GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MIP - Major intrinsic protein
Pfam: PF00230 (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: 227
Sequences: 3164
Seq/Len: 13.94
HH_delta: 0.006 (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
15_F105_L0.934733.970
82_A89_W0.820543.485
78_T92_A0.808823.435
142_F222_L0.801083.402
19_F109_L0.77553.293
142_F218_I0.690242.931
11_F98_A0.686112.914
82_A92_A0.681652.895
138_F215_G0.679862.887
151_V175_T0.675172.867
11_F94_V0.672622.856
15_F101_L0.656472.788
19_F106_G0.617062.621
144_G183_G0.612922.603
55_G177_G0.592462.516
138_F142_F0.582162.472
83_L221_I0.579512.461
10_K91_K0.553672.351
146_F223_A0.551342.341
96_I217_F0.502552.134
190_S196_A0.470972.000
79_L217_F0.458481.947
59_A173_G0.455461.934
197_L201_L0.455131.933
217_F221_I0.442721.880
65_F73_F0.428421.819
25_G54_W0.413141.755
17_G73_F0.412921.754
72_H95_Y0.407321.730
197_L213_W0.401141.704
210_W214_V0.400171.699
180_V189_A0.399891.698
79_L96_I0.383281.628
219_G223_A0.38291.626
144_G191_L0.37931.611
61_L65_F0.37541.594
179_L191_L0.365871.554
180_V184_G0.35441.505
209_F213_W0.353081.499
140_S186_Y0.341431.450
77_V152_I0.340851.448
58_L176_V0.330311.403
23_F109_L0.329671.400
89_W92_A0.326611.387
48_L52_L0.325261.381
137_A187_T0.319771.358
87_I92_A0.318741.354
128_P137_A0.315891.342
149_V220_A0.311811.324
108_L202_F0.310971.321
98_A102_G0.3051.295
78_T99_Q0.304211.292
176_V191_L0.303941.291
206_W209_F0.295541.255
146_F222_L0.293261.245
146_F226_L0.292351.242
108_L112_A0.29171.239
141_E187_T0.289011.227
80_A84_T0.288451.225
146_F150_L0.283911.206
18_T103_A0.282351.199
104_F205_I0.280191.190
92_A96_I0.278821.184
78_T87_I0.277411.178
104_F198_G0.275091.168
196_A200_A0.274471.166
20_L147_I0.271721.154
135_G139_F0.26781.137
170_L174_L0.26731.135
69_S95_Y0.265571.128
81_F87_I0.265541.128
51_A181_L0.265251.126
103_A107_A0.265141.126
104_F202_F0.264751.124
145_T220_A0.264671.124
8_W11_F0.263171.118
62_I169_P0.260761.107
89_W93_I0.25991.104
52_L177_G0.25851.098
140_S144_G0.258071.096
59_A170_L0.257641.094
29_V50_I0.2571.091
107_A199_P0.256561.090
142_F219_G0.254611.081
113_L140_S0.253631.077
26_C110_V0.251411.068
13_A68_I0.250041.062
65_F71_A0.249271.059
19_F105_L0.248411.055
72_H78_T0.247871.053
22_V26_C0.246371.046
78_T96_I0.245591.043
157_D227_Y0.245551.043
120_A123_I0.245341.042
24_F57_A0.244511.038
148_L176_V0.241321.025
21_L58_L0.241191.024
93_I97_I0.240951.023
75_P194_A0.240141.020
109_L143_I0.239791.018
140_S187_T0.239611.018
142_F215_G0.237871.010
138_F214_V0.236871.006
56_L178_A0.236521.004
80_A149_V0.234840.997
63_Y169_P0.234570.996
105_L108_L0.233630.992
102_G106_G0.23130.982
27_G110_V0.231110.981
64_A151_V0.230560.979
29_V33_N0.229970.977
100_F213_W0.229940.977
138_F211_V0.229440.974
61_L73_F0.229050.973
156_A172_I0.227860.968
197_L209_F0.225930.959
168_A172_I0.222750.946
76_A193_P0.22150.941
57_A61_L0.221310.940
217_F220_A0.221130.939
113_L186_Y0.220190.935
100_F197_L0.219550.932
62_I77_V0.21630.919
17_G21_L0.21590.917
79_L221_I0.213120.905
132_I137_A0.212460.902
96_I100_F0.212120.901
134_L211_V0.212030.900
215_G219_G0.211610.899
138_F210_W0.211450.898
82_A87_I0.209370.889
103_A198_G0.205640.873
48_L51_A0.205570.873
82_A93_I0.203290.863
104_F201_L0.202740.861
59_A63_Y0.202360.859
183_G189_A0.200610.852
45_G49_Q0.198010.841
18_T22_V0.196870.836
104_F197_L0.196440.834
63_Y171_A0.19620.833
136_Q140_S0.19590.832
14_E17_G0.195820.832
11_F15_F0.195040.828
133_S136_Q0.193610.822
30_A123_I0.193360.821
72_H77_V0.192970.819
101_L105_L0.192830.819
83_L224_A0.191070.811
59_A171_A0.190630.810
84_T153_L0.189240.804
139_F142_F0.188950.802
22_V103_A0.188830.802
56_L177_G0.188350.800
107_A202_F0.187540.796
83_L225_L0.186390.792
152_I172_I0.185530.788
