GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DnaB - DnaB-like helicase N terminal domain
Pfam: PF00772 (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: 103
Sequences: 2144
Seq/Len: 20.82
HH_delta: -0.06 (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
49_E69_E0.701562.534
32_P45_E0.682162.464
65_E68_D0.676242.442
16_L23_I0.605742.188
53_E65_E0.54881.982
23_I48_L0.546791.975
47_I57_I0.54331.962
46_A65_E0.513061.853
65_E69_E0.481991.741
63_A81_L0.473581.710
10_K87_N0.464871.679
29_K98_A0.462131.669
49_E65_E0.459891.661
29_K99_K0.452961.636
34_D102_K0.450221.626
42_R71_K0.449191.622
17_L62_V0.426951.542
89_P97_Y0.426681.541
71_K74_D0.415951.502
38_P41_R0.402061.452
95_E99_K0.396221.431
13_L40_H0.391791.415
16_L26_I0.384121.387
6_I37_D0.383481.385
46_A62_V0.383391.385
16_L47_I0.380631.375
44_F48_L0.374651.353
33_E41_R0.373491.349
64_E68_D0.372071.344
38_P42_R0.370751.339
12_L101_I0.360251.301
35_F44_F0.360251.301
10_K80_Y0.354751.281
25_E95_E0.353761.278
23_I51_Y0.353021.275
40_H80_Y0.351681.270
67_S72_L0.351331.269
59_P82_M0.343951.242
8_A101_I0.340471.230
43_I80_Y0.336641.216
63_A67_S0.33451.208
22_A94_L0.332021.199
15_A94_L0.329131.189
3_P36_Y0.324191.171
32_P48_L0.323221.167
72_L76_G0.323091.167
63_A72_L0.314871.137
94_L98_A0.303581.096
23_I27_I0.301921.090
49_E53_E0.300531.085
27_I51_Y0.300341.085
8_A100_I0.296971.072
4_Y36_Y0.294591.064
10_K40_H0.290551.049
78_I82_M0.288121.041
37_D40_H0.286741.036
13_L84_L0.282321.020
78_I86_N0.27610.997
79_E82_M0.273030.986
58_D93_N0.271320.980
56_P61_T0.271250.980
5_D64_E0.269480.973
99_K103_E0.269020.972
64_E67_S0.26860.970
66_L76_G0.261790.945
38_P74_D0.258630.934
51_Y57_I0.257470.930
14_G88_A0.256890.928
82_M86_N0.251930.910
79_E83_E0.248080.896
7_E10_K0.247340.893
45_E49_E0.245170.885
12_L30_L0.245080.885
26_I94_L0.24470.884
59_P63_A0.243140.878
93_N97_Y0.241490.872
57_I61_T0.239940.867
72_L75_I0.236380.854
20_P57_I0.235790.852
96_D99_K0.235730.851
42_R74_D0.230410.832
18_N89_P0.229530.829
31_S34_D0.22540.814
42_R45_E0.223950.809
40_H43_I0.223720.808
83_E86_N0.220220.795
72_L77_G0.219470.793
29_K95_E0.219150.791
64_E100_I0.218410.789
63_A82_M0.212580.768
80_Y84_L0.210770.761
15_A93_N0.210010.758
30_L44_F0.209230.756
50_L55_E0.208670.754
10_K83_E0.207410.749
19_D94_L0.205090.741
20_P62_V0.204290.738
76_G81_L0.20390.736
46_A49_E0.201650.728
63_A78_I0.201510.728
12_L94_L0.199730.721
19_D91_I0.198340.716
24_D51_Y0.196220.709
5_D8_A0.196090.708
26_I98_A0.195360.706
16_L20_P0.195270.705
55_E99_K0.191840.693
6_I10_K0.191230.691
5_D101_I0.191070.690
6_I40_H0.189890.686
18_N91_I0.189270.684
66_L75_I0.188490.681
88_A92_A0.187130.676
46_A69_E0.186550.674
56_P59_P0.185680.671
50_L61_T0.185450.670
73_K83_E0.185320.669
93_N96_D0.184650.667
22_A25_E0.18460.667
83_E87_N0.184510.666
15_A97_Y0.184040.665
43_I81_L0.184020.665
62_V66_L0.182380.659
49_E52_R0.181770.656
59_P78_I0.181610.656
18_N88_A0.18160.656
11_A60_I0.180010.650
65_E71_K0.17960.649
91_I98_A0.179380.648
68_D86_N0.178660.645
12_L35_F0.177040.639
21_E24_D0.177030.639
14_G89_P0.1770.639
14_G100_I0.176240.636
12_L97_Y0.175380.633
48_L52_R0.17450.630
45_E71_K0.172180.622
78_I83_E0.170950.617
37_D55_E0.169950.614
13_L44_F0.169140.611
50_L62_V0.169120.611
15_A26_I0.168160.607
20_P51_Y0.166650.602
22_A91_I0.166180.600
11_A101_I0.166080.600
5_D10_K0.165150.596
24_D27_I0.164830.595
16_L19_D0.164330.593
55_E96_D0.164230.593
88_A93_N0.163640.591
12_L60_I0.162270.586
15_A56_P0.162070.585
39_A51_Y0.161990.585
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
1b79A199.8-0.06
2r5uA199.7-0.056
2q6tA199.7-0.027
2r6aA199.7-0.026
3gxvA0.951599.7-0.017
3bgwA0.961299.70.011
2r6aC0.951599.50.163
4ehsA0.961283.10.776
1t3wA0.970963.80.807
1wixA0.941741.10.83

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