GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Asp - Eukaryotic aspartyl protease
Pfam: PF00026 (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: CL0129
Length: 317
Sequences: 3932
Seq/Len: 12.4
HH_delta: 0.042 (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
5_N14_T0.628083.776
53_F74_V0.566573.406
171_W313_G0.56393.390
238_C275_C0.506163.043
8_I28_V0.503143.025
143_L206_T0.502723.022
139_N308_E0.478952.880
213_L218_F0.478752.878
88_Q129_Q0.456232.743
182_V204_L0.454612.733
6_V17_V0.43852.636
248_T255_T0.437482.630
306_D311_R0.43352.606
169_L304_V0.422342.539
22_G207_G0.415062.495
262_D300_N0.400962.411
233_V238_C0.40012.405
4_I19_I0.392812.362
114_F310_N0.391112.351
45_Y53_F0.386442.323
8_I78_V0.359462.161
306_D309_N0.358972.158
171_W311_R0.358092.153
248_T257_T0.355392.137
170_V256_F0.353152.123
60_F91_G0.347832.091
222_I277_L0.346272.082
7_T14_T0.344592.072
246_D257_T0.340922.050
188_S250_T0.338642.036
142_S302_Y0.336252.022
204_L314_F0.334642.012
215_R219_D0.330431.987
73_L89_T0.32271.940
17_V26_T0.311681.874
213_L291_W0.308291.853
5_N16_R0.307561.849
10_T51_S0.300341.806
46_N49_K0.296781.784
115_P128_D0.29591.779
250_T255_T0.294411.770
206_T298_L0.293291.763
31_S46_N0.292981.761
259_P262_D0.287491.728
126_F130_L0.278691.676
112_L157_F0.271951.635
210_Y278_G0.269371.619
22_G205_D0.266171.600
128_D307_Y0.260951.569
160_Y304_V0.258491.554
184_L249_F0.25721.546
45_Y74_V0.25371.525
79_S84_T0.253111.522
60_F69_V0.252021.515
33_C39_C0.251761.514
7_T12_P0.251461.512
249_F293_L0.250741.507
214_P291_W0.249751.502
211_I296_P0.244051.467
160_Y165_Y0.243681.465
256_F301_Y0.23751.428
142_S156_T0.226871.364
20_D23_S0.226011.359
45_Y52_T0.225711.357
124_P132_Q0.223961.346
125_T128_D0.22381.346
130_L135_L0.223371.343
260_P263_Y0.222621.338
27_W64_Y0.220841.328
172_V314_F0.217551.308
205_D208_T0.216821.304
74_V92_L0.214461.289
77_T86_P0.213151.281
21_T207_G0.213011.281
278_G296_P0.212941.280
30_S92_L0.211741.273
293_L297_F0.211091.269
171_W304_V0.211081.269
130_L136_I0.2111.269
218_F222_I0.210971.268
166_D316_Q0.20921.258
298_L305_F0.208851.256
60_F71_G0.208191.252
79_S82_G0.207871.250
161_D164_K0.207431.247
26_T78_V0.206351.241
172_V251_F0.205341.235
215_R281_P0.204491.229
131_V139_N0.204081.227
36_C39_C0.203081.221
85_I126_F0.201891.214
184_L251_F0.20011.203
118_S125_T0.199361.199
225_L277_L0.196161.179
186_S250_T0.195991.178
78_V88_Q0.195431.175
298_L303_V0.194631.170
196_S200_Q0.194531.170
45_Y50_S0.194261.168
154_S164_K0.193981.166
9_G76_D0.193881.166
174_L312_I0.193841.165
140_V159_G0.193491.163
245_P263_Y0.192771.159
52_T76_D0.191761.153
4_I17_V0.191671.152
23_S207_G0.191111.149
182_V251_F0.190321.144
24_S113_G0.19031.144
141_F305_F0.190171.143
46_N50_S0.188471.133
50_S76_D0.187841.129
69_V93_A0.187661.128
185_D250_T0.187611.128
256_F297_F0.187591.128
165_Y315_A0.186751.123
188_S255_T0.186161.119
139_N307_Y0.184381.109
55_N72_N0.183571.104
72_N94_D0.183571.104
181_S201_Q0.183431.103
110_L126_F0.183151.101
45_Y92_L0.182861.099
246_D259_P0.18281.099
213_L217_I0.182391.097
184_L202_A0.182041.094
42_S107_D0.181551.092
208_T292_I0.180871.087
54_S87_N0.180651.086
10_T77_T0.180041.082
73_L123_Y0.181.082
140_V160_Y0.178811.075
218_F279_I0.178111.071
47_P53_F0.177361.066
11_P51_S0.176411.061
179_Y203_I0.175931.058
129_Q133_Q0.175621.056
247_L279_I0.175561.055
265_F278_G0.175351.054
165_Y302_Y0.175281.054
138_S308_E0.175021.052
64_Y207_G0.174821.051
234_Y238_C0.174411.049
17_V108_G0.17371.044
170_V254_V0.173141.041
19_I143_L0.173081.041
