GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
H2TH - Formamidopyrimidine-DNA glycosylase H2TH domain
Pfam: PF06831 (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: CL0303
Length: 92
Sequences: 2499
Seq/Len: 27.16
HH_delta: -0.012 (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
57_R66_E1.075982.727
39_I44_A1.01632.576
26_I53_I0.950172.408
63_S66_E0.929822.357
50_R80_E0.880522.232
29_A59_A0.852242.160
23_R60_S0.827742.098
12_A71_H0.79772.022
19_L29_A0.720741.827
12_A68_R0.697381.768
50_R73_A0.655771.662
16_A64_E0.644711.634
25_P28_A0.642631.629
15_F71_H0.632721.604
51_A73_A0.612831.553
57_R61_S0.587181.488
24_R32_D0.585761.485
73_A76_R0.580551.471
58_P61_S0.570891.447
16_A67_L0.565861.434
29_A35_V0.550981.396
11_D14_Y0.544291.380
14_Y18_R0.540781.371
64_E68_R0.524181.329
39_I74_I0.509731.292
70_L74_I0.503351.276
47_I74_I0.502041.272
27_K44_A0.502021.272
14_Y17_E0.490181.242
66_E69_R0.483061.224
13_E64_E0.474441.202
62_L66_E0.469751.191
50_R77_V0.444731.127
31_L45_D0.442421.121
71_H75_K0.441391.119
24_R29_A0.436951.107
77_V81_A0.425951.080
16_A20_R0.423031.072
19_L26_I0.421981.070
12_A16_A0.416891.057
39_I47_I0.412531.046
19_L67_L0.410011.039
13_E17_E0.404571.025
12_A15_F0.401571.018
3_P7_S0.398311.010
42_I47_I0.390850.991
16_A68_R0.390160.989
3_P36_I0.389380.987
50_R76_R0.388220.984
7_S75_K0.375680.952
75_K79_R0.374250.949
7_S10_F0.37290.945
80_E84_V0.365620.927
40_G55_P0.36480.925
5_P78_L0.364070.923
76_R80_E0.363450.921
10_F36_I0.360730.914
1_L37_A0.360610.914
25_P56_E0.359240.911
72_E76_R0.355670.901
33_Q45_D0.352140.893
27_K45_D0.348420.883
79_R83_E0.346710.879
24_R28_A0.344870.874
4_D37_A0.344820.874
2_G37_A0.339240.860
22_R59_A0.338230.857
22_R29_A0.338040.857
21_K60_S0.334390.848
33_Q37_A0.330360.837
69_R73_A0.324530.823
69_R72_E0.318490.807
47_I70_L0.311050.788
22_R35_V0.310260.786
53_I70_L0.307690.780
13_E68_R0.297320.754
43_Y78_L0.297290.753
80_E83_E0.293750.745
41_N45_D0.286590.726
51_A69_R0.285210.723
40_G48_L0.282080.715
62_L67_L0.281730.714
41_N55_P0.279430.708
39_I78_L0.27770.704
81_A84_V0.274360.695
78_L82_I0.274280.695
3_P9_E0.272990.692
8_D75_K0.272140.690
65_E69_R0.270870.687
18_R36_I0.269760.684
6_L75_K0.26860.681
27_K41_N0.268330.680
12_A72_E0.265360.673
65_E68_R0.264610.671
17_E64_E0.261420.663
30_L33_Q0.261280.662
62_L70_L0.257770.653
15_F19_L0.25060.635
8_D79_R0.249480.632
43_Y81_A0.24740.627
47_I77_V0.244830.621
31_L42_I0.242460.615
48_L53_I0.241850.613
20_R67_L0.241840.613
47_I51_A0.238280.604
38_G41_N0.238270.604
49_F55_P0.237980.603
75_K78_L0.233630.592
48_L59_A0.233110.591
38_G46_E0.231730.587
5_P10_F0.229610.582
3_P35_V0.227380.576
25_P84_V0.225180.571
8_D83_E0.225060.570
5_P82_I0.224550.569
30_L74_I0.224180.568
31_L41_N0.223940.568
53_I66_E0.223790.567
23_R58_P0.223140.566
25_P55_P0.221670.562
24_R80_E0.219940.557
63_S67_L0.219490.556
17_E61_S0.218730.554
50_R81_A0.218730.554
6_L78_L0.213960.542
13_E16_A0.211590.536
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
2xzfA199.9-0.012
3u6pA199.9-0.011
1k82A199.9-0.008
1ee8A199.9-0.003
1k3xA199.80.039
3twlA0.989199.80.065
3vk8A0.934899.80.092
1tdhA0.989199.70.158
3w0fA199.70.197
3doaA0.826198.20.595

Page generated in 0.0214 seconds.