GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RNase_PH_C - 3 exoribonuclease family domain 2
Pfam: PF03725 (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: 68
Sequences: 3209
Seq/Len: 47.19
HH_delta: 0.102 (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
10_I57_Q1.312233.109
20_T23_E0.935922.218
15_L60_E0.929352.202
55_E59_E0.927282.197
1_D37_G0.923642.188
54_S57_Q0.918112.175
7_T32_T0.907322.150
11_I16_V0.859832.037
9_G19_P0.847732.009
55_E66_K0.769231.823
33_L65_A0.721131.709
10_I30_S0.685121.623
1_D38_T0.662671.570
2_P37_G0.648051.535
15_L64_L0.61951.468
17_V64_L0.604711.433
57_Q60_E0.595721.411
63_E67_K0.569471.349
30_S51_S0.566831.343
35_V66_K0.521371.235
10_I15_L0.514521.219
1_D36_D0.506471.200
22_E26_L0.502951.192
16_V20_T0.490331.162
5_A34_A0.487611.155
12_D28_D0.47961.136
41_I63_E0.464411.100
56_D60_E0.455111.078
59_E63_E0.453231.074
8_V31_L0.426061.010
63_E66_K0.425881.009
43_T62_I0.419940.995
6_V17_V0.417430.989
35_V65_A0.411710.976
15_L61_A0.410450.973
8_V33_L0.402030.953
9_G27_S0.401630.952
46_K49_G0.387940.919
33_L62_I0.383320.908
56_D59_E0.369030.874
36_D40_N0.364870.865
7_T21_A0.36440.863
7_T34_A0.359890.853
19_P61_A0.358860.850
8_V64_L0.357170.846
16_V23_E0.35250.835
9_G29_S0.346590.821
11_I26_L0.345760.819
18_D23_E0.335810.796
60_E63_E0.330850.784
8_V65_A0.327540.776
14_E23_E0.325390.771
8_V61_A0.322780.765
22_E27_S0.320210.759
11_I14_E0.318560.755
12_D50_G0.31770.753
40_N51_S0.316830.751
31_L61_A0.3160.749
29_S48_G0.306770.727
30_S57_Q0.303530.719
28_D51_S0.30330.719
34_A49_G0.298180.707
44_L53_L0.295590.700
7_T26_L0.292470.693
14_E60_E0.290520.688
21_A39_G0.278520.660
9_G32_T0.277620.658
8_V17_V0.274820.651
14_E22_E0.274280.650
21_A44_L0.272950.647
11_I22_E0.272370.645
41_I46_K0.270210.640
13_G56_D0.269440.638
38_T41_I0.265170.628
9_G30_S0.264340.626
15_L19_P0.25970.615
55_E63_E0.258340.612
12_D26_L0.257570.610
39_G53_L0.256260.607
40_N54_S0.251320.595
56_D66_K0.248510.589
13_G30_S0.248210.588
11_I28_D0.246190.583
40_N59_E0.244050.578
15_L57_Q0.240350.569
45_Q49_G0.238340.565
39_G66_K0.238090.564
59_E66_K0.237280.562
11_I20_T0.237020.562
22_E28_D0.235930.559
51_S63_E0.235920.559
26_L32_T0.23410.555
33_L44_L0.233690.554
11_I23_E0.233670.554
2_P54_S0.233370.553
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
3m7nG0.985398.90.102
2nn6E0.985398.90.111
2po1B0.985398.90.114
1udnA198.90.119
2je6A0.985398.90.121
1r6lA198.90.122
2wnrA0.985398.90.123
2wp8A0.985398.90.124
2je6B0.970698.90.127
2nn6C0.985398.80.129

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