GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_S7 - Peptidase S7 Flavivirus NS3 serine protease
Pfam: PF00949 (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: CL0124
Length: 132
Sequences: 2051
Seq/Len: 15.54
HH_delta: 0.344 (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
105_N109_E1.754726.886
24_V102_P0.824043.234
102_P110_I0.694552.726
53_P110_I0.694162.724
24_V113_L0.69322.720
80_V88_G0.641242.516
24_V110_I0.610542.396
61_D77_G0.604752.373
61_D106_Q0.58642.301
54_S109_E0.52882.075
24_V53_P0.476811.871
23_G32_F0.46181.812
69_W118_V0.454261.783
53_P56_G0.435831.710
63_I106_Q0.402631.580
27_M31_V0.364251.429
32_F46_W0.359631.411
31_V45_R0.353131.386
67_G72_D0.34091.338
62_L106_Q0.337741.325
36_W40_R0.333631.309
58_V83_Y0.313351.230
30_G45_R0.304221.194
28_K49_K0.301721.184
52_D55_W0.29511.158
64_S103_I0.294981.158
56_G111_V0.294571.156
53_P104_F0.288361.132
72_D87_I0.28151.105
29_E45_R0.278331.092
87_I117_G0.276931.087
27_M30_G0.276471.085
83_Y88_G0.275461.081
62_L80_V0.273681.074
95_P98_S0.271591.066
22_I25_G0.263031.032
85_Y116_N0.259561.019
60_E77_G0.257481.010
69_W117_G0.256611.007
62_L111_V0.253130.993
34_T37_H0.25230.990
117_G121_G0.251210.986
28_K51_L0.248660.976
103_I114_Y0.247230.970
35_M114_Y0.246280.966
85_Y118_V0.246130.966
63_I75_W0.243460.955
67_G70_K0.243170.954
87_I116_N0.242610.952
73_L102_P0.241860.949
36_W39_T0.238770.937
63_I77_G0.238530.936
75_W79_E0.238380.935
24_V68_P0.236230.927
59_R66_G0.2340.918
70_K96_K0.233480.916
96_K117_G0.230450.904
90_I103_I0.230390.904
102_P114_Y0.228530.897
81_Q89_A0.228010.895
61_D87_I0.226420.889
79_E98_S0.22360.877
74_K89_A0.222550.873
35_M38_V0.219570.862
31_V121_G0.217260.853
35_M115_G0.215060.844
30_G71_L0.213960.840
91_D95_P0.212160.833
39_T42_A0.211670.831
118_V121_G0.210830.827
81_Q95_P0.210280.825
50_R53_P0.207240.813
44_L49_K0.20710.813
64_S78_E0.205630.807
23_G34_T0.202590.795
92_L104_F0.20190.792
37_H99_S0.201590.791
44_L54_S0.201440.791
64_S114_Y0.201330.790
48_G109_E0.200540.787
50_R54_S0.199050.781
85_Y117_G0.197970.777
69_W120_V0.197820.776
55_W110_I0.195490.767
105_N111_V0.19490.765
81_Q98_S0.194860.765
68_P79_E0.194670.764
40_R120_V0.194210.762
90_I114_Y0.192950.757
69_W95_P0.188630.740
35_M98_S0.187410.735
22_I102_P0.185840.729
40_R48_G0.184050.722
104_F114_Y0.183980.722
80_V83_Y0.182810.717
41_G49_K0.182760.717
55_W63_I0.182610.717
90_I94_F0.181140.711
87_I115_G0.179550.705
97_G100_G0.179490.704
25_G46_W0.178360.700
91_D114_Y0.176610.693
96_K120_V0.17650.693
58_V65_Y0.176240.692
24_V116_N0.175850.690
64_S76_H0.175780.690
23_G37_H0.174530.685
72_D118_V0.174080.683
68_P98_S0.173080.679
76_H82_Q0.171530.673
104_F116_N0.170640.670
26_V87_I0.169080.664
96_K121_G0.168990.663
59_R74_K0.168860.663
74_K95_P0.167780.658
38_V97_G0.166520.653
28_K52_D0.165170.648
86_G116_N0.16480.647
60_E106_Q0.16420.644
65_Y77_G0.164110.644
65_Y75_W0.163030.640
41_G96_K0.162680.638
22_I67_G0.162030.636
30_G33_H0.161810.635
74_K81_Q0.161540.634
48_G85_Y0.161460.634
28_K41_G0.16140.633
62_L104_F0.160340.629
32_F118_V0.160040.628
49_K52_D0.159310.625
71_L120_V0.159270.625
26_V52_D0.159210.625
28_K31_V0.15890.624
69_W121_G0.158650.623
43_A49_K0.158150.621
52_D56_G0.157940.620
53_P57_S0.157740.619
26_V29_E0.157060.616
49_K107_N0.157030.616
36_W86_G0.15650.614
72_D83_Y0.156160.613
89_A95_P0.155720.611
58_V87_I0.155570.611
78_E81_Q0.155070.609
41_G54_S0.154480.606
64_S115_G0.154340.606
64_S112_G0.154250.605
31_V55_W0.15330.602
36_W115_G0.153120.601
26_V110_I0.15310.601
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
3u1jB0.992499.90.344
3e90B0.992499.90.344
4a8cA199.90.345
2fomB0.992499.90.347
2ggvB0.992499.90.348
2fp7B0.992499.90.348
3pv2A199.90.352
3stjA199.90.364
1ky9A199.90.364
3stiA199.90.37

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