GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
cNMP_binding - Cyclic nucleotide-binding domain
Pfam: PF00027 (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: 91
Sequences: 14870
Seq/Len: 163.41
HH_delta: -0.02 (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
19_H76_R3.708123.822
29_K69_L2.317882.389
28_V72_S2.30642.378
31_S67_I2.230642.299
9_V12_R2.148042.214
24_L75_L2.113662.179
3_T73_E2.011052.073
6_K70_T1.961532.022
68_A72_S1.934631.994
5_K8_E1.889971.948
9_V67_I1.825251.882
2_K76_R1.821871.878
29_K41_I1.788231.843
4_Y74_V1.786591.842
78_P81_D1.738661.792
25_S73_E1.729931.783
13_Q65_T1.691551.744
29_K67_I1.678661.730
27_E44_F1.623831.674
28_V66_V1.619511.669
5_K71_D1.533821.581
17_C62_S1.524661.572
3_T71_D1.517971.565
79_R83_L1.474761.520
13_Q32_S1.473371.519
9_V65_T1.45591.501
31_S65_T1.451271.496
11_Y66_V1.448691.493
30_V66_V1.353391.395
12_R15_D1.344221.386
27_E70_T1.34281.384
45_L49_D1.34041.382
29_K44_F1.335061.376
6_K71_D1.304051.344
23_I28_V1.28891.329
12_R65_T1.273321.313
84_Q88_Q1.261541.300
27_E46_G1.241431.280
11_Y62_S1.240111.278
30_V45_L1.219921.258
27_E69_L1.18621.223
44_F69_L1.171731.208
8_E68_A1.143381.179
21_Y74_V1.134171.169
21_Y76_R1.122741.157
4_Y10_I1.098851.133
24_L73_E1.082051.115
20_I50_I1.071221.104
13_Q33_I1.019951.051
41_I44_F1.000191.031
81_D84_Q0.968880.999
19_H78_P0.963810.994
83_L87_Q0.950790.980
25_S47_P0.926180.955
21_Y51_F0.886170.913
7_G67_I0.829710.855
46_G49_D0.82320.849
23_I72_S0.821360.847
34_N37_G0.81740.843
4_Y68_A0.814690.840
82_F86_L0.806770.832
10_I28_V0.800790.825
28_V68_A0.796670.821
30_V64_F0.784890.809
2_K19_H0.771820.796
16_P61_P0.764270.788
23_I45_L0.748210.771
29_K39_E0.737120.760
4_Y72_S0.73510.758
59_G79_R0.722810.745
55_E62_S0.718930.741
4_Y8_E0.702580.724
45_L51_F0.693580.715
22_I75_L0.684560.706
2_K74_V0.676880.698
23_I26_G0.675190.696
10_I21_Y0.663870.684
18_D78_P0.661310.682
17_C55_E0.659750.680
11_Y64_F0.648910.669
20_I77_I0.648160.668
22_I50_I0.633030.653
20_I56_L0.631710.651
31_S39_E0.628840.648
28_V74_V0.608620.627
52_G62_S0.593960.612
56_L79_R0.588350.606
18_D79_R0.581640.600
51_F66_V0.577850.596
33_I39_E0.575030.593
33_I65_T0.568890.586
22_I77_I0.568820.586
30_V43_F0.562720.580
54_I58_T0.559590.577
20_I82_F0.550980.568
80_E84_Q0.54270.559
85_L89_D0.542070.559
84_Q87_Q0.527950.544
6_K69_L0.526690.543
28_V51_F0.525770.542
62_S66_V0.522910.539
4_Y28_V0.520490.537
85_L88_Q0.515380.531
55_E63_P0.508430.524
27_E72_S0.507820.523
34_N38_K0.500780.516
10_I72_S0.495690.511
68_A71_D0.495490.511
59_G83_L0.483060.498
5_K68_A0.478250.493
23_I48_G0.475010.490
25_S70_T0.473250.488
10_I74_V0.472070.487
4_Y21_Y0.471740.486
33_I37_G0.465230.480
30_V42_I0.464950.479
55_E64_F0.461210.475
23_I49_D0.451310.465
31_S41_I0.450140.464
32_S42_I0.448960.463
58_T61_P0.446010.460
9_V31_S0.444260.458
42_I64_F0.443920.458
54_I57_L0.437980.451
54_I64_F0.437790.451
34_N40_Q0.436390.450
54_I63_P0.433840.447
10_I68_A0.433020.446
10_I51_F0.424850.438
57_L82_F0.423650.437
86_L89_D0.423270.436
73_E76_R0.423180.436
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
3dn7A199.4-0.02
3d0sA199.4-0.012
3kccA199.4-0.01
3fx3A199.4-0.009
3e97A199.4-0.009
2gauA199.4-0.009
4ev0A199.4-0.008
3dkwA199.4-0.007
1zybA199.4-0.007
2oz6A199.3-0.001

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