GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HNH_2 - HNH endonuclease
Pfam: PF13391 (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: CL0263
Length: 66
Sequences: 1037
Seq/Len: 15.71
HH_delta: 0.702 (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
4_T54_L0.828423.099
4_T51_R0.79722.982
16_E55_H0.703872.633
51_R54_L0.653342.444
17_A47_G0.652292.440
16_E56_K0.592082.215
18_A55_H0.509041.904
18_A59_D0.460341.722
16_E52_P0.356261.333
55_H59_D0.343531.285
47_G58_F0.33541.255
14_L52_P0.331451.240
44_P47_G0.306061.145
14_L62_L0.300611.124
52_P56_K0.284851.065
26_G29_W0.283961.062
13_E62_L0.281791.054
15_L23_F0.279121.044
59_D65_I0.276811.035
14_L56_K0.275791.032
8_D13_E0.270651.012
26_G30_M0.269471.008
54_L63_F0.264560.990
18_A23_F0.263380.985
20_I46_N0.261770.979
2_V14_L0.257050.961
22_P61_G0.246910.924
56_K60_R0.245330.918
15_L49_L0.24480.916
21_V61_G0.242170.906
58_F61_G0.236740.886
19_H55_H0.234780.878
5_G17_A0.232910.871
20_I58_F0.232030.868
23_F61_G0.2310.864
21_V26_G0.230420.862
3_I65_I0.228620.855
8_D65_I0.227050.849
21_V30_M0.221360.828
53_D62_L0.217640.814
14_L57_L0.210940.789
7_R15_L0.207850.777
49_L59_D0.204890.766
17_A61_G0.203950.763
20_I48_L0.203040.759
3_I62_L0.200390.750
60_R63_F0.199160.745
16_E29_W0.197980.741
47_G61_G0.191320.716
7_R20_I0.190880.714
26_G44_P0.18880.706
2_V8_D0.188450.705
2_V5_G0.186170.696
20_I64_A0.180310.674
6_I43_S0.179090.670
12_W45_S0.176520.660
3_I54_L0.175760.657
21_V64_A0.173410.649
12_W43_S0.172930.647
54_L57_L0.172470.645
2_V49_L0.17050.638
25_L29_W0.170140.636
26_G43_S0.164640.616
14_L53_D0.164320.615
57_L62_L0.163990.613
25_L30_M0.163710.612
8_D12_W0.163230.611
21_V25_L0.163140.610
15_L61_G0.162090.606
24_S31_N0.159840.598
15_L57_L0.157950.591
7_R13_E0.156580.586
49_L53_D0.154180.577
21_V29_W0.153940.576
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
2qgpA0.772793.40.702
3htkC0.681815.90.847
3qwuA0.333313.50.851
1r6zP0.469710.60.858
3g27A0.83338.60.863
2nn6I0.33335.50.874
3uxjA0.90915.30.875
3mj0A0.42425.20.875
4aqtA0.87885.20.876
3nvqA0.93945.10.876
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