GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RuvB_C - Holliday junction DNA helicase ruvB C-terminus
Pfam: PF05491 (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: 76
Sequences: 32303
Seq/Len: 425.04
HH_delta: 0.107 (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
16_T34_A2.513362.152
20_N34_A2.396222.051
13_Y45_V2.336132.000
27_G30_T2.213511.895
59_T64_V2.137851.830
57_Q64_V2.09651.795
10_D49_Y2.03791.745
10_D53_I2.035561.743
18_I73_L1.94431.664
10_D45_V1.924991.648
7_D10_D1.865251.597
51_I58_R1.840471.576
16_T20_N1.8171.555
30_T33_A1.790761.533
18_I65_A1.717081.470
37_E41_T1.651531.414
15_K19_E1.63951.404
40_E43_E1.591691.363
43_E48_P1.536811.316
38_D41_T1.535971.315
14_L55_F1.414561.211
57_Q66_T1.384491.185
29_D39_K1.338371.146
71_E74_G1.334851.143
54_G68_K1.32151.131
16_T35_L1.307881.120
14_L18_I1.295111.109
44_D49_Y1.27511.092
15_K73_L1.243051.064
70_Y74_G1.242831.064
67_P71_E1.225161.049
29_D33_A1.217761.042
9_L45_V1.198791.026
14_L73_L1.190061.019
18_I70_Y1.188911.018
16_T19_E1.177551.008
66_T69_A1.161860.995
32_A39_K1.148870.984
44_D48_P1.142030.978
8_E12_R1.131610.969
54_G57_Q1.094960.937
28_L46_I1.088320.932
48_P51_I1.076780.922
48_P52_Q1.047140.896
68_K72_H1.027190.879
39_K43_E1.019260.873
68_K71_E1.01170.866
12_R15_K1.000040.856
12_R16_T0.996890.853
30_T34_A0.986580.845
17_L56_I0.982360.841
20_N26_V0.975570.835
9_L37_E0.957950.820
48_P58_R0.950810.814
38_D44_D0.942220.807
32_A42_I0.928710.795
18_I74_G0.926790.793
20_N30_T0.925960.793
31_L42_I0.919240.787
45_V49_Y0.910340.779
26_V30_T0.904720.775
7_D45_V0.899090.770
56_I63_R0.881360.755
28_L43_E0.87690.751
67_P70_Y0.871480.746
55_F72_H0.866140.741
41_T44_D0.858690.735
65_A70_Y0.855230.732
28_L63_R0.853570.731
37_E42_I0.849550.727
16_T31_L0.8430.722
43_E58_R0.842580.721
65_A69_A0.839250.718
51_I56_I0.81660.699
11_R15_K0.809250.693
19_E34_A0.80150.686
17_L31_L0.791430.678
14_L56_I0.788260.675
13_Y42_I0.770470.660
7_D49_Y0.768790.658
49_Y52_Q0.759580.650
6_L53_I0.758880.650
41_T45_V0.752490.644
28_L42_I0.751490.643
55_F68_K0.738440.632
70_Y73_L0.735720.630
46_I51_I0.730840.626
9_L49_Y0.730240.625
35_L42_I0.728060.623
9_L12_R0.725110.621
31_L56_I0.717360.614
13_Y37_E0.713130.610
49_Y53_I0.710570.608
28_L39_K0.656830.562
6_L10_D0.643360.551
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
2o0mA0.947498.80.107
4aikA0.960598.80.11
4em2A0.947498.70.121
3fm5A0.960598.70.126
2fxaA0.947498.70.126
3k0lA0.947498.70.131
3echA0.947498.70.139
3hsrA0.947498.70.141
3s2wA0.947498.70.142
4hblA0.947498.70.142

Page generated in 0.04 seconds.