GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Helicase_Sgs1 - Sgs1 RecQ helicase
Pfam: PF11408 (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: CL0426
Length: 80
Sequences: 2334
Seq/Len: 29.18
HH_delta: 0.15 (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
17_I21_N1.289013.213
46_T49_E1.076562.684
15_I67_F0.912052.274
8_A43_L0.846912.111
8_A71_L0.839392.092
9_Y40_A0.760811.897
15_I19_L0.756741.886
47_E65_K0.7411.847
59_Q62_K0.713361.778
38_K42_K0.708031.765
11_K70_T0.665181.658
39_M71_L0.654021.630
47_E51_S0.65291.628
65_K69_D0.649681.620
25_P29_N0.648921.618
19_L22_R0.61631.536
11_K73_R0.613611.530
51_S58_E0.589251.469
45_T49_E0.588811.468
39_M67_F0.568321.417
39_M56_I0.563671.405
19_L66_Y0.52981.321
12_L36_L0.524341.307
34_T54_V0.480161.197
50_F68_K0.479231.195
66_Y70_T0.453821.131
38_K54_V0.448991.119
17_I27_N0.444771.109
19_L23_M0.444061.107
15_I70_T0.442051.102
29_N32_S0.43541.085
26_P29_N0.428321.068
10_E13_R0.424991.059
38_K41_T0.418861.044
31_M56_I0.408971.020
26_P33_D0.403981.007
66_Y69_D0.396630.989
9_Y13_R0.386130.963
31_M36_L0.383790.957
69_D73_R0.382290.953
15_I18_N0.378140.943
14_E18_N0.377540.941
57_N60_Q0.376790.939
16_S33_D0.374930.935
38_K53_L0.371360.926
15_I66_Y0.361080.900
47_E61_R0.360230.898
51_S61_R0.350650.874
9_Y36_L0.346310.863
47_E68_K0.342960.855
23_M63_K0.339460.846
19_L67_F0.332110.828
31_M67_F0.327810.817
50_F61_R0.322040.803
20_S26_P0.321540.802
28_D57_N0.300050.748
28_D33_D0.298410.744
10_E37_K0.297490.742
37_K41_T0.293310.731
20_S23_M0.292460.729
39_M50_F0.290680.725
13_R33_D0.286440.714
50_F67_F0.283430.707
42_K53_L0.28140.701
31_M60_Q0.275520.687
18_N22_R0.275430.687
7_S10_E0.273520.682
7_S58_E0.268770.670
45_T69_D0.268730.670
44_P50_F0.26810.668
45_T72_M0.267550.667
35_I56_I0.25920.646
13_R36_L0.256610.640
70_T73_R0.255450.637
45_T68_K0.253360.632
16_S20_S0.244720.610
15_I50_F0.243680.607
15_I39_M0.243550.607
50_F64_F0.238250.594
9_Y37_K0.237440.592
24_N32_S0.236370.589
55_G60_Q0.234860.585
48_E51_S0.234660.585
40_A43_L0.232690.580
28_D32_S0.229990.573
44_P49_E0.228480.570
69_D72_M0.227080.566
33_D60_Q0.226960.566
35_I55_G0.225370.562
44_P68_K0.22530.562
28_D60_Q0.225070.561
53_L60_Q0.224570.560
49_E52_K0.22290.556
58_E61_R0.222890.556
32_S35_I0.221660.553
23_M58_E0.217410.542
43_L71_L0.216870.541
43_L47_E0.21540.537
37_K62_K0.214360.534
64_F68_K0.212720.530
8_A12_L0.212390.529
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
1wudA199.50.15
2dgzA0.987599.50.175
2e1fA0.987599.50.179
2rrdA199.50.191
2kv2A199.50.198
2rhfA0.9599.40.21
3safA199.40.246
2hbjA199.30.247
1yt3A0.987599.30.286
3cymA199.20.291

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