GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RRM_1 - RNA recognition motif (aka RRM RBD or RNP domain)
Pfam: PF00076 (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: 70
Sequences: 24372
Seq/Len: 348.17
HH_delta: -0.17 (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
48_S51_D2.462292.557
24_K47_E2.44082.535
11_T14_E2.217762.303
22_F58_E2.21082.296
14_E65_N2.089572.170
26_E47_E1.880361.953
49_E53_E1.727681.794
54_K58_E1.717211.784
63_K68_K1.702291.768
8_P67_R1.701081.767
18_F62_K1.545731.605
22_F59_L1.541461.601
1_L56_L1.519481.578
27_S45_E1.505771.564
16_R20_S1.449941.506
31_M41_Y1.409981.464
46_F55_A1.375371.429
12_E16_R1.373951.427
26_E45_E1.360831.413
19_F44_V1.357771.410
47_E51_D1.325821.377
64_I69_I1.299921.350
17_D20_S1.268251.317
61_G68_K1.183221.229
59_L62_K1.129421.173
63_K66_G1.128971.173
2_Y41_Y1.105191.148
7_P10_V1.104811.148
3_V19_F1.099511.142
53_E57_E1.085351.127
24_K51_D1.079741.121
9_D65_N1.078261.120
1_L52_A1.074551.116
4_G41_Y1.073961.115
30_V38_S1.058791.100
54_K57_E1.052411.093
8_P37_K1.033121.073
31_M43_F1.0181.057
15_L42_A1.005151.044
13_E17_D0.994111.033
10_V64_I0.990721.029
18_F59_L0.981351.019
19_F59_L0.966721.004
50_E54_K0.962571.000
7_P65_N0.956960.994
30_V42_A0.949310.986
18_F21_Q0.90990.945
10_V65_N0.890340.925
19_F55_A0.884160.918
14_E17_D0.863780.897
25_I46_F0.861060.894
25_I44_V0.859340.893
29_K32_R0.832450.865
18_F64_I0.819550.851
6_L42_A0.81910.851
8_P40_G0.817090.849
51_D55_A0.803150.834
7_P67_R0.794750.825
10_V14_E0.776860.807
13_E16_R0.766040.796
23_G46_F0.754260.783
5_N67_R0.753690.783
28_I42_A0.749830.779
1_L55_A0.734820.763
12_E30_V0.704120.731
49_E52_A0.691790.719
3_V44_V0.691330.718
51_D54_K0.681090.707
14_E18_F0.672770.699
56_L60_N0.67050.696
28_I44_V0.66790.694
15_L28_I0.666920.693
55_A59_L0.665830.692
2_Y43_F0.645590.671
21_Q59_L0.635320.660
25_I28_I0.632750.657
12_E28_I0.619710.644
33_N36_G0.614570.638
6_L10_V0.613290.637
18_F69_I0.605890.629
33_N37_K0.602170.625
33_N39_K0.597310.620
52_A56_L0.563360.585
3_V15_L0.560580.582
62_K69_I0.548810.570
33_N40_G0.539260.560
32_R36_G0.538950.560
46_F51_D0.530810.551
23_G51_D0.530430.551
31_M38_S0.511990.532
5_N68_K0.511240.531
41_Y45_E0.507130.527
16_R28_I0.50640.526
32_R35_S0.499770.519
29_K45_E0.496810.516
15_L30_V0.494850.514
10_V15_L0.492190.511
50_E53_E0.491490.510
21_Q62_K0.490710.510
53_E56_L0.490160.509
22_F55_A0.489090.508
4_G43_F0.465460.483
28_I31_M0.454330.472
1_L46_F0.450420.468
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
3pgwS199.1-0.17
4f25A0.985799-0.153
3q2sC199-0.153
3n9uC199-0.144
3s8sA199-0.141
2hglA0.985799-0.131
2fy1A199-0.129
1s79A0.985799-0.128
2f3jA198.9-0.12
2kn4A198.9-0.12

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