GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DND1_DSRM - double strand RNA binding domain from DEAD END PROTEIN 1
Pfam: PF14709 (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: CL0196
Length: 80
Sequences: 3321
Seq/Len: 41.51
HH_delta: 0.089 (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
4_V68_K1.513123.397
26_E33_K1.074982.414
2_S5_S1.047162.351
22_E40_V1.044352.345
37_Y67_A1.023082.297
24_V38_K0.981322.203
23_L37_Y0.97692.193
28_G31_H0.965712.168
34_L60_P0.820891.843
38_K45_E0.816161.832
8_N21_Y0.787141.767
70_S73_Q0.773481.737
73_Q77_Q0.746721.677
46_Y75_A0.702761.578
3_A73_Q0.679831.526
25_S36_L0.627891.410
36_L60_P0.626041.406
30_D33_K0.609331.368
62_S66_E0.59951.346
22_E38_K0.598831.344
40_V45_E0.596411.339
11_C19_P0.574871.291
63_T66_E0.565131.269
27_S34_L0.564531.267
3_A76_L0.563561.265
66_E70_S0.557881.253
2_S69_E0.533211.197
36_L58_T0.518391.164
6_L76_L0.509611.144
8_N12_Q0.506351.137
39_V75_A0.506281.137
3_A69_E0.505541.135
5_S9_E0.504031.132
20_V40_V0.496851.116
23_L68_K0.466271.047
32_R62_S0.463871.041
10_L14_N0.45891.030
74_Q78_A0.457551.027
5_S8_N0.456821.026
46_Y78_A0.454011.019
27_S36_L0.430130.966
70_S74_Q0.421360.946
7_L39_V0.408370.917
35_F65_K0.4020.903
38_K58_T0.396380.890
11_C15_K0.392890.882
2_S8_N0.388350.872
47_P74_Q0.388330.872
28_G33_K0.378370.850
15_K19_P0.3480.781
6_L73_Q0.347580.780
65_K69_E0.34020.764
75_A78_A0.332180.746
40_V43_G0.329730.740
7_L79_L0.327710.736
10_L75_A0.325070.730
38_K47_P0.324080.728
8_N68_K0.313920.705
11_C41_I0.313510.704
5_S69_E0.311350.699
74_Q77_Q0.310090.696
17_G42_P0.309520.695
23_L26_E0.305610.686
4_V21_Y0.30560.686
31_H34_L0.30360.682
11_C16_W0.301160.676
19_P39_V0.298310.670
10_L13_K0.297410.668
14_N19_P0.290920.653
9_E12_Q0.288520.648
66_E69_E0.284230.638
37_Y68_K0.282580.634
16_W43_G0.281980.633
5_S12_Q0.279120.627
40_V75_A0.277180.622
21_Y72_A0.275510.619
44_L47_P0.267250.600
61_S66_E0.258160.580
4_V10_L0.255060.573
7_L76_L0.252350.567
75_A79_L0.251670.565
44_L75_A0.251160.564
15_K18_P0.249850.561
11_C18_P0.249710.561
4_V8_N0.248230.557
29_P32_R0.244090.548
59_K74_Q0.243180.546
61_S70_S0.239860.539
34_L62_S0.238250.535
40_V46_Y0.2370.532
47_P75_A0.235940.530
2_S12_Q0.235760.529
10_L79_L0.23390.525
10_L76_L0.232080.521
3_A65_K0.231020.519
4_V69_E0.229650.516
20_V44_L0.228770.514
10_L16_W0.227370.510
28_G35_F0.227160.510
8_N18_P0.226650.509
59_K71_A0.225540.506
23_L64_K0.224350.504
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
2cpnA0.862599.50.089
3adlA0.862599.50.093
2khxA0.87599.50.097
1uhzA0.862599.50.097
3adjA0.87599.50.1
2l2nA0.862599.50.103
1ekzA0.8599.50.11
3adgA0.862599.50.114
1x49A0.862599.50.118
1di2A0.8599.50.123

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