GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RRM_5 - RNA recognition motif (aka RRM RBD or RNP domain)
Pfam: PF13893 (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: CL0221
Length: 56
Sequences: 19872
Seq/Len: 354.86
HH_delta: -0.152 (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
10_E29_A2.42272.477
8_F40_Q2.36252.416
30_S33_D2.349482.402
12_K29_A2.044972.091
31_V55_Y1.973342.018
35_Q55_Y1.840981.882
8_F41_L1.71411.753
36_K40_Q1.603251.639
2_Y6_S1.546931.582
45_Q50_P1.546171.581
31_V35_Q1.499511.533
13_K27_E1.499151.533
5_F26_V1.493641.527
29_A33_D1.474141.507
3_K6_S1.412661.444
4_L44_R1.403631.435
17_F23_F1.349811.380
38_I55_Y1.316721.346
46_F51_L1.288751.318
43_G50_P1.269861.298
28_F37_A1.265051.294
12_K27_E1.239131.267
34_A55_Y1.208371.236
10_E33_D1.201221.228
35_Q39_E1.196431.223
45_Q48_G1.185931.213
4_L41_L1.152751.179
1_L24_A1.125421.151
41_L44_R1.033791.057
16_I24_A1.026591.050
36_K39_E1.002351.025
4_L7_K0.991831.014
15_K18_K0.97510.997
32_E36_K0.945060.966
17_F25_F0.941620.963
42_N52_K0.920670.941
19_K22_G0.885310.905
11_V26_V0.881020.901
2_Y14_I0.881010.901
38_I53_V0.839040.858
4_L46_F0.829050.848
9_G28_F0.826930.846
5_F53_V0.819020.837
33_D36_K0.817370.836
5_F37_A0.813090.831
11_V28_F0.811380.830
14_I26_V0.769720.787
42_N53_V0.764910.782
43_G52_K0.759840.777
14_I24_A0.758320.775
33_D37_A0.727790.744
22_G49_R0.703090.719
18_K22_G0.698020.714
19_K23_F0.664280.679
1_L14_I0.660390.675
38_I54_S0.651850.667
17_F21_R0.645350.660
11_V14_I0.643240.658
41_L53_V0.62530.639
5_F41_L0.612110.626
25_F54_S0.611210.625
27_E54_S0.593930.607
35_Q38_I0.582120.595
37_A41_L0.564670.577
17_F20_K0.560870.573
4_L51_L0.555980.568
16_I19_K0.554240.567
38_I42_N0.553820.566
28_F33_D0.546780.559
14_I17_F0.539920.552
32_E35_Q0.536940.549
34_A38_I0.523220.535
40_Q44_R0.523210.535
44_R51_L0.519220.531
47_N50_P0.516730.528
10_E30_S0.514310.526
23_F27_E0.510640.522
46_F49_R0.50250.514
28_F34_A0.497690.509
31_V34_A0.494130.505
1_L16_I0.491240.502
7_K44_R0.490050.501
24_A46_F0.479920.491
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
3tytA198.6-0.152
3pgwS198.5-0.126
3u1lA0.982198.5-0.118
2wbrA0.982198.5-0.118
3pgwA198.5-0.116
2i2yA198.5-0.111
3zzyA198.5-0.11
4fxwA198.5-0.107
2pe8A198.5-0.106
3s6eA198.5-0.106

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