GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Calx-beta - Calx-beta domain
Pfam: PF03160 (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: 100
Sequences: 1605
Seq/Len: 16.05
HH_delta: 0.019 (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
48_Y66_G1.043823.755
74_E77_K1.012113.641
90_E93_E0.887963.195
86_D93_E0.68482.464
70_F77_K0.675282.429
33_V68_V0.674042.425
35_R38_G0.657592.366
60_D93_E0.617942.223
30_T80_N0.615852.216
86_D90_E0.548581.974
48_Y79_I0.519011.867
52_D61_Y0.505711.819
42_G72_P0.498041.792
32_T78_T0.492991.774
32_T76_S0.467331.681
15_F31_V0.460621.657
51_V98_R0.431811.554
81_I95_F0.42421.526
30_T78_T0.409771.474
46_V68_V0.401411.444
60_D90_E0.385321.386
16_S32_T0.372321.340
49_S98_R0.368781.327
52_D57_A0.366481.318
24_E90_E0.365521.315
43_P71_P0.363361.307
68_V77_K0.363351.307
17_S20_Y0.362591.304
57_A63_P0.356851.284
70_F74_E0.34751.250
62_S82_T0.342861.234
53_G94_T0.338861.219
35_R44_V0.337021.213
35_R39_S0.334591.204
55_A61_Y0.334171.202
45_T67_T0.324171.166
43_P72_P0.323691.165
47_N67_T0.318141.145
45_T69_T0.313781.129
43_P69_T0.291071.047
49_S65_S0.280941.011
46_V70_F0.276430.995
55_A60_D0.275420.991
34_T76_S0.271310.976
24_E93_E0.271010.975
51_V96_T0.268980.968
20_Y31_V0.259350.933
48_Y64_T0.258850.931
13_V46_V0.257320.926
50_T62_S0.25160.905
26_D85_D0.248580.894
52_D58_G0.241140.868
50_T61_Y0.240.863
31_V97_V0.239320.861
35_R70_F0.237870.856
53_G96_T0.236960.853
22_V29_V0.235990.849
50_T64_T0.235020.846
13_V44_V0.234150.842
24_E86_D0.232710.837
39_S42_G0.231710.834
28_T82_T0.227150.817
85_D91_G0.226460.815
28_T80_N0.223870.805
52_D55_A0.223820.805
85_D88_I0.222840.802
62_S65_S0.219710.790
22_V26_D0.219480.790
25_G85_D0.218180.785
83_I95_F0.214240.771
71_P77_K0.212350.764
33_V79_I0.211920.762
56_T59_S0.21110.759
31_V81_I0.199980.719
35_R42_G0.199130.716
35_R73_G0.197660.711
16_S34_T0.19720.709
22_V31_V0.19410.698
13_V42_G0.193990.698
52_D95_F0.190350.685
50_T63_P0.189670.682
14_S36_S0.186480.671
44_V69_T0.185580.668
16_S20_Y0.185520.667
12_T18_P0.185230.666
50_T57_A0.18480.665
41_D72_P0.183550.660
55_A90_E0.182850.658
38_G41_D0.180380.649
82_T88_I0.178610.643
14_S17_S0.176150.634
23_S30_T0.175640.632
24_E83_I0.175390.631
53_G87_D0.175140.630
58_G84_I0.174550.628
55_A58_G0.173640.625
20_Y29_V0.172810.622
15_F97_V0.169180.609
48_Y99_L0.168750.607
18_P29_V0.166840.600
79_I97_V0.164620.592
15_F83_I0.161760.582
54_T94_T0.16120.580
43_P75_T0.160570.578
23_S26_D0.159280.573
44_V47_N0.156630.564
66_G79_I0.154070.554
50_T55_A0.152950.550
35_R43_P0.150960.543
70_F99_L0.150920.543
91_G98_R0.14950.538
32_T49_S0.149470.538
13_V33_V0.149330.537
31_V85_D0.14820.533
14_S34_T0.14810.533
71_P74_E0.147760.532
29_V85_D0.14760.531
31_V95_F0.146310.526
18_P28_T0.145720.524
13_V70_F0.145680.524
41_D89_P0.145050.522
65_S78_T0.144450.520
17_S21_T0.144230.519
83_I90_E0.143460.516
37_G54_T0.142250.512
23_S49_S0.142250.512
57_A64_T0.140810.507
12_T91_G0.140710.506
24_E60_D0.140180.504
70_F79_I0.139940.503
94_T98_R0.139780.503
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
3rb5A0.9999.80.019
3us9A0.9999.80.022
3ginA199.80.041
2qvkA0.9499.80.057
3eadA0.9399.80.087
3e9tA0.9199.70.107
3rb5A0.9799.70.117
2lt9A0.9999.70.121
3fsoA0.9499.70.138
3us9A0.9899.70.151

Page generated in 0.0239 seconds.