GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CaMKII_AD - Calciumcalmodulin dependent protein kinase II Association
Pfam: PF08332 (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: CL0051
Length: 128
Sequences: 8079
Seq/Len: 63.12
HH_delta: 0.064 (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
20_D23_T1.964663.918
29_A120_V1.285292.563
25_A51_K1.258142.509
30_P47_L1.177442.348
86_G106_E1.172692.339
14_D18_T1.128472.251
111_Q120_V1.109522.213
15_A23_T0.985731.966
46_G49_F0.974291.943
17_Q67_T0.968171.931
88_Y104_A0.951111.897
8_L110_W0.914831.824
108_R122_H0.863141.721
21_P25_A0.850561.696
7_A11_R0.829661.655
6_A10_D0.818611.633
23_T26_K0.818511.632
51_K55_D0.814121.624
11_R23_T0.803681.603
109_V121_H0.791771.579
29_A113_R0.770471.537
22_E51_K0.751041.498
83_I109_V0.746411.489
28_Y122_H0.722311.441
11_R27_L0.718881.434
33_A50_H0.715481.427
76_L82_A0.708521.413
28_Y33_A0.697081.390
84_D110_W0.690321.377
29_A118_K0.689961.376
86_G108_R0.682431.361
113_R118_K0.676691.350
25_A47_L0.667111.330
113_R120_V0.666591.329
5_I112_K0.606451.209
48_E51_K0.605391.207
15_A27_L0.60531.207
48_E52_F0.604111.205
110_W119_I0.591451.180
81_A111_Q0.584131.165
22_E25_A0.578551.154
5_I82_A0.576991.151
81_A109_V0.575571.148
12_W27_L0.571731.140
12_W24_Y0.569151.135
47_L51_K0.567861.133
68_T89_T0.560661.118
15_A20_D0.554831.107
52_F56_H0.550391.098
73_H85_A0.542751.082
22_E26_K0.537951.073
28_Y50_H0.531591.060
45_E49_F0.524051.045
28_Y119_I0.517991.033
89_T103_Q0.514371.026
19_G58_L0.510541.018
11_R15_A0.507611.012
55_D59_A0.50611.009
49_F52_F0.505751.009
33_A121_H0.488640.975
31_D120_V0.483320.964
34_V121_H0.477260.952
13_N69_I0.474480.946
70_L87_V0.47390.945
85_A107_T0.473690.945
71_N87_V0.473420.944
78_G81_A0.467980.933
74_V84_D0.467270.932
5_I74_V0.462650.923
50_H54_F0.458990.915
9_F110_W0.458120.914
10_D14_D0.457520.912
44_R49_F0.456860.911
8_L27_L0.451650.901
14_D73_H0.450840.899
52_F55_D0.449250.896
13_N17_Q0.44810.894
9_F84_D0.445240.888
30_P118_K0.443550.885
34_V45_E0.437460.872
77_L83_I0.425460.849
88_Y106_E0.422980.844
108_R119_I0.413940.826
11_R26_K0.410930.820
83_I107_T0.410930.820
16_I67_T0.407980.814
107_T121_H0.407860.813
16_I24_Y0.403560.805
36_E121_H0.401270.800
87_V103_Q0.400010.798
29_A111_Q0.394430.787
9_F108_R0.391820.781
56_H59_A0.39160.781
85_A105_R0.389940.778
23_T27_L0.384970.768
111_Q121_H0.384660.767
46_G50_H0.384410.767
70_L89_T0.379530.757
21_P55_D0.378720.755
11_R14_D0.378290.754
36_E43_L0.376690.751
21_P24_Y0.37210.742
87_V105_R0.36910.736
25_A48_E0.368360.735
7_A10_D0.363810.726
20_D26_K0.363480.725
53_Y57_F0.353210.704
8_L112_K0.351110.700
12_W28_Y0.350990.700
14_D17_Q0.34960.697
10_D72_P0.348920.696
5_I8_L0.348480.695
15_A26_K0.347780.694
6_A72_P0.341980.682
115_G118_K0.341750.682
8_L119_I0.338610.675
110_W122_H0.337950.674
5_I9_F0.337280.673
8_L11_R0.336750.672
18_T23_T0.331110.660
47_L118_K0.3310.660
77_L81_A0.327130.652
12_W16_I0.324810.648
109_V120_V0.318270.635
10_D13_N0.316210.631
15_A18_T0.314330.627
31_D113_R0.312170.623
60_K64_G0.307830.614
60_K63_Q0.307550.613
86_G90_F0.306390.611
114_D118_K0.305640.610
5_I76_L0.30440.607
74_V82_A0.301320.601
88_Y108_R0.300180.599
24_Y54_F0.297020.592
12_W108_R0.291050.580
75_R83_I0.289840.578
72_P86_G0.289280.577
25_A50_H0.288690.576
22_E55_D0.287780.574
16_I21_P0.287040.572
59_A62_P0.2840.566
61_K95_K0.283370.565
72_P76_L0.283350.565
86_G110_W0.279840.558
13_N16_I0.27860.556
44_R53_Y0.273590.546
82_A112_K0.271970.542
9_F13_N0.271020.541
13_N122_H0.269890.538
35_F39_V0.26660.532
9_F119_I0.266540.532
19_G63_Q0.262090.523
92_F96_D0.261050.521
21_P51_K0.259620.518
62_P95_K0.258060.515
16_I106_E0.256410.511
81_A84_D0.25560.510
63_Q91_Q0.254940.508
34_V37_P0.253720.506
76_L79_D0.25320.505
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
3h51A0.968899.70.064
3f7sA0.968899.60.105
2ux0A0.992299.60.127
2f86B0.976699.60.128
3hx8A0.960999.50.146
3gzrA0.984499.50.161
3cu3A0.976699.50.17
4i4kA0.953199.50.179
3cnxA0.968899.50.179
3gwrA0.953199.50.184

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