180_L0.957711.151
22_I92_Y0.95681.150
32_A88_A0.954491.147
84_Q87_A0.951061.143
18_A102_T0.950521.142
143_K147_A0.950471.142
171_Q175_D0.946451.138
128_E132_E0.943191.134
9_L103_K0.942681.133
88_A91_E0.937011.126
94_Q98_Q0.936511.126
16_K19_R0.933471.122
127_A172_A0.929371.117
124_L172_A0.924991.112
19_R23_E0.920881.107
15_L106_L0.917061.102
36_Y81_R0.916811.102
43_S70_S0.906291.089
105_E109_E0.90041.082
127_A165_A0.896071.077
7_L187_L0.884641.063
32_A35_S0.882191.060
164_Q168_Q0.881991.060
116_Q182_Q0.872041.048
36_Y82_R0.871641.048
130_Q134_A0.864181.039
161_Q164_Q0.862991.037
74_P77_D0.859551.033
180_L184_K0.856811.030
125_E128_E0.852111.024
113_A179_A0.851441.023
144_R149_L0.850631.022
168_Q171_Q0.844591.015
116_Q179_A0.843981.014
132_E135_K0.822650.989
82_R86_K0.820590.986
152_E156_L0.817960.983
114_Y118_L0.814740.979
123_Q127_A0.803580.966
110_V183_L0.803580.966
123_Q175_D0.803210.965
138_L155_L0.802120.964
24_A28_Q0.798870.960
18_A21_Q0.792790.953
175_D179_A0.789690.949
177_Q180_L0.787130.946
140_I144_R0.778820.936
159_Q163_L0.778060.935
141_A158_A0.777060.934
179_A182_Q0.774810.931
156_L159_Q0.774090.930
142_E155_L0.768180.923
80_K84_Q0.767120.922
22_I26_E0.766750.922
173_Q177_Q0.766590.921
28_Q32_A0.765890.921
139_E142_E0.764270.919
102_T105_E0.75090.903
40_L71_L0.750640.902
25_A28_Q0.749530.901
120_A175_D0.749420.901
157_Q161_Q0.748510.900
8_A106_L0.748410.900
136_E140_I0.747260.898
104_R108_L0.746520.897
86_K89_K0.742630.893
21_Q98_Q0.738130.887
12_N109_E0.735690.884
109_E112_Q0.733930.882
117_L121_Q0.733060.881
118_L122_E0.729230.876
12_N106_L0.71940.865
121_Q180_L0.715940.861
25_A95_A0.714910.859
120_A176_L0.708050.851
16_K20_A0.703420.845
15_L103_K0.701150.843
127_A168_Q0.700440.842
35_S81_R0.694090.834
170_I173_Q0.693260.833
86_K90_A0.691540.831
18_A95_A0.687990.827
113_A186_L0.683320.821
28_Q91_E0.68190.820
89_K93_E0.677910.815
155_L159_Q0.676150.813
15_L99_L0.668420.803
14_D17_A0.665270.800
134_A161_Q0.664990.799
25_A88_A0.664260.798
45_S66_S0.664250.798
20_A24_A0.663770.798
91_E95_A0.663160.797
19_R103_K0.662850.797
175_D178_I0.659350.792
118_L121_Q0.654050.786
121_Q125_E0.653450.785
98_Q101_Q0.651320.783
96_K100_E0.65010.781
112_Q116_Q0.649630.781
106_L186_L0.647830.779
157_Q160_A0.640980.770
79_G83_A0.640530.770
30_K33_K0.639740.769
7_L10_Q0.637090.766
123_Q172_A0.636190.765
128_E131_L0.635380.764
119_Q123_Q0.631310.759
172_A175_D0.622650.748
145_Y150_I0.613910.738
81_R84_Q0.61330.737
89_K92_Y0.612910.737
117_L179_A0.612580.736
137_Q141_A0.606390.729
26_E30_K0.600190.721
160_A164_Q0.598240.719
23_E27_A0.595550.716
178_I182_Q0.587360.706
93_E97_A0.582470.700
33_K37_L0.580490.698
44_A67_V0.579560.697
100_E104_R0.577860.695
17_A20_A0.574260.690
127_A169_L0.563370.677
131_L165_A0.56320.677
141_A144_R0.56240.676
113_A182_Q0.556170.668
182_Q185_R0.549310.660
135_K138_L0.54820.659
103_K107_R0.545920.656
32_A84_Q0.54050.650
145_Y151_S0.539690.649
181_A184_K0.534960.643
105_E108_L0.534760.643
129_E133_L0.533390.641
115_Y118_L0.532040.639
14_D102_T0.529070.636
109_E113_A0.528190.635
90_A94_Q0.527940.635
116_Q120_A0.523910.630
117_L183_L0.523330.629
18_A99_L0.519720.625
156_L160_A0.519350.624
74_P81_R0.518210.623
121_Q124_L0.515140.619
165_A168_Q0.514920.619
166_Q169_L0.513070.617
107_R111_K0.509290.612
181_A185_R0.508760.611
29_I88_A0.503450.605
17_A24_A0.502010.603
134_A137_Q0.499530.600
69_L73_Q0.497740.598
133_L137_Q0.496960.597
87_A94_Q0.49690.597
116_Q119_Q0.496870.597
144_R154_D0.495930.596
35_S84_Q0.495680.596
98_Q102_T0.493690.593
26_E96_K0.493270.593
126_I129_E0.4930.593
39_Q72_S0.492230.592
122_E126_I0.491770.591
41_S70_S0.490720.590
14_D106_L0.488240.587
127_A131_L0.487580.586
127_A130_Q0.48250.580
26_E29_I0.482240.580
77_D80_K0.479260.576
150_I155_L0.477240.574
25_A92_Y0.476160.572
25_A91_E0.475390.571
8_A187_L0.472770.568
141_A145_Y0.471020.566
27_A31_A0.470030.565
79_G82_R0.466390.561
24_A27_A0.462780.556
21_Q25_A0.460.553
71_L74_P0.456930.549
31_A35_S0.456320.548
99_L102_T0.455520.548
101_Q104_R0.454740.547
167_L171_Q0.451230.542
20_A27_A0.450150.541
97_A101_Q0.448580.539
42_L69_L0.443380.533
58_P61_S0.441740.531
83_A90_A0.440330.529
94_Q97_A0.440190.529
173_Q176_L0.439050.528
170_I174_N0.438450.527
34_S37_L0.437310.526
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
1ek9A199.90.014
3pikA0.98499.90.025
3d5kA199.90.033
1yc9A199.90.039
3pikA0.994799.90.041
3d5kA0.994799.90.043
1yc9A0.994799.90.053
1ek9A0.98499.90.063
4dk0A0.797989.80.813
2f1mA0.707487.40.821

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