GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RNA_pol_A_CTD - Bacterial RNA polymerase alpha chain C terminal domain
Pfam: PF03118 (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: CL0198
Length: 66
Sequences: 1698
Seq/Len: 25.73
HH_delta: 0.053 (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
15_E28_K0.653252.375
43_E61_K0.646232.349
20_S59_E0.616932.243
32_I38_L0.603322.193
32_I41_Y0.532021.934
53_G56_S0.531641.933
33_H37_D0.525851.912
52_F57_L0.520191.891
12_T16_D0.427471.554
49_I52_F0.40941.488
58_E62_E0.385031.400
12_T35_V0.367921.338
42_S45_D0.357861.301
14_I24_Y0.347591.264
22_R26_C0.334311.215
39_V42_S0.325661.184
50_K53_G0.310081.127
36_G39_V0.307871.119
19_L22_R0.299941.090
22_R59_E0.298711.086
17_L64_L0.29351.067
52_F60_I0.291791.061
26_C52_F0.276581.006
45_D48_K0.275031.000
32_I45_D0.272060.989
24_Y28_K0.266890.970
47_L52_F0.265910.967
41_Y45_D0.263420.958
31_G49_I0.261570.951
57_L61_K0.260640.948
36_G40_K0.260410.947
14_I17_L0.257230.935
13_P18_G0.256090.931
23_A56_S0.255630.929
25_N29_R0.249350.907
61_K65_K0.24880.905
40_K49_I0.242160.880
51_N56_S0.239950.872
26_C51_N0.239870.872
10_L16_D0.23770.864
26_C56_S0.234940.854
50_K63_K0.232360.845
57_L64_L0.230170.837
49_I60_I0.230130.837
11_D15_E0.227550.827
23_A50_K0.226570.824
21_V25_N0.225870.821
19_L26_C0.225680.821
40_K44_E0.224620.817
16_D35_V0.223820.814
12_T15_E0.223130.811
13_P16_D0.219980.800
54_K57_L0.219160.797
13_P35_V0.217420.790
13_P33_H0.216570.787
41_Y64_L0.211760.770
10_L65_K0.211010.767
58_E65_K0.21090.767
15_E24_Y0.210270.764
25_N55_K0.209160.760
32_I37_D0.205140.746
10_L25_N0.204890.745
22_R38_L0.204230.743
49_I63_K0.203120.738
24_Y47_L0.201530.733
22_R48_K0.200830.730
38_L64_L0.200090.727
23_A52_F0.199450.725
59_E62_E0.197950.720
43_E65_K0.197090.717
21_V28_K0.196830.716
16_D46_L0.195790.712
55_K59_E0.195710.712
44_E65_K0.195130.709
37_D59_E0.192080.698
50_K56_S0.189480.689
47_L61_K0.188920.687
23_A26_C0.187620.682
12_T65_K0.185910.676
34_T44_E0.185340.674
31_G34_T0.184940.672
30_A40_K0.183080.666
41_Y48_K0.181540.660
30_A49_I0.180740.657
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
3gfkB199.20.053
4igcA199.20.053
4kn7A199.20.056
3lu0A199.20.056
2a6hA199.20.064
1cooA199.20.067
3k4gA199.20.076
1z3eB0.954599.20.09
1b22A198.50.298
1u9lA0.924298.30.352

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