GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GP120 - Envelope glycoprotein GP120
Pfam: PF00516 (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: 488
Sequences: 6078
Seq/Len: 12.45
HH_delta: 0.198 (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
263_T429_L1.196465.796
273_E315_E1.045065.063
210_K248_E0.778613.772
57_K255_E0.777533.767
333_N339_K0.767543.718
333_N340_T0.747723.622
45_P208_N0.734773.560
326_K329_E0.704873.415
210_K247_E0.701053.396
270_E315_E0.695153.368
270_E318_N0.692893.357
198_A204_I0.670793.250
52_N217_P0.668213.237
304_D395_R0.654123.169
255_E258_T0.652883.163
215_T255_E0.64213.111
211_K248_E0.640283.102
371_K393_P0.636123.082
270_E322_Q0.623873.022
257_I330_H0.621743.012
342_I440_N0.61742.991
255_E259_D0.606362.938
289_H294_A0.599812.906
332_N339_K0.569242.758
273_E422_T0.566572.745
342_I442_T0.556532.696
171_R402_M0.548762.659
280_G418_N0.541652.624
16_T59_N0.53822.607
154_K174_N0.52272.532
269_N322_Q0.513842.489
97_T102_N0.504752.445
249_E326_K0.496662.406
143_D171_R0.483082.340
209_D220_K0.481722.334
314_G388_D0.46592.257
325_E328_R0.463282.244
255_E262_K0.456972.214
318_N322_Q0.453232.196
154_K173_I0.452342.191
324_A376_W0.444282.152
289_H293_Q0.443052.146
290_I293_Q0.43942.129
81_K405_R0.434922.107
397_K400_V0.429412.080
315_E318_N0.429092.079
275_N422_T0.422252.046
309_H313_S0.422232.046
309_H391_T0.422062.045
13_K16_T0.407431.974
290_I295_F0.407211.973
142_R145_K0.405721.966
253_R456_S0.401691.946
318_N321_Q0.396141.919
300_D416_R0.393541.907
314_G371_K0.387561.878
321_Q324_A0.379811.840
137_I148_E0.370861.797
130_M280_G0.36881.787
284_R300_D0.366021.773
314_G317_N0.359011.739
148_E285_K0.357471.732
74_Q181_T0.357151.730
190_E361_G0.353931.715
211_K249_E0.352441.707
321_Q325_E0.352431.707
246_A249_E0.35061.699
405_R408_K0.347251.682
135_F150_A0.342941.661
158_V399_I0.340711.651
250_I324_A0.339131.643
324_A328_R0.338931.642
267_Q271_S0.336991.633
297_A300_D0.335571.626
47_E220_K0.335041.623
287_S294_A0.332471.611
477_K482_Q0.331961.608
211_K220_K0.329561.597
273_E277_T0.328341.591
141_I171_R0.327321.586
402_M405_R0.325711.578
128_E131_K0.325061.575
155_L171_R0.324661.573
269_N273_E0.322881.564
287_S300_D0.322031.560
255_E449_D0.319161.546
328_R376_W0.31911.546
143_D402_M0.317821.540
140_E174_N0.316431.533
287_S302_I0.315331.528
255_E261_A0.314471.523
211_K215_T0.314331.523
154_K159_P0.309781.501
250_I257_I0.309381.499
304_D307_Q0.308941.497
401_N408_K0.308391.494
93_D131_K0.307631.490
325_E329_E0.307531.490
66_E150_A0.303581.471
259_D449_D0.301761.462
263_T446_G0.299661.452
446_G449_D0.298421.446
143_D295_F0.297641.442
282_N287_S0.297421.441
137_I171_R0.296841.438
383_N386_T0.295731.433
287_S299_G0.293721.423
146_Q154_K0.292751.418
248_E269_N0.292081.415
271_S322_Q0.289931.405
140_E146_Q0.286621.389
353_I357_S0.282971.371
181_T408_K0.282391.368
288_I294_A0.281651.364
275_N420_T0.281191.362
94_V130_M0.276631.340
131_K157_V0.275911.337
45_P209_D0.275671.336
143_D153_Y0.275181.333
141_I174_N0.275021.332
153_Y171_R0.272741.321
312_I315_E0.270531.311
361_G420_T0.270011.308
351_P355_T0.268261.300
275_N315_E0.267821.297
137_I141_I0.267091.294
