GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MS_channel - Mechanosensitive ion channel
Pfam: PF00924 (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: 206
Sequences: 5457
Seq/Len: 26.49
HH_delta: 0.065 (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
196_L200_E1.069893.349
68_E73_E0.990083.099
77_E87_R0.970823.039
162_E169_E0.87412.736
198_I201_E0.830772.601
134_E197_E0.805012.520
198_I202_H0.796412.493
138_E142_E0.753962.360
66_R73_E0.725332.271
161_D171_R0.706592.212
147_N190_E0.678422.124
141_E145_R0.669882.097
123_P167_S0.664972.082
164_G169_E0.658682.062
160_V168_L0.651322.039
43_Q47_S0.627961.966
142_E146_S0.615811.928
135_E202_H0.615761.928
100_K104_S0.61291.919
66_R75_R0.602511.886
78_E85_R0.595141.863
121_E171_R0.589011.844
137_R193_K0.582271.823
125_D205_E0.575881.803
8_I12_G0.575761.802
139_K198_I0.551931.728
84_T98_N0.546751.712
137_R141_E0.531571.664
58_E82_R0.530431.660
151_F154_P0.520261.629
190_E194_R0.517411.620
68_E71_G0.508211.591
194_R197_E0.507721.589
147_N194_R0.505161.581
36_L39_G0.51.565
68_E107_V0.499311.563
140_I195_I0.490581.536
77_E93_I0.489821.533
135_E138_E0.488691.530
197_E201_E0.484011.515
134_E193_K0.472741.480
66_R89_W0.470331.472
139_K202_H0.469911.471
121_E169_E0.467991.465
124_V133_I0.466451.460
44_D47_S0.462691.448
88_T94_V0.461641.445
61_F84_T0.460731.442
143_A198_I0.457921.434
188_R192_R0.456111.428
123_P169_E0.452781.417
135_E139_K0.45051.410
68_E109_Y0.445051.393
124_V136_L0.44181.383
199_L204_I0.438951.374
128_T205_E0.43571.364
123_P164_G0.425891.333
94_V107_V0.421631.320
122_I195_I0.416691.304
144_L172_I0.416211.303
67_I76_V0.414361.297
134_E138_E0.412371.291
85_R93_I0.409651.282
126_Y163_I0.408961.280
142_E198_I0.407561.276
183_K186_E0.405561.270
142_E145_R0.404071.265
26_S29_A0.403141.262
125_D128_T0.402361.260
119_V171_R0.400221.253
143_A194_R0.400011.252
136_L170_F0.392891.230
16_I20_L0.38971.220
174_V191_I0.389521.219
124_V128_T0.38851.216
176_V187_I0.384941.205
139_K142_E0.372261.165
123_P126_Y0.372041.165
123_P166_S0.371481.163
70_G105_P0.369271.156
138_E141_E0.367451.150
70_G104_S0.363831.139
163_I168_L0.361511.132
116_R184_Y0.359241.125
165_D169_E0.35871.123
117_R175_Y0.356781.117
124_V199_L0.354361.109
5_R9_I0.353731.107
74_G86_L0.352891.105
72_V105_P0.351241.100
92_E107_V0.350551.097
193_K197_E0.348751.092
33_V42_F0.346281.084
17_L22_I0.344841.080
126_Y166_S0.343631.076
119_V173_R0.342541.072
118_V174_V0.334141.046
30_S33_V0.333721.045
126_Y168_L0.331141.037
65_D111_R0.329321.031
133_I137_R0.323351.012
124_V170_F0.319691.001
34_L38_I0.315960.989
76_V86_L0.313960.983
129_D135_E0.313430.981
186_E190_E0.3120.977
127_D205_E0.310460.972
62_K111_R0.310310.971
100_K103_S0.307810.964
121_E161_D0.305610.957
80_G85_R0.305410.956
88_T92_E0.305220.955
178_N183_K0.30520.955
100_K105_P0.304140.952
143_A191_I0.302650.947
184_Y188_R0.300870.942
127_D196_L0.300590.941
28_L37_A0.299470.937
185_W189_S0.299190.937
149_Y190_E0.295880.926
191_I195_I0.295510.925
189_S193_K0.294230.921
41_A46_I0.293840.920
12_G16_I0.293420.919
47_S99_S0.292020.914
139_K143_A0.289960.908
28_L32_G0.289790.907
146_S194_R0.288690.904
136_L139_K0.287190.899
123_P165_D0.28570.894
47_S103_S0.284650.891
145_R152_K0.283380.887
194_R198_I0.283030.886
93_I111_R0.279850.876
6_I10_I0.279790.876
139_K199_L0.277430.868
83_S95_I0.276980.867
147_N191_I0.276890.867
158_V172_I0.274280.859
124_V204_I0.271080.849
140_I172_I0.270230.846
144_L150_I0.269630.844
118_V188_R0.268470.840
69_I101_L0.266980.836
126_Y165_D0.266220.833
45_I51_S0.266110.833
34_L37_A0.263950.826
