GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Nup35_RRM - Nup533540-type RNA recognition motif
Pfam: PF05172 (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: 100
Sequences: 15154
Seq/Len: 151.54
HH_delta: 0.078 (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
63_N66_S2.142072.571
31_T62_D2.071242.486
21_Q79_S1.958982.351
18_A21_Q1.931232.318
16_P81_S1.706012.048
33_L62_D1.546581.856
8_W60_T1.485481.783
68_Q88_P1.458771.751
64_P68_Q1.361371.634
12_F85_G1.357151.629
64_P88_P1.339981.608
29_F73_K1.292941.552
25_H76_T1.275221.531
77_I83_M1.204731.446
31_T66_S1.203971.445
75_G83_M1.201761.442
9_V71_L1.197571.437
23_L27_S1.194811.434
33_L60_T1.15451.386
62_D66_S1.129261.355
26_F59_I1.117451.341
36_F39_L1.086921.305
22_V57_I1.079561.296
17_S79_S1.069031.283
9_V67_A1.063641.277
19_S23_L1.063351.276
68_Q72_Q1.054381.265
24_R27_S1.028531.234
7_T67_A1.020471.225
67_A88_P1.016971.221
41_S50_I1.014811.218
34_E60_T1.014161.217
61_Y70_A0.988881.187
7_T60_T0.976031.171
11_V26_F0.967551.161
78_F84_V0.961841.154
16_P52_S0.956931.149
77_I80_G0.95611.148
39_L56_W0.952251.143
38_V53_G0.930761.117
25_H73_K0.906511.088
14_F57_I0.892911.072
15_P79_S0.885751.063
7_T64_P0.867581.041
69_R72_Q0.866161.040
25_H78_F0.853361.024
65_L69_R0.846881.016
8_W36_F0.814510.978
73_K76_T0.794280.953
16_P55_N0.769430.923
20_N24_R0.765910.919
41_S49_P0.741110.889
71_L88_P0.740940.889
87_K90_D0.732890.880
66_S70_A0.720620.865
26_F73_K0.71850.862
26_F70_A0.717860.862
12_F56_W0.709420.851
12_F87_K0.704450.845
30_G61_Y0.693750.833
26_F86_V0.692290.831
19_S38_V0.689360.827
32_I59_I0.688030.826
38_V57_I0.685930.823
7_T33_L0.685690.823
35_H38_V0.68210.819
32_I61_Y0.670390.805
25_H28_S0.664090.797
6_E88_P0.659020.791
74_N85_G0.651820.782
20_N23_L0.646690.776
13_G85_G0.646660.776
74_N86_V0.634530.762
6_E64_P0.63140.758
36_F40_R0.623860.749
8_W34_E0.621120.745
58_H89_C0.618590.742
35_H59_I0.603910.725
25_H84_V0.601280.722
8_W89_C0.576570.692
21_Q24_R0.573830.689
22_V35_H0.570060.684
10_T56_W0.565920.679
15_P81_S0.563040.676
65_L68_Q0.558620.670
35_H57_I0.555690.667
19_S35_H0.550480.661
11_V59_I0.549840.660
66_S69_R0.542780.651
71_L86_V0.540530.649
13_G81_S0.539980.648
11_V22_V0.53790.646
9_V70_A0.535050.642
9_V61_Y0.51510.618
21_Q25_H0.487710.585
71_L74_N0.487530.585
11_V86_V0.484620.582
39_L58_H0.480650.577
76_T84_V0.480440.577
39_L53_G0.477310.573
19_S40_R0.475990.571
64_P67_A0.46980.564
22_V38_V0.459120.551
75_G85_G0.454060.545
9_V88_P0.454010.545
10_T58_H0.452480.543
23_L35_H0.450010.540
13_G83_M0.440320.528
7_T88_P0.427880.514
10_T87_K0.42430.509
32_I35_H0.413920.497
71_L87_K0.412220.495
23_L32_I0.405790.487
29_F66_S0.39680.476
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
3pgwS0.9299.40.078
1s79A0.9199.30.086
2lxiA0.8799.30.086
2kxnB0.8799.30.088
3q2sC0.9299.30.089
2jwnA0.9299.30.09
2cq4A0.9299.30.098
1h2vZ0.9299.30.1
2kn4A0.9299.30.103
3s8sA0.9299.30.103

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