GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
OmpA - OmpA family
Pfam: PF00691 (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: 97
Sequences: 8338
Seq/Len: 85.96
HH_delta: -0.049 (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
36_E78_Y2.476153.166
3_D10_S2.074912.653
52_S77_G1.941792.483
5_N47_Y1.941682.483
78_Y82_Q1.855832.373
7_S54_R1.718452.198
50_E54_R1.699422.173
60_K75_V1.658482.121
4_P42_T1.616172.067
18_D66_N1.615752.066
49_Q53_Q1.601292.048
87_N92_G1.567632.005
85_A92_G1.516981.940
53_Q57_E1.476441.888
18_D62_Y1.449141.853
42_T93_R1.428471.827
17_L62_Y1.284471.643
85_A95_R1.2781.634
38_H82_Q1.158381.481
45_A80_E1.143161.462
60_K64_V1.107471.416
34_E74_S1.093621.398
62_Y66_N1.082361.384
86_S92_G1.073831.373
49_Q81_S1.063531.360
45_A81_S1.060461.356
57_E60_K1.049761.342
34_E76_V1.022431.307
9_L62_Y0.99031.266
64_V70_P0.938161.200
40_D48_N0.926161.184
16_Q19_E0.923691.181
69_P72_R0.923071.180
43_G48_N0.921821.179
60_K73_I0.91531.170
89_T92_G0.888871.137
9_L13_S0.882681.129
32_Q74_S0.879871.125
14_Q62_Y0.87871.124
35_I60_K0.840031.074
21_A66_N0.838371.072
3_D6_S0.835061.068
57_E61_Q0.826821.057
35_I56_A0.826241.057
11_P14_Q0.822821.052
13_S16_Q0.816141.044
62_Y65_E0.813931.041
61_Q65_E0.813691.041
4_P40_D0.804651.029
60_K70_P0.803391.027
57_E75_V0.792451.013
33_I73_I0.792071.013
36_E76_V0.791261.012
88_D92_G0.781751.000
41_S93_R0.779680.997
64_V73_I0.773940.990
1_Y13_S0.768650.983
47_Y50_E0.766170.980
54_R57_E0.736250.941
87_N93_R0.728010.931
20_L24_L0.725430.928
38_H83_P0.695970.890
17_L59_V0.695860.890
36_E82_Q0.689880.882
4_P47_Y0.683510.874
53_Q77_G0.655570.838
22_K25_K0.653930.836
41_S87_N0.64620.826
21_A25_K0.646110.826
56_A77_G0.640920.820
14_Q18_D0.639550.818
4_P48_N0.638450.816
7_S58_A0.637580.815
91_E95_R0.632070.808
56_A75_V0.631250.807
2_F37_G0.62290.797
18_D22_K0.616080.788
15_E18_D0.613030.784
19_E22_K0.606270.775
61_Q64_V0.602470.770
23_I29_N0.600140.767
7_S51_L0.598790.766
53_Q75_V0.585920.749
10_S13_S0.580490.742
21_A63_L0.578250.739
68_I73_I0.57410.734
84_L95_R0.571130.730
58_A61_Q0.547870.701
89_T93_R0.539570.690
68_I72_R0.537210.687
47_Y51_L0.534740.684
9_L58_A0.533280.682
39_T48_N0.528050.675
47_Y80_E0.521620.667
2_F59_V0.521170.666
50_E53_Q0.517770.662
25_K69_P0.512130.655
37_G59_V0.511510.654
41_S83_P0.510870.653
37_G52_S0.510160.652
1_Y84_L0.502730.643
86_S89_T0.493390.631
42_T90_E0.487240.623
85_A93_R0.484430.619
38_H78_Y0.483640.618
44_S47_Y0.483170.618
21_A68_I0.478540.612
21_A62_Y0.476370.609
4_P43_G0.471630.603
88_D93_R0.457670.585
48_N80_E0.455220.582
46_E50_E0.450680.576
90_E93_R0.443980.568
25_K68_I0.440480.563
30_K72_R0.440170.563
37_G55_R0.43740.559
20_L23_I0.436990.559
3_D8_E0.430170.550
16_Q20_L0.429830.550
53_Q76_V0.425780.544
19_E23_I0.422390.540
22_K28_G0.412830.528
7_S50_E0.404610.517
67_G73_I0.402010.514
41_S88_D0.400320.512
89_T94_A0.397730.509
5_N43_G0.395160.505
49_Q79_G0.390820.500
52_S79_G0.388510.497
15_E19_E0.384550.492
49_Q52_S0.383580.491
25_K66_N0.380770.487
64_V67_G0.36920.472
90_E94_A0.363630.465
24_L72_R0.362330.463
85_A89_T0.362170.463
12_E15_E0.361820.463
41_S80_E0.360530.461
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
3ldtA0.979499.8-0.049
2zf8A199.8-0.04
2l26A0.979499.8-0.036
2hqsH0.989799.8-0.027
3s0yA0.979499.8-0.025
3khnA0.979499.8-0.015
3nb3A199.8-0.011
2aizP0.989799.8-0.009
3s06A0.979499.8-0.008
2k1sA0.979499.8-0.008

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