GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
dsrm - Double-stranded RNA binding motif
Pfam: PF00035 (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: 67
Sequences: 3672
Seq/Len: 54.81
HH_delta: -0.009 (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
2_K56_K1.56173.570
35_C55_A1.131892.587
36_T43_E1.013242.316
25_G28_H0.954112.181
32_R48_E0.85081.945
58_Q61_K0.8011.831
1_P64_L0.793481.814
44_Y63_A0.770121.760
34_I48_E0.725691.659
38_Y43_E0.723451.654
34_I46_E0.718431.642
61_K65_Q0.678721.551
1_P61_K0.666041.522
26_P29_H0.65681.501
50_S54_E0.656041.500
54_E58_Q0.636931.456
20_Y35_C0.6291.438
27_S31_P0.59471.359
36_T46_E0.594031.358
8_Y12_N0.577391.320
23_E31_P0.562361.285
3_S7_E0.559021.278
22_E34_I0.552121.262
62_K66_K0.534861.223
6_N10_Q0.527841.206
39_I44_Y0.519471.187
21_I36_T0.510091.166
51_S54_E0.49971.142
1_P57_Q0.490451.121
45_G63_A0.489621.119
3_S6_N0.474841.085
4_R64_L0.472821.081
28_H31_P0.465481.064
19_Y38_Y0.458181.047
58_Q62_K0.455411.041
37_V63_A0.451241.031
21_I35_C0.418770.957
19_Y36_T0.418480.957
49_G58_Q0.415520.950
49_G54_E0.415050.949
9_C14_F0.413290.945
2_K6_N0.410110.937
45_G66_K0.398040.910
45_G62_K0.392960.898
5_L37_V0.391760.895
24_E31_P0.372780.852
6_N16_P0.372480.851
47_G59_A0.371450.849
33_F53_K0.369190.844
24_E34_I0.364710.834
38_Y41_G0.352810.806
54_E57_Q0.352450.806
6_N56_K0.352110.805
9_C13_K0.343660.786
59_A63_A0.337660.772
29_H50_S0.33550.767
37_V45_G0.324470.742
53_K57_Q0.318450.728
7_E10_Q0.317940.727
22_E36_T0.317090.725
47_G62_K0.317060.725
38_Y44_Y0.30820.704
6_N18_Y0.306850.701
31_P52_K0.306520.701
25_G29_H0.305910.699
35_C56_K0.297560.680
1_P10_Q0.295860.676
25_G31_P0.289770.662
17_P20_Y0.288130.659
62_K65_Q0.284210.650
9_C39_I0.282520.646
1_P50_S0.28210.645
8_Y11_K0.282030.645
43_E46_E0.281980.645
9_C15_P0.277990.635
4_R61_K0.276930.633
10_Q16_P0.274980.629
42_K63_A0.274160.627
44_Y66_K0.274150.627
12_N29_H0.274090.626
29_H32_R0.271870.621
5_L67_L0.267810.612
14_F39_I0.267070.610
38_Y42_K0.265630.607
13_K16_P0.265530.607
24_E32_R0.264460.604
5_L64_L0.261790.598
7_E33_F0.261580.598
63_A66_K0.261390.597
63_A67_L0.260890.596
3_S10_Q0.256790.587
22_E46_E0.254670.582
23_E34_I0.253480.579
5_L60_A0.25160.575
38_Y63_A0.248720.569
3_S16_P0.247370.565
9_C44_Y0.246230.563
8_Y67_L0.245940.562
6_N60_A0.244790.560
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
1x49A0.985199.4-0.009
1qu6A0.985199.30
2l2nA0.985199.30
3adgA0.985199.30.003
3vyyA0.970199.30.009
1di2A0.970199.30.01
1ekzA0.970199.30.01
3adjA0.985199.30.01
3adlA0.970199.30.018
3llhA0.970199.30.021

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