GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GNVR - G-rich domain on putative tyrosine kinase
Pfam: PF13807 (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: 82
Sequences: 2676
Seq/Len: 32.63
HH_delta: 0.795 (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
26_R29_E0.80692.933
18_E21_E0.647542.354
57_K60_L0.639992.326
17_R21_E0.632042.298
73_G77_A0.578412.103
10_Q14_E0.569732.071
14_E18_E0.560632.038
16_K19_L0.511491.859
58_R61_I0.492951.792
65_G69_G0.491491.787
28_E31_R0.488361.775
60_L64_L0.474581.725
20_Y24_L0.470621.711
27_Y31_R0.448141.629
14_E17_R0.447561.627
15_I24_L0.41311.502
76_L80_R0.407951.483
6_Y10_Q0.387251.408
8_R12_D0.344351.252
23_L32_L0.336451.223
33_S38_V0.330491.201
52_K59_A0.328151.193
24_L28_E0.317951.156
33_S36_S0.316961.152
61_I64_L0.313331.139
10_Q13_V0.306681.115
69_G73_G0.295381.074
22_T26_R0.293291.066
67_F71_I0.291811.061
74_I78_F0.28981.053
28_E32_L0.286341.041
18_E25_Q0.285531.038
26_R33_S0.283731.031
31_R34_K0.280071.018
25_Q29_E0.277721.010
20_Y42_R0.270130.982
56_P61_I0.264270.961
7_L10_Q0.264120.960
27_Y30_A0.263260.957
53_P58_R0.262540.954
29_E33_S0.26160.951
77_A81_E0.259810.944
26_R36_S0.256750.933
20_Y26_R0.255020.927
23_L45_D0.254480.925
72_L75_G0.252680.919
66_L70_L0.251330.914
55_S61_I0.251280.913
58_R62_L0.249250.906
35_A38_V0.249090.905
50_P53_P0.247590.900
22_T29_E0.246350.896
16_K28_E0.242240.881
11_R17_R0.241370.877
15_I18_E0.236870.861
9_L12_D0.23630.859
74_I77_A0.236140.858
61_I65_G0.230270.837
43_I46_P0.224140.815
69_G76_L0.22070.802
19_L32_L0.219660.798
13_V17_R0.218850.796
42_R47_A0.218040.793
59_A63_A0.216050.785
66_L71_I0.216030.785
32_L35_A0.214990.782
13_V40_N0.214260.779
70_L74_I0.213320.775
30_A40_N0.212360.772
15_I28_E0.206080.749
23_L33_S0.204980.745
53_P56_P0.204570.744
6_Y27_Y0.204440.743
61_I68_L0.204170.742
24_L69_G0.203860.741
39_S47_A0.202410.736
13_V16_K0.201350.732
52_K57_K0.200660.729
22_T78_F0.200620.729
41_V47_A0.198930.723
66_L73_G0.197310.717
19_L22_T0.196940.716
12_D16_K0.195830.712
30_A41_V0.195790.712
44_V55_S0.195120.709
20_Y41_V0.195010.709
22_T25_Q0.194610.707
27_Y32_L0.193960.705
59_A62_L0.193360.703
24_L35_A0.190480.692
16_K27_Y0.189970.691
36_S41_V0.189520.689
72_L80_R0.186470.678
36_S39_S0.186320.677
59_A67_F0.186310.677
63_A66_L0.186170.677
67_F74_I0.185510.674
16_K48_I0.184520.671
21_E25_Q0.184520.671
6_Y41_V0.183920.669
46_P71_I0.181740.661
55_S58_R0.18080.657
30_A39_S0.180720.657
63_A70_L0.180350.656
15_I47_A0.178790.650
55_S59_A0.17850.649
60_L67_F0.178310.648
47_A50_P0.177780.646
25_Q32_L0.177750.646
66_L75_G0.177480.645
37_N45_D0.177410.645
71_I78_F0.176740.642
29_E39_S0.176720.642
51_D79_L0.176270.641
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
4e29A0.682951.90.795
2j7aC0.4268240.828
3orgA0.37821.30.832
3nd0A0.62214.30.844
3w03C0.353713.30.846
3hd7B0.951211.50.85
1ik9A0.70739.80.855
2kncB0.40249.50.855
3bj4A0.35379.10.856
2kluA0.39028.80.857
If you are interested in a protein containing this domain,
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