GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Bac_DNA_binding - Bacterial DNA-binding protein
Pfam: PF00216 (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: CL0548
Length: 90
Sequences: 3990
Seq/Len: 44.33
HH_delta: -0.044 (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
53_K78_K1.576593.351
22_E26_D1.377852.928
59_K68_K1.333322.834
54_E75_K1.194092.538
35_A40_E1.141032.425
8_K18_K1.136772.416
57_A70_E1.104452.347
20_D23_A0.999062.123
83_K87_E0.982542.088
61_R66_G0.96932.060
59_K70_E0.947162.013
52_V75_K0.92681.970
48_G79_F0.904821.923
51_S80_K0.884791.880
60_G71_I0.858161.824
17_S20_D0.805591.712
55_R76_K0.781711.661
10_I25_L0.75751.610
41_S49_T0.753971.602
19_K23_A0.746241.586
9_R31_V0.715461.521
28_L32_I0.713111.516
36_L52_V0.700451.489
61_R68_K0.682611.451
9_R13_K0.677321.439
21_V24_V0.674851.434
36_L85_L0.643421.367
29_F47_F0.633551.346
41_S51_S0.615091.307
54_E73_A0.612621.302
32_I42_V0.592031.258
45_P82_S0.585821.245
10_I28_L0.584191.242
51_S78_K0.580511.234
43_K49_T0.55741.185
16_L21_V0.547591.164
13_K34_E0.5471.163
57_A73_A0.5431.154
16_L24_V0.533071.133
62_N65_T0.497321.057
16_L20_D0.475151.010
9_R35_A0.473891.007
39_G75_K0.472331.004
14_T21_V0.467360.993
47_F82_S0.461250.980
50_F79_F0.459430.976
9_R34_E0.455170.967
8_K12_E0.446380.949
37_K88_A0.441910.939
13_K31_V0.43950.934
13_K30_D0.433940.922
55_R74_K0.427910.909
10_I14_T0.425640.905
64_K67_E0.419810.892
33_K85_L0.417740.888
29_F44_L0.41720.887
7_I22_E0.414180.880
1_M5_E0.411680.875
15_G23_A0.411020.874
2_T5_E0.410.871
25_L29_F0.408340.868
47_F50_F0.402520.855
31_V35_A0.400480.851
33_K88_A0.392240.834
10_I21_V0.384840.818
32_I50_F0.380340.808
7_I21_V0.376720.801
10_I24_V0.376280.800
27_A31_V0.370330.787
84_K87_E0.370320.787
4_K22_E0.364450.775
53_K76_K0.364120.774
23_A27_A0.361690.769
15_G20_D0.355890.756
28_L31_V0.353740.752
31_V34_E0.35330.751
74_K90_N0.352230.749
3_K26_D0.351370.747
34_E37_K0.349810.743
34_E38_E0.344080.731
29_F33_K0.338910.720
35_A38_E0.333270.708
1_M35_A0.321180.683
18_K26_D0.317260.674
36_L77_V0.316750.673
61_R64_K0.315380.670
30_D33_K0.312930.665
33_K37_K0.312470.664
48_G82_S0.310850.661
1_M40_E0.310620.660
62_N66_G0.306950.652
9_R12_E0.306310.651
5_E8_K0.305010.648
63_P66_G0.304340.647
62_N69_I0.303390.645
3_K7_I0.30280.644
9_R38_E0.301070.640
13_K27_A0.299180.636
62_N67_E0.298160.634
26_D30_D0.295910.629
14_T27_A0.291810.620
77_V89_V0.287780.612
11_A14_T0.280610.596
55_R58_R0.280260.596
57_A72_P0.277470.590
49_T80_K0.26570.565
77_V86_K0.262130.557
6_L44_L0.257110.546
3_K47_F0.256010.544
77_V84_K0.253130.538
74_K86_K0.252680.537
21_V28_L0.25010.532
21_V31_V0.249460.530
11_A18_K0.249310.530
35_A42_V0.248980.529
41_S80_K0.245870.523
60_G68_K0.245850.523
6_L10_I0.244840.520
55_R73_A0.244450.520
11_A21_V0.244250.519
66_G69_I0.243220.517
14_T25_L0.241650.514
25_L50_F0.24080.512
25_L28_L0.240530.511
43_K58_R0.240180.510
36_L42_V0.236490.503
58_R76_K0.235910.501
87_E90_N0.233280.496
55_R77_V0.232190.493
17_S21_V0.229770.488
43_K82_S0.228820.486
31_V44_L0.227840.484
12_E54_E0.22610.481
77_V85_L0.225860.480
30_D34_E0.225070.478
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
3rhiA199.8-0.044
2o97B199.8-0.035
1b8zA199.8-0.03
1mulA199.8-0.03
1p71A199.8-0.03
1exeA199.8-0.03
3c4iA199.8-0.028
1owfA199.8-0.023
1owfB199.8-0.021
2np2A199.8-0.015

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