GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_12 - Ribonuclease R winged-helix domain
Pfam: PF08461 (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: CL0123
Length: 66
Sequences: 46550
Seq/Len: 705.3
HH_delta: 0.156 (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
20_A32_E2.737562.289
6_I22_E2.617242.188
49_R57_I2.491792.084
15_G18_Q2.480182.074
43_E50_K2.413742.018
13_P57_I2.217261.854
49_R59_T2.199371.839
51_V57_I1.873611.567
39_L56_R1.669061.396
16_R36_R1.658531.387
50_K56_R1.647531.378
14_L22_E1.638471.370
36_R40_R1.580661.322
16_R32_E1.544681.292
13_P55_G1.527941.278
34_A38_R1.497251.252
13_P51_V1.495871.251
33_E37_R1.494741.250
8_A58_I1.455371.217
40_R43_E1.449591.212
33_E36_R1.417911.186
17_K21_E1.388721.161
6_I23_L1.381471.155
43_E48_T1.321311.105
16_R56_R1.303071.090
18_Q22_E1.299451.087
6_I14_L1.285031.075
14_L18_Q1.250261.045
3_I38_R1.237751.035
31_S34_A1.23741.035
6_I10_S1.23431.032
34_A37_R1.226731.026
41_A45_D1.22611.025
30_L34_A1.217611.018
17_K32_E1.215461.016
18_Q21_E1.214261.015
19_L39_L1.205661.008
10_S14_L1.202581.006
10_S22_E1.169960.978
51_V55_G1.128640.944
39_L48_T1.104790.924
43_E56_R1.096810.917
3_I35_V1.089180.911
40_R44_R1.008920.844
31_S37_R1.007720.843
4_L47_L0.996890.834
16_R35_V0.994370.831
30_L35_V0.991750.829
38_R41_A0.987970.826
17_K20_A0.969520.811
7_L14_L0.943090.789
32_E36_R0.941570.787
4_L8_A0.938350.785
17_K36_R0.934120.781
15_G55_G0.927230.775
20_A35_V0.923040.772
37_R40_R0.86780.726
16_R39_L0.860560.720
7_L48_T0.84180.704
3_I19_L0.812960.680
42_M47_L0.757690.634
6_I9_E0.744480.623
5_R8_A0.742180.621
23_L29_E0.740790.619
30_L41_A0.7220.604
3_I23_L0.70430.589
9_E12_K0.698070.584
40_R50_K0.696050.582
6_I19_L0.694240.581
19_L35_V0.693470.580
35_V39_L0.677750.567
50_K53_R0.673590.563
37_R41_A0.661890.553
5_R9_E0.646270.540
36_R52_G0.639780.535
46_G59_T0.638640.534
23_L30_L0.627350.525
20_A30_L0.616070.515
10_S18_Q0.603670.505
50_K54_Q0.602330.504
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
3hrsA0.909198.10.156
1on2A0.9091980.173
3b73A0.939497.90.186
2wteA0.909197.90.188
3fm5A0.924297.90.193
2h09A0.909197.90.198
2o0mA0.893997.90.201
3mq0A0.924297.80.209
2p8tA0.909197.80.211
4em2A0.909197.80.214

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