GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DYW_deaminase - DYW family of nucleic acid deaminases
Pfam: PF14432 (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: CL0109
Length: 116
Sequences: 1233
Seq/Len: 10.63
HH_delta: 0.922 (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
103_E116_K0.943284.362
69_I93_I0.823833.810
20_Q75_N0.758873.510
92_F96_I0.722273.340
6_I72_G0.701093.242
38_E87_G0.657643.041
93_I106_V0.473462.190
69_I78_V0.460852.131
23_L100_T0.429711.987
71_F75_N0.426341.972
28_K57_E0.397431.838
2_G82_L0.389251.800
26_K29_E0.386171.786
27_M99_I0.364641.686
9_H18_H0.360341.666
85_V93_I0.357561.654
85_V106_V0.355081.642
20_Q71_F0.347331.606
25_N29_E0.345081.596
27_M92_F0.334631.548
107_R112_F0.325841.507
108_D113_H0.320941.484
30_E98_K0.320561.483
3_C10_S0.318271.472
27_M95_F0.304221.407
22_E26_K0.301321.394
4_S78_V0.301041.392
86_C89_C0.296481.371
76_T102_R0.288211.333
69_I96_I0.271371.255
107_R113_H0.27041.251
69_I85_V0.265311.227
3_C12_V0.265261.227
107_R111_R0.261141.208
14_G62_Y0.258581.196
100_T109_S0.253931.174
5_W79_V0.251131.161
31_G34_P0.250221.157
36_T39_V0.249671.155
15_D18_H0.241471.117
5_W10_S0.240171.111
17_S21_S0.237541.099
4_S11_F0.237251.097
39_V43_V0.229351.061
108_D112_F0.225321.042
10_S79_V0.222431.029
37_K61_C0.218571.011
43_V59_S0.216331.000
23_L28_K0.209760.970
12_V61_C0.209550.969
42_D48_K0.208740.965
8_V75_N0.208610.965
12_V59_S0.207150.958
42_D46_E0.206770.956
24_I61_C0.194870.901
36_T48_K0.193830.896
105_I114_H0.192830.892
35_D87_G0.191810.887
34_P73_L0.19070.882
108_D115_F0.187420.867
111_R115_F0.186930.865
9_H71_F0.186570.863
104_I108_D0.182190.843
24_I27_M0.180530.835
22_E100_T0.180360.834
81_N90_H0.176030.814
23_L26_K0.175030.809
16_R21_S0.172190.796
45_E48_K0.170750.790
102_R108_D0.170340.788
44_D62_Y0.169340.783
34_P104_I0.168540.779
47_E79_V0.168540.779
77_R105_I0.166650.771
25_N101_G0.165490.765
32_Y88_D0.16540.765
76_T79_V0.165320.765
27_M96_I0.165290.764
5_W106_V0.162990.754
4_S59_S0.162160.750
14_G47_E0.162050.749
90_H97_S0.161910.749
68_A81_N0.160510.742
25_N30_E0.160410.742
35_D91_S0.159880.739
77_R106_V0.159670.738
8_V110_N0.15790.730
48_K60_L0.157390.728
19_P60_L0.155550.719
112_F115_F0.154210.713
84_R90_H0.154120.713
23_L38_E0.154060.712
10_S14_G0.15390.712
97_S113_H0.152480.705
46_E66_K0.151830.702
2_G80_K0.151350.700
104_I113_H0.150760.697
3_C114_H0.150260.695
86_C90_H0.150250.695
3_C47_E0.149190.690
41_H48_K0.147920.684
63_H89_C0.147890.684
10_S101_G0.147790.683
58_E61_C0.147620.683
90_H108_D0.147030.680
22_E27_M0.146720.679
23_L32_Y0.146530.678
92_F110_N0.146260.676
2_G81_N0.146130.676
15_D64_S0.1460.675
67_L72_G0.145660.674
78_V87_G0.145380.672
37_K79_V0.144940.670
12_V21_S0.144110.666
15_D74_I0.143550.664
41_H46_E0.143410.663
59_S109_S0.142810.660
74_I98_K0.142340.658
102_R107_R0.141970.657
3_C79_V0.141810.656
21_S116_K0.141540.655
97_S108_D0.141190.653
41_H78_V0.141180.653
64_S68_A0.140550.650
47_E59_S0.139840.647
78_V96_I0.139620.646
12_V79_V0.139410.645
28_K33_V0.13930.644
5_W109_S0.138070.639
1_G12_V0.137820.637
108_D111_R0.136890.633
10_S109_S0.136840.633
7_E70_A0.136430.631
22_E58_E0.136010.629
27_M30_E0.135020.624
5_W38_E0.134070.620
14_G26_K0.133870.619
86_C94_K0.133720.618
90_H113_H0.133590.618
25_N35_D0.133010.615
47_E105_I0.132920.615
10_S21_S0.132320.612
22_E73_L0.132050.611
26_K30_E0.131960.610
77_R100_T0.131790.609
47_E77_R0.131410.608
32_Y35_D0.13110.606
38_E41_H0.130880.605
15_D19_P0.130480.603
23_L70_A0.130310.603
24_I58_E0.130070.602
77_R103_E0.129940.601
14_G21_S0.129890.601
21_S24_I0.129490.599
104_I107_R0.129290.598
40_G87_G0.128070.592
71_F94_K0.128010.592
31_G48_K0.127950.592
36_T45_E0.127950.592
18_H102_R0.127910.592
81_N97_S0.127590.590
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
1svmA0.870732.40.922
1j0tA0.353427.10.925
1pm4A0.34487.60.941
4gdfA0.87077.10.942
1wmxA0.33625.90.944
1vddA0.6815.60.945
2o2kA0.5694.40.947
4h08A0.353440.948
3lnbA0.741430.951
3odcA0.43130.951
If you are interested in a protein containing this domain,
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