GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribonuclease_P - Ribonuclease P
Pfam: PF00825 (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: 111
Sequences: 1600
Seq/Len: 14.41
HH_delta: 0.031 (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
43_R82_D0.874693.608
68_E71_R0.69222.855
61_R65_R0.669912.763
46_F66_L0.664912.743
68_E72_L0.649572.679
60_N63_K0.641092.644
95_S98_E0.578172.385
48_V62_I0.551192.274
13_F45_G0.502912.074
63_K67_R0.490832.025
35_N82_D0.488252.014
56_A60_N0.462441.908
10_R14_Q0.453221.869
25_G102_E0.449891.856
44_V70_F0.428041.766
54_K57_V0.411621.698
85_F103_L0.411121.696
73_N100_E0.402551.660
16_V84_V0.395591.632
73_N104_K0.392571.619
5_E74_K0.372621.537
27_Y94_L0.371441.532
49_S52_V0.366071.510
72_L100_E0.364721.504
45_G84_V0.350981.448
24_S88_R0.328371.354
23_F32_Y0.324881.340
9_K12_E0.320881.324
69_A96_F0.315231.300
27_Y102_E0.315061.300
25_G105_K0.314831.299
65_R69_A0.308981.275
7_L16_V0.3061.262
31_Y86_I0.303861.253
65_R99_L0.302271.247
15_R33_L0.302181.246
65_R96_F0.292841.208
94_L102_E0.285521.178
53_G58_K0.283241.168
46_F70_F0.272581.124
96_F100_E0.27181.121
35_N39_Y0.268341.107
17_F47_S0.261151.077
48_V63_K0.260581.075
104_K108_K0.260251.074
32_Y81_Y0.259221.069
47_S86_I0.252821.043
100_E104_K0.243071.003
90_G94_L0.237330.979
29_V88_R0.234460.967
17_F86_I0.233840.965
22_R29_V0.23220.958
14_Q18_K0.230770.952
3_K8_K0.229590.947
105_K109_K0.223510.922
25_G106_L0.221090.912
34_P81_Y0.21940.905
66_L85_F0.218360.901
23_F106_L0.217390.897
5_E39_Y0.214410.884
24_S29_V0.213470.881
17_F31_Y0.212560.877
62_I91_A0.212460.876
30_L83_I0.212190.875
46_F67_R0.212010.875
69_A99_L0.211690.873
77_L107_L0.211480.872
54_K58_K0.211120.871
56_A63_K0.209910.866
67_R103_L0.208410.860
58_K93_E0.206090.850
94_L98_E0.204780.845
19_K101_K0.204120.842
76_E104_K0.203440.839
98_E101_K0.203110.838
19_K93_E0.200070.825
69_A103_L0.1990.821
61_R96_F0.195030.804
20_G33_L0.194760.803
14_Q17_F0.191990.792
21_K32_Y0.191910.792
70_F74_K0.191470.790
58_K92_L0.191290.789
52_V91_A0.190180.784
8_K47_S0.189450.781
15_R36_D0.187720.774
30_L85_F0.186850.771
20_G61_R0.183910.759
32_Y110_A0.182930.755
76_E108_K0.182910.754
48_V87_A0.182780.754
27_Y90_G0.182260.752
66_L103_L0.181720.750
47_S84_V0.180370.744
52_V87_A0.178480.736
97_E101_K0.176290.727
73_N76_E0.174550.720
12_E43_R0.173720.717
15_R19_K0.173250.715
3_K6_R0.17140.707
30_L106_L0.171030.705
36_D80_G0.170080.702
89_P92_L0.169810.700
69_A107_L0.16810.693
60_N67_R0.1670.689
52_V89_P0.1670.689
2_P5_E0.165320.682
49_S53_G0.16520.681
50_K53_G0.164610.679
10_R47_S0.164140.677
103_L107_L0.162940.672
101_K109_K0.162780.671
5_E70_F0.162340.670
91_A99_L0.161450.666
28_F66_L0.158720.655
13_F84_V0.158670.654
22_R88_R0.158340.653
69_A104_K0.158010.652
65_R68_E0.155740.642
54_K60_N0.155390.641
30_L56_A0.15520.640
87_A94_L0.154540.637
38_D79_P0.153980.635
53_G87_A0.153840.635
17_F88_R0.153730.634
24_S87_A0.152590.629
62_I92_L0.151940.627
70_F85_F0.151230.624
23_F110_A0.150360.620
24_S109_K0.149810.618
10_R86_I0.149610.617
102_E106_L0.14890.614
87_A91_A0.148280.612
34_P108_K0.148220.611
20_G53_G0.147550.609
24_S30_L0.147430.608
12_E82_D0.14740.608
35_N80_G0.147280.608
22_R31_Y0.147190.607
45_G88_R0.147050.607
31_Y53_G0.146550.605
35_N43_R0.146360.604
25_G29_V0.146120.603
28_F102_E0.145230.599
20_G31_Y0.144110.594
19_K33_L0.143910.594
2_P44_V0.141930.585
38_D80_G0.141840.585
31_Y84_V0.141720.585
101_K105_K0.14120.582
72_L75_P0.140690.580
14_Q49_S0.140660.580
30_L110_A0.140580.580
8_K45_G0.140550.580
69_A100_E0.140280.579
34_P80_G0.140220.578
74_K107_L0.140040.578
34_P75_P0.139160.574
76_E79_P0.13860.572
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
1nz0A0.97399.90.031
1a6fA0.96499.90.047
1d6tA0.96499.90.048
2ljpA0.96499.90.052
2bx2L0.828856.30.883
3r3tA0.333318.40.908
1cqmA0.306312.20.915
2e87A0.774812.10.915
1v7pC0.333310.20.918
1pt6A0.34239.50.919

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