GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AA_permease - Amino acid permease
Pfam: PF00324 (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: CL0062
Length: 478
Sequences: 10294
Seq/Len: 21.54
HH_delta: 0.291 (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
388_R392_K0.694473.264
129_T346_S0.691373.250
161_G254_A0.667443.137
122_I353_L0.652013.065
380_I418_I0.640323.010
231_K235_R0.620022.914
228_N231_K0.605482.846
39_G245_G0.580122.727
327_K330_A0.552532.597
343_L347_I0.540332.540
287_W291_I0.507022.383
40_I416_L0.505192.374
383_N417_G0.495842.331
415_I419_A0.495822.330
226_A232_T0.489732.302
3_F239_L0.480192.257
63_Y321_D0.4792.251
412_M416_L0.464132.181
30_G202_F0.462332.173
263_N282_Y0.459392.159
67_S75_G0.459052.158
328_F340_V0.458822.157
316_Y320_R0.456162.144
388_R391_K0.449632.113
67_S72_P0.44862.108
332_H335_N0.447582.104
319_A330_A0.442162.078
79_G318_M0.437682.057
224_E320_R0.411521.934
70_L388_R0.402511.892
409_F413_F0.401111.885
83_W345_S0.394741.855
122_I350_L0.394121.852
48_S383_N0.393381.849
225_E313_R0.388231.825
340_V344_V0.384571.808
152_I156_A0.383311.802
126_L350_L0.382811.799
70_L384_I0.382081.796
51_E390_R0.37931.783
129_T342_I0.378121.777
133_L343_L0.376071.768
238_L242_L0.371411.746
260_P263_N0.368611.733
130_L134_F0.366391.722
387_I415_I0.363441.708
23_I31_A0.362851.705
148_I152_I0.36271.705
137_R141_K0.361661.700
384_I418_I0.357181.679
319_A329_F0.355651.672
235_R239_L0.353981.664
40_I44_L0.353741.663
327_K340_V0.350851.649
66_A78_A0.349451.642
133_L339_Y0.343621.615
228_N232_T0.341071.603
48_S414_A0.339011.593
36_L249_V0.338191.590
34_A205_A0.336271.581
70_L74_L0.333771.569
411_P415_I0.327911.541
335_N339_Y0.325471.530
386_Y414_A0.324741.526
311_A345_S0.323881.522
22_A31_A0.322981.518
78_A381_L0.322261.515
232_T235_R0.320271.505
125_I349_S0.31991.504
59_A224_E0.318921.499
391_K394_K0.316481.487
56_F68_R0.315071.481
90_I349_S0.314181.477
242_L246_V0.311641.465
54_R404_P0.310221.458
333_P339_Y0.309561.455
121_A353_L0.309111.453
132_N305_N0.308971.452
329_F333_P0.307551.446
290_W294_A0.307141.444
312_S342_I0.307011.443
228_N235_R0.304951.433
3_F243_R0.304561.431
158_I250_L0.303651.427
229_P234_P0.303231.425
111_P114_W0.302151.420
322_G327_K0.301031.415
126_L346_S0.298541.403
329_F332_H0.298151.401
76_F80_W0.296681.394
412_M415_I0.290951.367
170_G173_N0.290731.366
330_A340_V0.285191.340
246_V250_L0.283781.334
340_V343_L0.282861.329
32_P253_Y0.282661.329
66_A381_L0.282591.328
315_L324_L0.281451.323
122_I126_L0.278961.311
53_S65_Y0.27761.305
7_I243_R0.276611.300
222_L309_Y0.275621.295
230_R404_P0.27511.293
125_I353_L0.274591.291
111_P115_V0.273081.284
161_G258_A0.272981.283
80_W324_L0.272431.280
151_L155_I0.271881.278
69_G385_S0.271491.276
36_L40_I0.271311.275
71_G74_L0.27121.275
10_I244_I0.27081.273
44_L416_L0.269131.265
156_A160_V0.268511.262
347_I351_L0.266661.253
281_Q289_A0.263121.237
328_F331_R0.262791.235
129_T133_L0.261351.228
46_A237_T0.260591.225
153_A295_G0.258331.214
328_F332_H0.257681.211
142_I146_L0.255921.203
315_L341_A0.255191.199
41_I420_A0.254741.197
214_V375_N0.253071.189
329_F344_V0.251941.184
129_T343_L0.251881.184
134_F335_N0.251311.181
151_L247_F0.250491.177
327_K331_R0.248911.170
94_A125_I0.247961.165
64_A68_R0.246111.157
187_F202_F0.246011.156
