GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TatD_DNase - TatD related DNase
Pfam: PF01026 (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: CL0034
Length: 255
Sequences: 10898
Seq/Len: 42.74
HH_delta: 0.114 (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
114_E144_E1.487813.900
238_S241_E1.102592.890
78_E122_E1.023472.683
248_E252_R0.92912.435
244_Q248_E0.900992.362
119_L122_E0.888432.329
241_E244_Q0.863412.263
76_E79_E0.860072.254
230_A233_E0.850122.228
114_E145_Y0.844882.214
30_A251_K0.802522.103
165_K194_A0.789862.070
165_K169_D0.786652.062
143_K170_L0.783912.055
46_E50_Q0.774252.029
247_Y251_K0.771612.022
243_A248_E0.767792.012
201_L253_L0.749141.964
118_E145_Y0.743291.948
190_E193_K0.73891.937
21_E25_E0.722561.894
173_Y199_R0.720331.888
49_S85_R0.704711.847
119_L123_L0.703631.844
115_R118_E0.681761.787
118_E122_E0.681481.786
121_K145_Y0.677851.777
45_L49_S0.671811.761
189_R193_K0.668661.753
78_E123_L0.656181.720
22_R220_E0.64961.703
161_P194_A0.64571.692
17_P50_Q0.643811.687
78_E119_L0.62721.644
98_Y137_E0.617821.619
30_A56_Y0.615851.614
166_K169_D0.61241.605
247_Y250_A0.608721.595
124_N151_R0.60821.594
190_E194_A0.600271.573
152_V172_C0.59611.562
130_H205_D0.590211.547
198_D244_Q0.5871.539
140_E144_E0.584831.533
18_E21_E0.584261.531
23_A31_I0.57541.508
139_L166_K0.571881.499
42_E46_E0.571131.497
136_E140_E0.570891.496
161_P165_K0.566581.485
58_A90_A0.563811.478
244_Q249_N0.561311.471
229_Q233_E0.558141.463
46_E49_S0.555141.455
173_Y253_L0.549411.440
237_I242_L0.54591.431
186_K190_E0.538291.411
29_S247_Y0.538011.410
84_N123_L0.536441.406
225_P229_Q0.532281.395
201_L249_N0.530971.392
74_L115_R0.5221.368
20_L24_R0.505761.326
43_R46_E0.504141.321
120_A127_V0.499921.310
243_A247_Y0.496121.300
173_Y252_R0.494131.295
189_R230_A0.491821.289
117_L127_V0.49151.288
197_L237_I0.489951.284
75_E78_E0.489161.282
197_L245_I0.488661.281
110_E137_E0.486681.276
136_E166_K0.481611.262
111_E115_R0.480821.260
34_V128_S0.475771.247
24_R53_D0.473521.241
37_D40_D0.472551.239
20_L51_Y0.472291.238
192_I241_E0.472131.237
18_E22_R0.467961.227
78_E84_N0.463221.214
237_I241_E0.461971.211
17_P21_E0.461851.211
160_S163_E0.461381.209
161_P190_E0.456431.196
131_C138_L0.450711.181
22_R25_E0.449111.177
75_E79_E0.440331.154
173_Y201_L0.439361.152
49_S87_K0.438661.150
31_I55_V0.436971.145
124_N255_G0.43491.140
141_I145_Y0.432031.132
226_K229_Q0.431231.130
248_E251_K0.430821.129
118_E121_K0.430611.129
110_E114_E0.428131.122
26_A225_P0.425461.115
121_K146_G0.425281.115
198_D252_R0.421711.105
246_I250_A0.420871.103
114_E118_E0.419871.101
228_A239_L0.419471.099
242_L246_I0.414911.088
33_I44_V0.412631.082
197_L241_E0.411981.080
249_N252_R0.410461.076
239_L243_A0.40871.071
114_E141_I0.407621.068
48_A57_P0.398131.044
232_A242_L0.397491.042
57_P88_V0.39391.032
58_A128_S0.393581.032
199_R252_R0.39341.031
162_E165_K0.391471.026
72_E75_E0.391161.025
17_P51_Y0.390861.024
32_I254_F0.387391.015
73_D76_E0.386541.013
115_R119_L0.383231.004
176_F200_I0.380230.997
202_L228_A0.377810.990
76_E80_L0.37330.978
155_H205_D0.370010.970
43_R47_L0.368890.967
166_K170_L0.36680.961
139_L143_K0.362060.949
182_F210_A0.361770.948
197_L235_K0.361420.947
105_D108_V0.35880.940
79_E84_N0.358680.940
83_L123_L0.356570.935
83_L125_L0.355340.931
74_L119_L0.355230.931
153_I253_L0.355210.931
168_L199_R0.354830.930
23_A28_V0.35280.925
186_K189_R0.351190.920
111_E114_E0.347490.911
175_S201_L0.342430.898
201_L250_A0.340770.893
45_L85_R0.340480.892
79_E85_R0.338420.887
240_E244_Q0.337880.886
34_V58_A0.337230.884
143_K166_K0.33690.883
173_Y249_N0.33690.883
202_L246_I0.336540.882
48_A55_V0.336350.882
32_I250_A0.335220.879
24_R29_S0.33520.879
90_A95_G0.334920.878
20_L55_V0.332010.870
42_E76_E0.330630.867
187_K190_E0.330280.866
113_F129_I0.329670.864
162_E166_K0.328490.861
21_E24_R0.326890.857
196_P199_R0.325370.853
44_V57_P0.322640.846
71_E75_E0.317650.833
107_E110_E0.316890.831
106_K110_E0.316420.829
