GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RNase_PH - 3 exoribonuclease family domain 1
Pfam: PF01138 (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: CL0329
Length: 132
Sequences: 3806
Seq/Len: 28.83
HH_delta: 0.04 (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
9_T128_D1.027273.365
30_C121_A0.978943.207
22_S27_K0.959813.144
32_V125_A0.927763.039
6_S22_S0.924153.028
30_C104_V0.890752.918
10_G128_D0.719912.358
8_E22_S0.717222.350
16_D60_F0.670532.197
13_P25_N0.646352.117
86_L122_A0.629922.064
29_I107_L0.620772.034
7_I21_V0.611092.002
28_V106_V0.604791.981
7_I124_L0.592281.940
12_L31_S0.591771.939
5_I23_L0.553821.814
21_V117_A0.539641.768
7_I120_N0.52351.715
32_V102_V0.506411.659
20_R27_K0.46231.515
92_L95_Y0.461.507
23_L117_A0.445811.461
42_N48_E0.437331.433
24_G110_D0.432671.417
83_E87_R0.42781.402
19_A124_L0.41941.374
34_G98_W0.416441.364
104_V122_A0.397341.302
86_L126_L0.384271.259
39_P42_N0.383881.258
80_S83_E0.381221.249
32_V129_A0.376791.234
90_I100_I0.376551.234
123_C127_L0.376121.232
59_P68_G0.373241.223
3_R113_N0.371021.215
16_D130_G0.368081.206
37_E40_P0.367281.203
15_A31_S0.365151.196
34_G131_I0.360941.182
12_L15_A0.352551.155
102_V122_A0.350291.148
17_G32_V0.346991.137
66_R72_D0.340691.116
34_G96_P0.337651.106
40_P48_E0.336751.103
104_V118_A0.333371.092
56_E71_P0.332131.088
116_D119_I0.330451.083
66_R69_G0.324431.063
9_T124_L0.322911.058
42_N46_D0.322081.055
33_K101_H0.320061.049
17_G125_A0.312231.023
90_I126_L0.309671.015
35_P98_W0.307321.007
74_E78_L0.307251.007
35_P101_H0.299410.981
74_E114_L0.296010.970
56_E75_E0.294070.963
71_P76_R0.293890.963
66_R71_P0.293490.961
21_V121_A0.293130.960
6_S20_R0.286320.938
21_V120_N0.285670.936
63_P66_R0.284850.933
35_P39_P0.282910.927
5_I120_N0.277580.909
48_E92_L0.275240.902
3_R111_G0.274990.901
89_S123_C0.274080.898
120_N124_L0.272730.893
18_S29_I0.271270.889
28_V117_A0.269760.884
68_G72_D0.26850.880
12_L29_I0.267070.875
34_G129_A0.266780.874
11_V20_R0.266760.874
34_G100_I0.266260.872
104_V121_A0.265670.870
3_R23_L0.261950.858
72_D76_R0.261910.858
36_I98_W0.260580.854
95_Y132_P0.260320.853
15_A18_S0.260010.852
8_E20_R0.259850.851
48_E83_E0.257060.842
102_V126_L0.256730.841
67_R71_P0.255570.837
34_G130_G0.254020.832
72_D75_E0.251280.823
109_D113_N0.250570.821
37_E99_Q0.250160.820
8_E11_V0.250130.819
38_P42_N0.249240.817
26_T117_A0.248720.815
57_F61_A0.24830.813
28_V104_V0.247950.812
23_L116_D0.247480.811
19_A121_A0.247070.809
11_V27_K0.244470.801
33_K103_D0.24190.792
113_N117_A0.238790.782
109_D114_L0.23720.777
61_A66_R0.23710.777
16_D33_K0.235580.772
109_D115_L0.234560.768
17_G128_D0.234320.768
56_E66_R0.234180.767
53_V82_L0.232950.763
12_L19_A0.232890.763
15_A33_K0.232360.761
85_A88_S0.232340.761
89_S92_L0.232230.761
82_L104_V0.229770.753
14_R63_P0.229590.752
100_I126_L0.228950.750
30_C122_A0.228930.750
11_V14_R0.228720.749
55_V75_E0.228680.749
30_C102_V0.227590.746
24_G111_G0.226930.743
56_E105_Q0.226930.743
78_L113_N0.226870.743
22_S25_N0.226180.741
52_T99_Q0.225260.738
40_P43_E0.22390.734
80_S87_R0.220080.721
82_L119_I0.21750.713
62_S109_D0.216670.710
116_D120_N0.215850.707
21_V28_V0.215380.706
110_D113_N0.215250.705
76_R79_S0.215230.705
96_P132_P0.21330.699
48_E87_R0.213140.698
3_R24_G0.212840.697
46_D67_R0.207410.679
25_N110_D0.206760.677
45_D97_R0.206150.675
53_V122_A0.205860.674
111_G117_A0.205790.674
51_L75_E0.200610.657
28_V118_A0.19660.644
37_E98_W0.196150.643
16_D34_G0.195010.639
78_L114_L0.193270.633
52_T101_H0.192240.630
56_E103_D0.190660.625
59_P74_E0.190020.623
4_P24_G0.189820.622
86_L90_I0.189710.622
91_L98_W0.187590.615
10_G17_G0.187260.613
40_P98_W0.18680.612
55_V115_L0.186740.612
26_T113_N0.186550.611
30_C53_V0.186090.610
26_T111_G0.185750.609
58_S77_E0.185160.607
86_L102_V0.184630.605
45_D48_E0.184560.605
23_L113_N0.18380.602
80_S84_R0.182770.599
63_P67_R0.181410.594
55_V78_L0.181330.594
30_C106_V0.181030.593
51_L60_F0.180970.593
71_P101_H0.180650.592
31_S105_Q0.180210.590
52_T103_D0.178580.585
78_L115_L0.178240.584
77_E84_R0.178190.584
61_A114_L0.178070.583
63_P76_R0.176710.579
57_F75_E0.176640.579
74_E113_N0.176560.578
46_D83_E0.175930.576
19_A128_D0.17590.576
55_V118_A0.175630.575
8_E13_P0.174950.573
85_A119_I0.174830.573
48_E68_G0.173010.567
24_G113_N0.172920.566
9_T127_L0.171430.562
47_A97_R0.171190.561
104_V114_L0.170690.559
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
3m7nD0.97731000.04
2nn6B0.97731000.043
2wnrB0.977399.90.05
2nn6F0.977399.90.058
2wp8B0.984899.90.062
2je6B0.977399.90.062
2po1A0.977399.90.07
3dd6A0.984899.90.071
3m7nG0.969799.90.086
2po1B0.969799.90.088

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