GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Beta-Casp - Beta-Casp domain
Pfam: PF10996 (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. )
Length: 126
Sequences: 1315
Seq/Len: 10.44
HH_delta: 0.091 (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_D109_N0.430492.888
117_Q123_G0.421292.827
113_F126_L0.374552.513
119_P124_R0.277951.865
1_A25_V0.275291.847
103_L109_N0.269551.809
8_L23_I0.26361.769
10_E14_E0.261361.754
89_G115_G0.253651.702
22_P80_G0.253331.700
78_L82_K0.250471.681
104_A111_I0.209861.408
70_D73_K0.204471.372
118_A121_T0.2031.362
21_V81_P0.197651.326
27_S95_R0.197071.322
31_A66_V0.196961.322
72_S99_Y0.196351.317
26_D99_Y0.194791.307
55_K58_N0.193811.300
100_L104_A0.193571.299
68_S71_E0.192941.295
84_V103_L0.191271.283
2_Q37_Y0.188961.268
111_I125_R0.185821.247
5_L63_F0.183731.233
92_E122_L0.180081.208
93_G97_R0.179611.205
99_Y103_L0.179521.204
5_L85_I0.178931.201
66_V75_L0.17841.197
87_S93_G0.177271.189
91_L96_S0.176761.186
84_V99_Y0.175751.179
22_P81_P0.174561.171
1_A30_A0.172241.156
2_Q90_M0.1721.154
90_M116_Y0.171631.152
86_A94_G0.170281.143
27_S72_S0.168281.129
26_D95_R0.167931.127
25_V31_A0.167351.123
90_M115_G0.165471.110
76_N98_H0.164451.103
2_Q116_Y0.162251.089
88_S115_G0.162031.087
22_P64_K0.160841.079
87_S92_E0.16081.079
8_L12_W0.160361.076
59_P63_F0.160021.074
32_K67_K0.159731.072
90_M123_G0.159241.068
46_E50_R0.15691.053
103_L106_D0.15691.053
28_P95_R0.155311.042
82_K103_L0.150821.012
25_V87_S0.150791.012
3_E91_L0.150151.007
89_G116_Y0.149911.006
7_I11_Y0.149761.005
4_L8_L0.149711.004
76_N103_L0.148470.996
35_E38_K0.14810.994
90_M93_G0.146720.984
101_K105_S0.146610.984
107_P119_P0.146250.981
86_A103_L0.146020.980
37_Y106_D0.145530.976
11_Y15_G0.145320.975
115_G123_G0.144660.971
3_E48_I0.1420.953
50_R54_D0.1420.953
27_S30_A0.141670.951
2_Q89_G0.14160.950
11_Y96_S0.141250.948
99_Y123_G0.140740.944
84_V94_G0.139810.938
12_W21_V0.139610.937
52_F58_N0.138190.927
37_Y93_G0.138150.927
1_A92_E0.137990.926
13_K125_R0.137560.923
35_E39_S0.13740.922
29_M89_G0.137320.921
45_S48_I0.136090.913
12_W20_D0.135650.910
3_E12_W0.135570.910
89_G93_G0.135380.908
50_R107_P0.135040.906
10_E59_P0.133210.894
79_S82_K0.133180.894
14_E59_P0.132840.891
9_D60_F0.13230.888
72_S98_H0.132260.887
4_L12_W0.132120.886
67_K71_E0.130950.879
42_E64_K0.130910.878
100_L122_L0.130730.877
13_K54_D0.130490.876
36_Y40_Y0.130340.875
38_K41_P0.130280.874
41_P44_L0.130190.874
121_T126_L0.12980.871
25_V30_A0.129190.867
17_L22_P0.129110.866
62_N83_V0.128240.860
24_Y78_L0.128090.859
54_D67_K0.127990.859
54_D58_N0.127260.854
51_K84_V0.127130.853
26_D93_G0.127120.853
7_I91_L0.126260.847
2_Q115_G0.126220.847
97_R122_L0.125570.843
37_Y42_E0.125520.842
9_D22_P0.125430.842
4_L9_D0.124940.838
74_E119_P0.124910.838
60_F63_F0.12470.837
111_I126_L0.124690.837
28_P84_V0.124410.835
116_Y119_P0.124390.835
24_Y75_L0.124160.833
24_Y99_Y0.123490.829
72_S76_N0.123470.828
13_K53_E0.123230.827
72_S95_R0.1230.825
87_S95_R0.1230.825
102_R105_S0.1230.825
100_L118_A0.12260.823
31_A73_K0.122330.821
26_D84_V0.122050.819
43_W91_L0.121770.817
2_Q29_M0.121370.814
39_S42_E0.12130.814
90_M117_Q0.120980.812
35_E67_K0.120750.810
40_Y45_S0.120330.807
37_Y116_Y0.120160.806
16_K119_P0.119580.802
35_E49_Q0.119540.802
79_S109_N0.11910.799
66_V71_E0.118950.798
31_A85_I0.11890.798
96_S100_L0.118730.797
42_E53_E0.118480.795
33_V36_Y0.117670.790
50_R67_K0.117080.786
91_L124_R0.117040.785
44_L48_I0.116690.783
17_L78_L0.116430.781
100_L111_I0.116430.781
12_W16_K0.11590.778
12_W82_K0.11580.777
3_E32_K0.115390.774
62_N65_F0.115380.774
102_R108_R0.115220.773
10_E13_K0.115160.773
78_L81_P0.114890.771
29_M93_G0.114720.770
4_L7_I0.114670.769
104_A109_N0.114560.769
93_G117_Q0.114530.768
66_V105_S0.114240.766
117_Q124_R0.114060.765
3_E60_F0.113770.763
117_Q120_G0.113760.763
12_W17_L0.113730.763
91_L111_I0.113180.759
33_V38_K0.113150.759
21_V24_Y0.113130.759
28_P87_S0.113040.758
3_E97_R0.113030.758
29_M116_Y0.112650.756
89_G123_G0.112020.752
6_L44_L0.111650.749
93_G99_Y0.111650.749
69_V98_H0.11130.747
60_F81_P0.110820.744
51_K83_V0.110530.742
22_P75_L0.110270.740
64_K68_S0.110230.740
51_K55_K0.109940.738
16_K107_P0.10990.737
31_A35_E0.109490.735
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
3iekA0.96831000.091
2i7tA0.968399.90.216
2xr1A0.984199.90.285
3af5A0.976299.90.289
2ycbA0.976299.90.299
2i7xA0.960399.90.323
3zq4A0.769898.50.7
3bk2A0.75498.30.718
2az4A0.738193.20.85
3sbxA0.539740.70.907

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