GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MscL - Large-conductance mechanosensitive channel MscL
Pfam: PF01741 (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: 128
Sequences: 1340
Seq/Len: 10.47
HH_delta: 0.038 (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
32_N36_N0.833363.402
3_K7_D0.814223.324
4_E92_K0.632552.582
29_A32_N0.54922.242
38_I68_I0.533522.178
33_S37_D0.530282.165
85_F89_L0.526912.151
113_T116_E0.524872.143
17_L21_V0.523772.138
34_L38_I0.487171.989
69_P72_A0.482881.971
15_V94_I0.478441.953
4_E95_N0.476591.946
113_T119_T0.47281.930
55_L70_Y0.460131.878
56_F67_V0.441171.801
28_T32_N0.435111.776
17_L20_G0.415031.694
34_L73_F0.407041.662
112_K115_E0.404591.652
114_C117_L0.402141.642
1_M89_L0.391341.598
115_E119_T0.359371.467
1_M85_F0.350361.430
56_F65_A0.340551.390
37_D72_A0.334391.365
101_E104_E0.334131.364
15_V90_I0.325931.331
120_E126_K0.325851.330
75_N79_N0.320591.309
118_L122_R0.318571.301
117_L122_R0.309071.262
119_T124_L0.297251.214
9_I84_A0.297251.214
29_A79_N0.296451.210
79_N83_I0.288711.179
32_N79_N0.287971.176
98_K101_E0.286951.171
7_D95_N0.285691.166
110_A116_E0.284881.163
21_V28_T0.28481.163
37_D76_A0.28191.151
14_V34_L0.28151.149
44_G52_F0.278961.139
52_F74_L0.277251.132
70_Y74_L0.276931.131
100_K103_K0.273331.116
72_A76_A0.273311.116
5_F8_F0.272921.114
33_S73_F0.270821.106
32_N35_V0.268191.095
7_D99_K0.264821.081
4_E88_F0.262521.072
4_E93_P0.258671.056
30_I77_L0.256961.049
111_P116_E0.255441.043
56_F59_L0.252771.032
10_M14_V0.250441.022
37_D73_F0.247821.012
57_I68_I0.24581.003
58_V66_V0.244690.999
114_C119_T0.236810.967
5_F85_F0.234590.958
37_D69_P0.231450.945
20_G95_N0.231050.943
9_I20_G0.231030.943
9_I81_L0.228160.931
56_F69_P0.228090.931
58_V67_V0.226270.924
99_K102_E0.225460.920
23_I28_T0.225360.920
40_M75_N0.224870.918
116_E119_T0.224650.917
42_L46_L0.223790.914
96_K100_K0.21970.897
25_A29_A0.219620.897
116_E124_L0.219230.895
75_N83_I0.219180.895
111_P114_C0.217240.887
16_D19_V0.214070.874
23_I27_F0.211130.862
120_E123_D0.210860.861
22_V90_I0.210750.860
25_A83_I0.210690.860
93_P96_K0.209760.856
22_V43_I0.206460.843
42_L68_I0.206440.843
40_M43_I0.203580.831
117_L125_L0.20340.830
51_D54_D0.202330.826
74_L78_I0.201320.822
51_D75_N0.199690.815
121_I125_L0.199410.814
117_L121_I0.197950.808
49_G55_L0.197790.807
55_L58_V0.197670.807
46_L68_I0.196440.802
115_E124_L0.195980.800
75_N78_I0.19490.796
91_V95_N0.194750.795
2_L7_D0.194730.795
52_F78_I0.194060.792
14_V30_I0.193820.791
14_V26_A0.193760.791
56_F63_A0.193340.789
40_M44_G0.192040.784
39_I86_V0.190450.778
28_T86_V0.190280.777
112_K117_L0.189560.774
19_V91_V0.189110.772
47_F55_L0.188670.770
2_L81_L0.186340.761
21_V25_A0.18630.761
81_L85_F0.186040.760
53_S75_N0.18580.759
89_L93_P0.183720.750
3_K6_K0.182930.747
2_L64_G0.182770.746
122_R126_K0.182060.743
44_G71_G0.181540.741
11_R98_K0.180140.735
11_R14_V0.179850.734
122_R125_L0.179740.734
114_C125_L0.179660.733
4_E7_D0.178170.727
117_L123_D0.177950.726
17_L24_G0.177030.723
42_L47_F0.176130.719
74_L77_L0.174560.713
33_S72_A0.174390.712
30_I33_S0.174260.711
55_L74_L0.173160.707
22_V35_V0.172580.705
85_F92_K0.171990.702
43_I83_I0.170620.697
112_K116_E0.170420.696
70_Y73_F0.170210.695
110_A123_D0.169510.692
42_L66_V0.1690.690
48_G52_F0.167840.685
47_F86_V0.167740.685
27_F80_F0.167490.684
20_G45_L0.167240.683
99_K103_K0.167130.682
5_F9_I0.166560.680
16_D35_V0.165640.676
114_C122_R0.165610.676
40_M52_F0.165610.676
113_T124_L0.163680.668
59_L63_A0.162850.665
56_F66_V0.162050.662
98_K102_E0.160460.655
57_I66_V0.160270.654
38_I42_L0.159890.653
14_V19_V0.158310.646
13_N22_V0.158270.646
101_E108_A0.158080.645
28_T40_M0.158070.645
39_I82_I0.157860.644
59_L65_A0.157780.644
13_N16_D0.157390.643
12_G16_D0.157210.642
13_N25_A0.156870.640
77_L81_L0.156080.637
87_V90_I0.155940.637
22_V86_V0.15590.636
63_A66_V0.155720.636
76_A79_N0.155580.635
21_V30_I0.155370.634
5_F84_A0.155160.633
11_R15_V0.154410.630
23_I29_A0.154320.630
10_M91_V0.153540.627
119_T122_R0.153250.626
14_V91_V0.152450.622
47_F50_P0.152320.622
9_I94_I0.152030.621
36_N107_E0.151840.620
12_G27_F0.151570.619
103_K106_A0.151380.618
72_A77_L0.151290.618
15_V22_V0.151270.618
22_V79_N0.150950.616
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
2oarA0.96091000.038
3hzqA0.72661000.236
2yfvC0.179717.80.94
3pk1B0.2031140.942
3p5nA0.679710.50.945
3m91B0.23449.40.946
3rlbA0.78128.70.947
2wscJ0.34388.70.947
1jb0J0.32038.30.947
3vouA0.8758.20.947

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