GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DDE_1 - DDE superfamily endonuclease
Pfam: PF03184 (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: CL0219
Length: 217
Sequences: 1321
Seq/Len: 6.09
HH_delta: 0.588 (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
12_T167_K0.280532.850
7_F57_E0.274682.791
108_D140_N0.229122.328
164_G168_A0.210582.140
107_F111_V0.201082.043
123_D128_H0.19922.024
107_F120_L0.198872.021
156_Q159_D0.196491.996
152_T156_Q0.195421.986
193_T196_D0.194241.974
9_M48_V0.193471.966
166_F201_I0.193471.966
89_S98_L0.185971.890
111_V142_I0.182691.856
202_S206_N0.17691.797
60_P110_R0.172091.749
102_W107_F0.170211.729
58_K205_W0.166061.687
49_L61_P0.162931.655
50_C205_W0.162351.650
4_S54_A0.161651.642
89_S95_T0.157391.599
11_E128_H0.15711.596
107_F118_V0.156031.585
7_F107_F0.155961.585
135_Q139_S0.15251.550
89_S92_G0.151621.541
8_N159_D0.149771.522
8_N156_Q0.147521.499
28_S32_K0.146891.493
111_V118_V0.144511.468
124_S150_N0.143161.455
150_N153_H0.14281.451
103_L108_D0.142691.450
70_P73_F0.138681.409
137_C142_I0.135031.372
9_M120_L0.133871.360
201_I205_W0.133551.357
158_L162_V0.133031.352
119_L145_V0.132391.345
10_D123_D0.131681.338
108_D111_V0.13061.327
94_M99_F0.130031.321
125_H128_H0.130021.321
173_K203_K0.129771.319
87_A101_E0.129731.318
126_S129_I0.129421.315
197_A201_I0.129411.315
61_P201_I0.128011.301
150_N159_D0.127561.296
152_T159_D0.126661.287
178_I182_G0.124321.263
9_M102_W0.123161.251
70_P75_N0.122421.244
121_L147_L0.118971.209
68_K90_E0.118891.208
3_P7_F0.118311.202
118_V142_I0.117781.197
101_E105_K0.117351.192
64_I94_M0.117141.190
35_V38_Q0.11611.180
8_N13_G0.115781.176
133_F144_L0.115271.171
108_D136_L0.114251.161
52_N56_G0.113811.156
5_N116_R0.113771.156
106_V109_P0.112991.148
103_L137_C0.112881.147
44_R47_T0.111741.135
150_N156_Q0.111531.133
32_K38_Q0.11041.122
125_H150_N0.110381.122
47_T63_V0.110341.121
63_V198_I0.110321.121
62_L98_L0.108871.106
71_R74_W0.108351.101
156_Q160_V0.108311.101
124_S147_L0.108091.098
122_L133_F0.105491.072
124_S128_H0.103611.053
103_L142_I0.102111.038
10_D128_H0.101751.034
5_N115_G0.101221.028
147_L150_N0.100351.020
194_L197_A0.100041.016
51_C158_L0.11.016
17_G43_R0.098641.002
72_C75_N0.098531.001
93_W127_S0.098441.000
200_W204_A0.098340.999
136_L140_N0.098080.997
67_G74_W0.09630.978
205_W208_V0.096040.976
8_N157_P0.095980.975
196_D199_R0.095550.971
171_R175_L0.095420.970
7_F55_G0.095240.968
52_N55_G0.094970.965
96_T99_F0.09470.962
8_N152_T0.094660.962
198_I202_S0.094590.961
53_S57_E0.094250.958
28_S31_N0.093910.954
6_I201_I0.093880.954
93_W128_H0.093690.952
162_V208_V0.093580.951
69_R73_F0.093450.950
106_V110_R0.093310.948
10_D152_T0.092410.939
134_K138_K0.091380.928
4_S55_G0.091370.928
143_I149_P0.091270.927
151_T163_F0.091180.926
51_C102_W0.090950.924
175_L180_E0.090690.921
37_G40_S0.090020.915
195_L199_R0.089550.910
86_Y161_G0.089220.907
7_F145_V0.089210.906
60_P99_F0.089160.906
151_T208_V0.089120.906
155_L159_D0.088970.904
131_P135_Q0.088770.902
95_T122_L0.088730.902
177_W200_W0.08860.900
36_P39_K0.088460.899
58_K208_V0.088290.897
148_P155_L0.087960.894
61_P158_L0.087590.890
67_G88_S0.087040.884
132_E146_F0.08680.882
62_L87_A0.08650.879
108_D139_S0.086060.874
42_K47_T0.085970.874
135_Q138_K0.085850.872
71_R75_N0.085850.872
18_M108_D0.085780.872
204_A207_S0.085770.871
74_W92_G0.085750.871
179_I183_N0.085370.867
137_C143_I0.084770.861
67_G71_R0.084640.860
177_W181_N0.084550.859