313_R338_P0.245771.155
330_A333_P0.245471.154
44_L413_F0.24411.147
97_A297_L0.243971.147
101_L116_W0.243751.146
331_R340_V0.242921.142
387_I414_A0.24241.139
380_I384_I0.2411.133
411_P414_A0.240631.131
409_F412_M0.240161.129
141_K145_I0.240091.128
280_A288_L0.238151.119
128_I304_A0.237951.118
332_H339_Y0.237331.115
157_F161_G0.235261.106
417_G421_L0.235091.105
130_L133_L0.234871.104
155_I159_I0.232491.093
278_I281_Q0.232411.092
8_G147_T0.231911.090
60_G63_Y0.231241.087
146_L302_S0.230841.085
30_G187_F0.230451.083
38_A209_A0.230061.081
199_F202_F0.228991.076
68_R393_F0.228371.073
160_V280_A0.227041.067
63_Y317_A0.226451.064
39_G213_F0.226181.063
94_A304_A0.226061.063
223_A233_I0.224661.056
141_K144_F0.223611.051
370_I374_S0.223581.051
85_S375_N0.223411.050
5_I222_L0.222841.047
110_L115_V0.222721.047
140_G144_F0.222411.045
93_E303_S0.222161.044
168_G171_P0.221881.043
407_S410_G0.221871.043
49_L62_F0.22131.040
55_R404_P0.221251.040
387_I391_K0.220631.037
218_S310_A0.22031.035
384_I388_R0.219431.031
46_A241_V0.218891.029
124_F304_A0.218791.028
6_S240_S0.218491.027
186_N189_P0.218041.025
227_K232_T0.217691.023
133_L337_V0.217221.021
128_I305_N0.21571.014
339_Y343_L0.215611.013
150_K299_S0.215121.011
33_L202_F0.214931.010
102_Q113_T0.214671.009
21_F25_A0.214091.006
313_R316_Y0.213721.005
260_P282_Y0.211490.994
114_W122_I0.210850.991
258_A279_A0.210140.988
3_F6_S0.209780.986
58_S64_A0.209480.985
97_A124_F0.209190.983
45_V383_N0.208690.981
285_G288_L0.208460.980
50_A54_R0.20820.979
87_I91_A0.208170.978
49_L382_I0.208030.978
250_L254_A0.207750.976
365_N368_L0.206370.970
281_Q286_P0.206110.969
410_G414_A0.206070.969
67_S321_D0.205780.967
48_S407_S0.204720.962
312_S341_A0.204670.962
43_L238_L0.204090.959
125_I346_S0.203670.957
89_A93_E0.203310.956
43_L47_L0.202830.953
170_G174_G0.202830.953
66_A74_L0.201880.949
308_L312_S0.201740.948
230_R235_R0.201680.948
217_E221_I0.201530.947
83_W315_L0.201470.947
32_P256_T0.201410.947
51_E54_R0.200820.944
320_R330_A0.200550.943
245_G249_V0.200450.942
332_H336_G0.200080.940
387_I418_I0.200020.940
331_R336_G0.199660.938
308_L346_S0.199240.936
126_L130_L0.199080.936
346_S350_L0.198720.934
52_M386_Y0.197790.930
407_S413_F0.197750.929
390_R394_K0.197570.929
380_I421_L0.196640.924
299_S302_S0.196550.924
9_G306_A0.196280.923
136_V309_Y0.195920.921
143_E305_N0.195850.921
278_I282_Y0.194630.915
134_F138_V0.194320.913
210_F376_L0.193310.909
92_A211_F0.192320.904
107_F110_L0.191910.902
86_Y307_S0.190320.895
38_A210_F0.190150.894
338_P341_A0.189440.890
239_L242_L0.1890.888
28_P256_T0.188650.887
82_Y86_Y0.187820.883
214_V371_S0.187720.882
287_W290_W0.187240.880
410_G413_F0.187150.880
128_I308_L0.186640.877
389_F393_F0.186270.875
131_L142_I0.185780.873
70_L385_S0.185520.872
168_G172_S0.18550.872
333_P336_G0.184850.869
167_F173_N0.184490.867
89_A92_A0.184370.867
327_K332_H0.184290.866
328_F344_V0.183370.862
413_F417_G0.182660.859
47_L408_P0.182650.858
47_L238_L0.182510.858
15_L251_T0.182430.857
66_A385_S0.182180.856
367_L371_S0.182080.856
200_S203_F0.182070.856
17_L96_A0.181190.852
206_L210_F0.181170.852
72_P323_L0.180930.850
21_F365_N0.180580.849
333_P337_V0.180330.848
42_V216_F0.179960.846
22_A26_A0.179470.844
63_Y79_G0.17940.843
15_L154_L0.179090.842
33_L36_L0.178530.839
416_L420_A0.177590.835
