GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GHMP_kinases_C - GHMP kinases C terminal
Pfam: PF08544 (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: 85
Sequences: 4558
Seq/Len: 53.62
HH_delta: 0.113 (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
9_D12_L1.171142.526
66_C75_V1.110582.395
51_A64_A1.018212.196
3_K7_E0.910431.964
4_A12_L0.892121.924
18_N44_E0.884751.908
2_I6_A0.783811.691
43_A64_A0.782091.687
68_D71_D0.735591.587
38_E42_A0.726791.568
52_K63_F0.725241.564
14_G50_G0.70381.518
46_N78_A0.702691.516
40_K51_A0.679691.466
19_E22_E0.675621.457
12_L15_E0.674151.454
41_E45_E0.667771.440
77_E81_E0.663921.432
36_I62_V0.660711.425
76_A80_R0.656991.417
73_E76_A0.649371.401
54_S61_T0.641291.383
42_A82_H0.603961.303
37_D41_E0.599771.294
4_A16_L0.585521.263
4_A13_L0.585351.262
4_A9_D0.574711.240
17_M50_G0.558081.204
56_S60_P0.557521.202
42_A46_N0.556521.200
3_K6_A0.515461.112
71_D74_R0.504671.088
52_K60_P0.498671.076
38_E41_E0.493061.063
17_M63_F0.487971.052
74_R78_A0.486681.050
72_A76_A0.478231.031
73_E77_E0.471221.016
11_E15_E0.465051.003
40_K62_V0.464251.001
55_G59_G0.459640.991
78_A82_H0.454090.979
12_L16_L0.452050.975
21_Q40_K0.447540.965
32_L53_M0.44520.960
17_M52_K0.443010.955
78_A81_E0.442950.955
30_E37_D0.435450.939
20_N52_K0.434060.936
45_E78_A0.429580.927
43_A75_V0.420560.907
43_A48_A0.419220.904
40_K44_E0.412010.889
54_S63_F0.404210.872
38_E82_H0.391850.845
16_L20_N0.387140.835
35_E38_E0.38270.825
21_Q53_M0.375130.809
21_Q29_R0.374470.808
69_E73_E0.372520.803
74_R77_E0.365660.789
21_Q32_L0.362880.783
52_K56_S0.358910.774
33_T53_M0.352350.760
14_G49_L0.351410.758
36_I53_M0.346970.748
43_A62_V0.343390.741
51_A62_V0.342070.738
46_N75_V0.341670.737
44_E48_A0.339640.733
56_S61_T0.335370.723
39_L62_V0.335070.723
69_E72_A0.332950.718
66_C72_A0.332240.717
32_L37_D0.330480.713
55_G60_P0.329030.710
31_V52_K0.329010.710
42_A45_E0.328580.709
34_P38_E0.328560.709
45_E82_H0.326590.704
43_A47_G0.326150.703
53_M56_S0.32590.703
54_S64_A0.324940.701
43_A51_A0.322590.696
29_R33_T0.320820.692
20_N28_Y0.318160.686
18_N22_E0.317720.685
43_A79_L0.317060.684
22_E53_M0.316330.682
31_V60_P0.315050.680
9_D15_E0.314860.679
48_A75_V0.314280.678
77_E80_R0.314190.678
68_D72_A0.313150.675
35_E39_L0.312710.674
13_L65_L0.307890.664
54_S60_P0.307070.662
29_R56_S0.303320.654
49_L68_D0.302420.652
74_R81_E0.300780.649
22_E28_Y0.29940.646
46_N74_R0.2980.643
36_I63_F0.294420.635
21_Q60_P0.290680.627
22_E44_E0.28940.624
75_V78_A0.289060.623
5_L13_L0.288190.622
33_T36_I0.286230.617
69_E82_H0.285280.615
75_V79_L0.285120.615
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
3gonA0.988299.30.113
2a2cA0.964799.30.123
2pg9A0.988299.20.142
1pieA0.976599.20.144
3v2uC0.976599.20.147
3k85A0.988299.20.147
2cz9A0.976599.20.147
3k17A0.964799.20.162
1wuuA0.976599.10.171
4hacA0.964799.10.178

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