GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribonuclease_3 - Ribonuclease III domain
Pfam: PF00636 (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: 114
Sequences: 2875
Seq/Len: 25.22
HH_delta: 0.137 (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
52_G55_K0.884952.810
17_E21_E0.796312.528
57_L101_V0.783652.488
18_Y22_K0.708612.250
12_K16_S0.696662.212
49_V93_L0.625361.985
49_V95_P0.616881.959
48_A98_L0.610211.937
8_D103_E0.609771.936
64_I92_V0.607981.930
16_S35_R0.603231.915
49_V98_L0.595381.890
48_A102_F0.581191.845
9_A12_K0.557991.772
47_L102_F0.50911.616
41_N99_A0.507751.612
53_L105_L0.505211.604
26_L30_Q0.498931.584
10_V110_Y0.498541.583
41_N96_K0.484241.537
40_S43_F0.482621.532
4_E8_D0.471431.497
10_V13_L0.465551.478
96_K100_D0.457791.453
9_A35_R0.438221.391
101_V104_A0.43061.367
45_A99_A0.429431.363
4_E100_D0.428941.362
11_L106_I0.42871.361
102_F106_I0.426861.355
15_V39_V0.425911.352
26_L34_L0.42541.351
63_E94_P0.401561.275
2_R20_F0.399241.268
49_V54_H0.394011.251
4_E103_E0.385341.223
17_E110_Y0.384321.220
48_A65_Q0.377761.199
105_L109_I0.36881.171
51_L102_F0.358261.137
11_L44_L0.352261.118
29_G32_T0.34641.100
27_N30_Q0.346131.099
28_E31_L0.340621.081
34_L37_A0.340311.080
45_A49_V0.339581.078
63_E66_R0.334011.060
42_K95_P0.326971.038
44_L106_I0.310630.986
108_A112_D0.306230.972
45_A98_L0.303160.963
8_D39_V0.300980.956
32_T35_R0.297080.943
12_K35_R0.289310.919
30_Q33_K0.285010.905
12_K39_V0.279720.888
47_L50_K0.278050.883
4_E28_E0.274870.873
42_K46_R0.267770.850
30_Q34_L0.266550.846
32_T36_S0.257630.818
23_Y26_L0.25750.818
19_L35_R0.25480.809
15_V47_L0.253010.803
54_H98_L0.245580.780
13_L17_E0.244930.778
12_K15_V0.241520.767
41_N100_D0.240740.764
49_V55_K0.24030.763
38_L112_D0.240060.762
96_K101_V0.240040.762
61_P64_I0.239810.761
105_L113_S0.234070.743
62_F66_R0.232160.737
10_V14_L0.230980.733
44_L102_F0.22930.728
41_N95_P0.228190.724
41_N44_L0.227920.724
60_E63_E0.227510.722
19_L31_L0.22730.722
9_A32_T0.226710.720
43_F47_L0.22580.717
20_F31_L0.225190.715
4_E39_V0.225120.715
63_E91_Q0.224160.712
21_E46_R0.223810.711
18_Y38_L0.223430.709
10_V107_G0.219950.698
1_E62_F0.218770.695
59_Q97_V0.218010.692
4_E96_K0.217480.690
5_F39_V0.215160.683
59_Q62_F0.214750.682
48_A101_V0.212190.674
35_R44_L0.212020.673
40_S99_A0.209740.666
97_V100_D0.209260.664
12_K96_K0.208440.662
8_D100_D0.205210.652
54_H63_E0.204010.648
46_R50_K0.200420.636
18_Y21_E0.199510.633
44_L99_A0.199470.633
1_E91_Q0.197990.629
5_F12_K0.195360.620
2_R6_L0.19420.617
91_Q95_P0.193030.613
5_F28_E0.192140.610
19_L38_L0.190420.605
94_P97_V0.18810.597
100_D103_E0.187260.595
3_L14_L0.186560.592
21_E24_P0.185360.589
3_L108_A0.185190.588
39_V103_E0.183130.581
2_R5_F0.182510.579
19_L28_E0.181220.575
40_S98_L0.180720.574
6_L111_L0.179980.571
34_L38_L0.178770.568
42_K101_V0.178550.567
11_L108_A0.177360.563
33_K37_A0.176690.561
23_Y47_L0.176350.560
45_A95_P0.175990.559
21_E52_G0.175980.559
61_P65_Q0.175790.558
56_Y105_L0.174140.553
1_E4_E0.173380.550
32_T96_K0.173130.550
64_I93_L0.172580.548
41_N50_K0.17240.547
38_L43_F0.17180.545
21_E25_N0.169070.537
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
2qvwA0.754499.90.137
3c4bA199.90.137
2qvwA0.763299.90.144
3n3wA0.798299.90.156
3o2rA0.798299.90.165
3rv1A0.80799.90.167
3rv0A0.80799.80.182
1o0wA0.798299.80.185
2a11A0.798299.80.192
2nugA0.745699.80.201

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