GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NUDIX - NUDIX domain
Pfam: PF00293 (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: 134
Sequences: 20251
Seq/Len: 151.13
HH_delta: 0.125 (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
54_K60_D2.34573.087
11_N15_K2.133172.807
39_I48_A1.919722.526
15_K112_P1.867072.457
20_K107_E1.807472.379
44_S47_E1.791072.357
32_W109_K1.727722.274
112_P115_E1.715242.257
43_E51_R1.62032.132
7_V49_A1.557292.049
17_L108_V1.49181.963
111_V119_L1.481031.949
45_P85_I1.384291.822
10_F88_I1.363751.795
50_R54_K1.329231.749
52_E56_E1.307031.720
15_K110_W1.302591.714
46_E50_R1.287971.695
7_V53_L1.271061.673
20_K106_S1.251681.647
109_K119_L1.202311.582
18_L111_V1.194251.572
52_E55_E1.16381.532
39_I45_P1.146461.509
17_L110_W1.138081.498
21_R33_E1.128321.485
11_N110_W1.102941.451
66_L69_L1.067481.405
43_E48_A1.030541.356
47_E50_R1.029341.355
53_L61_V1.009151.328
35_P57_T1.008961.328
115_E118_E1.008921.328
19_I105_I1.003881.321
6_G34_L0.990091.303
48_A51_R0.988591.301
10_F90_E0.950121.250
69_L85_I0.933391.228
20_K32_W0.926111.219
7_V89_A0.897271.181
66_L85_I0.875751.152
37_G52_E0.867031.141
45_P87_F0.862981.136
6_G36_G0.860761.133
98_I101_Q0.857261.128
6_G86_F0.851971.121
23_R106_S0.839561.105
19_I108_V0.797181.049
8_I34_L0.790361.040
9_I53_L0.787841.037
20_K30_G0.782531.030
5_V48_A0.775831.021
21_R24_S0.772871.017
91_L94_E0.770361.014
11_N14_G0.757070.996
32_W111_V0.753350.991
19_I35_P0.750920.988
62_S92_P0.74550.981
22_S25_P0.739910.974
63_P90_E0.732250.964
71_S83_I0.726230.956
50_R64_L0.726220.956
72_Y77_G0.725030.954
54_K57_T0.721250.949
115_E119_L0.717530.944
22_S106_S0.715360.941
65_E90_E0.699460.920
6_G84_V0.698750.920
61_V64_L0.689030.907
61_V89_A0.68480.901
40_E52_E0.680070.895
53_L57_T0.67080.883
73_P76_S0.664170.874
33_E36_G0.661760.871
111_V116_L0.659270.868
50_R53_L0.658650.867
72_Y75_P0.653760.860
86_F89_A0.643490.847
50_R62_S0.642410.845
38_G82_E0.633380.834
118_E122_N0.631460.831
12_E90_E0.628880.828
82_E86_F0.626910.825
111_V117_L0.624320.822
73_P78_D0.615990.811
43_E47_E0.611220.804
4_A38_G0.599650.789
75_P78_D0.598250.787
33_E38_G0.596050.784
97_E100_P0.595190.783
89_A92_P0.59440.782
63_P66_L0.593710.781
111_V115_E0.589960.776
100_P103_E0.587530.773
51_R55_E0.584920.770
36_G120_L0.580380.764
5_V49_A0.579480.763
69_L83_I0.578830.762
62_S91_L0.575450.757
10_F113_P0.571450.752
10_F16_V0.568090.748
94_E97_E0.566860.746
101_Q104_E0.564760.743
62_S90_E0.561680.739
53_L89_A0.557590.734
49_A87_F0.556650.733
65_E88_I0.556280.732
18_L32_W0.554630.730
23_R30_G0.554570.730
59_L91_L0.550040.724
60_D93_S0.54820.721
19_I57_T0.546870.720
64_L90_E0.542670.714
20_K109_K0.537360.707
14_G113_P0.535580.705
16_V34_L0.533470.702
112_P117_L0.532660.701
74_S77_G0.525990.692
49_A53_L0.525180.691
105_I108_V0.517690.681
10_F14_G0.517570.681
30_G106_S0.514710.677
19_I33_E0.513010.675
50_R61_V0.512750.675
33_E105_I0.512480.674
18_L121_L0.510780.672
54_K58_G0.50980.671
116_L120_L0.509370.670
21_R30_G0.504580.664
50_R60_D0.503940.663
63_P91_L0.502550.661
5_V36_G0.499560.657
67_L88_I0.499160.657
73_P77_G0.496670.654
68_G71_S0.490660.646
37_G56_E0.489360.644
109_K115_E0.488130.642
92_P95_Q0.487790.642
52_E104_E0.487020.641
72_Y76_S0.484430.637
12_E92_P0.484310.637
117_L121_L0.48420.637
12_E15_K0.474140.624
113_P117_L0.470510.619
16_V113_P0.469180.617
67_L70_F0.457520.602
37_G40_E0.455280.599
114_D117_L0.450190.592
100_P105_I0.448380.590
6_G38_G0.447190.588
6_G33_E0.442590.582
118_E121_L0.434760.572
56_E104_E0.433290.570
10_F13_D0.430580.567
18_L116_L0.428180.563
32_W107_E0.427070.562
102_D105_I0.426640.561
35_P53_L0.424730.559
71_S74_S0.423860.558
50_R63_P0.420260.553
31_Y120_L0.419790.552
40_E43_E0.41490.546
67_L71_S0.412670.543
98_I108_V0.411930.542
5_V45_P0.405810.534
23_R33_E0.405180.533
4_A36_G0.404380.532
70_F84_V0.402550.530
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
3grnA0.955299.70.125
3i7uA0.925499.70.134
3exqA0.947899.70.139
3u53A0.962799.70.142
3gwyA0.940399.70.146
4dywA0.955299.70.147
2fkbA0.955299.70.148
3q93A0.947899.70.156
2yvpA0.970199.70.156
3q1pA0.932899.70.158

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