289_H295_F0.265511.286
250_I267_Q0.263681.277
294_A297_A0.263531.277
280_G416_R0.263361.276
324_A375_T0.262051.270
208_N211_K0.26181.268
283_T287_S0.261581.267
158_V171_R0.261491.267
382_S386_T0.261371.266
45_P220_K0.259891.259
250_I319_T0.259881.259
283_T302_I0.259411.257
267_Q456_S0.25921.256
275_N418_N0.258921.254
280_G302_I0.258761.254
213_N217_P0.255921.240
213_N255_E0.255511.238
209_D213_N0.25541.237
93_D128_E0.255241.237
198_A209_D0.254671.234
171_R174_N0.253281.227
143_D290_I0.252021.221
261_A331_F0.251471.218
130_M301_I0.251231.217
346_S446_G0.249491.209
81_K181_T0.248881.206
319_T376_W0.244971.187
102_N105_T0.243631.180
174_N179_V0.241811.171
283_T416_R0.240841.167
280_G393_P0.240321.164
16_T62_E0.238861.157
342_I345_P0.238661.156
128_E157_V0.236411.145
13_K467_E0.236391.145
137_I142_R0.236051.144
248_E251_I0.235651.142
322_Q325_E0.235161.139
317_N324_A0.235041.139
418_N422_T0.234531.136
54_N255_E0.234221.135
134_S149_Y0.234011.134
149_Y285_K0.233971.133
295_F300_D0.233491.131
485_R488_R0.233411.131
93_D157_V0.233121.129
281_N302_I0.233091.129
62_E451_R0.231151.120
137_I146_Q0.230821.118
257_I331_F0.230141.115
285_K297_A0.229891.114
90_N136_N0.229051.110
188_S196_Y0.228611.108
332_N340_T0.228531.107
47_E208_N0.228231.106
479_R482_Q0.227081.100
265_I429_L0.225011.090
148_E180_I0.224751.089
259_D262_K0.22271.079
137_I145_K0.221171.071
299_G416_R0.220471.068
211_K217_P0.220351.068
148_E177_T0.22011.066
384_N387_N0.219171.062
137_I140_E0.218711.060
290_I294_A0.217471.054
249_E329_E0.216951.051
386_T389_T0.216051.047
61_V456_S0.215431.044
285_K299_G0.215191.043
328_R340_T0.215061.042
188_S361_G0.213081.032
145_K293_Q0.212011.027
52_N215_T0.211531.025
255_E263_T0.211141.023
202_F465_E0.210841.021
149_Y154_K0.210811.021
136_N142_R0.210651.021
277_T422_T0.21051.020
142_R290_I0.209461.015
125_N128_E0.209171.013
449_D452_D0.208851.012
90_N93_D0.208811.012
152_F157_V0.208231.009
355_T368_N0.20771.006
130_M153_Y0.207591.006
3_V7_Y0.207531.005
257_I332_N0.20751.005
14_E198_A0.20721.004
140_E145_K0.205990.998
416_R420_T0.205750.997
351_P405_R0.204710.992
159_P173_I0.204140.989
296_Y299_G0.20410.989
127_K130_M0.202990.983
263_T268_L0.201140.974
250_I272_V0.199860.968
263_T346_S0.199680.967
270_E273_E0.199580.967
395_R401_N0.199260.965
57_K262_K0.198910.964
4_T7_Y0.196030.950
274_I356_H0.195060.945
174_N180_I0.194610.943
143_D148_E0.194470.942
282_N302_I0.19410.940
281_N287_S0.193470.937
312_I371_K0.193380.937
148_E179_V0.193280.936
55_M215_T0.192540.933
45_P210_K0.192530.933
74_Q177_T0.192010.930
59_N62_E0.191930.930
141_I290_I0.191340.927
74_Q405_R0.189430.918
328_R332_N0.189060.916
267_Q270_E0.187510.908
313_S422_T0.187320.907
287_S416_R0.187150.907
371_K391_T0.186110.902
232_K271_S0.184860.896
126_E130_M0.184270.893
249_E269_N0.183870.891
142_R402_M0.183760.890
344_N440_N0.183720.890
261_A347_S0.183650.890
249_E322_Q0.183440.889
211_K251_I0.183410.889
351_P408_K0.181550.880
157_V171_R0.181280.878
311_N422_T0.18070.875
47_E209_D0.180370.874
151_L174_N0.180220.873
210_K251_I0.179950.872
446_G451_R0.179510.870
13_K177_T0.179180.868
198_A206_K0.179110.868
324_A332_N0.178790.866
68_I198_A0.177960.862
