GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ORF6N - ORF6N domain
Pfam: PF10543 (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. )
Length: 88
Sequences: 523
Seq/Len: 5.94
HH_delta: 0.833 (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
28_T31_R0.865644.827
6_E11_R0.489312.729
31_R62_G0.437562.440
31_R59_S0.40122.237
64_S71_T0.39032.177
58_K72_R0.386392.155
28_T62_G0.359322.004
83_A86_V0.325831.817
80_R83_A0.316281.764
59_S62_G0.315941.762
27_K63_I0.31351.748
27_K31_R0.295131.646
83_A87_K0.28961.615
64_S69_K0.257221.434
6_E9_G0.24961.392
67_I70_R0.241441.346
58_K64_S0.227531.269
30_N48_Q0.227171.267
27_K30_N0.224991.255
48_Q75_Y0.222271.239
64_S68_G0.212351.184
26_T30_N0.209521.168
3_Q20_E0.20871.164
6_E10_Q0.206891.154
39_R83_A0.204911.143
13_M17_D0.203611.135
54_L58_K0.202811.131
58_K63_I0.197981.104
16_E76_L0.195941.093
82_Y85_L0.192041.071
44_K87_K0.188661.052
80_R84_M0.186811.042
14_T76_L0.1861.037
5_I13_M0.185611.035
40_F81_G0.184491.029
52_E56_E0.179911.003
17_D20_E0.175960.981
68_G71_T0.175510.979
30_N34_K0.17540.978
32_N35_R0.173120.965
58_K68_G0.172370.961
56_E66_N0.172320.961
80_R88_I0.169150.943
52_E55_K0.168960.942
80_R87_K0.168850.942
33_F77_F0.166970.931
37_K46_Y0.166120.926
80_R86_V0.166050.926
15_D77_F0.163980.914
35_R62_G0.163450.911
39_R79_E0.163230.910
21_L86_V0.162670.907
18_L45_D0.161810.902
67_I71_T0.160070.893
66_N70_R0.158980.887
22_Y86_V0.155260.866
51_G54_L0.154150.860
84_M88_I0.153170.854
4_I8_R0.152760.852
6_E16_E0.151830.847
66_N69_K0.151390.844
19_A22_Y0.150190.838
23_G87_K0.147510.823
54_L71_T0.145890.814
49_L57_L0.145720.813
51_G73_N0.145420.811
68_G72_R0.145130.809
4_I9_G0.144620.806
36_N40_F0.144030.803
10_Q20_E0.143460.800
4_I13_M0.141910.791
19_A29_I0.140580.784
83_A88_I0.140470.783
22_Y82_Y0.139720.779
31_R34_K0.138820.774
49_L76_L0.138770.774
26_T74_L0.138670.773
17_D25_E0.138570.773
28_T32_N0.138450.772
58_K61_L0.138170.771
13_M21_L0.137830.769
57_L66_N0.135550.756
24_V32_N0.135030.753
39_R87_K0.135020.753
29_I39_R0.134690.751
3_Q8_R0.134130.748
60_Q63_I0.133860.746
57_L68_G0.133190.743
78_T81_G0.132750.740
18_L82_Y0.132680.740
56_E67_I0.132610.739
15_D19_A0.132390.738
16_E70_R0.132210.737
8_R53_E0.132050.736
21_L24_V0.131450.733
54_L73_N0.131290.732
14_T74_L0.131190.732
3_Q17_D0.131180.732
30_N75_Y0.130870.730
27_K34_K0.129620.723
29_I88_I0.128970.719
11_R20_E0.127870.713
3_Q16_E0.127790.713
45_D82_Y0.12740.710
82_Y87_K0.126310.704
58_K69_K0.12450.694
27_K58_K0.123730.690
85_L88_I0.122920.685
28_T59_S0.122560.683
32_N88_I0.122120.681
37_K51_G0.121410.677
46_Y87_K0.12110.675
6_E87_K0.12090.674
60_Q64_S0.120750.673
21_L83_A0.120170.670
45_D80_R0.119650.667
58_K71_T0.118990.664
63_I69_K0.118620.661
14_T46_Y0.118250.659
59_S63_I0.116390.649
57_L67_I0.115940.647
50_T70_R0.115870.646
45_D81_G0.115670.645
15_D30_N0.115580.645
45_D77_F0.115240.643
31_R35_R0.114510.639
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
1y6uA0.727387.50.833
1j9iA0.7573.50.855
3h0gB0.87563.90.864
1twfB0.87563.50.864
3sqnA0.931858.90.868
1l0oC0.465957.60.869
1l9zH0.62554.90.871
3iydF0.62553.30.872
4kn7X0.625530.872
1qpzA0.784152.30.873
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0164 seconds.