GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Hjc - Archaeal holliday junction resolvase (hjc)
Pfam: PF01870 (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: 88
Sequences: 1223
Seq/Len: 13.9
HH_delta: 0.087 (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
42_K50_Y0.887833.822
2_F43_S0.718913.095
7_V17_V0.698353.006
17_V30_A0.641992.764
4_R19_R0.537492.314
38_A63_S0.487462.099
7_V28_I0.482582.078
7_V19_R0.482432.077
15_F30_A0.387251.667
15_F32_K0.36731.581
8_K12_E0.364631.570
30_A39_I0.353771.523
7_V11_W0.351031.511
8_K11_W0.313331.349
21_A65_R0.301611.298
60_K64_K0.291931.257
57_E61_E0.281351.211
9_I13_R0.280941.209
15_F37_L0.271061.167
54_E57_E0.270681.165
32_K35_R0.262281.129
6_L20_A0.260471.121
36_Y66_F0.257991.111
32_K37_L0.252691.088
31_G34_G0.246791.062
26_G29_I0.242341.043
40_E55_Q0.230470.992
7_V30_A0.229830.989
52_E55_Q0.228620.984
29_I38_A0.225160.969
38_A59_L0.222720.959
25_G58_K0.222270.957
58_K62_F0.217090.935
21_A66_F0.216380.932
20_A55_Q0.213120.917
3_E42_K0.213120.917
11_W17_V0.207590.894
56_V60_K0.207070.891
31_G66_F0.20510.883
21_A29_I0.203690.877
25_G51_L0.203620.877
6_L10_L0.203010.874
5_E47_D0.20230.871
2_F41_V0.196720.847
23_S64_K0.195580.842
16_A33_G0.195540.842
60_K63_S0.19510.840
61_E64_K0.192330.828
16_A48_K0.190930.822
51_L55_Q0.190140.819
55_Q59_L0.187640.808
3_E40_E0.187420.807
44_T55_Q0.186670.804
2_F55_Q0.185640.799
40_E44_T0.178930.770
6_L9_I0.177980.766
49_I66_F0.175860.757
48_K61_E0.174380.751
35_R47_D0.172130.741
11_W36_Y0.168960.727
42_K51_L0.168610.726
53_K57_E0.168340.725
33_G64_K0.168170.724
18_V31_G0.166380.716
8_K47_D0.166170.715
52_E59_L0.165750.714
59_L64_K0.165750.714
12_E48_K0.163430.704
23_S65_R0.163380.703
2_F22_G0.162060.698
56_V67_G0.160890.693
4_R61_E0.159730.688
9_I12_E0.159280.686
56_V62_F0.159160.685
54_E61_E0.159110.685
54_E58_K0.157430.678
61_E65_R0.15640.673
44_T58_K0.155910.671
23_S62_F0.155030.667
8_K13_R0.152960.659
18_V36_Y0.151570.653
5_E54_E0.151540.652
4_R8_K0.150820.649
12_E22_G0.150810.649
4_R16_A0.15050.648
9_I56_V0.149850.645
44_T50_Y0.14980.645
35_R53_K0.149610.644
43_S50_Y0.149560.644
13_R19_R0.149360.643
15_F56_V0.149250.643
26_G62_F0.149240.642
51_L62_F0.149130.642
34_G45_S0.148970.641
11_W51_L0.148550.640
11_W34_G0.147830.636
33_G45_S0.14740.635
55_Q66_F0.146970.633
38_A44_T0.146750.632
20_A37_L0.1460.629
27_D42_K0.145710.627
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
1gefA199.80.087
1ob8A199.80.103
2eo0A0.988699.80.145
1hh1A0.988699.80.152
2wcwA199.80.153
3fovA199.50.335
1y88A0.965998.40.59
1xmxA0.977393.10.79
2vldA0.943291.70.799
4f0qA0.988669.30.844

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