145_K148_E0.177310.859
142_R293_Q0.176950.857
313_S389_T0.176710.856
361_G419_I0.176690.856
2_W7_Y0.176460.855
209_D215_T0.176410.855
356_H369_T0.175830.852
346_S431_T0.175810.852
284_R287_S0.175680.851
157_V174_N0.175680.851
155_L400_V0.175680.851
288_I293_Q0.174840.847
287_S297_A0.172850.837
189_F413_P0.172840.837
293_Q302_I0.172720.837
130_M151_L0.172620.836
314_G390_I0.172230.834
287_S293_Q0.1720.833
261_A353_I0.1710.828
209_D217_P0.170510.826
267_Q322_Q0.169960.823
2_W6_Y0.169010.819
16_T465_E0.168890.818
189_F255_E0.168630.817
331_F339_K0.168530.816
321_Q376_W0.168530.816
14_E45_P0.168530.816
174_N402_M0.167590.812
177_T401_N0.167130.810
174_N399_I0.167040.809
174_N293_Q0.166870.808
312_I345_P0.166730.808
158_V173_I0.166650.807
142_R149_Y0.166360.806
190_E202_F0.166310.806
155_L397_K0.166270.806
150_A405_R0.166040.804
288_I295_F0.165240.801
177_T181_T0.164980.799
467_E475_K0.16490.799
94_V157_V0.164760.798
281_N416_R0.164550.797
208_N269_N0.164160.795
446_G452_D0.164140.795
273_E424_N0.16410.795
94_V149_Y0.163910.794
13_K465_E0.163850.794
4_T8_G0.163730.793
420_T467_E0.163620.793
261_A446_G0.163270.791
66_E329_E0.16320.791
130_M399_I0.163160.790
287_S295_F0.16260.788
215_T257_I0.161820.784
284_R302_I0.161220.781
314_G318_N0.161030.780
138_T174_N0.160510.778
13_K401_N0.160370.777
143_D255_E0.160160.776
142_R171_R0.160120.776
93_D154_K0.160120.776
370_S376_W0.160050.775
321_Q370_S0.159890.775
140_E179_V0.159760.774
179_V410_M0.159760.774
406_V410_M0.158970.770
5_V8_G0.158620.768
132_N149_Y0.158340.767
345_P370_S0.157390.762
361_G418_N0.156810.760
131_K154_K0.156270.757
408_K422_T0.155760.755
284_R296_Y0.155370.753
217_P220_K0.155160.752
148_E288_I0.155060.751
315_E319_T0.154850.750
272_V319_T0.154420.748
174_N198_A0.154240.747
482_Q486_E0.154160.747
258_T331_F0.153670.744
311_N314_G0.153010.741
52_N66_E0.152680.740
45_P211_K0.152650.740
432_R435_G0.152330.738
52_N150_A0.152310.738
344_N442_T0.152240.738
389_T418_N0.152050.737
181_T405_R0.151680.735
146_Q180_I0.151330.733
74_Q136_N0.151030.732
331_F443_F0.150980.731
319_T323_V0.150420.729
328_R342_I0.150410.729
94_V300_D0.150280.728
2_W5_V0.150240.728
465_E469_L0.149970.727
275_N317_N0.149360.724
280_G285_K0.149350.724
62_E66_E0.148650.720
190_E232_K0.148570.720
94_V131_K0.148520.720
3_V6_Y0.14850.719
145_K174_N0.148230.718
351_P400_V0.147970.717
351_P401_N0.147930.717
250_I322_Q0.14760.715
273_E420_T0.147280.714
351_P369_T0.147180.713
217_P255_E0.146440.709
208_N215_T0.146350.709
170_Y174_N0.145530.705
94_V280_G0.145470.705
137_I149_Y0.145460.705
141_I144_K0.14540.704
342_I346_S0.145230.704
138_T142_R0.145090.703
171_R177_T0.144560.700
280_G309_H0.144450.700
55_M263_T0.144440.700
145_K154_K0.144290.699
309_H393_P0.144180.698
88_T143_D0.143710.696
255_E295_F0.143330.694
432_R441_E0.143070.693
397_K401_N0.143050.693
268_L429_L0.142810.692
371_K392_L0.142780.692
288_I297_A0.142760.692
145_K354_T0.14250.690
142_R181_T0.141840.687
324_A342_I0.141820.687
312_I392_L0.141750.687
13_K18_T0.141640.686
275_N313_S0.141630.686
342_I376_W0.141410.685
252_I257_I0.141350.685
145_K408_K0.141330.685
317_N323_V0.141310.685
141_I160_I0.141140.684
