GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
F-protein - Negative factor (F-Protein) or Nef
Pfam: PF00469 (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: 220
Sequences: 2393
Seq/Len: 10.88
HH_delta: 0.043 (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
50_V60_I1.146734.584
106_H206_Y0.990643.960
118_F197_V0.870433.479
169_E172_E0.865333.459
178_C184_Q0.846763.385
52_Q55_E0.806793.225
203_R207_R0.786353.143
165_V197_V0.736782.945
100_L137_I0.704192.815
121_Q125_E0.700492.800
174_G177_N0.678462.712
203_R209_I0.677652.709
203_R206_Y0.67292.690
209_I213_L0.663572.652
102_I206_Y0.661192.643
102_I106_H0.624842.498
115_E160_F0.619932.478
161_K201_D0.619192.475
105_S159_L0.589152.355
121_Q191_P0.587492.348
169_E197_V0.569332.276
7_S10_V0.565852.262
122_R133_N0.542432.168
106_H203_R0.540872.162
122_R125_E0.52442.096
66_K76_D0.509232.035
10_V13_P0.506622.025
168_E172_E0.491411.964
165_V183_A0.490911.962
43_G55_E0.485811.942
99_K102_I0.483541.933
119_Y124_Q0.476461.904
50_V72_C0.47271.889
185_Q193_G0.466381.864
65_T73_A0.464891.858
207_R212_E0.45041.800
185_Q189_D0.444441.776
111_K122_R0.434891.738
60_I72_C0.434781.738
10_V15_L0.432791.730
202_S206_Y0.42661.705
98_Y150_I0.396591.585
119_Y191_P0.394161.575
206_Y209_I0.393411.572
98_Y102_I0.387821.550
125_E191_P0.373841.494
178_C185_Q0.369991.479
7_S13_P0.365421.461
45_S211_R0.358131.431
62_S68_Q0.356851.426
99_K110_E0.354141.416
65_T68_Q0.34721.388
7_S11_G0.34511.379
14_E21_R0.341661.366
60_I68_Q0.339381.357
9_S13_P0.315551.261
124_Q143_N0.313551.253
155_T218_F0.311771.246
146_P155_T0.308761.234
75_L133_N0.308221.232
9_S18_R0.306011.223
19_L117_I0.305031.219
173_E184_Q0.304281.216
177_N184_Q0.30311.212
165_V169_E0.302141.208
99_K103_D0.301721.206
142_Q155_T0.298491.193
2_G7_S0.298471.193
152_Y160_F0.29751.189
20_R56_K0.292371.169
104_L131_V0.291131.164
152_Y209_I0.288321.152
10_V14_E0.279071.115
67_Q76_D0.274191.096
169_E191_P0.271891.087
110_E119_Y0.270751.082
188_M191_P0.267181.068
167_P197_V0.266921.067
131_V137_I0.265541.061
18_R21_R0.263691.054
105_S152_Y0.261891.047
93_L133_N0.261311.044
65_T69_N0.259551.037
105_S209_I0.259081.036
102_I203_R0.258711.034
66_K72_C0.258441.033
168_E178_C0.257721.030
171_E174_G0.250391.001
122_R131_V0.249670.998
213_L216_E0.249290.996
121_Q189_D0.246190.984
161_K207_R0.241690.966
2_G11_G0.240970.963
137_I142_Q0.238360.953
201_D207_R0.236140.944
45_S71_D0.235340.941
57_H62_S0.235090.940
19_L22_T0.234510.937
176_N184_Q0.232780.930
69_N195_V0.230370.921
88_R102_I0.22860.914
3_K6_K0.225610.902
185_Q188_M0.224130.896
119_Y218_F0.223990.895
14_E71_D0.223020.891
213_L217_Y0.221580.886
68_Q72_C0.219320.877
150_I160_F0.21850.873
209_I212_E0.216710.866
67_Q71_D0.21640.865
159_L205_A0.214360.857
156_F160_F0.214020.855
98_Y209_I0.212610.850
1_G6_K0.211790.847
75_L125_E0.211470.845
82_E133_N0.209570.838
67_Q191_P0.208780.835
121_Q124_Q0.205770.822
119_Y161_K0.205770.822
131_V135_Q0.205510.821
105_S115_E0.205210.820
10_V19_L0.20430.817
73_A76_D0.204070.816
17_E80_E0.203680.814
150_I163_V0.20260.810
57_H60_I0.201910.807
74_W77_S0.201580.806
100_L104_L0.201410.805
66_K70_A0.200520.801
170_E174_G0.199860.799
99_K109_K0.198870.795
9_S14_E0.198870.795
177_N183_A0.197540.790
106_H202_S0.197250.788
93_L137_I0.197080.788
62_S67_Q0.196540.786
213_L220_D0.195860.783
119_Y193_G0.195370.781
217_Y220_D0.194860.779
49_A64_N0.191310.765
214_H220_D0.191190.764
165_V168_E0.191040.764
50_V63_S0.190940.763
117_I122_R0.189770.759
66_K73_A0.18950.757
191_P197_V0.189390.757
50_V57_H0.189040.756
161_K212_E0.189010.755
121_Q193_G0.188860.755
13_P18_R0.188480.753
