GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RRM_2 - RNA recognition motif 2
Pfam: PF04059 (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: 97
Sequences: 15195
Seq/Len: 156.65
HH_delta: 0.016 (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
54_S57_A2.209572.592
14_T17_M2.004242.351
29_K53_T1.917592.249
17_M71_P1.7452.047
25_H64_A1.629331.911
31_D53_T1.609371.888
60_R64_A1.590691.866
55_P83_Y1.477871.733
11_N77_K1.46451.718
3_T51_N1.423131.669
59_I83_Y1.421861.668
7_R80_E1.410981.655
55_P59_I1.394671.636
58_A83_Y1.279161.500
36_P47_Y1.277381.498
25_H65_F1.266841.486
4_V62_Y1.259651.477
53_T57_A1.143121.341
19_I23_D1.1211.315
15_Q19_I1.111561.304
69_K78_V1.110181.302
4_V58_A1.105451.297
52_F61_F1.089761.278
32_F51_N1.089741.278
35_L44_N1.086051.274
59_I63_K1.075941.262
31_D51_N1.075431.261
10_P13_Y1.068481.253
20_Q23_D1.064081.248
22_L50_V1.043781.224
18_L48_A1.040841.221
6_I22_L1.027811.206
21_I68_K1.004251.178
70_W79_C0.996681.169
69_K76_K0.977671.147
67_G78_V0.972281.140
11_N43_C0.963191.130
12_K71_P0.939361.102
16_E20_Q0.932481.094
10_P71_P0.891281.045
5_M47_Y0.88471.038
62_Y83_Y0.878281.030
25_H28_G0.875641.027
29_K57_A0.874111.025
60_R63_K0.865191.015
21_I65_F0.862171.011
11_N46_G0.845950.992
7_R82_S0.844410.990
7_R47_Y0.833870.978
65_F68_K0.830780.974
35_L48_A0.823530.966
57_A60_R0.819210.961
36_P49_F0.806410.946
17_M20_Q0.788770.925
13_Y70_W0.779890.915
18_L33_F0.763550.896
28_G52_F0.746580.876
56_Q60_R0.733640.861
10_P77_K0.72830.854
15_Q35_L0.716450.840
66_N80_E0.705220.827
22_L65_F0.702870.824
22_L61_F0.690810.810
21_I70_W0.686680.805
21_I24_E0.684850.803
34_Y37_I0.682490.801
61_F65_F0.6780.795
38_D43_C0.667610.783
22_L81_I0.665640.781
13_Y71_P0.664130.779
13_Y17_M0.651460.764
33_F48_A0.649340.762
21_I79_C0.649120.761
9_I13_Y0.646850.759
62_Y81_I0.633930.744
76_K79_C0.616830.723
6_I18_L0.610390.716
30_Y52_F0.609460.715
3_T34_Y0.604240.709
8_N80_E0.587990.690
30_Y33_F0.581840.682
15_Q33_F0.581530.682
4_V61_F0.580790.681
49_F84_A0.580610.681
62_Y66_N0.577910.678
82_S85_R0.567610.666
16_E19_I0.566980.665
3_T32_F0.560780.658
8_N77_K0.559420.656
65_F81_I0.557390.654
4_V52_F0.557340.654
57_A61_F0.555710.652
3_T84_A0.535490.628
33_F50_V0.527260.618
6_I81_I0.525950.617
67_G80_E0.518310.608
9_I48_A0.514350.603
55_P58_A0.513870.603
6_I50_V0.507470.595
38_D45_L0.500630.587
71_P76_K0.498820.585
52_F57_A0.492560.578
8_N78_V0.487970.572
5_M49_F0.481060.564
56_Q59_I0.473470.555
30_Y50_V0.472150.554
17_M21_I0.466030.547
37_I42_K0.462360.542
38_D46_G0.459660.539
46_G77_K0.453220.532
36_P44_N0.450940.529
49_F82_S0.446080.523
22_L30_Y0.438770.515
64_A68_K0.436570.512
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
3q2sC0.938199.50.016
3n9uC0.938199.40.023
3pgwS0.938199.40.029
2m2bA0.927899.40.043
2kn4A0.917599.40.047
3p5tL0.907299.40.051
3s8sA0.917599.40.052
3ns6A0.907299.40.057
2leaA0.917599.40.059
1rk8A0.938199.40.059

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