GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RNA_pol_Rpb2_45 - RNA polymerase beta subunit external 1 domain
Pfam: PF10385 (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: 66
Sequences: 2078
Seq/Len: 31.48
HH_delta: 0.082 (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
34_D38_K1.7124.723
8_K38_K1.040892.872
14_E62_Y0.987832.725
31_A39_F0.973652.686
32_P41_D0.940672.595
34_D40_I0.915812.527
24_Y61_D0.855942.361
55_V59_E0.774562.137
46_A55_V0.763212.106
3_K14_E0.72742.007
32_P40_I0.696491.922
56_P59_E0.535951.479
45_P52_F0.533841.473
16_L62_Y0.510181.408
9_V33_L0.507861.401
25_V48_Y0.485791.340
45_P54_M0.483741.335
3_K62_Y0.447831.236
48_Y52_F0.446371.231
43_R54_M0.418971.156
4_V60_V0.418061.153
23_K49_R0.410931.134
8_K37_G0.397651.097
22_E49_R0.394321.088
26_I52_F0.393371.085
46_A53_I0.378241.044
24_Y62_Y0.365681.009
5_K8_K0.365451.008
31_A41_D0.362481.000
23_K48_Y0.36160.998
33_L39_F0.359880.993
19_D22_E0.359020.990
42_E57_P0.334840.924
45_P53_I0.333040.919
5_K12_E0.332740.918
17_T20_E0.331020.913
25_V59_E0.329860.910
31_A63_M0.32810.905
19_D50_G0.315440.870
43_R56_P0.311890.860
19_D26_I0.306420.845
4_V9_V0.30480.841
25_V55_V0.298730.824
2_R65_V0.290240.801
2_R64_D0.290130.800
3_K12_E0.285630.788
48_Y59_E0.280140.773
63_M66_S0.278760.769
30_N33_L0.277250.765
48_Y53_I0.270970.748
10_T13_I0.266680.736
12_E62_Y0.265750.733
2_R28_Q0.260540.719
33_L37_G0.256250.707
2_R30_N0.250990.692
53_I66_S0.249880.689
61_D66_S0.248590.686
18_A21_E0.246150.679
22_E62_Y0.246030.679
19_D23_K0.245370.677
7_G57_P0.245270.677
15_Y19_D0.245230.677
7_G38_K0.244970.676
22_E54_M0.242810.670
46_A60_V0.24120.665
17_T22_E0.239190.660
23_K56_P0.238840.659
14_E20_E0.236570.653
11_D14_E0.236010.651
46_A54_M0.234850.648
24_Y49_R0.232350.641
31_A45_P0.228780.631
27_A46_A0.227010.626
5_K10_T0.224760.620
25_V61_D0.224150.618
33_L40_I0.222290.613
19_D51_E0.221790.612
17_T30_N0.220970.610
3_K24_Y0.219570.606
45_P50_G0.219370.605
51_E64_D0.215350.594
15_Y51_E0.214710.592
6_N58_E0.21450.592
50_G64_D0.214190.591
43_R52_F0.20780.573
46_A64_D0.207680.573
53_I59_E0.207250.572
10_T19_D0.204560.564
6_N35_E0.20430.564
1_Y28_Q0.203390.561
25_V52_F0.20170.556
27_A63_M0.199830.551
25_V46_A0.199060.549
20_E65_V0.198610.548
6_N36_D0.197870.546
15_Y23_K0.19690.543
33_L63_M0.196750.543
41_D57_P0.196090.541
29_A50_G0.19590.540
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
3lu0C199.70.082
4kn7C199.70.082
2a6hC0.984899.10.389
4igcC198.10.571
1twfB0.954597.70.617
4aybB0.651589.80.776
3ttgA0.909110.30.883
1vlyA0.9091100.883
1uf2K0.87887.50.889
3girA0.90916.50.893

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