GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribonuc_L-PSP - Endoribonuclease L-PSP
Pfam: PF01042 (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: CL0534
Length: 121
Sequences: 6007
Seq/Len: 49.64
HH_delta: -0.02 (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
46_R88_E1.996643.079
68_K116_E1.777942.742
53_E63_L1.742152.687
42_E84_E1.543472.380
40_D43_E1.465332.260
61_A65_D1.451092.238
52_I117_A1.4352.213
27_V111_A1.402362.163
56_L119_A1.395872.153
42_E81_A1.377732.125
53_E57_A1.322592.040
44_Q112_L1.291031.991
72_Y102_V1.285561.983
46_R50_D1.264231.950
103_G106_A1.239251.911
30_D33_T1.216741.876
17_A120_V1.181551.822
50_D89_F1.164821.796
71_V82_V1.138291.756
69_V117_A1.105381.705
47_Q51_N1.05171.622
22_F118_I1.050121.620
21_V61_A1.006621.552
78_D112_L0.982231.515
41_I45_T0.968721.494
17_A67_V0.934631.441
50_D53_E0.901291.390
16_R21_V0.872291.345
16_R19_D0.872031.345
62_S65_D0.868641.340
46_R89_F0.85751.322
100_T116_E0.852981.315
70_T116_E0.850461.312
47_Q50_D0.844271.302
76_M103_G0.842721.300
28_G111_A0.841531.298
20_T120_V0.812711.253
81_A84_E0.797371.230
53_E89_F0.789591.218
73_L101_T0.786761.213
85_V88_E0.782911.207
21_V59_A0.778531.201
28_G48_A0.772431.191
19_D120_V0.761161.174
66_V119_A0.737591.138
83_N99_R0.732341.129
106_A110_G0.722371.114
74_T78_D0.714851.102
73_L82_V0.705361.088
69_V86_W0.700881.081
46_R85_V0.698581.077
86_W99_R0.69351.070
26_Q55_I0.689821.064
42_E85_V0.67881.047
25_G114_E0.674911.041
66_V117_A0.671941.036
36_V111_A0.668171.030
57_A62_S0.666281.028
14_A55_I0.661761.021
72_Y100_T0.649921.002
16_R61_A0.642620.991
23_I117_A0.642020.990
23_I55_I0.627480.968
66_V90_F0.619020.955
42_E46_R0.617110.952
75_D78_D0.616560.951
74_T106_A0.614230.947
30_D35_Q0.607430.937
43_E46_R0.60540.934
70_T100_T0.603120.930
74_T112_L0.593810.916
78_D81_A0.592480.914
49_L86_W0.59220.913
49_L89_F0.590770.911
72_Y104_V0.590040.910
38_P43_E0.576610.889
56_L61_A0.574520.886
74_T104_V0.572830.883
45_T82_V0.5720.882
63_L66_V0.568920.877
15_V98_A0.559350.863
20_T118_I0.552480.852
20_T67_V0.547850.845
84_E88_E0.537180.828
39_G43_E0.53580.826
30_D47_Q0.51680.797
14_A59_A0.514950.794
54_R57_A0.514640.794
84_E87_K0.514270.793
26_Q51_N0.513490.792
63_L89_F0.512450.790
17_A22_F0.509610.786
68_K118_I0.505250.779
17_A20_T0.492820.760
72_Y116_E0.490430.756
45_T113_V0.488270.753
14_A21_V0.47880.738
35_Q109_P0.474190.731
10_P87_K0.465370.718
42_E88_E0.46030.710
24_S98_A0.450460.695
16_R59_A0.44730.690
8_I13_Q0.446970.689
26_Q52_I0.438110.676
48_A115_I0.437230.674
70_T118_I0.434950.671
71_V99_R0.428370.661
77_S106_A0.422120.651
29_I34_G0.421490.650
41_I78_D0.418250.645
41_I113_V0.416220.642
27_V109_P0.414750.640
18_G120_V0.412960.637
40_D81_A0.412880.637
8_I11_Y0.412720.637
65_D120_V0.412450.636
79_F101_T0.411970.635
80_P84_E0.409320.631
48_A52_I0.402190.620
74_T110_G0.401210.619
50_D54_R0.398130.614
76_M106_A0.397960.614
67_V120_V0.39730.613
69_V115_I0.396910.612
26_Q48_A0.396750.612
41_I82_V0.394460.608
104_V107_L0.394040.608
51_N54_R0.391370.604
54_R58_A0.390980.603
85_V89_F0.390260.602
10_P84_E0.382270.590
49_L63_L0.381740.589
56_L66_V0.379210.585
40_D112_L0.375690.579
73_L76_M0.375670.579
66_V69_V0.369850.570
8_I109_P0.366850.566
57_A60_G0.366810.566
69_V90_F0.364820.563
79_F83_N0.361750.558
39_G112_L0.3610.557
38_P41_I0.359280.554
83_N86_W0.357860.552
29_I111_A0.357070.551
41_I81_A0.355960.549
45_T85_V0.355860.549
23_I52_I0.355730.549
28_G44_Q0.353280.545
74_T105_S0.352810.544
21_V55_I0.351810.543
13_Q51_N0.348240.537
68_K100_T0.346540.534
78_D103_G0.344950.532
108_P111_A0.339860.524
56_L60_G0.338670.522
49_L115_I0.33820.522
35_Q38_P0.335750.518
83_N101_T0.332620.513
75_D112_L0.33260.513
71_V115_I0.332570.513
13_Q58_A0.332260.512
41_I112_L0.33140.511
79_F108_P0.32880.507
78_D106_A0.324740.501
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
3m1xA0.9835100-0.02
3quwA0.9752100-0.019
3l7qA0.9835100-0.019
3k0tA0.9752100-0.017
3r0pA0.9835100-0.012
1xrgA0.9835100-0.008
3vczA0.9835100-0.008
2b33A0.9835100-0.008
3lybA0.9835100-0.007
1x25A0.9835100-0.004

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