GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PRA-PH - Phosphoribosyl-ATP pyrophosphohydrolase
Pfam: PF01503 (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: CL0231
Length: 83
Sequences: 2746
Seq/Len: 33.08
HH_delta: 0.168 (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
32_G39_I1.143462.625
32_G36_G1.141662.621
51_A78_E1.137962.613
20_T59_Y1.001612.300
10_Q14_E0.932982.142
30_K33_E0.919882.112
54_L65_L0.89422.053
38_L54_L0.884242.030
52_D78_E0.839121.927
54_L61_L0.825771.896
41_A49_E0.816941.876
49_E52_D0.70231.612
27_R64_L0.674131.548
36_G39_I0.670771.540
38_L50_V0.660711.517
38_L57_L0.621221.426
9_D66_A0.61221.406
5_H66_A0.602931.384
15_A18_G0.600581.379
46_D49_E0.594541.365
5_H72_L0.540991.242
5_H9_D0.533511.225
36_G40_E0.524491.204
31_L57_L0.490541.126
16_P21_K0.487411.119
51_A74_E0.484251.112
71_D74_E0.477631.097
12_K66_A0.469831.079
8_I72_L0.469681.078
15_A21_K0.468741.076
34_E37_E0.467161.073
47_K68_M0.463481.064
35_A39_I0.463451.064
54_L58_L0.448251.029
22_E26_L0.448231.029
27_R67_S0.447471.027
8_I62_L0.446261.025
31_L60_H0.437811.005
42_A64_L0.426220.979
37_E56_D0.425580.977
9_D12_K0.42040.965
28_L39_I0.415650.954
58_L61_L0.413670.950
23_L26_L0.413130.949
29_K39_I0.411730.945
10_Q13_K0.410460.942
29_K32_G0.409750.941
77_D80_H0.404840.929
73_D76_F0.403630.927
26_L29_K0.393660.904
24_L67_S0.389410.894
34_E56_D0.388840.893
73_D77_D0.38770.890
31_L38_L0.385030.884
70_I74_E0.382920.879
9_D71_D0.380930.875
59_Y63_G0.379390.871
35_A57_L0.377060.866
51_A75_V0.375020.861
28_L43_K0.373930.859
21_K25_D0.367270.843
47_K70_I0.362480.832
13_K77_D0.346010.794
12_K15_A0.34580.794
5_H71_D0.344480.791
29_K40_E0.332570.764
7_T10_Q0.331740.762
45_G49_E0.33170.762
45_G68_M0.32850.754
53_E56_D0.327480.752
8_I24_L0.327410.752
70_I75_V0.324660.745
73_D80_H0.317570.729
42_A68_M0.317190.728
29_K36_G0.315970.725
6_R71_D0.313710.720
74_E77_D0.310650.713
59_Y66_A0.310210.712
40_E44_N0.306180.703
34_E53_E0.303850.698
42_A50_V0.303340.696
20_T63_G0.298280.685
32_G40_E0.298230.685
64_L68_M0.297860.684
47_K51_A0.297550.683
48_E78_E0.296010.680
55_A79_V0.289240.664
19_S30_K0.289080.664
41_A50_V0.288570.663
12_K24_L0.288340.662
27_R31_L0.287480.660
47_K74_E0.286670.658
37_E53_E0.285330.655
62_L72_L0.283730.651
33_E37_E0.283580.651
6_R10_Q0.283480.651
14_E18_G0.281730.647
28_L35_A0.280650.644
72_L76_F0.280590.644
51_A70_I0.274830.631
9_D16_P0.2740.629
52_D79_V0.273020.627
28_L32_G0.272940.627
41_A44_N0.27180.624
65_L75_V0.269870.620
32_G35_A0.268020.615
24_L64_L0.264480.607
27_R60_H0.262940.604
31_L64_L0.262890.604
18_G25_D0.257690.592
18_G21_K0.257140.590
48_E52_D0.255180.586
6_R9_D0.254890.585
28_L31_L0.253080.581
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
3craA199.50.168
2yf4A199.50.192
2rfpA199.40.212
1yvwA199.40.225
2a7wA199.30.245
1yxbA199.30.281
2yxhA0.951899.20.286
3nl9A199.20.287
1y6xA0.951899.20.293
2a3qA1990.356

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