GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Opacity - Opacity family porin protein
Pfam: PF02462 (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. )
Clan: CL0193
Length: 132
Sequences: 1854
Seq/Len: 14.05
HH_delta: 0.249 (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
106_Y122_H0.542083.046
56_G89_L0.526812.960
50_K94_Y0.459882.584
40_S87_G0.452682.544
54_Y105_G0.441372.480
9_R44_D0.419432.357
103_D127_G0.397952.236
100_L130_Y0.394812.218
14_Y35_Q0.392352.205
60_A85_G0.387952.180
96_I102_L0.378392.126
97_T100_L0.327031.838
108_Y122_H0.32051.801
54_Y91_G0.312631.757
5_F10_I0.304341.710
93_G103_D0.299031.680
51_F94_Y0.297361.671
13_D38_G0.290551.633
61_Y82_T0.290131.630
13_D40_S0.280771.578
93_G101_T0.280621.577
100_L128_V0.279521.571
9_R42_I0.259671.459
51_F92_V0.254881.432
58_R87_G0.247651.391
93_G129_R0.246021.382
95_D101_T0.244031.371
47_L52_K0.237341.334
8_W43_Y0.237151.332
4_D44_D0.234941.320
38_G87_G0.227211.277
105_G125_S0.21631.215
13_D107_R0.214881.207
11_A42_I0.21421.204
103_D129_R0.213281.198
40_S58_R0.20611.158
38_G58_R0.205031.152
43_Y46_D0.204291.148
104_A126_L0.20181.134
89_L105_G0.199721.122
47_L53_P0.19961.122
4_D7_D0.199141.119
36_S62_N0.197751.111
8_W41_A0.197631.110
102_L126_L0.190241.069
54_Y103_D0.189131.063
64_I83_K0.189121.063
56_G60_A0.183941.034
42_I107_R0.182741.027
99_N130_Y0.182471.025
101_T129_R0.181561.020
13_D87_G0.176210.990
49_S53_P0.16740.941
40_S56_G0.167010.938
36_S109_N0.166420.935
45_F55_I0.166130.933
11_A40_S0.164880.926
48_N79_N0.164730.926
56_G107_R0.162560.913
62_N85_G0.158340.890
101_T131_R0.156370.879
50_K55_I0.156070.877
37_L41_A0.155880.876
61_Y84_L0.154440.868
45_F86_L0.154440.868
87_G107_R0.152970.860
80_S83_K0.15140.851
5_F8_W0.151120.849
31_E80_S0.150930.848
95_D98_P0.150340.845
29_T32_V0.149310.839
44_D129_R0.149180.838
36_S40_S0.149090.838
47_L55_I0.148470.834
15_A54_Y0.148060.832
42_I93_G0.147830.831
38_G85_G0.147820.831
96_I128_V0.146420.823
50_K96_I0.145730.819
40_S107_R0.145150.816
123_E130_Y0.144780.813
59_V68_V0.142470.801
42_I56_G0.14220.799
89_L107_R0.14140.794
30_K79_N0.141280.794
97_T102_L0.140480.789
44_D93_G0.139820.786
2_G11_A0.139660.785
38_G60_A0.139540.784
52_K101_T0.139260.782
2_G9_R0.138730.779
30_K66_Y0.13770.774
4_D131_R0.137450.772
22_N30_K0.136390.766
37_L63_H0.136280.766
111_W121_T0.136150.765
19_K65_K0.134210.754
49_S97_T0.134030.753
100_L131_R0.133550.750
33_K126_L0.132670.745
52_K95_D0.131130.737
16_R35_Q0.131110.737
15_A20_W0.130970.736
121_T128_V0.13080.735
23_N28_N0.129560.728
15_A37_L0.129260.726
36_S111_W0.129010.725
9_R12_A0.128960.725
95_D125_S0.128740.723
21_N31_E0.128180.720
16_R19_K0.126960.713
96_I109_N0.126890.713
121_T125_S0.125090.703
45_F48_N0.124270.698
81_I84_L0.123770.695
36_S123_E0.123530.694
23_N68_V0.123510.694
63_H126_L0.122540.689
23_N39_L0.12220.687
108_Y120_K0.121550.683
31_E68_V0.121340.682
64_I82_T0.121040.680
53_P92_V0.120160.675
11_A89_L0.120080.675
96_I99_N0.119990.674
51_F130_Y0.11960.672
28_N33_K0.119430.671
56_G105_G0.119410.671
9_R107_R0.118470.666
48_N53_P0.118240.664
96_I100_L0.11790.662
66_Y79_N0.117530.660
11_A125_S0.117520.660
34_A41_A0.116280.653
59_V80_S0.116270.653
95_D131_R0.115870.651
84_L88_A0.115530.649
65_K80_S0.114960.646
34_A80_S0.11480.645
2_G44_D0.11430.642
80_S101_T0.114090.641
64_I111_W0.11360.638
122_H125_S0.113580.638
6_G43_Y0.112180.630
2_G60_A0.111980.629
82_T85_G0.111860.629
22_N79_N0.11180.628
67_T80_S0.110770.622
13_D56_G0.110290.620
58_R105_G0.110280.620
62_N111_W0.110170.619
94_Y104_A0.109950.618
84_L89_L0.109720.616
44_D87_G0.109670.616
83_K110_Y0.109450.615
63_H82_T0.109110.613
17_Y98_P0.108830.611
125_S131_R0.108790.611
51_F61_Y0.108440.609
87_G103_D0.108160.608
43_Y52_K0.107930.606
120_K126_L0.107790.606
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
1p4tA0.924299.70.249
2k0lA0.992499.60.288
2x27X199.60.296
3qraA0.924299.60.309
1qjpA0.954599.60.311
3nb3A0.954599.60.312
2f1vA0.992499.60.335
2jmmA0.863699.50.345
2lhfA0.909199.50.363
1ormA0.901599.40.385

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