GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribonuc_red_lgN - Ribonucleotide reductase all-alpha domain
Pfam: PF00317 (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. )
Length: 83
Sequences: 1623
Seq/Len: 19.55
HH_delta: 0.084 (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
37_M56_A0.811532.951
33_M56_A0.592472.155
11_L16_L0.590822.149
19_D23_K0.552362.009
27_T30_E0.54281.974
54_E58_E0.534851.945
29_Q64_S0.518151.884
57_E61_D0.490651.784
55_W58_E0.488681.777
61_D65_N0.479551.744
35_V75_L0.466711.697
33_M57_E0.466061.695
60_Y64_S0.419111.524
33_M60_Y0.408061.484
12_Y16_L0.405471.475
34_R79_G0.392371.427
33_M37_M0.391021.422
3_L32_F0.386191.405
51_D54_E0.381661.388
32_F63_L0.349861.272
9_K12_Y0.347441.264
40_A59_F0.343461.249
17_L80_T0.33911.233
72_T76_S0.335181.219
39_L74_T0.32911.197
9_K13_D0.326141.186
63_L70_P0.323581.177
29_Q33_M0.322151.172
31_M34_R0.32081.167
14_R66_Q0.317411.154
34_R38_A0.316921.153
54_E57_E0.316651.152
20_E82_R0.311731.134
53_M57_E0.311311.132
29_Q60_Y0.310221.128
38_A78_A0.293961.069
55_W59_F0.286951.044
16_L31_M0.272240.990
74_T78_A0.270760.985
11_L31_M0.26990.982
62_L67_K0.269860.981
18_K22_G0.265250.965
8_A12_Y0.263410.958
71_A82_R0.261420.951
40_A56_A0.257580.937
51_D55_W0.253040.920
14_R77_N0.24310.884
68_F79_G0.240690.875
19_D25_I0.239770.872
4_S8_A0.238470.867
24_V72_T0.237230.863
32_F75_L0.237180.863
31_M35_V0.231370.841
71_A77_N0.229720.835
53_M56_A0.228380.831
6_N10_V0.225090.819
23_K27_T0.22280.810
23_K61_D0.221310.805
37_M57_E0.220850.803
68_F71_A0.218220.794
28_P32_F0.216510.787
40_A55_W0.214040.778
15_Y73_P0.213220.775
38_A41_S0.212920.774
4_S38_A0.209530.762
57_E60_Y0.208780.759
39_L59_F0.208430.758
5_Y29_Q0.200450.729
35_V78_A0.199780.727
3_L69_I0.193410.703
7_A76_S0.191180.695
41_S58_E0.190280.692
31_M80_T0.185980.676
26_E73_P0.185820.676
18_K24_V0.18490.672
52_R55_W0.184520.671
8_A28_P0.184010.669
19_D51_D0.183430.667
76_S82_R0.181540.660
3_L81_K0.181310.659
16_L24_V0.180380.656
5_Y33_M0.179810.654
58_E61_D0.179680.653
4_S7_A0.179670.653
26_E33_M0.178230.648
24_V51_D0.175450.638
63_L69_I0.174430.634
61_D64_S0.172520.627
17_L82_R0.171190.623
9_K59_F0.167990.611
36_A78_A0.167570.609
37_M55_W0.165570.602
66_Q69_I0.164640.599
37_M53_M0.164450.598
4_S66_Q0.163390.594
68_F75_L0.16330.594
5_Y9_K0.163140.593
7_A77_N0.162580.591
55_W68_F0.162030.589
32_F60_Y0.161910.589
31_M75_L0.161820.589
39_L78_A0.161640.588
18_K26_E0.161030.586
34_R68_F0.160430.583
32_F64_S0.160080.582
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
3k8tA0.879599.80.084
3hncA0.879599.80.106
3o0qA199.80.111
2xapA0.951899.80.122
2wghA0.879599.80.148
1peqA0.891699.70.223
1l1lA199.60.263
2xw6A0.578317.90.886
3p9aA0.939814.90.89
3ilvA0.843410.60.897

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