GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
tRNA_anti-codon - OB-fold nucleic acid binding domain
Pfam: PF01336 (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: CL0021
Length: 75
Sequences: 13432
Seq/Len: 179.09
HH_delta: 0.159 (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
4_E52_R2.243632.921
2_T54_R2.113022.751
54_R71_K2.034622.649
31_V69_V1.763322.296
58_K68_I1.61432.102
52_R73_E1.598582.081
46_K49_D1.47061.915
5_G22_L1.468871.913
8_T28_S1.457661.898
56_K70_P1.386151.805
31_V53_V1.381871.799
21_T28_S1.358711.769
9_S21_T1.355231.765
20_F31_V1.324471.725
4_E50_I1.258861.639
2_T52_R1.190621.550
8_T23_E1.168851.522
20_F33_F1.123231.462
7_V20_F1.108151.443
56_K68_I1.082991.410
60_Y66_E1.081831.409
17_I32_V1.071731.395
23_E28_S1.008161.313
6_R50_I0.969741.263
21_T30_Q0.962961.254
49_D74_I0.945741.231
19_F30_Q0.936461.219
24_D27_G0.912741.188
45_L72_I0.908061.182
15_G35_N0.883131.150
29_I67_L0.876211.141
34_F68_I0.802851.045
10_I46_K0.785211.022
57_V65_L0.774481.008
7_V51_V0.765970.997
55_G67_L0.751420.978
57_V67_L0.746680.972
33_F69_V0.741220.965
59_R65_L0.731640.953
32_V66_E0.726690.946
7_V45_L0.716570.933
37_E40_R0.704710.918
9_S47_E0.702140.914
22_L51_V0.697230.908
29_I55_G0.683790.890
36_E40_R0.670420.873
3_V22_L0.664210.865
33_F72_I0.660070.859
23_E48_G0.647240.843
30_Q66_E0.642370.836
40_R44_K0.638710.832
10_I47_E0.617710.804
38_Y41_F0.614090.800
35_N39_E0.606040.789
32_V60_Y0.603230.785
3_V67_L0.602930.785
10_I13_S0.596520.777
10_I20_F0.59530.775
3_V29_I0.59490.775
37_E41_F0.593370.773
41_F45_L0.590840.769
5_G31_V0.590180.768
19_F32_V0.587580.765
6_R23_E0.587530.765
41_F44_K0.581920.758
58_K66_E0.579580.755
40_R43_E0.57770.752
8_T21_T0.574690.748
26_T29_I0.564640.735
69_V72_I0.554560.722
22_L29_I0.551340.718
39_E42_R0.540530.704
20_F45_L0.535220.697
1_V67_L0.534760.696
7_V10_I0.529020.689
16_K35_N0.528470.688
32_V68_I0.526860.686
36_E39_E0.526690.686
53_V69_V0.522080.680
10_I18_V0.511890.667
5_G53_V0.510850.665
13_S16_K0.505260.658
3_V53_V0.475180.619
54_R73_E0.470090.612
22_L53_V0.469760.612
18_V38_Y0.466590.608
60_Y63_G0.46530.606
59_R62_G0.462370.602
22_L31_V0.459650.598
24_D62_G0.454840.592
38_Y42_R0.44920.585
39_E43_E0.447240.582
1_V57_V0.446050.581
1_V55_G0.441820.575
20_F69_V0.430150.560
17_I34_F0.425120.554
33_F38_Y0.418360.545
54_R70_P0.40610.529
15_G39_E0.405810.528
41_F72_I0.397620.518
45_L51_V0.394260.513
35_N38_Y0.392580.511
18_V41_F0.390150.508
5_G29_I0.389940.508
6_R48_G0.387580.505
15_G36_E0.385050.501
12_R17_I0.383630.500
5_G51_V0.381490.497
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
4joiA0.973398.60.159
2hpiA0.973398.50.17
4gopB0.973398.50.174
2pi2A0.973398.50.185
3kdfD0.973398.40.19
4h02A198.40.198
3bjuA198.40.208
4gnxB0.973398.40.211
3a74A0.986798.30.232
4ex5A0.986798.30.235

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