GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ScdA_N - Domain of Unknown function (DUF542)
Pfam: PF04405 (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: 56
Sequences: 931
Seq/Len: 16.62
HH_delta: 0.056 (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
38_C48_V0.720552.761
21_K51_E0.690382.645
22_Y51_E0.674312.584
50_E54_A0.480761.842
44_D47_E0.475751.823
9_V16_A0.441891.693
4_T7_E0.430411.649
24_I37_A0.428971.644
8_I34_L0.421971.617
2_D35_E0.418791.605
46_E50_E0.397561.523
6_G10_A0.36461.397
17_R21_K0.34431.319
47_E51_E0.328421.258
8_I15_A0.326391.251
24_I32_R0.319921.226
15_A52_L0.305541.171
3_Q7_E0.305131.169
15_A19_F0.300981.153
18_V52_L0.299751.148
3_Q11_E0.298421.143
45_P49_L0.289771.110
38_C45_P0.286171.096
22_Y48_V0.284191.089
49_L53_N0.281841.080
27_C30_G0.279151.070
24_I29_G0.270831.038
12_D15_A0.255650.980
32_R41_K0.251650.964
24_I41_K0.250110.958
35_E39_E0.249750.957
26_F29_G0.249630.956
29_G37_A0.247930.950
47_E50_E0.246580.945
15_A26_F0.231140.886
21_K50_E0.221470.849
18_V22_Y0.214610.822
25_D28_C0.213760.819
29_G40_E0.209570.803
18_V48_V0.209230.802
3_Q8_I0.208490.799
10_A22_Y0.208240.798
10_A16_A0.206430.791
9_V14_R0.205550.788
47_E54_A0.202920.777
5_V9_V0.202860.777
19_F43_L0.201980.774
3_Q46_E0.201280.771
27_C37_A0.199620.765
8_I42_G0.198820.762
32_R37_A0.196210.752
32_R40_E0.194510.745
36_E40_E0.192980.739
42_G50_E0.191570.734
23_G41_K0.190440.730
6_G29_G0.188660.723
11_E39_E0.187440.718
16_A26_F0.184380.706
43_L48_V0.183110.702
8_I20_R0.181330.695
3_Q53_N0.181240.694
36_E45_P0.180510.692
28_C32_R0.17890.685
37_A41_K0.178250.683
25_D30_G0.178060.682
9_V26_F0.176550.676
5_V52_L0.175580.673
25_D41_K0.173430.664
51_E54_A0.173290.664
34_L38_C0.172110.659
21_K39_E0.170220.652
46_E54_A0.169280.649
13_P38_C0.169170.648
10_A18_V0.166840.639
20_R34_L0.166780.639
17_R39_E0.166450.638
5_V20_R0.165850.635
25_D34_L0.164860.632
16_A28_C0.163880.628
17_R53_N0.163720.627
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
2k5eA199.30.056
2k53A0.982199.30.083
2fi0A199.10.176
2kebA166.70.764
3ziuA0.946452.20.783
3ss7X150.70.785
4arcA0.946437.40.8
4e2i20.87534.60.804
1rqgA0.946432.90.806
2awiA0.982131.10.808

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