GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HNH_4 - HNH endonuclease
Pfam: PF13395 (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: 54
Sequences: 3644
Seq/Len: 67.48
HH_delta: 0.058 (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_C44_C2.106673.530
4_C41_C1.350912.264
21_D38_V1.281062.147
41_C44_C1.279582.144
19_E46_R1.256542.106
19_E42_K1.230972.063
3_Y40_C1.08911.825
2_P39_L1.005241.684
21_D45_N0.982581.646
25_P28_R0.982051.646
21_D48_K0.976911.637
42_K46_R0.933251.564
27_S50_N0.892041.495
20_I37_L0.858481.439
40_C45_N0.811711.360
1_C44_C0.757421.269
8_I18_Y0.71161.192
2_P38_V0.699611.172
1_C41_C0.69811.170
26_R32_D0.672171.126
6_K41_C0.667871.119
18_Y39_L0.655681.099
3_Y38_V0.637391.068
23_I38_V0.629081.054
45_N49_G0.616141.032
1_C4_C0.589620.988
28_R50_N0.571760.958
21_D40_C0.564710.946
9_S12_N0.55370.928
43_E47_S0.537340.900
38_V48_K0.493430.827
19_E45_N0.473630.794
7_P10_I0.461080.773
10_I18_Y0.443990.744
2_P34_F0.441080.739
19_E40_C0.441050.739
32_D37_L0.440640.738
31_D35_W0.440190.738
3_Y48_K0.438580.735
2_P37_L0.41960.703
11_E18_Y0.412550.691
43_E46_R0.406330.681
46_R49_G0.405660.680
22_H45_N0.40450.678
7_P12_N0.398580.668
24_I29_G0.387840.650
6_K10_I0.380090.637
33_S37_L0.371720.623
20_I32_D0.368810.618
20_I39_L0.350130.587
8_I39_L0.34470.578
24_I28_R0.340610.571
26_R29_G0.339230.568
6_K43_E0.337280.565
6_K11_E0.330230.553
2_P20_I0.329780.553
24_I30_G0.320910.538
8_I41_C0.314620.527
37_L46_R0.308250.517
26_R37_L0.304340.510
22_H32_D0.298050.499
12_N18_Y0.295810.496
3_Y23_I0.293370.492
7_P11_E0.293330.492
36_N48_K0.291320.488
19_E22_H0.290190.486
23_I36_N0.286020.479
2_P23_I0.284230.476
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
2qgpA0.907499.10.058
3m7kA0.944496.10.565
1e7lA0.888990.70.658
7ceiB0.870489.70.665
1fr2B0.870488.30.674
2jb0B0.8704880.675
2pu3A179.60.707
3plwA0.8889660.734
1w4rA0.759357.80.747
2orvA0.833354.40.752

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