129_I154_F0.314360.824
238_S242_L0.313940.823
163_E166_K0.313630.822
94_I116_Q0.313240.821
131_C135_H0.312590.819
71_E115_R0.310820.815
151_R154_F0.308520.809
245_I249_N0.306610.804
117_L121_K0.306250.803
168_L198_D0.303010.794
94_I127_V0.302830.794
229_Q239_L0.30240.793
237_I245_I0.301170.789
139_L167_F0.300820.788
20_L31_I0.300080.787
22_R26_A0.300070.787
202_L231_L0.299150.784
164_A174_F0.297890.781
83_L91_I0.297310.779
109_Q112_V0.297140.779
232_A239_L0.296460.777
130_H155_H0.295590.775
228_A232_A0.295420.774
45_L48_A0.293850.770
251_K255_G0.293760.770
245_I248_E0.291540.764
192_I231_L0.291380.764
197_L244_Q0.288160.755
110_E140_E0.287320.753
220_E223_N0.285940.749
176_F192_I0.284860.747
110_E141_I0.284130.745
44_V48_A0.283980.744
141_I144_E0.283590.743
143_K169_D0.282080.739
161_P191_L0.281940.739
112_V115_R0.28150.738
30_A53_D0.281010.737
224_I227_V0.280530.735
223_N226_K0.280180.734
121_K147_P0.278060.729
240_E248_E0.277290.727
154_F167_F0.276620.725
238_S244_Q0.275870.723
33_I55_V0.274690.720
23_A26_A0.274630.720
42_E79_E0.272970.715
95_G98_Y0.272870.715
56_Y89_V0.272150.713
140_E143_K0.271560.712
41_W44_V0.269070.705
108_V111_E0.268140.703
180_I231_L0.268010.702
129_I138_L0.267570.701
156_C177_S0.266640.699
113_F117_L0.264980.695
74_L78_E0.264820.694
77_L116_Q0.264030.692
117_L145_Y0.262630.688
108_V112_V0.262440.688
239_L242_L0.259470.680
151_R255_G0.258730.678
91_I94_I0.258260.677
201_L254_F0.256530.672
107_E111_E0.256410.672
41_W45_L0.253740.665
156_C174_F0.253440.664
179_A182_F0.253290.664
202_L224_I0.253160.664
241_E245_I0.252580.662
98_Y110_E0.251980.660
35_S41_W0.251530.659
103_E106_K0.251310.659
161_P164_A0.251270.659
142_L172_C0.250880.658
188_V191_L0.250550.657
121_K124_N0.249570.654
154_F175_S0.249120.653
32_I58_A0.248940.652
98_Y106_K0.248580.652
228_A242_L0.248130.650
135_H163_E0.247990.650
22_R222_S0.246290.646
41_W57_P0.245560.644
231_L242_L0.243710.639
16_R19_V0.243420.638
49_S86_P0.24340.638
120_A125_L0.239510.628
193_K241_E0.239270.627
168_L196_P0.238960.626
171_G199_R0.238430.625
244_Q252_R0.238290.625
164_A194_A0.236160.619
97_D155_H0.236150.619
179_A188_V0.235620.618
28_V224_I0.23490.616
36_T40_D0.233870.613
159_G163_E0.233580.612
58_A254_F0.232740.610
21_E51_Y0.232280.609
136_E163_E0.23190.608
228_A246_I0.22970.602
104_E107_E0.22870.599
153_I254_F0.228380.599
128_S254_F0.227910.597
229_Q232_A0.227520.596
126_P253_L0.227330.596
161_P187_K0.227240.596
29_S251_K0.226960.595
39_E42_E0.226560.594
19_V220_E0.226250.593
66_A112_V0.225980.592
192_I235_K0.22590.592
123_L126_P0.225670.591
32_I89_V0.225460.591
88_V125_L0.225320.591
167_F172_C0.22530.591
176_F179_A0.225260.590
231_L235_K0.224650.589
152_V253_L0.223470.586
175_S203_E0.222810.584
94_I97_D0.221940.582
38_P73_D0.221910.582
120_A123_L0.220760.579
250_A254_F0.220450.578
45_L57_P0.219890.576
116_Q120_A0.219780.576
168_L171_G0.219550.575
38_P41_W0.219550.575
155_H158_S0.218290.572
45_L59_L0.217950.571
44_V47_L0.217080.569
74_L122_E0.216220.567
137_E140_E0.215930.566
116_Q119_L0.215080.564
91_I125_L0.215050.564
42_E80_L0.213550.560
227_V230_A0.212850.558
157_F160_S0.212240.556
126_P151_R0.212060.556
165_K168_L0.211710.555
35_S44_V0.211460.554
41_W59_L0.210910.553
42_E45_L0.210860.553
64_W104_E0.210560.552
97_D132_R0.210050.551
39_E43_R0.208920.548
78_E115_R0.208880.547
236_G242_L0.208640.547
32_I56_Y0.207960.545
34_V206_A0.207620.544
151_R155_H0.206740.542
19_V23_A0.206530.541
174_F195_I0.206140.540
30_A247_Y0.205840.540
72_E76_E0.205220.538
83_L88_V0.204580.536
90_A254_F0.20430.535
128_S154_F0.203890.534
138_L146_G0.203660.534
23_A220_E0.203340.533
193_K236_G0.203140.532
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
3rcmA0.98821000.114
1j6oA0.98431000.131
2gzxA0.98431000.142
1xwyA0.98431000.142
1zzmA0.98041000.148
3ipwA0.98431000.159
1yixA0.97651000.166
2xioA0.98041000.19
2y1hA0.96861000.2
3gg7A0.93731000.203

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