GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DDT - DDT domain
Pfam: PF02791 (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: 61
Sequences: 319
Seq/Len: 5.23
HH_delta: 0.738 (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
9_M17_F0.212941.886
34_A38_N0.182121.613
22_G31_F0.165561.466
36_L42_G0.164651.458
9_M18_G0.156361.385
20_V47_I0.150691.334
6_D19_E0.150421.332
8_L46_E0.149371.323
7_L28_L0.142491.262
11_W46_E0.142011.258
56_L59_E0.137851.221
10_V17_F0.136611.210
24_S35_L0.135671.201
49_C52_L0.135571.201
26_F43_L0.133571.183
18_G44_L0.13331.180
42_G45_A0.132871.177
30_D40_P0.132251.171
24_S37_C0.126721.122
2_E40_P0.126161.117
25_P28_L0.124541.103
22_G45_A0.124461.102
7_L55_L0.124071.099
34_A48_H0.123371.093
16_T20_V0.122851.088
6_D20_V0.122191.082
28_L59_E0.121791.079
3_A23_L0.121721.078
6_D9_M0.121091.072
28_L41_S0.121091.072
54_A58_D0.11971.060
4_F50_A0.116311.030
26_F47_I0.116161.029
24_S40_P0.115941.027
10_V31_F0.11581.026
11_W50_A0.113191.002
21_L51_L0.112991.001
11_W43_L0.112790.999
15_N32_E0.112710.998
32_E36_L0.112190.994
6_D38_N0.111240.985
50_A57_A0.11060.979
36_L40_P0.109790.972
5_G8_L0.109060.966
5_G12_E0.108180.958
4_F19_E0.107120.949
3_A59_E0.106910.947
35_L45_A0.104960.930
14_L24_S0.104830.928
5_G32_E0.103710.918
13_F32_E0.101520.899
27_T33_Q0.100140.887
24_S43_L0.099870.884
27_T30_D0.097710.865
52_L56_L0.097620.865
14_L23_L0.097510.864
48_H53_K0.097160.860
20_V35_L0.09690.858
5_G9_M0.096340.853
30_D33_Q0.0960.850
40_P45_A0.095510.846
26_F48_H0.094410.836
43_L48_H0.09420.834
18_G58_D0.093340.827
45_A58_D0.093290.826
21_L50_A0.092950.823
28_L32_E0.092740.821
11_W24_S0.092520.819
2_E35_L0.092480.819
9_M28_L0.091940.814
12_E36_L0.091810.813
12_E39_D0.091580.811
18_G55_L0.091410.810
30_D49_C0.091020.806
45_A51_L0.090850.805
36_L54_A0.089820.795
20_V54_A0.089510.793
25_P43_L0.089350.791
18_G25_P0.08810.780
13_F39_D0.087860.778
34_A51_L0.087750.777
6_D21_L0.087520.775
21_L38_N0.087430.774
29_D46_E0.086990.770
21_L56_L0.086870.769
8_L11_W0.086770.768
7_L32_E0.086660.767
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
2y9yB191.10.738
2wx4A0.721312.40.862
4ieuA0.737711.60.863
3elnA0.737711.60.863
1ujnA0.96729.20.869
3q3eA0.85257.60.874
3ibvA0.93445.70.881
3jszA0.88525.30.882
3mt5A0.83614.60.885
2a90A0.98364.10.888
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