GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SIS_2 - SIS domain
Pfam: PF13580 (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: CL0067
Length: 138
Sequences: 2638
Seq/Len: 19.12
HH_delta: 0.21 (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_A134_I1.191134.107
101_I131_M0.899883.103
31_A106_V0.861492.970
41_C107_L0.838872.892
123_A133_V0.823472.839
125_E128_E0.785952.710
27_L132_K0.75582.606
31_A132_K0.687732.371
101_I107_L0.567171.955
121_E124_E0.540451.863
41_C122_A0.53571.847
125_E129_R0.532511.836
109_V123_A0.530911.830
36_G104_G0.515041.776
72_A75_D0.49691.713
40_V53_F0.475031.638
22_E26_D0.453921.565
17_Q20_A0.451071.555
28_I106_V0.446621.540
109_V119_V0.441081.521
126_A131_M0.428931.479
40_V108_I0.419961.448
31_A36_G0.414841.430
89_E124_E0.400111.379
20_A23_K0.395751.364
64_N85_L0.392851.354
34_N104_G0.390871.348
32_L38_I0.380231.311
44_G114_G0.369041.272
53_F57_L0.367711.268
30_E34_N0.365131.259
41_C119_V0.363681.254
124_E128_E0.359051.238
11_E15_E0.358011.234
32_L67_L0.352631.216
88_D91_F0.348311.201
110_I136_L0.348311.201
10_L13_V0.337531.164
107_L126_A0.33581.158
28_I38_I0.33351.150
73_L77_A0.331531.143
51_S55_A0.320551.105
36_G102_R0.318981.100
94_Q98_L0.313011.079
93_R97_A0.31211.076
55_A58_G0.311961.076
92_A122_A0.310581.071
89_E121_E0.310091.069
82_S85_L0.308681.064
52_H56_D0.306661.057
40_V50_A0.306171.056
106_V134_I0.305941.055
96_L125_E0.300961.038
57_L61_F0.300751.037
27_L106_V0.297221.025
90_G94_Q0.296351.022
23_K27_L0.293481.012
95_L118_N0.293391.012
86_E89_E0.291651.006
27_L31_A0.29151.005
19_E23_K0.291211.004
111_S114_G0.289830.999
103_P130_G0.288270.994
55_A59_G0.287130.990
82_S87_Y0.285360.984
43_N118_N0.285060.983
28_I134_I0.279170.963
24_A27_L0.278420.960
94_Q97_A0.277330.956
81_I85_L0.275870.951
101_I125_E0.274810.947
92_A125_E0.27240.939
124_E127_K0.272120.938
77_A80_A0.266690.919
23_K34_N0.265930.917
39_F95_L0.263380.908
27_L30_E0.262150.904
67_L97_A0.260770.899
39_F101_I0.258410.891
56_D112_N0.258350.891
109_V133_V0.257370.887
28_I32_L0.256230.883
46_S114_G0.255210.880
45_H56_D0.255150.880
65_R80_A0.251940.869
57_L68_L0.250820.865
23_K26_D0.247650.854
17_Q21_I0.247390.853
40_V54_A0.247240.852
51_S74_N0.24710.852
49_I56_D0.246330.849
57_L63_V0.24550.846
18_A21_I0.245430.846
26_D29_A0.243640.840
30_E132_K0.243530.840
80_A84_D0.242540.836
51_S77_A0.239970.827
126_A133_V0.239330.825
27_L134_I0.239170.825
59_G81_I0.23730.818
80_A83_N0.235270.811
127_K133_V0.234570.809
91_F95_L0.232910.803
92_A121_E0.229570.792
107_L131_M0.228190.787
120_I135_A0.227550.785
106_V132_K0.226880.782
45_H116_S0.22650.781
39_F71_I0.226010.779
49_I110_I0.224520.774
113_S116_S0.223880.772
49_I112_N0.222460.767
120_I124_E0.222380.767
54_A70_A0.222340.767
132_K135_A0.218290.753
43_N116_S0.217960.751
88_D117_P0.216690.747
22_E29_A0.21590.744
38_I108_I0.215510.743
117_P121_E0.215460.743
49_I52_H0.214770.740
72_A77_A0.214690.740
29_A33_R0.21340.736
45_H52_H0.211020.728
66_I69_P0.210570.726
77_A82_S0.209760.723
49_I109_V0.208510.719
11_E16_T0.207150.714
46_S116_S0.207080.714
30_E33_R0.206480.712
37_R69_P0.205690.709
45_H111_S0.205580.709
28_I108_I0.205340.708
53_F108_I0.204280.704
46_S110_I0.20150.695
46_S113_S0.201210.694
52_H83_N0.200740.692
36_G103_P0.200220.690
122_A126_A0.200170.690
83_N87_Y0.199550.688
48_A83_N0.198920.686
48_A51_S0.198640.685
25_A29_A0.198560.685
43_N112_N0.198090.683
127_K132_K0.197610.681
39_F69_P0.197310.680
24_A28_I0.194230.670
26_D30_E0.192730.664
63_V67_L0.190270.656
89_E96_L0.190240.656
36_G105_D0.189680.654
45_H49_I0.189260.653
43_N113_S0.188930.651
56_D113_S0.188560.650
34_N103_P0.187920.648
55_A80_A0.187680.647
18_A22_E0.186230.642
21_I25_A0.186180.642
87_Y90_G0.18590.641
111_S116_S0.184990.638
38_I106_V0.18390.634
125_E131_M0.183120.631
126_A130_G0.182120.628
20_A24_A0.181960.627
89_E92_A0.18020.621
37_R105_D0.177690.613
102_R105_D0.177520.612
46_S112_N0.17730.611
82_S86_E0.177120.611
22_E33_R0.176440.608
43_N47_A0.175580.605
16_T34_N0.174140.600
42_G45_H0.173160.597
93_R121_E0.172750.596
19_E22_E0.172230.594
77_A88_D0.171750.592
16_T30_E0.171490.591
44_G113_S0.171410.591
84_D88_D0.171080.590
96_L107_L0.170980.590
20_A27_L0.170170.587
55_A60_L0.169830.586
45_H112_N0.169110.583
81_I87_Y0.169060.583
24_A108_I0.169010.583
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
3trjA0.956599.80.21
3cvjA0.985599.80.229
2i2wA0.985599.70.256
1x92A0.956599.70.266
1tk9A0.978399.70.274
2xblA0.985599.70.278
2yvaA0.956599.70.281
1nriA0.992899.60.328
3etnA0.826199.60.33
4bb9A0.985599.60.333

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