283_T288_I0.140860.682
16_T408_K0.140130.679
255_E370_S0.140060.679
257_I261_A0.140010.678
481_V486_E0.139990.678
408_K418_N0.139920.678
321_Q328_R0.13970.677
287_S291_G0.139360.675
267_Q324_A0.139280.675
126_E129_E0.139230.675
148_E154_K0.139170.674
96_N102_N0.13910.674
297_A357_S0.139030.674
14_E52_N0.138780.672
177_T400_V0.138620.672
280_G301_I0.138460.671
1_L4_T0.138110.669
148_E171_R0.138070.669
68_I431_T0.137610.667
420_T424_N0.137340.665
326_K351_P0.137150.664
281_N288_I0.136980.664
280_G307_Q0.136730.662
397_K402_M0.136480.661
312_I319_T0.136470.661
481_V485_R0.135980.659
93_D149_Y0.135890.658
198_A208_N0.135780.658
8_G12_W0.135740.658
202_F257_I0.135410.656
181_T401_N0.134990.654
224_T297_A0.134850.653
249_E271_S0.134790.653
255_E413_P0.13470.653
296_Y300_D0.134260.650
275_N424_N0.134080.650
160_I376_W0.134040.649
104_T125_N0.133920.649
346_S351_P0.133870.649
480_V485_R0.133870.649
357_S428_L0.133710.648
174_N187_V0.133690.648
257_I267_Q0.133460.647
97_T126_E0.133410.646
288_I299_G0.133310.646
275_N389_T0.133260.646
307_Q313_S0.132720.643
66_E148_E0.13250.642
177_T477_K0.132380.641
181_T293_Q0.13220.640
284_R299_G0.131950.639
339_K442_T0.131470.637
148_E295_F0.131310.636
277_T313_S0.130740.633
143_D174_N0.130460.632
253_R267_Q0.130430.632
17_T198_A0.130380.632
311_N391_T0.130340.631
140_E293_Q0.130280.631
476_A481_V0.130260.631
280_G300_D0.130140.630
345_P440_N0.130010.630
46_L208_N0.129950.630
280_G287_S0.129480.627
130_M154_K0.129380.627
277_T315_E0.129370.627
4_T10_P0.129340.627
251_I269_N0.129170.626
149_Y288_I0.129070.625
282_N300_D0.128720.624
148_E153_Y0.128580.623
232_K361_G0.128530.623
151_L157_V0.128340.622
261_A429_L0.128310.622
482_Q485_R0.128270.621
405_R431_T0.128130.621
137_I180_I0.128110.621
93_D127_K0.127810.619
141_I146_Q0.127560.618
325_E376_W0.127520.618
323_V429_L0.127340.617
189_F479_R0.126980.615
324_A446_G0.126940.615
9_V12_W0.12680.614
81_K84_P0.126580.613
171_R399_I0.126560.613
289_H300_D0.126360.612
437_N440_N0.126260.612
179_V289_H0.126020.611
3_V8_G0.125990.610
44_I466_I0.125980.610
140_E482_Q0.125380.607
272_V345_P0.125320.607
277_T420_T0.124980.605
332_N342_I0.124870.605
388_D391_T0.124610.604
16_T45_P0.124570.603
44_I482_Q0.124470.603
480_V486_E0.124460.603
412_A415_I0.124220.602
71_L188_S0.124160.602
480_V488_R0.123960.601
145_K179_V0.123450.598
329_E413_P0.12320.597
198_A211_K0.123070.596
353_I446_G0.122860.595
104_T439_N0.12260.594
465_E475_K0.122570.594
280_G288_I0.122470.593
353_I431_T0.122080.591
355_T395_R0.122040.591
307_Q311_N0.121940.591
255_E324_A0.121490.589
270_E275_N0.121430.588
293_Q482_Q0.121410.588
66_E251_I0.12140.588
324_A377_N0.121370.588
317_N321_Q0.121330.588
90_N94_V0.12120.587
7_Y10_P0.121060.586
321_Q383_N0.120910.586
361_G369_T0.120790.585
189_F329_E0.120740.585
140_E154_K0.120720.585
45_P408_K0.12060.584
320_L324_A0.120190.582
97_T104_T0.120140.582
312_I317_N0.120080.582
329_E332_N0.120060.582
202_F220_K0.119860.581
377_N383_N0.119650.580
46_L471_V0.119560.579
434_G441_E0.119350.578
5_V10_P0.119240.578
263_T295_F0.119090.577
151_L173_I0.118720.575
251_I326_K0.118710.575
92_T136_N0.118540.574
141_I399_I0.118440.574