23_S205_D0.171861.033
45_Y76_D0.171551.031
189_I245_P0.17151.031
235_S238_C0.171321.030
165_Y169_L0.170581.026
204_L293_L0.170521.025
93_A96_Y0.17021.023
18_L66_D0.170111.023
172_V182_V0.169431.019
20_D207_G0.168371.012
17_V110_L0.168351.012
15_F28_V0.168291.012
23_S64_Y0.16791.009
19_I155_L0.16721.005
131_V136_I0.166150.999
156_T159_G0.163220.981
204_L312_I0.163120.981
140_V304_V0.16250.977
175_V201_Q0.159770.961
112_L141_F0.158220.951
175_V181_S0.158050.950
303_V314_F0.157910.949
50_S53_F0.157710.948
61_S70_S0.157430.946
153_G158_G0.157430.946
6_V26_T0.156870.943
221_I247_L0.156850.943
109_I207_G0.156540.941
29_P107_D0.155440.935
54_S75_S0.155070.932
221_I279_I0.154620.930
53_F92_L0.154320.928
143_L155_L0.154290.928
26_T110_L0.15310.920
204_L305_F0.152950.920
219_D223_K0.151210.909
169_L316_Q0.151130.909
75_S87_N0.150380.904
75_S89_T0.14940.898
86_P133_Q0.148520.893
219_D281_P0.147990.890
22_G208_T0.147960.890
127_L136_I0.14740.886
180_W307_Y0.147250.885
77_T84_T0.147220.885
258_I263_Y0.146740.882
114_F177_S0.145680.876
78_V90_F0.145610.875
22_G206_T0.145590.875
304_V315_A0.145150.873
10_T13_Q0.144990.872
222_I225_L0.144970.872
130_L157_F0.143540.863
203_I292_I0.143440.862
160_Y169_L0.143410.862
262_D299_R0.143230.861
174_L180_W0.142560.857
39_C44_F0.142530.857
2_Y295_S0.142120.854
117_L179_Y0.141990.854
212_Y280_Q0.141540.851
21_T205_D0.140260.843
144_Y164_K0.140020.842
220_A223_K0.140.842
27_W93_A0.139950.841
76_D90_F0.139530.839
3_Y16_R0.139330.838
66_D106_F0.138940.835
20_D27_W0.137890.829
146_N153_G0.137870.829
145_L295_S0.136150.819
27_W69_V0.135590.815
114_F174_L0.135460.814
233_V239_N0.135370.814
182_V312_I0.135250.813
85_I130_L0.135050.812
307_Y310_N0.134620.809
113_G274_Y0.134240.807
224_A227_G0.133960.805
8_I90_F0.133870.805
22_G64_Y0.133670.804
244_L260_P0.13360.803
177_S310_N0.133530.803
124_P129_Q0.132880.799
235_S239_N0.132810.798
185_D253_G0.132750.798
247_L255_T0.132680.798
147_P299_R0.132650.798
209_S295_S0.132150.795
128_D132_Q0.132120.794
74_V90_F0.131460.790
160_Y171_W0.131460.790
202_A291_W0.131350.790
32_N72_N0.131150.788
234_Y239_N0.130820.787
22_G109_I0.130650.785
18_L106_F0.12960.779
217_I291_W0.12920.777
47_P72_N0.128970.775
203_I208_T0.12880.774
129_Q132_Q0.128630.773
7_T79_S0.128020.770
124_P128_D0.127740.768
169_L302_Y0.12770.768
115_P124_P0.127360.766
29_P96_Y0.126770.762
9_G12_P0.126550.761
25_D118_S0.126470.760
116_S178_G0.12550.755
6_V15_F0.125010.752
141_F180_W0.124940.751
131_V307_Y0.124920.751
244_L264_I0.124420.748
247_L263_Y0.124240.747
128_D139_N0.124060.746
174_L177_S0.123990.745
173_P311_R0.123940.745
246_D260_P0.123720.744
166_D315_A0.1230.739
244_L263_Y0.122670.738
142_S159_G0.122440.736
73_L118_S0.122170.735
211_I297_F0.122030.734
15_F107_D0.121750.732
186_S248_T0.120880.727
298_L304_V0.120630.725
232_G235_S0.120590.725
20_D205_D0.120440.724
297_F314_F0.119710.720
50_S56_Q0.11970.720
131_V134_G0.119230.717
203_I293_L0.119120.716
174_L310_N0.119030.716
263_Y279_I0.1190.715
189_I247_L0.11880.714
189_I224_A0.118680.714
109_I208_T0.118550.713
156_T164_K0.118390.712
63_S68_S0.118380.712
212_Y292_I0.118350.712
53_F56_Q0.118290.711
30_S33_C0.118280.711
56_Q75_S0.118270.711
114_F307_Y0.118020.710
47_P74_V0.117470.706
236_V277_L0.117370.706
210_Y265_F0.117340.705
47_P92_L0.117110.704
171_W314_F0.117110.704
169_L313_G0.117070.704
13_Q45_Y0.116970.703
130_L134_G0.116650.701
15_F29_P0.11650.700
208_T212_Y0.116460.700
190_G224_A0.116160.698
2_Y145_L0.116070.698
181_S203_I0.1160.697
23_S109_I0.114440.688