124_F128_I0.177450.834
97_A300_A0.177080.832
63_Y67_S0.177010.832
386_Y390_R0.176990.832
158_I161_G0.176810.831
74_L381_L0.176440.829
73_A77_A0.176220.828
168_G173_N0.175770.826
83_W87_I0.175210.824
95_T367_L0.174710.821
262_D266_L0.174340.819
390_R410_G0.174280.819
312_S345_S0.174250.819
89_A371_S0.174020.818
308_L342_I0.173960.818
267_T278_I0.173890.817
19_S252_S0.17350.815
374_S378_V0.173170.814
243_R247_F0.172750.812
263_N266_L0.172660.812
294_A298_I0.172480.811
41_I416_L0.172230.810
140_G305_N0.172060.809
123_I127_L0.171990.808
376_L421_L0.171250.805
133_L342_I0.170830.803
4_M144_F0.170630.802
31_A252_S0.17020.800
235_R238_L0.169940.799
100_F297_L0.169860.798
351_L354_L0.169670.797
332_H337_V0.169180.795
127_L301_F0.169170.795
286_P290_W0.168920.794
58_S68_R0.168730.793
231_K234_P0.168360.791
409_F415_I0.167860.789
18_G368_L0.167690.788
227_K230_R0.167450.787
25_A204_A0.167220.786
62_F217_E0.167130.786
55_R394_K0.166450.782
166_F171_P0.166440.782
6_S219_I0.166330.782
387_I411_P0.166270.781
81_A378_V0.166160.781
204_A208_F0.165950.780
167_F171_P0.165430.778
199_F203_F0.165280.777
225_E316_Y0.165180.776
53_S220_A0.165130.776
109_G115_V0.164870.775
331_R339_Y0.164830.775
90_I94_A0.164670.774
59_A316_Y0.164330.772
45_V421_L0.164250.772
381_L385_S0.163910.770
308_L345_S0.163880.770
16_F154_L0.163390.768
405_F408_P0.163060.766
153_A292_V0.162970.766
7_I147_T0.162310.763
202_F206_L0.161680.760
110_L116_W0.16160.760
132_N342_I0.161580.759
147_T150_K0.160450.754
91_A367_L0.160420.754
284_G288_L0.160340.754
157_F280_A0.159930.752
44_L48_S0.159690.751
95_T372_T0.159660.750
327_K333_P0.159570.750
133_L335_N0.159460.749
344_V348_I0.159280.749
237_T240_S0.159070.748
169_G172_S0.158780.746
327_K336_G0.158420.745
228_N234_P0.157770.742
311_A315_L0.157710.741
10_I240_S0.157590.741
97_A301_F0.15750.740
35_Y252_S0.15740.740
115_V123_I0.157350.740
30_G201_G0.157130.739
132_N309_Y0.157030.738
251_T255_L0.156650.736
92_A368_L0.156580.736
383_N418_I0.156380.735
143_E150_K0.156290.735
16_F150_K0.155950.733
69_G388_R0.155880.733
8_G11_I0.155540.731
11_I150_K0.154980.728
229_P232_T0.154240.725
46_A216_F0.154220.725
35_Y211_F0.154170.725
15_L19_S0.154010.724
32_P36_L0.153690.722
63_Y75_G0.153630.722
171_P174_G0.153490.721
107_F123_I0.153040.719
277_V293_N0.152720.718
296_I300_A0.152530.717
108_P111_P0.152080.715
143_E302_S0.152010.714
21_F24_A0.151610.713
251_T276_F0.151550.712
107_F111_P0.15150.712
347_I350_L0.150890.709
7_I10_I0.150740.708
61_G66_A0.150410.707
167_F172_S0.150190.706
186_N190_G0.149840.704
372_T375_N0.149770.704
87_I345_S0.149710.704
9_G307_S0.14910.701
291_I295_G0.149090.701
165_L170_G0.148880.700
33_L37_I0.148570.698
316_Y332_H0.148490.698
374_S389_F0.148250.697
43_L242_L0.148020.696
341_A344_V0.147680.694
168_G174_G0.147470.693
253_Y257_L0.147220.692
224_E316_Y0.14650.689
102_Q110_L0.146170.687
357_S360_P0.146130.687
187_F199_F0.146080.687
52_M65_Y0.146020.686
101_L107_F0.146020.686
3_F240_S0.146010.686
226_A236_A0.145970.686
417_G420_A0.145420.683
391_K415_I0.145390.683
13_T300_A0.145330.683
12_G248_Y0.145270.683
201_G204_A0.145150.682
155_I247_F0.144930.681
104_W290_W0.144720.680
276_F292_V0.144640.680
101_L297_L0.144450.679
361_G365_N0.144150.678
69_G389_F0.144060.677
139_S143_E0.143950.677
22_A209_A0.143860.676
