GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
THAP - THAP domain
Pfam: PF05485 (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: 84
Sequences: 989
Seq/Len: 11.77
HH_delta: 0.038 (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
21_F61_F0.707923.800
60_D77_T0.547662.940
5_V51_I0.498392.675
29_R73_D0.435672.339
57_E60_D0.418312.245
36_A79_F0.401522.155
21_F53_S0.353891.900
45_P49_S0.352861.894
46_T49_S0.332981.787
19_S61_F0.331141.777
36_A77_T0.330571.774
3_C8_C0.329081.766
70_L74_A0.298561.603
18_V54_R0.294881.583
60_D74_A0.29021.558
29_R32_K0.289531.554
31_K35_K0.276661.485
19_S53_S0.226731.217
57_E77_T0.22251.194
30_R49_S0.221011.186
42_W45_P0.219041.176
37_C49_S0.215871.159
61_F70_L0.215671.158
22_R50_R0.210551.130
39_R42_W0.20961.125
46_T71_K0.20931.123
30_R34_L0.204281.097
61_F74_A0.202731.088
30_R47_K0.198811.067
25_K47_K0.190111.020
32_K35_K0.18520.994
32_K36_A0.182670.981
53_S61_F0.181390.974
18_V53_S0.18130.973
59_D71_K0.179710.965
19_S68_R0.179220.962
28_E32_K0.179050.961
71_K74_A0.173530.931
34_L39_R0.1680.902
20_F53_S0.166630.894
2_K13_S0.16590.891
55_H76_P0.165530.889
37_C51_I0.164760.884
23_F45_P0.164620.884
23_F51_I0.163770.879
7_G80_L0.163590.878
12_S17_G0.161780.868
34_L37_C0.161380.866
64_S68_R0.160890.864
23_F53_S0.157260.844
30_R45_P0.155680.836
60_D70_L0.155530.835
67_R72_P0.155260.833
5_V39_R0.15520.833
57_E74_A0.154840.831
46_T79_F0.154610.830
13_S35_K0.154130.827
57_E78_L0.151110.811
5_V8_C0.150850.810
30_R42_W0.150410.807
59_D74_A0.150040.805
54_R80_L0.149170.801
23_F34_L0.148640.798
68_R74_A0.148160.795
66_K73_D0.144890.778
36_A80_L0.14060.755
37_C42_W0.140550.754
61_F68_R0.138990.746
54_R57_E0.138660.744
5_V37_C0.137980.741
59_D72_P0.136640.733
65_S68_R0.135390.727
2_K48_N0.135040.725
42_W49_S0.135030.725
7_G31_K0.13420.720
35_K38_G0.133790.718
39_R45_P0.13330.716
18_V49_S0.132840.713
44_K47_K0.132670.712
25_K30_R0.132260.710
36_A60_D0.13210.709
5_V11_S0.132030.709
12_S20_F0.131670.707
17_G58_P0.13080.702
63_R69_R0.130720.702
23_F37_C0.130220.699
15_K31_K0.129410.695
61_F71_K0.128660.691
27_P31_K0.127940.687
46_T51_I0.127540.685
16_P20_F0.12710.682
63_R68_R0.127020.682
50_R54_R0.126740.680
36_A74_A0.125120.672
13_S28_E0.125120.672
23_F49_S0.123310.662
39_R49_S0.123010.660
6_P39_R0.122990.660
70_L75_V0.122220.656
68_R71_K0.121630.653
34_L41_D0.121490.652
15_K54_R0.121350.651
21_F68_R0.121320.651
7_G28_E0.121150.650
34_L45_P0.121030.650
6_P44_K0.11880.638
26_D47_K0.11840.636
22_R67_R0.11830.635
17_G63_R0.117710.632
37_C41_D0.117690.632
65_S72_P0.117470.631
29_R77_T0.116950.628
21_F69_R0.115820.622
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
2d8rA0.988199.80.038
2jtgA0.988199.80.046
2lauA0.845299.70.135
2jm3A0.88199.50.265
3kdeC0.833399.40.334
1v5pA0.48814.40.908
2aw2A0.95244.30.909
2h8bA0.22624.30.909
1h67A0.6194.30.909
3ljuX0.58333.90.911

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