GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DDE_Tnp_4 - DDE superfamily endonuclease
Pfam: PF13359 (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: 158
Sequences: 2912
Seq/Len: 18.43
HH_delta: 0.896 (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
33_Q84_Y0.760163.697
34_I124_F0.722233.512
36_C120_V0.651983.171
118_I122_R0.476212.316
117_R121_E0.424732.065
4_T128_K0.413522.011
34_I42_I0.401441.952
54_H57_T0.396461.928
33_Q49_W0.376891.833
7_P27_N0.372571.812
37_D41_R0.360591.754
103_T106_E0.354021.722
81_D121_E0.353791.720
119_I122_R0.352841.716
149_I152_A0.352731.715
51_G55_D0.34781.691
138_L146_A0.342171.664
40_G126_R0.337891.643
23_G29_S0.332141.615
36_C123_A0.322731.569
49_W58_I0.317651.545
33_Q44_Y0.309011.503
121_E124_F0.286891.395
34_I123_A0.284361.383
5_H29_S0.283181.377
37_D43_I0.280031.362
145_K149_I0.277931.352
80_G90_L0.275211.338
141_S144_E0.26881.307
110_N114_S0.267461.301
29_S51_G0.261411.271
42_I123_A0.254171.236
147_P151_L0.253661.234
92_T95_K0.251871.225
133_I153_C0.25051.218
134_L153_C0.249081.211
127_L153_C0.245281.193
9_Q12_S0.244621.190
127_L154_C0.239071.163
20_F23_G0.237831.157
121_E125_G0.236721.151
133_I149_I0.236441.150
35_V78_L0.235741.146
40_G122_R0.232711.132
33_Q62_S0.23271.132
23_G26_K0.232461.130
56_S83_G0.229611.117
81_D117_R0.227171.105
110_N113_H0.223911.089
116_A119_I0.220791.074
152_A155_V0.219551.068
8_I11_P0.219451.067
33_Q80_G0.219261.066
122_R126_R0.216521.053
141_S145_K0.215781.049
22_S25_K0.214641.044
49_W53_V0.212581.034
55_D81_D0.212111.031
145_K148_Q0.211941.031
117_R120_V0.211841.030
40_G119_I0.211281.027
21_Y25_K0.210871.025
4_T32_V0.210291.023
31_K55_D0.206441.004
144_E148_Q0.204350.994
17_Q22_S0.203880.991
91_L94_Y0.203770.991
102_L106_E0.203350.989
79_L116_A0.203240.988
87_S90_L0.203120.988
151_L155_V0.203050.987
94_Y109_F0.202220.983
36_C119_I0.199970.972
120_V124_F0.198870.967
2_D117_R0.198650.966
17_Q21_Y0.197850.962
94_Y99_G0.197850.962
53_V58_I0.195950.953
149_I153_C0.195430.950
2_D81_D0.193690.942
9_Q20_F0.193410.941
17_Q20_F0.193240.940
108_E111_R0.192190.935
138_L141_S0.19090.928
146_A152_A0.190880.928
4_T24_K0.18990.923
77_Y91_L0.189740.923
12_S18_R0.18920.920
99_G103_T0.189090.920
100_R103_T0.186850.909
150_I154_C0.185710.903
102_L107_K0.185420.902
111_R115_S0.184840.899
5_H23_G0.184210.896
147_P150_I0.183940.894
126_R139_R0.182630.888
2_D55_D0.182320.887
128_K135_R0.182070.885
149_I154_C0.178920.870
65_L68_L0.178330.867
19_E22_S0.177230.862
32_V150_I0.176740.859
83_G121_E0.176630.859
60_R88_P0.17660.859
147_P152_A0.176310.857
54_H83_G0.17610.856
83_G86_L0.175670.854
77_Y85_P0.175340.853
50_P53_V0.173260.843
30_L146_A0.171470.834
94_Y106_E0.170780.831
59_F62_S0.170550.829
104_P107_K0.170280.828
145_K152_A0.16970.825
2_D121_E0.168850.821
33_Q58_I0.168320.819
81_D84_Y0.16810.817
81_D120_V0.166830.811
104_P108_E0.165740.806
102_L110_N0.164020.798
118_I125_G0.163840.797
12_S17_Q0.163680.796
133_I139_R0.163570.795
89_Y92_T0.163020.793
22_S26_K0.162920.792
58_I61_Q0.162650.791
5_H22_S0.16180.787
143_P148_Q0.161540.786
125_G130_R0.161420.785
136_G139_R0.160820.782
127_L134_L0.160590.781
12_S19_E0.159920.778
103_T107_K0.159490.776
9_Q18_R0.158470.771
34_I120_V0.158210.769
55_D117_R0.158120.769
53_V57_T0.157770.767
80_G92_T0.156990.763
104_P109_F0.156980.763
100_R105_E0.15670.762
32_V47_V0.155290.755
82_S114_S0.155140.754
119_I123_A0.154740.753
23_G27_N0.154150.750
57_T60_R0.153480.746
132_R139_R0.153480.746
128_K137_R0.153320.746
100_R107_K0.152930.744
82_S115_S0.152820.743
85_P95_K0.152750.743
47_V147_P0.15210.740
3_G125_G0.151730.738
145_K150_I0.151210.735
17_Q28_H0.150150.730
8_I23_G0.149090.725
46_S62_S0.148840.724
54_H82_S0.148770.723
35_V44_Y0.148450.722
41_R131_F0.147930.719
143_P147_P0.147920.719
137_R151_L0.147590.718
122_R125_G0.147460.717
42_I147_P0.146910.714
147_P153_C0.146460.712
18_R22_S0.146160.711
147_P154_C0.145740.709
22_S31_K0.145460.707
56_S85_P0.145190.706
150_I155_V0.145150.706
135_R145_K0.145130.706
91_L95_K0.144490.703
5_H9_Q0.143970.700
55_D121_E0.14390.700
144_E147_P0.143750.699
140_L149_I0.143480.698
27_N30_L0.143370.697
77_Y109_F0.143360.697
90_L94_Y0.142980.695
45_V151_L0.142680.694
39_D87_S0.142450.693
143_P146_A0.142070.691
4_T7_P0.1420.691
11_P18_R0.14150.688
107_K110_N0.141440.688
35_V131_F0.141310.687
9_Q17_Q0.141030.686
79_L113_H0.140830.685
20_F24_K0.140140.682
66_D88_P0.139660.679
99_G107_K0.139330.678
140_L145_K0.139040.676
113_H127_L0.1390.676
4_T19_E0.138930.676
56_S59_F0.138430.673
54_H121_E0.13840.673
5_H31_K0.138360.673
44_Y67_R0.138070.671
135_R138_L0.138060.671
8_I17_Q0.13790.671
79_L112_R0.137670.669
45_V154_C0.13760.669
124_F128_K0.1370.666
40_G118_I0.136990.666
94_Y110_N0.136960.666
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
4fw1A0.835449.50.896
1cxqA0.816542.20.901
3kksA0.772235.20.904
1c0mA0.797533.90.905
4fw2A0.835428.90.908
1bcoA0.860827.20.91
1musA0.810124.80.911
3av9A0.759518.70.916
1ex4A0.772217.60.917
1j27A0.3924160.918
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