121_E162_E0.261310.818
162_E192_R0.260410.815
67_I101_L0.259560.813
159_V189_S0.256990.804
57_F60_P0.256610.803
149_Y183_K0.255680.800
59_R62_K0.255590.800
42_F50_I0.254930.798
161_D169_E0.250630.785
44_D99_S0.250550.784
120_V192_R0.249850.782
58_E83_S0.249530.781
149_Y187_I0.248810.779
12_G15_I0.246890.773
118_V176_V0.246370.771
87_R91_G0.246320.771
141_E158_V0.245560.769
128_T133_I0.244410.765
143_A147_N0.243390.762
122_I163_I0.243360.762
32_G35_G0.243350.762
68_E72_V0.241350.756
25_S29_A0.24090.754
91_G175_Y0.24020.752
23_D26_S0.239830.751
136_L140_I0.236990.742
117_R173_R0.236790.741
30_S34_L0.236610.741
33_V37_A0.236390.740
67_I86_L0.235490.737
58_E85_R0.232370.727
159_V171_R0.231910.726
164_G167_S0.23090.723
144_L191_I0.230040.720
43_Q99_S0.229310.718
140_I198_I0.228980.717
148_P152_K0.227540.712
15_I19_I0.227160.711
163_I195_I0.227130.711
138_E145_R0.227070.711
139_K204_I0.225910.707
10_I14_L0.225330.705
150_I174_V0.224960.704
128_T136_L0.224160.702
38_I46_I0.223780.701
29_A32_G0.222910.698
41_A61_F0.222310.696
40_F43_Q0.222120.695
118_V184_Y0.22210.695
16_I19_I0.221970.695
63_V79_I0.221490.693
54_I102_I0.221280.693
150_I187_I0.219820.688
133_I136_L0.219740.688
119_V175_Y0.219490.687
93_I113_S0.216830.679
46_I50_I0.216530.678
13_I16_I0.216520.678
151_F177_K0.2160.676
133_I196_L0.215790.676
149_Y186_E0.21550.675
11_V15_I0.215020.673
133_I170_F0.215020.673
75_R87_R0.214710.672
163_I192_R0.214670.672
85_R95_I0.214070.670
129_D197_E0.211960.664
44_D48_N0.211690.663
136_L199_L0.211420.662
177_K182_E0.211240.661
31_L35_G0.208820.654
160_V192_R0.207830.651
146_S198_I0.207460.649
140_I144_L0.206440.646
187_I190_E0.20620.646
89_W109_Y0.205920.645
140_I143_A0.205830.644
90_D117_R0.205440.643
157_R173_R0.204810.641
61_F67_I0.20370.638
199_L202_H0.203670.638
168_L196_L0.201870.632
37_A42_F0.200840.629
48_N99_S0.200230.627
18_S23_D0.199970.626
34_L41_A0.198120.620
190_E193_K0.197720.619
139_K201_E0.197630.619
40_F45_I0.197560.618
123_P163_I0.197320.618
80_G83_S0.196890.616
69_I105_P0.196450.615
137_R189_S0.196370.615
32_G36_L0.195930.613
87_R93_I0.195410.612
29_A34_L0.19540.612
56_L102_I0.194820.610
51_S102_I0.19470.610
6_I9_I0.194640.609
45_I102_I0.193660.606
40_F44_D0.193620.606
160_V193_K0.193530.606
120_V174_V0.192930.604
108_N111_R0.192140.601
69_I96_I0.190630.597
9_I13_I0.189450.593
126_Y167_S0.18920.592
70_G100_K0.188460.590
144_L174_V0.188160.589
52_G74_G0.187260.586
9_I12_G0.186530.584
136_L143_A0.186530.584
61_F106_I0.186510.584
160_V163_I0.186380.583
33_V36_L0.185620.581
32_G43_Q0.185320.580
156_P159_V0.185080.579
126_Y164_G0.184650.578
92_E109_Y0.184060.576
39_G52_G0.18280.572
87_R113_S0.181990.570
129_D200_E0.181720.569
96_I105_P0.181640.569
75_R89_W0.181490.568
133_I140_I0.180610.565
61_F101_L0.180520.565
145_R155_E0.18030.564
136_L198_I0.179550.562
89_W175_Y0.179240.561
128_T138_E0.178520.559
115_Y177_K0.178410.559
31_L120_V0.177850.557
73_E109_Y0.177610.556
144_L156_P0.17720.555
141_E156_P0.177020.554
38_I42_F0.176470.552
185_W188_R0.176240.552
45_I50_I0.17530.549
197_E200_E0.175170.548
30_S50_I0.174290.546
28_L33_V0.173470.543
158_V161_D0.173260.542
165_D168_L0.172950.541
150_I154_P0.172110.539
134_E141_E0.171570.537
30_S35_G0.171330.536
24_V30_S0.171120.536
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
2vv5A0.9661000.065
4hw9A0.97091000.087
3udcA0.9661000.117
2do3A0.310738.40.926
2e6zA0.247624.50.932
1mwwA0.398123.80.933
3mlqE0.30119.30.935
1nz9A0.233160.937
2qn6B0.417515.70.938
3iv3A0.5874150.938

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