GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HEAT_2 - HEAT repeats
Pfam: PF13646 (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: CL0020
Length: 88
Sequences: 10369
Seq/Len: 117.83
HH_delta: 0.086 (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
17_R42_D1.450762.969
11_D16_V0.998572.044
41_K69_K0.90071.843
48_R73_D0.829151.697
53_R82_A0.820581.679
22_R50_A0.817981.674
42_D47_V0.801771.641
14_P44_D0.7931.623
37_I66_A0.789541.616
42_D51_A0.728631.491
25_G54_A0.70541.444
74_D79_V0.692541.417
64_I68_I0.690081.412
11_D20_A0.682641.397
35_A38_E0.673141.378
3_A6_Q0.651521.333
22_R53_R0.650361.331
10_N38_E0.649551.329
48_R74_D0.640921.312
21_A36_L0.637141.304
41_K66_A0.615991.261
18_A50_A0.605471.239
14_P18_A0.602381.233
32_A63_A0.590241.208
49_R82_A0.584331.196
66_A69_K0.57961.186
70_L83_A0.572291.171
3_A7_L0.569891.166
50_A53_R0.560511.147
22_R85_E0.558591.143
71_L84_A0.556851.140
19_E22_R0.553451.133
35_A39_L0.547071.120
34_P62_E0.536241.097
82_A85_E0.528311.081
33_I37_I0.526051.077
39_L51_A0.520881.066
53_R85_E0.51671.057
49_R53_R0.51561.055
5_L35_A0.508791.041
80_R84_A0.505561.035
56_G86_A0.504951.033
18_A22_R0.494651.012
77_E80_R0.494511.012
69_K72_Q0.487530.998
40_L51_A0.487110.997
39_L42_D0.484820.992
33_I60_D0.480350.983
45_P49_R0.477760.978
54_A58_I0.477220.977
24_L32_A0.472990.968
71_L83_A0.472710.967
39_L47_V0.469540.961
21_A25_G0.465310.952
17_R39_L0.462980.948
64_I87_L0.46190.945
66_A70_L0.459650.941
17_R47_V0.456860.935
28_G59_G0.456390.934
40_L66_A0.444120.909
65_P69_K0.443580.908
21_A39_L0.440550.902
52_A83_A0.440110.901
52_A70_L0.439980.900
65_P68_I0.438780.898
52_A86_A0.435420.891
46_M49_R0.431350.883
45_P76_D0.430150.880
19_E23_A0.429450.879
53_R57_R0.426960.874
34_P38_E0.423440.867
8_L24_L0.418240.856
26_E57_R0.412690.845
55_L63_A0.412250.844
37_I62_E0.411820.843
42_D48_R0.410870.841
67_L86_A0.409760.839
52_A67_L0.409450.838
7_L16_V0.404740.828
4_L20_A0.403960.827
49_R78_V0.403410.826
37_I63_A0.398720.816
14_P45_P0.398310.815
48_R51_A0.398120.815
33_I58_I0.397340.813
74_D83_A0.393320.805
10_N35_A0.390840.800
19_E50_A0.388870.796
81_E85_E0.388840.796
50_A82_A0.388630.795
67_L83_A0.387810.794
7_L11_D0.387510.793
19_E46_M0.387280.793
78_V81_E0.385280.789
50_A54_A0.385110.788
18_A49_R0.383830.786
25_G28_G0.381390.781
31_E62_E0.380860.779
40_L52_A0.376090.770
4_L23_A0.375930.769
45_P48_R0.374270.766
73_D83_A0.373930.765
40_L55_L0.372190.762
70_L73_D0.3660.749
34_P37_I0.363510.744
71_L87_L0.357840.732
21_A51_A0.356780.730
36_L54_A0.354460.725
48_R79_V0.354130.725
13_D16_V0.353820.724
37_I41_K0.351090.719
7_L20_A0.348910.714
82_A86_A0.344590.705
4_L7_L0.34310.702
56_G67_L0.342620.701
59_G63_A0.342060.700
48_R70_L0.341870.700
28_G58_I0.341360.699
52_A79_V0.341320.699
69_K73_D0.340890.698
11_D17_R0.333590.683
70_L79_V0.331130.678
22_R25_G0.330950.677
41_K70_L0.330460.676
15_Q46_M0.329670.675
44_D47_V0.324850.665
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
1te4A0.977398.90.086
3ltmA0.977398.80.121
1te4A0.965998.80.121
3ltjA0.977398.80.121
3ltmA0.977398.80.124
3ltjA0.977398.80.126
1oyzA0.977398.70.14
1oyzA0.954598.60.187
2vglB0.977398.40.245
4fddA0.977398.30.275

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