GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CTD_bind - RNA polymerase II-binding domain
Pfam: PF04818 (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: 64
Sequences: 752
Seq/Len: 11.75
HH_delta: -0.015 (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
1_K37_H0.444412.603
51_Q54_L0.303741.779
44_P47_R0.299791.756
5_L53_L0.293881.721
9_N13_Q0.285691.673
10_D14_N0.282331.653
13_Q60_R0.281411.648
51_Q55_N0.275591.614
5_L50_V0.24451.432
10_D13_Q0.241871.417
35_F54_L0.240661.409
45_E49_K0.235371.378
43_D46_V0.2321.359
9_N56_I0.224511.315
6_Y49_K0.214241.255
8_A34_A0.20961.228
13_Q56_I0.203421.191
55_N59_E0.202251.184
53_L63_F0.201571.181
48_K55_N0.200641.175
26_A29_P0.193451.133
12_L25_P0.192411.127
2_L49_K0.191861.124
20_P24_A0.190541.116
14_N18_K0.184411.080
14_N23_F0.18331.074
45_E51_Q0.18141.062
27_F52_R0.18111.061
2_L6_Y0.18011.055
14_N27_F0.176621.034
36_A59_E0.174261.021
50_V61_N0.173931.019
36_A40_K0.170650.999
46_V49_K0.169260.991
13_Q62_I0.167770.983
19_N26_A0.167220.979
18_K22_E0.167140.979
8_A16_K0.162770.953
4_L34_A0.162730.953
56_I60_R0.161110.944
25_P28_S0.159610.935
1_K41_N0.155850.913
37_H49_K0.152280.892
24_A31_L0.152190.891
23_F26_A0.15160.888
27_F30_V0.150130.879
35_F39_Y0.149210.874
14_N20_P0.147410.863
16_K52_R0.146670.859
25_P55_N0.146670.859
49_K52_R0.146040.855
11_I15_S0.145470.852
7_L36_A0.144990.849
49_K53_L0.141940.831
49_K57_W0.140570.823
33_D45_E0.140460.823
9_N60_R0.140180.821
26_A33_D0.140090.820
35_F61_N0.139930.820
38_A44_P0.139660.818
29_P34_A0.139160.815
29_P39_Y0.139140.815
48_K51_Q0.137530.805
2_L28_S0.137310.804
12_L63_F0.137160.803
36_A51_Q0.13670.801
27_F62_I0.136590.800
31_L48_K0.136130.797
7_L54_L0.134980.791
10_D15_S0.134860.790
48_K52_R0.134370.787
31_L40_K0.133150.780
38_A46_V0.132390.775
45_E61_N0.132090.774
20_P27_F0.13160.771
5_L34_A0.130790.766
16_K24_A0.128770.754
47_R51_Q0.128360.752
44_P58_E0.12770.748
32_P37_H0.127090.744
2_L22_E0.127090.744
6_Y11_I0.126690.742
16_K60_R0.126290.740
7_L11_I0.126040.738
7_L47_R0.125860.737
3_A14_N0.125570.735
28_S40_K0.12530.734
35_F63_F0.124120.727
36_A44_P0.124090.727
6_Y9_N0.123980.726
1_K7_L0.12340.723
12_L24_A0.122590.718
12_L45_E0.122170.716
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
2km4A199.5-0.015
4flbA0.953199.50.003
4fu3A0.984499.50.01
3d9jA0.984499.30.109
1sz9A0.937599.20.137
3cljA198.90.279
1x5bA0.921980.80.745
1dvpA0.921978.30.751
1juqA0.968873.80.761
1mhqA0.968871.10.765

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