181_T357_S0.118420.574
280_G283_T0.11840.574
251_I257_I0.118370.573
245_L272_V0.118350.573
140_E289_H0.118110.572
62_E467_E0.11810.572
376_W467_E0.117860.571
146_Q174_N0.11770.570
68_I392_L0.117640.570
150_A251_I0.117610.570
155_L395_R0.116970.567
145_K482_Q0.11690.566
328_R377_N0.116680.565
147_K154_K0.116480.564
473_P478_R0.116450.564
188_S366_Y0.116380.564
141_I154_K0.116220.563
140_E148_E0.116160.563
177_T408_K0.116130.563
476_A479_R0.116080.562
472_A478_R0.116070.562
346_S354_T0.116010.562
142_R180_I0.115990.562
275_N324_A0.115950.562
323_V371_K0.115870.561
2_W8_G0.115820.561
141_I179_V0.115810.561
411_Y414_P0.115730.561
251_I267_Q0.115550.560
4_T12_W0.115510.560
145_K370_S0.115390.559
187_V410_M0.115260.558
208_N220_K0.115170.558
399_I402_M0.115170.558
15_A19_L0.115140.558
288_I393_P0.115130.558
131_K413_P0.115080.558
315_E422_T0.1150.557
147_K401_N0.114950.557
309_H422_T0.114680.556
314_G319_T0.114470.555
376_W388_D0.114240.553
161_D382_S0.114190.553
478_R488_R0.114160.553
294_A300_D0.114140.553
326_K330_H0.114020.552
138_T154_K0.114010.552
318_N323_V0.113870.552
293_Q351_P0.113860.552
190_E376_W0.113860.552
392_L431_T0.113490.550
5_V12_W0.113420.549
215_T220_K0.113390.549
140_E354_T0.113350.549
285_K288_I0.113060.548
153_Y290_I0.113010.547
146_Q173_I0.112790.546
146_Q162_N0.112460.545
346_S371_K0.112460.545
279_P307_Q0.112380.544
52_N213_N0.112190.544
293_Q405_R0.112060.543
262_K449_D0.112040.543
97_T127_K0.112020.543
187_V290_I0.111930.542
345_P354_T0.111640.541
125_N130_M0.111610.541
288_I370_S0.111610.541
202_F347_S0.111550.540
280_G297_A0.11150.540
154_K179_V0.111320.539
179_V357_S0.111180.539
7_Y12_W0.111130.538
179_V416_R0.110690.536
279_P389_T0.110520.535
346_S353_I0.109840.532
280_G304_D0.109830.532
482_Q487_K0.109690.531
11_V18_T0.10960.531
297_A428_L0.109470.530
220_K431_T0.109390.530
311_N420_T0.109320.530
47_E211_K0.109090.528
28_V188_S0.109070.528
481_V488_R0.109040.528
295_F400_V0.108990.528
96_N104_T0.108940.528
478_R485_R0.108920.528
126_E307_Q0.10860.526
468_P472_A0.10850.526
361_G416_R0.10850.526
11_V14_E0.108460.525
287_S296_Y0.10830.525
90_N137_I0.108180.524
263_T449_D0.108170.524
149_Y413_P0.108130.524
326_K405_R0.108050.523
422_T467_E0.107990.523
404_Q409_A0.107950.523
321_Q375_T0.107870.523
479_R486_E0.107840.522
154_K157_V0.107750.522
273_E312_I0.107690.522
74_Q401_N0.107610.521
468_P473_P0.107510.521
105_T437_N0.107130.519
96_N125_N0.107080.519
224_T406_V0.107050.519
16_T211_K0.106970.518
481_V487_K0.106820.518
289_H297_A0.106760.517
272_V294_A0.106660.517
152_F174_N0.106490.516
147_K174_N0.106440.516
363_E367_C0.106370.515
411_Y421_C0.106340.515
62_E68_I0.106150.514
317_N376_W0.106120.514
405_R449_D0.105880.513
177_T467_E0.105840.513
295_F299_G0.105840.513
283_T300_D0.105730.512
16_T482_Q0.105620.512
304_D418_N0.105430.511
142_R148_E0.105050.509
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
3jwdA0.73771000.198
4jzzA0.72131000.237
4j6rG0.70491000.252
4dkpA0.70291000.253
2ny1A0.63111000.332
3lqaG0.64751000.34
2bf1A0.62091000.35
4i3sG0.3771000.668
3tygA0.38321000.756
4jpkA0.31351000.805

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