GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Bac_DnaA_C - Bacterial dnaA protein helix-turn-helix
Pfam: PF08299 (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: CL0123
Length: 70
Sequences: 1387
Seq/Len: 19.81
HH_delta: -0.089 (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
2_I40_A0.706952.563
2_I6_I0.679662.464
52_G57_G0.675272.448
37_M63_V0.644192.335
16_S19_D0.578222.096
61_S64_I0.545221.977
6_I21_R0.539671.956
17_V21_R0.537051.947
36_A55_F0.529891.921
7_E11_E0.487491.767
10_A17_V0.477351.731
34_Q65_H0.474791.721
50_E53_R0.449881.631
13_F35_V0.41641.510
2_I54_Y0.378211.371
37_M66_A0.37791.370
55_F66_A0.369741.340
2_I46_L0.359081.302
30_V34_Q0.340271.234
35_V39_L0.336111.219
45_G50_E0.335371.216
19_D24_S0.332671.206
34_Q37_M0.326561.184
6_I55_F0.320341.161
46_L50_E0.305881.109
52_G58_R0.303611.101
31_E70_I0.296921.076
8_A11_E0.291141.055
60_H64_I0.288561.046
49_S61_S0.271420.984
41_R67_I0.269910.979
21_R54_Y0.269130.976
37_M55_F0.264930.960
8_A16_S0.264790.960
9_V13_F0.264130.958
6_I17_V0.260160.943
40_A55_F0.258960.939
41_R68_R0.255560.926
25_R65_H0.253620.919
34_Q62_T0.251720.913
23_K58_R0.249520.905
23_K26_K0.249370.904
7_E50_E0.249350.904
4_D45_G0.248740.902
3_E7_E0.244120.885
6_I54_Y0.241880.877
26_K30_V0.24030.871
6_I20_I0.238320.864
34_Q47_S0.238060.863
41_R60_H0.236580.858
13_F32_A0.235680.854
24_S43_L0.23480.851
63_V66_A0.232010.841
61_S69_K0.231420.839
65_H69_K0.230540.836
35_V38_Y0.226770.822
53_R67_I0.226050.820
46_L54_Y0.224860.815
1_T11_E0.224670.814
36_A40_A0.223680.811
51_I63_V0.221950.805
51_I60_H0.215750.782
50_E69_K0.21560.782
5_I44_T0.214280.777
22_S29_I0.214090.776
49_S53_R0.20910.758
4_D8_A0.208920.757
3_E54_Y0.208540.756
11_E14_G0.205930.747
37_M62_T0.205590.745
48_L67_I0.204080.740
16_S45_G0.199780.724
52_G56_G0.198180.718
27_R31_E0.198120.718
7_E17_V0.19650.712
4_D14_G0.195730.710
38_Y42_E0.195290.708
8_A12_Y0.194710.706
25_R60_H0.19240.698
20_I30_V0.191230.693
3_E67_I0.19120.693
4_D12_Y0.190020.689
45_G48_L0.189850.688
5_I51_I0.186880.677
49_S57_G0.186850.677
7_E23_K0.185980.674
39_L43_L0.185690.673
8_A42_E0.184890.670
32_A37_M0.184820.670
17_V20_I0.184340.668
20_I36_A0.183820.666
38_Y70_I0.183750.666
47_S59_D0.183720.666
35_V70_I0.181570.658
4_D7_E0.181070.656
4_D38_Y0.181010.656
46_L53_R0.180260.653
14_G54_Y0.179140.649
24_S29_I0.178590.647
31_E58_R0.178430.647
40_A43_L0.178210.646
33_R62_T0.177760.644
22_S42_E0.175770.637
40_A44_T0.174850.634
3_E27_R0.173310.628
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
1j1vA199.9-0.089
3pvvA0.985799.9-0.071
2z4sA0.985799.70.132
1l8qA199.50.253
3nbxX0.928697.80.624
2dhrA0.9429960.727
2fxaA0.785789.70.787
1hsjA0.985789.10.789
3k0lA0.785788.90.79
3g3zA0.785788.90.79

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