GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RNA_helicase - RNA helicase
Pfam: PF00910 (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: CL0023
Length: 107
Sequences: 22280
Seq/Len: 208.22
HH_delta: 0.217 (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_I104_T1.921623.130
58_F103_I1.276942.080
17_E21_D1.243862.026
59_G105_S1.105341.801
17_E20_K1.100021.792
12_S75_R1.06361.733
57_D106_N1.052291.714
13_T17_E1.023541.667
43_F46_G1.022121.665
15_A102_I1.011921.648
45_D48_Q0.941731.534
16_K79_S0.911291.484
6_P9_I0.861551.403
27_G30_T0.86051.402
30_T34_V0.854061.391
59_G106_N0.853221.390
42_K45_D0.852151.388
29_P32_D0.818121.333
23_L26_I0.798111.300
27_G32_D0.797781.300
44_W47_Y0.796321.297
42_K46_G0.789051.285
71_S74_I0.77191.257
29_P33_S0.727551.185
38_N42_K0.726821.184
30_T33_S0.721671.176
13_T16_K0.715771.166
2_W103_I0.712491.161
41_D46_G0.710861.158
76_L82_F0.707911.153
75_R79_S0.705511.149
37_R40_G0.696981.135
28_E34_V0.695071.132
26_I54_I0.688451.121
15_A54_I0.683811.114
44_W48_Q0.672461.095
39_P42_K0.672081.095
74_I78_S0.664081.082
47_Y51_P0.659341.074
40_G44_W0.657331.071
32_D35_Y0.654581.066
48_Q51_P0.642641.047
38_N41_D0.639211.041
30_T35_Y0.63511.035
69_D72_E0.632471.030
72_E76_L0.63211.030
99_K103_I0.625231.018
102_I105_S0.622121.013
81_P85_N0.621751.013
46_G51_P0.612360.998
31_K34_V0.609420.993
41_D44_W0.607470.990
72_E75_R0.600770.979
70_E74_I0.596850.972
73_L78_S0.59090.963
28_E32_D0.589320.960
27_G36_T0.585490.954
28_E31_K0.58510.953
69_D74_I0.582790.949
28_E33_S0.580210.945
52_V102_I0.572150.932
7_P60_Q0.567180.924
19_A52_V0.565310.921
4_Y60_Q0.560980.914
12_S56_D0.559380.911
81_P84_P0.557320.908
61_D69_D0.553690.902
39_P43_F0.553170.901
2_W105_S0.549360.895
5_G8_G0.547380.892
99_K102_I0.54670.891
46_G50_Q0.546070.890
19_A26_I0.53720.875
31_K35_Y0.534270.870
53_V101_V0.534230.870
3_I14_L0.534220.870
5_G10_G0.527850.860
52_V100_L0.526010.857
43_F47_Y0.522030.850
16_K20_K0.519870.847
1_I4_Y0.519430.846
75_R78_S0.518320.844
58_F70_E0.516470.841
29_P35_Y0.511910.834
35_Y38_N0.509250.830
3_I15_A0.504180.821
41_D48_Q0.501870.818
57_D61_D0.500860.816
40_G43_F0.498440.812
5_G11_K0.49520.807
22_L52_V0.495170.807
33_S36_T0.495130.807
74_I77_I0.493570.804
58_F61_D0.493370.804
99_K105_S0.489910.798
60_Q106_N0.48970.798
79_S82_F0.484810.790
50_Q53_V0.483510.788
34_V38_N0.481860.785
29_P34_V0.479510.781
36_T42_K0.470960.767
32_D39_P0.464780.757
60_Q63_D0.457910.746
43_F48_Q0.455310.742
27_G35_Y0.453130.738
37_R43_F0.450390.734
72_E79_S0.449710.733
37_R42_K0.449460.732
22_L25_H0.44850.731
70_E77_I0.448330.730
41_D45_D0.444350.724
70_E73_L0.442380.721
1_I102_I0.441670.719
36_T40_G0.437660.713
4_Y59_G0.430250.701
8_G11_K0.429840.700
28_E35_Y0.425070.692
41_D47_Y0.423060.689
46_G49_G0.422090.688
15_A52_V0.419510.683
56_D106_N0.419330.683
73_L77_I0.4180.681
38_N43_F0.416680.679
7_P59_G0.41570.677
31_K41_D0.412960.673
63_D71_S0.410360.668
44_W64_G0.408510.665
35_Y40_G0.408120.665
32_D36_T0.407990.665
78_S85_N0.406430.662
27_G31_K0.405480.661
40_G46_G0.401020.653
39_P45_D0.400650.653
37_R41_D0.398110.649
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
3cf2A0.943999.30.217
3cf2A0.943999.30.218
3m6aA199.30.224
1r6bX0.925299.30.225
1qvrA0.925299.30.232
3pfiA0.962699.30.234
3t15A0.981399.30.235
3hwsA0.981399.20.243
3f9vA0.934699.20.247
3pxiA0.915999.20.248

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