GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NERD - Nuclease-related domain
Pfam: PF08378 (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: CL0236
Length: 115
Sequences: 1043
Seq/Len: 9.07
HH_delta: 0.784 (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
27_N39_E0.475393.042
42_H55_V0.4492.873
5_G57_N0.399052.553
9_V55_V0.349842.238
54_E84_Q0.343052.195
56_K84_Q0.32452.076
85_V89_A0.316172.023
85_V88_Q0.277461.775
10_A42_H0.266991.708
26_H42_H0.266121.703
17_L22_Y0.264681.693
6_E54_E0.242761.553
40_I43_L0.230851.477
52_V89_A0.224851.439
64_G80_N0.218021.395
22_Y46_T0.216521.385
10_A26_H0.213361.365
45_I50_I0.206271.320
39_E42_H0.203091.299
11_E15_K0.202911.298
6_E56_K0.202331.295
72_Q78_F0.202151.293
24_V44_V0.200611.284
41_D56_K0.199181.274
41_D54_E0.186431.193
52_V85_V0.184431.180
52_V92_L0.184341.179
22_Y44_V0.18221.166
5_G55_V0.181851.163
30_L38_R0.181261.160
62_I72_Q0.181021.158
71_F77_E0.180151.153
3_A57_N0.17581.125
83_E87_R0.17541.122
90_Q93_K0.16921.083
18_P22_Y0.169181.082
54_E81_P0.168621.079
27_N42_H0.158281.013
4_A8_R0.156851.004
69_Q77_E0.155530.995
29_R79_K0.153430.982
57_N72_Q0.153270.981
60_G72_Q0.152760.977
39_E54_E0.152020.973
9_V53_I0.151360.968
41_D84_Q0.150840.965
89_A93_K0.150470.963
39_E88_Q0.149530.957
52_V88_Q0.148930.953
34_Q65_D0.147940.947
27_N38_R0.145050.928
13_L44_V0.14490.927
50_I96_L0.144680.926
9_V13_L0.144080.922
54_E88_Q0.142110.909
63_Y73_E0.141910.908
65_D68_G0.141250.904
30_L95_L0.140810.901
90_Q94_N0.140530.899
86_R90_Q0.14020.897
60_G64_G0.139090.890
7_Q19_D0.138750.888
86_R93_K0.138520.886
84_Q88_Q0.138420.886
13_L24_V0.138310.885
91_A95_L0.132720.849
66_E83_E0.132590.848
17_L60_G0.132580.848
44_V53_I0.132290.846
79_K86_R0.131910.844
27_N60_G0.131870.844
10_A39_E0.131280.840
42_H49_G0.131090.839
34_Q55_V0.130420.834
70_W81_P0.130370.834
61_K74_N0.128420.822
48_K51_F0.128170.820
51_F82_L0.12790.818
12_R18_P0.127720.817
8_R46_T0.127350.815
48_K53_I0.12690.812
11_E16_H0.126310.808
48_K94_N0.126030.806
81_P84_Q0.125580.803
70_W78_F0.125320.802
64_G68_G0.124440.796
92_L95_L0.123930.793
72_Q75_K0.123070.787
51_F62_I0.12280.786
64_G70_W0.121960.780
7_Q15_K0.121790.779
23_H43_L0.121530.778
10_A27_N0.121210.776
68_G95_L0.120080.768
4_A75_K0.119930.767
52_V76_K0.119790.766
5_G30_L0.11960.765
66_E75_K0.119130.762
20_D50_I0.11890.761
46_T49_G0.118450.758
3_A7_Q0.118230.756
5_G84_Q0.117980.755
84_Q87_R0.117710.753
40_I88_Q0.117390.751
13_L23_H0.116540.746
10_A24_V0.116350.744
61_K73_E0.115310.738
12_R94_N0.114220.731
29_R38_R0.113970.729
20_D63_Y0.113920.729
9_V12_R0.11290.722
68_G83_E0.112060.717
4_A7_Q0.112050.717
35_G58_W0.1120.717
13_L79_K0.111460.713
68_G73_E0.110630.708
76_K94_N0.11050.707
46_T51_F0.110430.707
44_V93_K0.109850.703
83_E86_R0.109530.701
54_E80_N0.109130.698
15_K96_L0.108960.697
59_S72_Q0.108930.697
58_W88_Q0.108410.694
44_V84_Q0.10830.693
66_E86_R0.108280.693
16_H22_Y0.108090.692
40_I52_V0.108030.691
79_K84_Q0.107870.690
3_A35_G0.107350.687
11_E19_D0.107290.686
3_A10_A0.106940.684
25_F40_I0.105610.676
18_P74_N0.104750.670
74_N96_L0.104640.669
23_H59_S0.104610.669
83_E89_A0.104070.666
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
2wcwA0.782695.40.784
1y88A0.878395.40.784
3fovA0.8174950.791
1gefA0.747894.30.798
2eo0A0.782692.20.813
1hh1A0.921791.80.815
1xmxA0.782688.60.828
1ob8A0.808787.20.831
2vldA0.739171.10.856
3h1tA0.852242.10.878
If you are interested in a protein containing this domain,
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