GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribonucleas_3_3 - Ribonuclease-III-like
Pfam: PF14622 (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: CL0539
Length: 128
Sequences: 3334
Seq/Len: 26.05
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
39_E117_R1.024083.295
73_G76_K0.730652.351
39_E43_Q0.688522.215
22_N99_V0.664792.139
78_I99_V0.620531.997
115_A118_K0.620251.996
85_E90_S0.610691.965
70_K93_D0.604841.946
40_Y44_R0.594211.912
30_D101_E0.575821.853
69_A96_L0.573471.845
38_S56_R0.57321.844
107_I119_F0.569891.834
14_Y79_R0.561491.807
34_G38_S0.526871.695
36_V120_I0.515691.659
70_K91_G0.50761.633
118_K122_K0.49981.608
104_I119_F0.495961.596
70_K96_L0.489931.576
62_N97_A0.487291.568
69_A100_F0.483921.557
74_L103_L0.472951.522
31_A34_G0.464761.495
32_V108_Y0.456671.469
12_K23_E0.455891.467
24_R42_F0.450811.450
61_S64_T0.444981.432
26_E98_D0.431181.387
94_K98_D0.418441.346
68_I100_F0.407461.311
15_A21_N0.397381.279
26_E30_D0.397341.278
50_G53_T0.396221.275
5_L111_S0.394391.269
62_N94_K0.392721.264
26_E101_E0.392271.262
32_V35_L0.391291.259
40_Y121_Q0.388341.249
31_A56_R0.382131.229
39_E108_Y0.379941.222
100_F104_I0.377071.213
9_L74_L0.376091.210
10_T79_R0.369781.190
36_V113_F0.365991.178
117_R121_Q0.365381.176
114_E117_R0.365171.175
5_L103_L0.36481.174
53_T56_R0.356881.148
66_A96_L0.3531.136
36_V116_A0.348131.120
33_L104_I0.347951.120
30_D60_V0.346751.116
7_Q20_P0.345481.112
6_L79_R0.342611.102
23_E26_E0.340911.097
111_S115_A0.340561.096
116_A120_I0.339751.093
37_V60_V0.335471.079
70_K75_D0.332181.069
32_V105_G0.327131.053
41_L52_L0.326721.051
66_A97_A0.323491.041
9_L99_V0.322931.039
72_L100_F0.320691.032
12_K22_N0.319061.027
3_E6_L0.317191.021
99_V102_A0.316681.019
55_L58_N0.315321.015
104_I120_I0.312861.007
115_A119_F0.307490.989
9_L103_L0.301790.971
49_E52_L0.298310.960
108_Y113_F0.297970.959
48_D51_E0.294970.949
84_E87_S0.292380.941
10_T15_A0.290860.936
7_Q21_N0.290520.935
63_E93_D0.289660.932
43_Q121_Q0.28840.928
35_L113_F0.286530.922
112_G116_A0.285930.920
24_R28_L0.285390.918
106_A110_D0.280950.904
36_V117_R0.274090.882
89_G92_S0.273230.879
41_L56_R0.273020.878
112_G115_A0.272780.878
66_A70_K0.271640.874
51_E55_L0.27160.874
34_G56_R0.258610.832
63_E67_E0.255030.821
60_V101_E0.254670.819
35_L39_E0.254040.817
11_H27_F0.250370.806
14_Y82_P0.24940.802
88_G92_S0.248050.798
84_E92_S0.242060.779
65_L100_F0.241480.777
69_A99_V0.240140.773
59_L64_T0.23990.772
31_A38_S0.236860.762
6_L10_T0.234870.756
97_A101_E0.233360.751
22_N102_A0.229230.738
84_E89_G0.229070.737
5_L77_L0.228880.736
103_L107_I0.227810.733
12_K21_N0.226890.730
30_D98_D0.226710.729
12_K61_S0.226140.728
51_E54_R0.225330.725
8_A106_A0.224280.722
34_G37_V0.223610.719
26_E49_E0.222590.716
24_R27_F0.221460.713
75_D96_L0.220920.711
12_K95_V0.219480.706
34_G60_V0.21880.704
88_G91_G0.218190.702
15_A20_P0.215090.692
98_D101_E0.215070.692
78_I96_L0.2140.689
113_F117_R0.211790.681
56_R65_L0.21050.677
33_L60_V0.209760.675
40_Y105_G0.209010.672
118_K121_Q0.208580.671
66_A93_D0.206990.666
12_K15_A0.20490.659
49_E98_D0.204030.656
87_S90_S0.202810.653
27_F34_G0.202370.651
4_L25_L0.200350.645
28_L109_L0.200190.644
80_W95_V0.198580.639
31_A35_L0.197540.636
5_L9_L0.197430.635
26_E60_V0.196950.634
38_S41_L0.196750.633
42_F56_R0.196560.632
12_K92_S0.19580.630
23_E98_D0.195770.630
40_Y59_L0.195670.630
27_F60_V0.195250.628
33_L65_L0.194470.626
6_L9_L0.19440.625
68_I71_Q0.193540.623
114_E118_K0.193370.622
7_Q10_T0.193030.621
81_G84_E0.192950.621
43_Q122_K0.192420.619
31_A53_T0.19160.616
65_L104_I0.190350.612
37_V68_I0.189710.610
33_L120_I0.189440.610
62_N98_D0.189310.609
103_L111_S0.1890.608
4_L109_L0.188230.606
70_K73_G0.186730.601
54_R57_S0.183860.592
9_L72_L0.18370.591
29_G105_G0.182610.588
30_D50_G0.182050.586
11_H14_Y0.181630.584
54_R58_N0.180710.581
14_Y62_N0.180390.580
55_L59_L0.180310.580
44_R47_A0.180090.579
13_S27_F0.179020.576
92_S95_V0.177710.572
94_K99_V0.177580.571
69_A73_G0.177460.571
6_L77_L0.176750.569
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
3n3wA0.98441000.04
3o2rA0.98441000.041
3rv0A11000.069
3c4bA11000.07
1o0wA199.90.073
3rv1A199.90.074
2a11A199.90.085
2qvwA0.906299.90.087
2nugA0.937599.90.095
2qvwA0.945399.90.128

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