GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Laminin_G_2 - Laminin G domain
Pfam: PF02210 (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: CL0004
Length: 128
Sequences: 3748
Seq/Len: 29.28
HH_delta: 0.058 (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
57_H73_D1.033944.994
53_D57_H0.866724.186
31_L59_V0.465532.249
12_Y23_S0.387791.873
97_Y102_P0.381171.841
33_V61_I0.368831.781
25_E32_V0.357951.729
97_Y100_G0.353821.709
33_V68_V0.335741.622
24_L61_I0.331051.599
60_S71_T0.322381.557
24_L33_V0.321581.553
56_W121_R0.319351.542
61_I68_V0.316861.530
27_V32_V0.310611.500
53_D73_D0.295861.429
13_I22_L0.295711.428
115_G119_C0.293611.418
11_L22_L0.288471.393
22_L33_V0.284581.375
62_S69_T0.281521.360
9_L12_Y0.279841.352
5_S8_G0.27941.350
30_R46_F0.277331.340
26_L29_G0.274081.324
100_G119_C0.270371.306
30_R47_S0.270371.306
51_L72_V0.265131.281
69_T79_S0.264171.276
71_T76_S0.259831.255
76_S79_S0.259581.254
61_I70_L0.258891.250
63_R66_N0.257031.241
79_S86_S0.255481.234
7_N27_V0.246561.191
15_S92_P0.244451.181
98_I123_L0.242421.171
82_L85_S0.235931.140
116_F120_I0.233351.127
52_N57_H0.233251.127
71_T77_V0.232381.122
12_Y21_F0.232311.122
25_E34_R0.231951.120
11_L24_L0.230741.114
67_R81_S0.229991.111
35_Y63_R0.227681.100
9_L23_S0.220971.067
37_L63_R0.218581.056
36_N41_E0.217081.049
91_D94_G0.216581.046
6_P52_N0.214561.036
71_T119_C0.210881.019
40_S43_V0.209331.011
26_L51_L0.207761.004
11_L96_L0.207091.000
64_D67_R0.2071.000
49_S75_Q0.199840.965
5_S64_D0.199360.963
45_T80_E0.198350.958
8_G77_V0.197510.954
5_S18_N0.197050.952
32_V44_T0.195910.946
66_N86_S0.195720.945
41_E46_F0.194720.941
51_L57_H0.190250.919
80_E85_S0.189620.916
89_S92_P0.189320.914
10_L13_I0.187960.908
64_D69_T0.185020.894
51_L60_S0.183130.885
21_F34_R0.18170.878
42_I45_T0.18160.877
43_V66_N0.179420.867
41_E45_T0.177230.856
6_P49_S0.176630.853
12_Y15_S0.176540.853
40_S67_R0.175720.849
62_S83_P0.173970.840
57_H72_V0.173570.838
83_P89_S0.173190.837
35_Y68_V0.173130.836
53_D119_C0.172860.835
35_Y43_V0.17280.835
37_L90_L0.172740.834
17_D91_D0.172550.833
37_L40_S0.17150.828
85_S89_S0.171230.827
80_E84_S0.171060.826
11_L14_G0.168460.814
103_E106_Q0.167570.809
105_N120_I0.167530.809
31_L35_Y0.167040.807
35_Y92_P0.166840.806
9_L100_G0.166430.804
34_R103_E0.166270.803
32_V45_T0.165970.802
30_R63_R0.165470.799
69_T76_S0.165350.799
56_W59_V0.165280.798
21_F38_G0.164520.795
11_L62_S0.16410.793
120_I125_V0.163820.791
48_N78_S0.163520.790
82_L86_S0.162040.783
77_V80_E0.161720.781
34_R43_V0.161520.780
25_E113_T0.160670.776
67_R79_S0.16020.774
23_S96_L0.159820.772
29_G50_N0.159290.769
21_F97_Y0.158460.765
7_N114_P0.158290.765
60_S74_G0.158210.764
71_T78_S0.157050.759
15_S18_N0.156960.758
78_S93_D0.156940.758
6_P50_N0.156470.756
5_S55_Q0.156010.754
14_G18_N0.155860.753
81_S85_S0.155550.751
43_V46_F0.155350.750
41_E82_L0.15490.748
13_I92_P0.154680.747
26_L100_G0.153770.743
47_S74_G0.153450.741
50_N67_R0.153080.739
86_S94_G0.152330.736
30_R51_L0.151560.732
50_N54_G0.150870.729
65_G94_G0.150370.726
14_G21_F0.14940.722
64_D91_D0.149350.721
49_S79_S0.148680.718
11_L123_L0.147560.713
86_S92_P0.147540.713
74_G78_S0.14750.712
14_G41_E0.147350.712
16_E58_K0.146780.709
104_S113_T0.146530.708
76_S115_G0.146090.706
80_E86_S0.145820.704
116_F125_V0.14560.703
41_E44_T0.14490.700
22_L61_I0.144470.698
15_S123_L0.143890.695
25_E36_N0.142740.689
12_Y115_G0.140760.680
58_K122_D0.140550.679
13_I56_W0.140010.676
94_G117_V0.139510.674
14_G96_L0.139470.674
72_V98_I0.13920.672
78_S83_P0.139110.672
84_S89_S0.139010.671
63_R68_V0.13780.666
115_G121_R0.137670.665
18_N24_L0.137330.663
50_N105_N0.137220.663
62_S72_V0.136940.661
92_P115_G0.136320.658
13_I63_R0.135990.657
7_N28_D0.13530.654
58_K74_G0.134850.651
58_K98_I0.134670.650
94_G97_Y0.134620.650
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
1h30A0.984499.80.058
3sh4A0.984499.80.066
1pz7A0.984499.80.067
2jd4A0.984499.70.069
1dykA0.976699.70.071
1d2sA0.953199.70.072
1f5fA0.992299.70.074
2jd4A0.984499.70.074
3v64A0.984499.70.076
3qcwA0.992299.70.079

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