GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SnoaL_4 - SnoaL-like domain
Pfam: PF13577 (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: CL0051
Length: 127
Sequences: 5532
Seq/Len: 43.56
HH_delta: 0.122 (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
24_D27_E1.723784.039
90_V108_G1.117732.619
115_V124_S1.042772.443
117_E120_G1.032532.419
34_E51_R0.992582.325
86_V114_L0.932852.186
12_L114_L0.912892.139
32_F36_A0.893422.093
50_G53_A0.87732.055
19_A27_E0.858762.012
29_A55_R0.83681.960
113_E125_S0.827681.939
18_R22_T0.824551.932
33_T124_S0.805671.888
27_E30_D0.767881.799
37_V125_S0.751791.761
36_A54_I0.737671.728
116_R121_W0.729181.708
7_A10_R0.715971.677
21_D70_H0.706141.654
33_T117_E0.686771.609
88_S110_Y0.66271.553
117_E122_R0.658881.544
15_R27_E0.649461.522
33_T122_R0.615181.441
10_R14_A0.603251.413
82_D116_R0.595961.396
29_A51_R0.59311.390
88_S112_D0.590581.384
85_T113_E0.584481.369
84_A121_W0.57551.348
83_T113_E0.560521.313
9_I84_A0.559461.311
11_D15_R0.556231.303
83_T115_V0.538881.263
55_R59_R0.533911.251
56_A60_A0.532621.248
25_W29_A0.530711.243
8_A116_R0.528221.238
114_L123_I0.511961.199
87_R111_T0.510841.197
19_A24_D0.502171.177
19_A31_L0.4991.169
9_I77_V0.494561.159
10_R75_P0.492051.153
15_R31_L0.487911.143
20_L28_W0.482081.129
52_D56_A0.482061.129
18_R76_V0.480261.125
26_E55_R0.47951.123
49_R53_A0.475161.113
74_N89_Y0.468931.099
33_T115_V0.465541.091
13_I114_L0.46131.081
75_P88_S0.459371.076
50_G54_I0.458271.074
80_D83_T0.450211.055
29_A52_D0.449681.054
16_Y31_L0.446061.045
87_R109_R0.441891.035
52_D55_R0.44021.031
13_I112_D0.438481.027
26_E29_A0.433541.016
16_Y32_F0.430871.009
93_T105_W0.424830.995
112_D123_I0.412580.967
79_V84_A0.411630.964
13_I86_V0.410720.962
32_F54_I0.405940.951
15_R19_A0.398150.933
59_R63_D0.391110.916
73_T89_Y0.390710.915
13_I88_S0.388220.910
53_A56_A0.385720.904
90_V110_Y0.381720.894
7_A11_D0.381660.894
54_I58_L0.38030.891
56_A59_R0.379330.889
32_F123_I0.37830.886
16_Y20_L0.376270.882
71_M91_L0.374910.878
37_V49_R0.368450.863
77_V84_A0.362270.849
28_W58_L0.361260.846
17_A72_V0.356840.836
51_R55_R0.351380.823
16_Y28_W0.350530.821
34_E117_E0.346210.811
117_E124_S0.345310.809
12_L123_I0.342250.802
111_T125_S0.339570.796
35_D124_S0.336670.789
85_T111_T0.335970.787
73_T91_L0.335580.786
12_L31_L0.33360.782
23_G62_F0.330120.773
9_I121_W0.329010.771
9_I114_L0.328560.770
91_L105_W0.328540.770
15_R30_D0.325760.763
17_A21_D0.319390.748
19_A30_D0.319050.747
27_E31_L0.318560.746
30_D122_R0.317630.744
113_E124_S0.311860.731
29_A54_I0.308850.724
78_D85_T0.307850.721
80_D85_T0.307680.721
89_Y109_R0.303760.712
18_R21_D0.298450.699
39_D125_S0.297510.697
25_W59_R0.296550.695
15_R120_G0.293910.689
9_I12_L0.289150.677
91_L107_G0.288960.677
38_F41_P0.285840.670
76_V87_R0.284360.666
51_R54_I0.284060.666
32_F38_F0.283240.664
12_L15_R0.27770.651
58_L61_R0.272310.638
65_F94_H0.271030.635
30_D51_R0.267470.627
22_T27_E0.266570.625
26_E30_D0.264580.620
26_E59_R0.259560.608
37_V47_R0.258980.607
48_Y57_F0.258480.606
8_A12_L0.258120.605
68_T94_H0.256260.600
33_T36_A0.25620.600
13_I123_I0.255970.600
14_A18_R0.250350.587
42_G61_R0.248350.582
86_V123_I0.248250.582
14_A17_A0.246430.577
24_D30_D0.246420.577
16_Y112_D0.241890.567
61_R65_F0.241220.565
35_D50_G0.239940.562
36_A51_R0.239890.562
53_A57_F0.238650.559
14_A74_N0.237290.556
34_E122_R0.231530.542
79_V82_D0.230540.540
68_T92_A0.229790.538
58_L62_F0.229650.538
93_T104_L0.227990.534
86_V112_D0.225880.529
90_V109_R0.224790.527
14_A75_P0.224620.526
16_Y110_Y0.224190.525
20_L106_S0.22340.523
25_W28_W0.220520.517
41_P58_L0.220420.516
114_L121_W0.220120.516
48_Y53_A0.219870.515
17_A90_V0.219670.515
18_R87_R0.218390.512
8_A11_D0.216290.507
25_W62_F0.215260.504
60_A63_D0.214510.503
88_S92_A0.213370.500
72_V88_S0.213020.499
7_A52_D0.211820.496
9_I13_I0.210360.493
10_R86_V0.210050.492
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
3b8lA0.984399.50.122
3ef8A0.976499.50.127
3a76A0.976499.50.132
2chcA0.952899.50.138
3ejvA199.50.14
3f7sA0.960699.50.154
3h51A0.968599.50.157
4gb5A199.50.158
2rfrA0.960699.50.172
3hx8A0.952899.40.184

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