GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Helicase_C - Helicase conserved C-terminal domain
Pfam: PF00271 (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: CL0023
Length: 78
Sequences: 30750
Seq/Len: 394.23
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
11_A34_I2.424672.921
11_A28_K2.101262.531
9_K35_R1.860672.241
11_A25_I1.811232.182
28_K33_E1.743362.100
27_K31_S1.71392.065
57_F71_I1.65491.994
55_V74_A1.595831.922
13_I42_I1.562491.882
45_E69_Q1.540091.855
24_E28_K1.539181.854
14_H17_M1.475621.778
44_G66_E1.467451.768
43_L47_I1.439451.734
39_A43_L1.357371.635
18_S21_E1.355761.633
61_P67_Y1.351021.627
23_Q27_K1.308351.576
57_F70_R1.250661.507
73_R76_R1.226571.478
17_M25_I1.15271.389
21_E25_I1.115121.343
28_K34_I1.105671.332
44_G70_R1.073321.293
17_M21_E1.063721.281
41_D66_E1.030661.242
29_F52_A1.018681.227
25_I37_L0.989691.192
19_Q23_Q0.986711.189
25_I28_K0.966571.164
52_A74_A0.93891.131
30_N51_D0.934861.126
29_F37_L0.932321.123
21_E24_E0.889771.072
72_G75_G0.887711.069
69_Q73_R0.887241.069
63_S66_E0.878381.058
8_I36_V0.831551.002
13_I43_L0.811480.978
24_E27_K0.8060.971
32_G35_R0.787760.949
61_P70_R0.770730.928
57_F60_P0.760850.917
27_K30_N0.753790.908
12_I17_M0.748350.901
72_G76_R0.745140.898
68_I71_I0.742530.894
9_K34_I0.734430.885
25_I34_I0.724520.873
20_K24_E0.718290.865
53_S77_I0.712870.859
22_R42_I0.710740.856
11_A35_R0.708850.854
36_V40_T0.689770.831
8_I35_R0.687180.828
62_W67_Y0.678580.817
62_W66_E0.676330.815
12_I38_I0.675230.813
13_I26_L0.653870.788
20_K23_Q0.644160.776
41_D62_W0.639890.771
40_T75_G0.635360.765
10_V36_V0.625910.754
26_L30_N0.623480.751
15_G42_I0.613310.739
13_I22_R0.611070.736
48_D77_I0.601050.724
69_Q76_R0.57310.690
12_I25_I0.571750.689
10_V38_I0.556420.670
32_G51_D0.552780.666
9_K33_E0.543290.654
26_L49_L0.538150.648
7_G10_V0.537990.648
41_D44_G0.528340.636
22_R45_E0.526510.634
67_Y71_I0.521210.628
44_G69_Q0.519890.626
61_P66_E0.517580.623
41_D70_R0.510260.615
15_G22_R0.500640.603
64_P68_I0.490920.591
19_Q22_R0.489350.589
28_K31_S0.475320.573
50_P53_S0.474320.571
41_D61_P0.473990.571
46_G73_R0.473360.570
48_D62_W0.459340.553
13_I39_A0.458910.553
41_D59_D0.45720.551
57_F67_Y0.456820.550
9_K28_K0.451520.544
44_G49_L0.450680.543
12_I16_D0.444830.536
30_N50_P0.442290.533
23_Q26_L0.441360.532
60_P65_E0.439720.530
42_I69_Q0.436340.526
9_K32_G0.428560.516
54_H58_Y0.427110.515
35_R39_A0.423670.510
39_A42_I0.42050.507
71_I74_A0.418510.504
42_I48_D0.415170.500
45_E66_E0.414890.500
17_M22_R0.412610.497
15_G40_T0.394090.475
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
2db3A199.4-0.089
2v1xA199.4-0.072
4gl2A199.4-0.071
3dmqA199.4-0.07
1oywA199.4-0.066
3mwyW199.4-0.061
1wp9A199.4-0.061
3i5xA199.4-0.06
3sqwA199.4-0.06
3eaqA199.4-0.058

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