GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
rve - Integrase core domain
Pfam: PF00665 (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: CL0219
Length: 120
Sequences: 12301
Seq/Len: 102.51
HH_delta: 0.039 (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
99_P105_Q1.882022.949
29_V113_N1.677882.629
10_Q33_D1.39352.184
111_R114_R1.345372.108
38_I112_F1.265671.983
57_K87_W1.21511.904
41_F58_R1.203291.886
6_G9_W1.193151.870
14_T117_K1.184241.856
98_T106_N1.154441.809
7_E69_R1.13581.780
75_N97_F1.127941.768
48_T51_A1.126731.766
87_W91_L1.111521.742
111_R115_T1.105591.733
73_T95_H1.097331.720
8_R70_V1.09481.716
88_C93_I1.061811.664
33_D108_F1.025561.607
70_V96_V1.01411.589
11_I73_T1.002741.571
114_R118_R1.000721.568
49_A53_L0.992591.556
109_V113_N0.950381.489
10_Q109_V0.940441.474
88_C95_H0.929421.457
11_I71_I0.925161.450
72_R96_V0.897851.407
85_E95_H0.896911.406
53_L87_W0.889141.393
75_N100_P0.855131.340
14_T27_L0.845641.325
106_N109_V0.836741.311
102_T105_Q0.825331.293
8_R33_D0.817931.282
98_T105_Q0.779341.221
13_F78_E0.777031.218
80_T97_F0.744761.167
11_I30_F0.739341.159
10_Q106_N0.73791.156
76_G79_F0.733371.149
8_R72_R0.722181.132
13_F43_V0.720451.129
45_S48_T0.720011.128
29_V109_V0.719071.127
99_P102_T0.707021.108
45_S51_A0.701161.099
15_P26_Y0.688811.079
28_L79_F0.686221.075
84_F88_C0.684351.072
77_S80_T0.67431.057
26_Y46_K0.66341.040
14_T113_N0.657561.030
42_P58_R0.654941.026
10_Q108_F0.649021.017
53_L57_K0.648341.016
5_P35_S0.647651.015
39_Y62_K0.636310.997
36_R108_F0.635680.996
9_W30_F0.634330.994
30_F55_A0.632690.992
50_E54_R0.62590.981
5_P34_Y0.624770.979
31_I109_V0.615180.964
17_P24_R0.613470.961
110_E113_N0.612420.960
86_A90_H0.608650.954
15_P24_R0.600230.941
57_K91_L0.588910.923
53_L83_A0.585740.918
77_S81_S0.580830.910
46_K78_E0.580120.909
111_R118_R0.580050.909
115_T118_R0.576810.904
42_P54_R0.575810.902
11_I79_F0.568380.891
72_R98_T0.567030.889
106_N110_E0.566020.887
104_Q107_G0.563730.883
28_L55_A0.554210.869
31_I36_R0.553080.867
81_S84_F0.549870.862
13_F28_L0.549240.861
9_W59_A0.54380.852
49_A83_A0.542610.850
30_F59_A0.539790.846
60_I68_P0.539030.845
59_A63_R0.536320.840
50_E83_A0.533230.836
28_L52_A0.531740.833
57_K61_E0.525470.823
31_I108_F0.525030.823
32_D35_S0.524570.822
73_T79_F0.52130.817
70_V94_K0.519750.815
31_I38_I0.50710.795
86_A89_K0.506480.794
27_L116_L0.505060.791
83_A86_A0.502790.788
61_E64_G0.500760.785
82_H86_A0.499020.782
115_T119_R0.49360.774
85_E89_K0.493020.773
27_L40_A0.490530.769
28_L51_A0.486370.762
75_N80_T0.485450.761
103_P113_N0.479870.752
72_R105_Q0.47670.747
56_L60_I0.475420.745
64_G68_P0.4750.744
78_E81_S0.473860.743
39_Y59_A0.472990.741
112_F115_T0.467890.733
51_A54_R0.462040.724
49_A81_S0.460710.722
59_A64_G0.456540.715
17_P22_G0.455010.713
13_F26_Y0.454560.712
31_I112_F0.451710.708
61_E65_G0.445620.698
29_V112_F0.443650.695
60_I91_L0.442190.693
113_N116_L0.440470.690
56_L73_T0.437930.686
37_F63_R0.430530.675
9_W12_D0.430220.674
59_A65_G0.428620.672
71_I84_F0.426580.669
72_R106_N0.426430.668
24_R44_S0.420960.660
50_E53_L0.41990.658
40_A116_L0.41910.657
113_N117_K0.418350.656
109_V112_F0.414740.650
73_T97_F0.413350.648
69_R93_I0.405610.636
87_W90_H0.404760.634
10_Q72_R0.402020.630
9_W68_P0.398980.625
11_I28_L0.398760.625
60_I65_G0.397930.624
55_A58_R0.392470.615
112_F116_L0.392220.615
96_V105_Q0.390940.613
44_S51_A0.38930.610
75_N101_Y0.383770.601
41_F59_A0.38350.601
41_F55_A0.383480.601
25_V45_S0.382880.600
65_G68_P0.382870.600
54_R58_R0.382780.600
75_N103_P0.382250.599
98_T102_T0.380480.596
75_N98_T0.378060.592
14_T29_V0.376870.591
62_K65_G0.372810.584
24_R42_P0.365360.573
103_P107_G0.362790.569
51_A55_A0.359080.563
17_P21_K0.355710.557
29_V38_I0.353580.554
13_F52_A0.353240.554
6_G10_Q0.352810.553
13_F79_F0.352540.552
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
1c0mA0.958399.80.039
4fw1A0.958399.70.045
1cxqA0.958399.70.047
4fw2A0.958399.70.063
3oymA0.958399.70.091
1bcoA0.97599.70.094
2x78A0.9599.70.103
3hphA0.916799.70.11
3kksA0.883399.70.111
1ex4A0.916799.70.12

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