127_S163_F0.084470.858
198_I203_K0.084280.856
42_K150_N0.084230.856
42_K45_V0.084130.855
148_P157_P0.083610.850
196_D204_A0.083570.849
147_L151_T0.083390.847
99_F103_L0.083290.846
118_V137_C0.083150.845
169_H172_K0.082890.842
203_K206_N0.082780.841
69_R72_C0.082730.841
11_E125_H0.082460.838
103_L178_I0.082310.836
50_C57_E0.082140.835
6_I109_P0.08210.834
147_L153_H0.081790.831
107_F142_I0.08160.829
102_W120_L0.081580.829
45_V49_L0.081560.829
43_R47_T0.081480.828
100_L133_F0.081370.827
58_K166_F0.081140.824
202_S209_T0.08080.821
61_P65_F0.08050.818
86_Y89_S0.080460.818
62_L99_F0.080360.817
14_F170_Y0.080290.816
204_A208_V0.080160.814
196_D203_K0.080090.814
9_M49_L0.07980.811
100_L136_L0.079720.810
43_R46_T0.079690.810
51_C199_R0.079560.808
61_P64_I0.079480.808
37_G41_D0.079330.806
43_R51_C0.079150.804
151_T156_Q0.079090.804
169_H209_T0.078820.801
47_T92_G0.078810.801
90_E101_E0.07880.801
8_N158_L0.078560.798
29_K32_K0.078280.795
137_C174_L0.078110.794
128_H167_K0.077870.791
127_S166_F0.077640.789
6_I27_R0.077630.789
62_L106_V0.077450.787
60_P166_F0.077050.783
67_G87_A0.076950.782
67_G70_P0.076850.781
47_T94_M0.07680.780
5_N118_V0.076410.776
137_C146_F0.076390.776
65_F68_K0.0760.772
10_D90_E0.075790.770
103_L118_V0.075640.769
3_P176_Q0.075640.769
29_K37_G0.075620.768
160_V165_P0.075150.764
173_K176_Q0.074970.762
15_F92_G0.074530.757
13_G17_G0.074520.757
100_L130_S0.074450.756
73_F195_L0.074140.753
99_F102_W0.074120.753
168_A172_K0.074060.753
122_L157_P0.073940.751
98_L102_W0.073710.749
13_G127_S0.073640.748
48_V198_I0.073620.748
11_E147_L0.073520.747
50_C162_V0.073430.746
193_T198_I0.073380.746
15_F20_P0.073350.745
68_K71_R0.073280.745
64_I93_W0.073230.744
50_C158_L0.073190.744
9_M122_L0.073140.743
95_T98_L0.073090.743
10_D124_S0.072960.741
159_D163_F0.072770.739
94_M98_L0.072760.739
55_G135_Q0.072580.737
149_P159_D0.072410.736
35_V53_S0.072370.735
99_F122_L0.072320.735
118_V141_N0.072310.735
23_T28_S0.072280.734
152_T155_L0.072130.733
181_N184_N0.072130.733
178_I181_N0.072060.732
30_K51_C0.072010.732
145_V203_K0.071940.731
5_N117_P0.071870.730
9_M50_C0.071720.729
165_P169_H0.071610.728
65_F70_P0.071490.726
27_R31_N0.071470.726
121_L145_V0.071360.725
16_Y197_A0.071150.723
61_P128_H0.071130.723
108_D116_R0.07090.720
206_N209_T0.07090.720
88_S202_S0.070820.720
100_L132_E0.070790.719
51_C162_V0.070720.719
136_L139_S0.070680.718
46_T52_N0.070450.716
137_C144_L0.070440.716
13_G94_M0.070410.715
15_F64_I0.070390.715
147_L163_F0.070390.715
8_N163_F0.070360.715
93_W159_D0.070260.714
23_T31_N0.070.711
12_T163_F0.069890.710
54_A105_K0.069660.708
8_N64_I0.069590.707
141_N168_A0.069410.705
7_F62_L0.069350.705
202_S205_W0.069330.704
28_S98_L0.06930.704
11_E123_D0.069280.704
8_N23_T0.069220.703
132_E135_Q0.069210.703
66_K74_W0.06920.703
153_H163_F0.069140.703
159_D165_P0.069130.702
66_K151_T0.069090.702
172_K176_Q0.069090.702
175_L183_N0.069090.702
199_R203_K0.069070.702
95_T208_V0.069030.701
153_H159_D0.069030.701
179_I182_G0.069030.701
62_L101_E0.068990.701
147_L158_L0.068920.700
117_P143_I0.068910.700
111_V141_N0.068860.700
103_L111_V0.068770.699
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
2f7tA0.792699.70.588
3f2kA0.792699.70.593
3hotA0.792699.60.62
2x78A0.677456.60.924
3kksA0.635946.40.928
4fw1A0.709734.20.933
1cxqA0.7327310.934
3oymA0.834130.50.935
1c0mA0.705128.80.935
3av9A0.645228.60.936
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