GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
IMS - impBmucBsamB family
Pfam: PF00817 (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: 149
Sequences: 3672
Seq/Len: 24.64
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
86_R124_A1.262743.493
24_A63_L1.024682.835
14_R72_R0.994912.752
124_A128_E0.955842.644
86_R128_E0.94012.601
3_M133_A0.914462.530
93_E141_P0.903662.500
69_D72_R0.857442.372
53_L65_V0.848222.347
12_R39_N0.799662.212
123_Q127_E0.794882.199
3_M131_L0.784712.171
20_G41_E0.728892.017
76_A79_R0.725392.007
120_R124_A0.722932.000
125_I133_A0.691821.914
87_F124_A0.673851.864
14_R69_D0.644911.784
13_R76_A0.630571.745
95_Y101_F0.62261.722
3_M80_L0.618291.711
85_Y92_V0.617171.707
81_A100_L0.61141.691
21_R64_V0.601911.665
89_S102_L0.567651.570
55_E59_L0.565251.564
24_A65_V0.543371.503
8_A12_R0.527191.459
118_A135_I0.519441.437
8_A23_V0.51431.423
15_D18_L0.506061.400
52_P55_E0.501791.388
117_L121_L0.49351.365
119_R123_Q0.4931.364
10_V72_R0.492841.363
5_A9_S0.490781.358
75_E79_R0.485421.343
87_F120_R0.475751.316
84_L102_L0.474621.313
138_A143_L0.472031.306
24_A35_V0.467571.294
41_E44_A0.454541.258
36_I68_P0.452531.252
11_E73_Y0.447971.239
51_M59_L0.446281.235
104_V117_L0.442261.224
26_V53_L0.438721.214
10_V76_A0.437931.212
119_R122_R0.428751.186
83_I128_E0.427241.182
55_E58_A0.427091.182
11_E69_D0.426651.180
1_I84_L0.417971.156
38_A49_P0.412191.140
82_E85_Y0.410821.137
72_R75_E0.40641.124
118_A137_I0.400891.109
35_V38_A0.398591.103
54_A58_A0.398341.102
70_P74_R0.397871.101
107_S111_F0.397571.100
15_D66_V0.396781.098
1_I133_A0.392071.085
6_F10_V0.390961.082
13_R72_R0.389891.079
113_G116_A0.387161.071
72_R76_A0.387111.071
84_L100_L0.381371.055
12_R41_E0.380381.052
107_S117_L0.37971.050
12_R19_R0.379031.049
101_F141_P0.377721.045
71_E75_E0.377461.044
13_R130_G0.371571.028
45_A62_D0.370531.025
107_S110_L0.36561.011
139_P143_L0.360680.998
107_S112_G0.356310.986
12_R23_V0.354170.980
24_A60_C0.352210.974
83_I124_A0.351220.972
35_V47_V0.35080.971
81_A85_Y0.350780.970
83_I129_T0.350690.970
35_V56_A0.347430.961
23_V66_V0.346710.959
45_A60_C0.344470.953
26_V33_G0.344220.952
18_L23_V0.343380.950
1_I102_L0.343060.949
83_I87_F0.338710.937
115_E119_R0.338530.937
77_S81_A0.333080.921
24_A47_V0.331970.918
40_Y43_R0.330160.913
140_N143_L0.325960.902
80_L129_T0.325710.901
37_A43_R0.319140.883
51_M56_A0.318610.881
136_G147_A0.31810.880
48_R51_M0.316590.876
5_A12_R0.314120.869
10_V14_R0.308420.853
4_D134_S0.303930.841
57_L63_L0.303490.840
87_F121_L0.303470.840
81_A94_V0.300990.833
42_A63_L0.300590.832
122_R135_I0.298440.826
79_R129_T0.297190.822
12_R20_G0.29610.819
47_V63_L0.295380.817
138_A144_A0.295270.817
83_I125_I0.293810.813
92_V100_L0.292740.810
56_A60_C0.291230.806
126_A130_G0.289220.800
53_L60_C0.284460.787
126_A132_T0.280870.777
125_I129_T0.278720.771
116_A119_R0.277290.767
37_A49_P0.274930.761
57_L65_V0.274090.758
40_Y44_A0.273810.758
84_L121_L0.273730.757
99_E145_K0.273650.757
34_R49_P0.272740.755
7_F68_P0.270410.748
123_Q126_A0.269760.746
51_M55_E0.268750.744
76_A131_L0.268070.742
7_F70_P0.267280.739
104_V118_A0.266540.737
124_A127_E0.266470.737
38_A47_V0.264870.733
19_R126_A0.263690.730
116_A120_R0.263090.728
94_V97_P0.259360.718
3_M6_F0.259270.717
5_A40_Y0.259180.717
104_V107_S0.256770.710
84_L94_V0.254890.705
18_L64_V0.25440.704
36_I49_P0.254030.703
22_P60_C0.253660.702
14_R76_A0.253420.701
26_V34_R0.251350.695
11_E15_D0.251180.695
90_P108_L0.246940.683
48_R59_L0.246310.681
75_E78_E0.245720.680
114_E137_I0.242240.670
27_S67_P0.241040.667
98_D145_K0.240880.666
60_C63_L0.238720.660
11_E14_R0.237360.657
79_R128_E0.235710.652
109_R120_R0.234380.648
54_A57_L0.234380.648
21_R62_D0.231660.641
96_S99_E0.231510.640
8_A37_A0.231370.640
26_V68_P0.229830.636
79_R82_E0.229270.634
10_V13_R0.229230.634
9_S37_A0.226690.627
8_A39_N0.226160.626
78_E82_E0.2240.620
143_L147_A0.223260.618
35_V65_V0.222930.617
28_G69_D0.222610.616
25_V66_V0.222410.615
134_S148_A0.220540.610
120_R123_Q0.220030.609
22_P39_N0.219880.608
106_G112_G0.219820.608
89_S108_L0.219710.608
27_S34_R0.218930.606
27_S33_G0.217890.603
82_E86_R0.217710.602
20_G39_N0.215020.595
104_V137_I0.214750.594
57_L61_P0.214360.593
93_E101_F0.214360.593
4_D148_A0.213010.589
11_E25_V0.212960.589
89_S92_V0.212850.589
123_Q128_E0.210850.583
77_S98_D0.209580.580
74_R97_P0.208670.577
53_L57_L0.20760.574
91_R103_D0.207420.574
106_G110_L0.205060.567
91_R106_G0.204870.567
139_P146_L0.202140.559
12_R21_R0.201590.558
81_A84_L0.201360.557
110_L113_G0.200820.556
142_L146_L0.200270.554
28_G67_P0.200160.554
36_I43_R0.199440.552
26_V36_I0.198520.549
37_A40_Y0.198140.548
22_P62_D0.19810.548
83_I86_R0.197890.547
81_A92_V0.195890.542
74_R78_E0.195560.541
90_P106_G0.195360.540
25_V37_A0.194960.539
117_L120_R0.19390.536
38_A48_R0.193260.535
7_F97_P0.192850.534
2_D7_F0.192340.532
5_A43_R0.191940.531
38_A43_R0.191170.529
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
4irkB0.9933100-0.063
4f4yA0.9933100-0.052
1jx4A0.9933100-0.048
3pzpA0.9664100-0.044
3gqcA0.9933100-0.041
3bq0A0.9933100-0.041
4dezA0.9799100-0.041
1im4A0.9933100-0.03
1t94A0.9664100-0.026
3osnA0.9664100-0.017

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