146_P217_Y0.18840.753
80_E133_N0.187940.751
175_E192_H0.187120.748
71_D124_Q0.185530.742
100_L109_K0.184890.739
115_E206_Y0.184640.738
193_G197_V0.184610.738
166_D169_E0.184540.738
201_D212_E0.183890.735
189_D195_V0.182280.729
161_K209_I0.182220.728
121_Q192_H0.178770.715
45_S52_Q0.177360.709
99_K203_R0.175130.700
161_K199_K0.173950.695
102_I152_Y0.173690.694
48_G53_D0.172680.690
79_E122_R0.171760.687
17_E21_R0.17150.686
150_I209_I0.171480.685
1_G5_S0.171460.685
211_R220_D0.171380.685
97_T100_L0.170750.683
168_E183_A0.17060.682
155_T203_R0.169950.679
44_A47_K0.169880.679
76_D192_H0.168280.673
14_E45_S0.166920.667
11_G21_R0.166060.664
52_Q56_K0.1660.664
13_P111_K0.165770.663
79_E133_N0.165570.662
80_E98_Y0.164620.658
48_G58_G0.164510.658
45_S55_E0.162140.648
15_L21_R0.161850.647
119_Y152_Y0.16130.645
99_K111_K0.160850.643
169_E207_R0.159770.639
68_Q73_A0.159290.637
102_I156_F0.158430.633
173_E177_N0.158310.633
100_L131_V0.157920.631
93_L100_L0.157470.629
65_T71_D0.156540.626
119_Y201_D0.156530.626
204_L210_A0.156470.625
66_K71_D0.15620.624
169_E173_E0.156110.624
210_A215_P0.155590.622
75_L189_D0.155360.621
137_I143_N0.154080.616
80_E88_R0.15370.614
14_E22_T0.153590.614
7_S14_E0.152610.610
46_G75_L0.152050.608
67_Q70_A0.151660.606
54_L58_G0.151470.605
183_A193_G0.151280.605
201_D209_I0.150050.600
168_E192_H0.149790.599
171_E177_N0.149630.598
67_Q199_K0.14960.598
14_E155_T0.149490.598
191_P207_R0.14920.596
106_H168_E0.148890.595
102_I137_I0.148370.593
9_S21_R0.147960.591
69_N73_A0.147080.588
168_E199_K0.147030.588
45_S69_N0.147010.588
216_E219_K0.1470.588
9_S20_R0.146610.586
57_H219_K0.146410.585
58_G74_W0.146240.585
131_V142_Q0.146110.584
170_E173_E0.145510.582
132_Y138_F0.145260.581
4_W13_P0.145170.580
167_P170_E0.145120.580
97_T110_E0.144070.576
194_E198_W0.143790.575
190_D194_E0.143170.572
57_H71_D0.143030.572
130_Y134_E0.14260.570
56_K62_S0.142530.570
15_L20_R0.142510.570
2_G19_L0.142390.569
165_V173_E0.142090.568
105_S202_S0.141670.566
102_I115_E0.141650.566
61_T64_N0.141270.565
76_D203_R0.141250.565
165_V170_E0.140830.563
206_Y213_L0.140820.563
48_G51_S0.140670.562
213_L219_K0.140090.560
60_I75_L0.139960.559
117_I189_D0.139840.559
86_P90_Q0.139430.557
115_E152_Y0.138760.555
166_D178_C0.138580.554
60_I67_Q0.138560.554
62_S66_K0.138480.554
76_D106_H0.138370.553
46_G58_G0.137640.550
68_Q76_D0.137320.549
14_E165_V0.137110.548
62_S71_D0.136980.548
99_K115_E0.136960.547
21_R56_K0.13660.546
20_R169_E0.136080.544
60_I73_A0.135260.541
156_F219_K0.13470.538
82_E125_E0.134470.537
174_G183_A0.134450.537
67_Q119_Y0.13420.536
121_Q169_E0.134050.536
102_I109_K0.133770.535
2_G5_S0.133730.535
13_P56_K0.133610.534
110_E117_I0.132930.531
15_L124_Q0.132880.531
47_K51_S0.132560.530
209_I216_E0.132140.528
74_W78_D0.13210.528
10_V133_N0.131990.528
74_W125_E0.131990.528
170_E193_G0.131910.527
181_H185_Q0.131760.527
47_K54_L0.13170.526
197_V218_F0.131480.526
10_V20_R0.131460.525
104_L135_Q0.131080.524
168_E193_G0.130970.523
57_H63_S0.130430.521
43_G47_K0.129780.519
76_D133_N0.129740.519
211_R218_F0.128340.513
7_S20_R0.128310.513
12_W16_R0.128150.512
111_K207_R0.12810.512
199_K203_R0.127790.511
110_E114_L0.127530.510
57_H72_C0.127320.509
17_E20_R0.127140.508
96_M101_A0.126740.507
82_E122_R0.126570.506
170_E183_A0.126280.505
99_K107_F0.125990.504
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
4en2B0.91821000.043
3reaA0.74091000.17
3ik5A0.651000.254
2vikA0.18642.90.984
3j39n0.10912.80.984
3iz5q0.10912.80.984
3izcq0.10912.70.984
4dexB0.47732.60.984
3j3bn0.10912.50.984
2ys2A0.12.30.985

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