GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NUDIX_4 - NUDIX domain
Pfam: PF14815 (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: CL0261
Length: 114
Sequences: 16386
Seq/Len: 143.74
HH_delta: 0.059 (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
47_E53_S2.336323.207
6_R10_R2.232023.064
15_K91_E1.854742.546
33_S41_E1.759762.416
10_R96_S1.755082.409
37_D40_E1.738592.387
36_E44_E1.682632.310
96_S99_E1.681072.308
26_W93_Q1.492972.050
13_L95_V1.447351.987
12_L92_G1.336621.835
45_W49_Q1.318341.810
43_E47_E1.310671.799
12_L94_W1.293121.775
45_W48_E1.244131.708
16_R27_E1.236761.698
59_P75_H1.218971.673
15_K90_E1.118041.535
62_T75_H1.102861.514
39_E43_E1.097771.507
38_D75_H1.090821.498
29_P50_L1.054391.448
36_E41_E1.036721.423
59_P62_T1.004671.379
40_E43_E0.965821.326
38_D77_Y0.936621.286
10_R94_W0.928041.274
14_E92_G0.915711.257
14_E89_P0.905821.244
33_S38_D0.903841.241
14_E29_P0.891861.224
31_I45_W0.882181.211
99_E102_Q0.872681.198
95_V101_D0.872551.198
41_E44_E0.855721.175
46_L54_I0.846371.162
15_K26_W0.8151.119
54_I79_V0.807331.108
26_W95_V0.807061.108
27_E30_L0.792951.089
34_D45_W0.788061.082
14_E27_E0.786231.079
43_E57_V0.773931.062
15_K24_G0.762741.047
17_P23_A0.759981.043
42_L46_L0.741011.017
89_P92_G0.733411.007
81_V84_D0.72760.999
17_P90_E0.709110.973
58_E78_E0.708450.973
66_V71_R0.707470.971
55_R82_S0.699590.960
54_I57_V0.695510.955
6_R94_W0.692950.951
7_S10_R0.674730.926
57_V80_E0.672020.923
27_E32_E0.669870.920
47_E50_L0.65180.895
55_R80_E0.642860.883
9_G97_L0.639420.878
31_I34_D0.62420.857
32_E72_W0.62320.856
24_G90_E0.617280.847
95_V99_E0.616380.846
44_E48_E0.608430.835
62_T73_T0.600230.824
65_H70_R0.598550.822
18_E90_E0.589870.810
46_L50_L0.588930.809
64_K73_T0.586050.805
31_I49_Q0.579130.795
55_R81_V0.577890.793
58_E80_E0.570060.783
56_S80_E0.562960.773
9_G96_S0.562150.772
43_E56_S0.55970.768
6_R9_G0.55850.767
7_S82_S0.557410.765
60_L78_E0.549330.754
43_E55_R0.547740.752
6_R80_E0.547240.751
43_E46_L0.546450.750
72_W76_V0.545060.748
6_R78_E0.544950.748
7_S81_V0.532450.731
28_F76_V0.528270.725
11_V28_F0.523740.719
69_H72_W0.520460.715
63_V76_V0.518840.712
95_V100_L0.508930.699
96_S101_D0.508340.698
27_E89_P0.50250.690
13_L26_W0.497690.683
64_K71_R0.491720.675
66_V70_R0.48940.672
16_R89_P0.486990.669
26_W91_E0.486530.668
53_S83_A0.486420.668
73_T76_V0.485830.667
65_H68_S0.482470.662
17_P24_G0.482440.662
45_W88_E0.478780.657
56_S81_V0.471220.647
52_L81_V0.470440.646
57_V78_E0.467940.642
13_L93_Q0.463850.637
62_T65_H0.462490.635
97_L100_L0.460020.632
75_H78_E0.459360.631
14_E50_L0.45640.627
56_S59_P0.454810.624
43_E53_S0.454450.624
15_K93_Q0.454010.623
93_Q99_E0.451760.620
66_V69_H0.450220.618
18_E23_A0.448390.616
67_F70_R0.447780.615
47_E51_G0.445990.612
57_V79_V0.442320.607
42_L77_Y0.439530.603
7_S84_D0.43680.600
30_L70_R0.435320.598
27_E76_V0.426150.585
16_R24_G0.422610.580
36_E40_E0.419070.575
93_Q96_S0.416350.572
25_L74_I0.415530.570
49_Q88_E0.414190.569
56_S79_V0.413210.567
11_V14_E0.412940.567
16_R32_E0.408020.560
11_V97_L0.408010.560
32_E41_E0.40790.560
17_P89_P0.404090.555
7_S80_E0.403980.555
50_L89_P0.397720.546
97_L101_D0.39720.545
15_K25_L0.395970.544
9_G98_E0.395480.543
34_D41_E0.39220.538
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
3fspA0.991299.70.059
1x51A199.60.137
3eesA199.60.139
1mutA199.60.139
2rrkA199.60.143
3gwyA199.60.147
3hhjA199.60.15
3grnA199.60.15
3r03A199.60.151
3q93A0.991299.60.191

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