301_Y314_F0.114080.686
127_L139_N0.113540.683
218_F225_L0.113540.683
21_T206_T0.113510.682
85_I135_L0.113290.681
65_G207_G0.113260.681
31_S44_F0.112930.679
113_G117_L0.112510.676
69_V91_G0.112030.674
70_S95_S0.111760.672
146_N156_T0.111750.672
87_N129_Q0.111550.671
62_I69_V0.111540.671
217_I220_A0.111410.670
60_F93_A0.111310.669
286_D289_D0.111310.669
58_K92_L0.111270.669
157_F296_P0.111150.668
9_G50_S0.111040.668
65_G203_I0.11070.666
184_L187_I0.110540.665
213_L221_I0.109630.659
236_V264_I0.109410.658
251_F293_L0.109070.656
25_D117_L0.108910.655
64_Y111_G0.108860.654
251_F256_F0.108750.654
232_G238_C0.108590.653
169_L315_A0.108240.651
46_N52_T0.107960.649
210_Y280_Q0.107840.648
202_A293_L0.107650.647
207_G295_S0.107450.646
16_R107_D0.107440.646
25_D73_L0.10720.645
10_T52_T0.10680.642
258_I301_Y0.10670.641
40_A44_F0.106610.641
64_Y67_G0.10660.641
78_V84_T0.106490.640
175_V182_V0.105810.636
169_L204_L0.105780.636
179_Y209_S0.105740.636
302_Y315_A0.105450.634
29_P32_N0.105380.634
209_S212_Y0.105370.633
26_T126_F0.105310.633
292_I295_S0.105080.632
2_Y27_W0.104980.631
144_Y302_Y0.104970.631
202_A251_F0.104910.631
91_G123_Y0.104820.630
169_L314_F0.104820.630
30_S58_K0.104680.629
22_G67_G0.104280.627
225_L244_L0.104130.626
297_F301_Y0.103730.624
203_I209_S0.103570.623
259_P300_N0.10340.622
65_G208_T0.103220.621
25_D109_I0.103210.621
275_C299_R0.103060.620
186_S194_V0.102950.619
233_V276_Y0.102460.616
143_L295_S0.102320.615
262_D301_Y0.102220.615
206_T303_V0.1020.613
208_T296_P0.10190.613
164_K256_F0.101790.612
36_C40_A0.101740.612
156_T302_Y0.101740.612
222_I236_V0.101630.611
35_S270_G0.101610.611
162_P165_Y0.101270.609
294_G306_D0.10090.607
233_V236_V0.100720.606
172_V253_G0.100690.605
303_V312_I0.100580.605
205_D209_S0.10050.604
65_G109_I0.100450.604
249_F258_I0.100440.604
138_S142_S0.10040.604
125_T129_Q0.100350.603
70_S94_D0.100250.603
113_G203_I0.099630.599
222_I226_G0.09950.598
19_I110_L0.099420.598
9_G13_Q0.09940.598
188_S191_G0.099280.597
175_V183_P0.098690.593
185_D252_G0.098520.592
202_A209_S0.098480.592
262_D276_Y0.098260.591
256_F303_V0.098250.591
172_V175_V0.098230.591
236_V240_S0.098220.591
140_V171_W0.097920.589
29_P64_Y0.09790.589
18_L23_S0.097830.588
22_G209_S0.097710.587
92_L144_Y0.097420.586
301_Y316_Q0.097250.585
80_I130_L0.097240.585
141_F307_Y0.097070.584
174_L178_G0.097030.583
211_I279_I0.096980.583
297_F303_V0.096830.582
23_S295_S0.096780.582
80_I153_G0.096580.581
131_V308_E0.096570.581
224_A228_S0.096570.581
164_K302_Y0.096540.580
112_L127_L0.096470.580
143_L298_L0.096410.580
278_G295_S0.096080.578
225_L260_P0.095980.577
48_S72_N0.095660.575
80_I255_T0.095560.575
240_S243_S0.095540.574
220_A224_A0.095440.574
267_I288_S0.095390.573
24_S125_T0.095290.573
17_V28_V0.095160.572
51_S54_S0.095050.571
85_I88_Q0.095040.571
212_Y281_P0.094980.571
259_P316_Q0.094790.570
245_P260_P0.094770.570
143_L305_F0.094730.570
25_D113_G0.094630.569
49_K269_D0.094570.569
200_Q291_W0.09450.568
80_I126_F0.094440.568
31_S72_N0.094310.567
188_S194_V0.094220.566
171_W309_N0.094140.566
184_L200_Q0.094130.566
196_S199_G0.094010.565
133_Q219_D0.093770.564
5_N197_S0.093530.562
77_T87_N0.093260.561
109_I112_L0.093120.560
11_P76_D0.093050.559
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
3psgA0.98111000.042
2x0bA0.99371000.048
3qvcA0.96211000.065
4aa9A0.96851000.068
1tzsA0.99371000.069
4aucA0.96851000.071
3k1wA0.99371000.075
3cmsA0.96851000.079
1am5A0.97791000.079
1qdmA0.99681000.083

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