48_S386_Y0.143490.674
158_I254_A0.143260.673
299_S305_N0.142920.672
19_S22_A0.142740.671
263_N267_T0.142550.670
103_F293_N0.142550.670
304_A307_S0.142340.669
14_G248_Y0.142230.668
48_S417_G0.14220.668
59_A317_A0.142190.668
102_Q109_G0.14210.668
11_I247_F0.141890.667
165_L168_G0.141790.666
30_G186_N0.141350.664
410_G415_I0.141290.664
313_R317_A0.141190.664
52_M69_G0.140850.662
282_Y286_P0.140630.661
157_F251_T0.140440.660
354_L357_S0.140390.660
415_I418_I0.140090.658
286_P289_A0.140080.658
37_I40_I0.13910.654
70_L381_L0.138930.653
101_L124_F0.13890.653
90_I93_E0.138520.651
6_S236_A0.138430.651
62_F221_I0.137960.648
407_S414_A0.137770.648
66_A70_L0.137360.646
67_S323_L0.13730.645
215_G219_I0.137270.645
62_F382_I0.137190.645
44_L417_G0.136980.644
287_W294_A0.136890.643
95_T355_L0.136830.643
265_G268_A0.136740.643
60_G317_A0.136640.642
218_S306_A0.136620.642
244_I305_N0.136610.642
139_S305_N0.136360.641
331_R335_N0.136350.641
8_G143_E0.136330.641
131_L135_G0.136170.640
78_A84_L0.136160.640
96_A99_S0.136070.640
8_G12_G0.135920.639
123_I126_L0.135790.638
98_G101_L0.135710.638
172_S257_L0.135310.636
12_G16_F0.135120.635
412_M419_A0.134970.634
113_T116_W0.134960.634
356_G360_P0.134910.634
368_L372_T0.134810.634
95_T98_G0.134760.633
93_E299_S0.134420.632
65_Y386_Y0.134360.632
319_A325_P0.133980.630
375_N378_V0.133970.630
103_F290_W0.133790.629
167_F174_G0.133690.628
265_G281_Q0.133490.627
52_M389_F0.133140.626
126_L189_P0.132980.625
99_S296_I0.132890.625
5_I8_G0.132670.624
42_V375_N0.132630.623
135_G138_V0.132530.623
7_I244_I0.132510.623
27_G30_G0.132440.622
166_F174_G0.132210.621
250_L253_Y0.131310.617
98_G124_F0.131060.616
13_T211_F0.130840.615
379_Y382_I0.130710.614
122_I125_I0.13070.614
239_L243_R0.130610.614
160_V285_G0.13050.613
166_F257_L0.130450.613
26_A205_A0.130280.612
62_F82_Y0.130170.612
8_G305_N0.129780.610
38_A213_F0.129720.610
85_S89_A0.129580.609
12_G150_K0.129480.609
23_I26_A0.129410.608
211_F371_S0.129370.608
84_L374_S0.129250.607
243_R250_L0.129220.607
100_F103_F0.1290.606
160_V283_S0.128780.605
160_V165_L0.128730.605
343_L346_S0.128670.605
82_Y378_V0.128660.605
264_L268_A0.128550.604
50_A237_T0.128480.604
33_L188_P0.128440.604
212_A248_Y0.128390.603
15_L247_F0.128270.603
51_E57_P0.128260.603
225_E338_P0.128260.603
11_I16_F0.128220.603
46_A50_A0.128210.603
257_L260_P0.128150.602
234_P237_T0.127930.601
342_I346_S0.12780.601
279_A292_V0.127640.600
307_S311_A0.127590.600
85_S374_S0.127350.599
214_V379_Y0.127170.598
366_W370_I0.127150.598
44_L420_A0.126910.596
43_L241_V0.126850.596
416_L419_A0.126820.596
86_Y90_I0.126690.595
150_K302_S0.126590.595
56_F69_G0.126540.595
221_I310_A0.126540.595
384_I415_I0.126430.594
91_A94_A0.12640.594
329_F340_V0.126320.594
81_A85_S0.126290.594
93_E304_A0.126220.593
334_K339_Y0.126160.593
32_P249_V0.126150.593
319_A324_L0.125880.592
130_L145_I0.125850.592
283_S286_P0.125180.588
60_G64_A0.124830.587
35_Y276_F0.124830.587
66_A73_A0.124070.583
44_L407_S0.124050.583
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
3l1lA0.88281000.291
4djkA0.93311000.311
3giaA0.87241000.319
2jlnA0.849498.90.846
2a65A0.926898.50.871
2xq2A0.8975980.891
3dh4A0.897597.90.894
4ainA0.824396.70.917
2wswA0.7782950.929
3j1zP0.290832.40.961

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