56_L174_L0.184330.783
61_L71_A0.184270.783
201_L204_G0.184130.782
132_I186_Y0.183770.780
26_C107_A0.183590.780
148_L152_I0.183520.779
121_A127_T0.183320.779
47_W50_I0.183030.777
132_I136_Q0.18280.776
80_A224_A0.182420.775
195_R199_P0.18230.774
76_A220_A0.181350.770
189_A212_Y0.18120.770
13_A69_S0.180220.765
20_L61_L0.180050.765
211_V216_P0.178470.758
196_A216_P0.177550.754
31_A37_S0.17740.753
53_A181_L0.177110.752
113_L139_F0.176970.752
22_V110_V0.176540.750
208_Y212_Y0.176480.749
134_L138_F0.176410.749
46_G49_Q0.174320.740
72_H99_Q0.173970.739
150_L226_L0.172260.732
69_S72_H0.170370.724
116_D136_Q0.170120.722
126_T190_S0.168460.715
88_S91_K0.168440.715
26_C106_G0.167440.711
111_Y202_F0.166910.709
121_A125_A0.165370.702
177_G181_L0.165140.701
179_L189_A0.164770.700
94_V98_A0.164570.699
138_F218_I0.164040.697
155_V171_A0.163730.695
67_P227_Y0.162920.692
184_G189_A0.162560.690
112_A139_F0.16110.684
23_F147_I0.160560.682
194_A198_G0.160560.682
158_D227_Y0.160480.682
211_V215_G0.160470.681
18_T194_A0.158930.675
100_F198_G0.158470.673
10_K13_A0.157620.669
113_L136_Q0.156990.667
163_P170_L0.156850.666
18_T21_L0.156690.665
63_Y170_L0.156380.664
63_Y167_L0.15590.662
15_F19_F0.155880.662
200_A205_I0.155120.659
198_G202_F0.154070.654
214_V218_I0.153130.650
193_P213_W0.153070.650
121_A203_S0.152630.648
196_A213_W0.152530.648
145_T149_V0.152360.647
48_L181_L0.152330.647
126_T212_Y0.151580.644
155_V175_T0.151510.643
123_I128_P0.151210.642
20_L60_A0.151160.642
149_V152_I0.150860.641
87_I94_V0.149880.637
81_F86_R0.149660.636
21_L176_V0.149490.635
23_F106_G0.149470.635
19_F102_G0.149060.633
52_L181_L0.148860.632
154_A157_D0.148830.632
97_I101_L0.148740.632
115_P136_Q0.147110.625
63_Y173_G0.147090.625
190_S212_Y0.146840.624
139_F143_I0.146680.623
214_V217_F0.146220.621
160_R163_P0.146090.620
14_E18_T0.145790.619
188_G192_N0.145770.619
204_G209_F0.145110.616
210_W216_P0.14480.615
50_I54_W0.144590.614
80_A85_G0.144420.613
13_A70_G0.144190.612
190_S195_R0.143990.611
90_K93_I0.143610.610
70_G95_Y0.143290.609
9_R13_A0.143210.608
126_T129_P0.142920.607
147_I151_V0.14280.606
24_F31_A0.142120.604
196_A212_Y0.141920.603
146_F219_G0.141740.602
46_G185_P0.141460.601
11_F101_L0.140970.599
147_I183_G0.140280.596
24_F178_A0.140040.595
88_S94_V0.13990.594
157_D160_R0.139810.594
134_L207_D0.139650.593
27_G182_A0.139170.591
81_F152_I0.139060.591
137_A211_V0.138470.588
32_L36_T0.138420.588
54_W180_V0.1380.586
31_A185_P0.137960.586
64_A67_P0.137860.585
33_N36_T0.13780.585
195_R200_A0.137430.584
175_T179_L0.137110.582
220_A224_A0.136780.581
145_T199_P0.136680.580
88_S92_A0.136640.580
18_T58_L0.136390.579
23_F113_L0.136370.579
208_Y211_V0.135620.576
103_A106_G0.135420.575
31_A186_Y0.135380.575
61_L64_A0.135150.574
10_K95_Y0.134830.573
21_L147_I0.134760.572
215_G218_I0.134760.572
147_I175_T0.134450.571
74_N192_N0.134240.570
200_A204_G0.134220.570
151_V171_A0.134210.570
221_I224_A0.13410.569
51_A189_A0.133970.569
150_L154_A0.133820.568
195_R210_W0.133590.567
153_L223_A0.133560.567
128_P211_V0.13340.567
123_I126_T0.133360.566
19_F23_F0.133170.566
84_T223_A0.132120.561
156_A168_A0.132080.561
72_H87_I0.131930.560
11_F100_F0.131310.558
31_A35_S0.131020.556
28_S32_L0.130640.555
116_D133_S0.130470.554
31_A51_A0.130130.553
67_P171_A0.130030.552
77_V149_V0.130020.552
79_L92_A0.129940.552
32_L49_Q0.129530.550
151_V155_V0.129160.549
23_F144_G0.129130.548
49_Q181_L0.128880.547
23_F140_S0.128730.547
62_I152_I0.128460.546
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
3iyzA0.97361000.006
3cn5A0.98681000.008
2zz9A0.97361000.018
1j4nA0.99121000.03
3d9sA0.95591000.033
3gd8A0.95591000.035
1ldfA0.97361000.046
2b6oA0.95591000.052
3llqA0.96041000.054
2w2eA0.97361000.056

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