GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
F5_F8_type_C - F58 type C domain
Pfam: PF00754 (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: CL0202
Length: 129
Sequences: 5535
Seq/Len: 42.91
HH_delta: 0.092 (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
72_E113_T1.730874.108
72_E82_T1.5053.572
43_D108_R1.3933.306
73_Y83_V1.161892.757
73_Y107_A1.115032.646
70_K82_T1.099062.608
70_K113_T1.022532.427
72_E111_R1.009092.395
74_S109_Y0.944062.240
41_Q111_R0.892432.118
20_A40_I0.864892.053
49_T106_K0.85732.035
76_D79_N0.844132.003
70_K115_T0.81981.946
35_D38_Q0.816341.937
22_D27_T0.73961.755
74_S80_W0.735831.746
47_P106_K0.718351.705
82_T85_S0.679351.612
17_A20_A0.658411.563
73_Y105_V0.654431.553
114_V124_V0.632431.501
43_D109_Y0.626881.488
54_S96_V0.605671.437
74_S77_G0.605061.436
68_S115_T0.577491.371
55_I126_I0.571941.357
30_C124_V0.568421.349
80_W111_R0.565481.342
47_P75_N0.560711.331
41_Q77_G0.55711.322
41_Q109_Y0.533061.265
20_A42_I0.523971.243
39_W113_T0.519411.233
44_L110_I0.514871.222
57_F66_P0.50351.195
28_A58_R0.502181.192
24_D27_T0.495491.176
50_I107_A0.486351.154
57_F65_R0.46741.109
73_Y110_I0.46351.100
51_S104_P0.442631.050
52_G98_T0.439491.043
69_F86_Q0.438911.042
52_G101_F0.43241.026
31_S38_Q0.427341.014
53_I84_A0.425231.009
49_T104_P0.424871.008
21_F42_I0.42461.008
20_A126_I0.4231.004
74_S78_S0.417950.992
53_I69_F0.417530.991
66_P69_F0.417170.990
112_I127_A0.410740.975
44_L48_Y0.404390.960
75_N107_A0.402510.955
30_C58_R0.401250.952
99_I102_F0.396530.941
68_S85_S0.393340.933
41_Q80_W0.392450.931
39_W111_R0.389050.923
44_L50_I0.387250.919
28_A125_S0.386480.917
47_P108_R0.385080.914
93_S97_V0.383150.909
74_S79_N0.381070.904
23_G128_E0.369840.878
58_R61_G0.369820.878
54_S98_T0.368840.875
53_I71_I0.363910.864
38_Q123_W0.361450.858
44_L109_Y0.36060.856
107_A110_I0.352860.837
76_D109_Y0.349550.830
92_N95_S0.346470.822
81_T105_V0.34640.822
75_N81_T0.345130.819
71_I112_I0.341760.811
76_D80_W0.341390.810
17_A21_F0.334560.794
73_Y81_T0.333650.792
25_P56_Q0.330790.785
56_Q96_V0.329660.782
71_I110_I0.327410.777
74_S108_R0.324580.770
70_K85_S0.322640.766
41_Q74_S0.320490.761
57_F114_V0.317460.753
30_C63_N0.294030.698
28_A127_A0.289620.687
30_C123_W0.289190.686
19_N22_D0.288470.685
37_P113_T0.285160.677
29_W32_N0.284750.676
95_S98_T0.282820.671
120_N124_V0.281810.669
30_C125_S0.279570.663
58_R127_A0.278760.662
17_A22_D0.278420.661
55_I112_I0.277610.659
123_W126_I0.276310.656
77_G80_W0.272840.648
57_F126_I0.270580.642
101_F104_P0.26860.637
94_G97_V0.266760.633
69_F84_A0.265640.630
52_G99_I0.265110.629
102_F105_V0.264650.628
66_P124_V0.262780.624
57_F69_F0.259490.616
66_P114_V0.259460.616
53_I110_I0.258550.614
96_V100_S0.258370.613
71_I83_V0.258020.612
80_W109_Y0.256350.608
48_Y51_S0.255030.605
55_I69_F0.254830.605
58_R125_S0.251880.598
45_G108_R0.25180.598
69_F99_I0.25030.594
83_V105_V0.247150.587
37_P115_T0.243270.577
54_S99_I0.243170.577
89_G92_N0.241740.574
62_N93_S0.237860.564
22_D128_E0.237510.564
90_N97_V0.233920.555
29_W40_I0.233450.554
75_N106_K0.232660.552
21_F128_E0.232280.551
18_S21_F0.231520.549
44_L108_R0.230730.548
31_S123_W0.230380.547
97_V101_F0.228420.542
53_I112_I0.228050.541
40_I44_L0.227720.540
69_F114_V0.227430.540
55_I99_I0.22560.535
19_N24_D0.225520.535
28_A31_S0.224920.534
120_N123_W0.224340.532
27_T59_N0.222460.528
58_R63_N0.222290.528
21_F40_I0.221470.526
52_G100_S0.220810.524
30_C34_D0.220660.524
46_K108_R0.220570.523
27_T31_S0.21880.519
40_I126_I0.217240.516
40_I127_A0.215330.511
79_N82_T0.215320.511
46_K70_K0.21490.510
101_F105_V0.214770.510
121_N124_V0.214040.508
36_S115_T0.213190.506
100_S103_P0.210420.499
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
2zxqA0.984599.70.092
4a41A0.961299.70.099
4a3zA0.930299.70.132
3gglA0.976799.70.136
2v5dA0.96999.70.137
3f2zA0.976799.70.138
4a4aA0.90799.70.141
1k3iA0.945799.70.149
2j1aA0.96999.60.157
1w8oA0.96999.60.163

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