GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Aa_trans - Transmembrane amino acid transporter protein
Pfam: PF01490 (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: 409
Sequences: 17341
Seq/Len: 42.4
HH_delta: 0.322 (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
220_D223_K0.698432.908
370_K374_R0.686572.859
75_R83_K0.678132.824
4_S219_K0.675912.814
4_S7_S0.620412.583
44_A239_F0.600372.500
223_K229_K0.578212.408
321_W324_Y0.573872.390
229_K233_I0.569132.370
129_I335_F0.565322.354
75_R80_P0.557592.322
270_V274_I0.555082.311
8_A218_M0.547752.281
302_L312_S0.543932.265
123_S126_V0.531322.212
5_W9_F0.530342.208
370_K373_K0.528552.201
9_F233_I0.496372.067
315_N318_S0.494512.059
5_W233_I0.485632.022
325_L329_I0.482382.009
35_L194_F0.478191.991
367_L371_L0.471791.964
299_E303_F0.463921.932
13_I237_I0.460411.917
344_F349_S0.441751.839
320_R324_Y0.437031.820
368_Y372_F0.432761.802
78_F82_G0.426451.776
87_D301_L0.425131.770
320_R323_R0.416681.735
236_I240_I0.416561.735
232_S236_I0.414581.726
217_E296_N0.4091.703
79_G82_G0.403141.679
28_F36_G0.402881.678
78_F370_K0.399521.664
167_I171_S0.397321.654
315_N321_W0.396651.652
9_F237_I0.394951.645
6_F10_F0.393491.638
145_K149_Y0.39091.628
84_W88_I0.389331.621
181_P185_V0.384991.603
259_G262_L0.380821.586
126_V130_I0.376731.569
367_L370_K0.37671.569
125_Y129_I0.37281.552
216_S303_F0.365841.523
16_I238_C0.364661.518
12_L234_S0.364571.518
156_F160_Y0.358821.494
187_P190_S0.355561.481
45_L49_Y0.354931.478
48_Y232_S0.354781.477
5_W229_K0.353181.471
53_L365_A0.352181.466
180_V184_P0.34481.436
52_Y232_S0.344241.433
245_F249_G0.34091.419
249_G254_G0.337731.406
39_L197_A0.336941.403
313_P322_L0.336181.400
313_P323_R0.33361.389
145_K148_R0.329121.370
321_W325_L0.328391.367
249_G252_A0.328161.366
344_F348_I0.326441.359
150_L154_G0.326251.358
163_V167_I0.326051.358
260_N264_N0.324791.352
180_V185_V0.323081.345
160_Y164_I0.321811.340
239_F243_L0.320051.333
246_G250_Y0.318891.328
56_R372_F0.318361.326
165_V169_I0.313911.307
105_I131_F0.309831.290
126_V129_I0.309171.287
350_L354_L0.309151.287
152_I156_F0.308911.286
91_F298_L0.308511.285
133_L137_P0.307931.282
43_V201_I0.304271.267
314_K318_S0.300671.252
8_A230_V0.29981.248
190_S193_G0.299731.248
317_P321_W0.298911.245
214_I292_F0.298281.242
135_V287_Y0.296851.236
249_G253_F0.294521.226
318_S321_W0.29381.223
348_I352_G0.292621.218
146_S149_Y0.291621.214
220_D229_K0.289691.206
48_Y52_Y0.289491.205
322_L326_I0.288971.203
81_K85_F0.288661.202
273_I277_I0.288121.200
101_Y287_Y0.284241.184
151_S155_L0.283811.182
179_G182_S0.283621.181
229_K232_S0.283121.179
282_S285_L0.281471.172
329_I333_L0.280971.170
179_G183_P0.280861.169
78_F366_L0.279081.162
250_Y254_G0.279071.162
336_L340_F0.278021.158
263_L266_P0.277041.154
233_I236_I0.275711.148
143_N148_R0.27551.147
80_P84_W0.275291.146
109_L127_W0.275251.146
324_Y327_R0.270911.128
51_M231_L0.26981.123
131_F135_V0.269421.122
56_R59_N0.267971.116
149_Y154_G0.267771.115
182_S185_V0.267061.112
74_A86_V0.267041.112
6_F9_F0.266781.111
41_V243_L0.26671.111
191_F194_F0.26661.110
296_N299_E0.266531.110
366_L370_K0.266491.110
49_Y53_L0.265811.107
176_E179_G0.265281.105
262_L265_L0.265011.103
343_N346_D0.264731.102
5_W230_V0.264311.101
101_Y286_S0.264261.100
261_I266_P0.263831.099
315_N322_L0.263131.096
44_A205_F0.261761.090
168_Y172_Y0.261741.090
326_I330_L0.260011.083
35_L187_P0.259551.081
209_P213_P0.259131.079
181_P184_P0.258971.078
129_I133_L0.25861.077
34_V38_I0.257121.071
125_Y128_I0.256741.069
246_G251_L0.256711.069
294_A298_L0.256091.066
345_G349_S0.255981.066
77_A371_L0.25581.065
323_R327_R0.255381.063
122_I126_V0.255271.063
349_S353_A0.255161.062
27_A31_S0.254961.062
346_D349_S0.253991.058
287_Y334_S0.253551.056
128_I132_A0.252631.052
274_I278_L0.251981.049
251_L254_G0.251221.046
328_I331_V0.251211.046
349_S352_G0.250921.045
240_I244_L0.250271.042
254_G257_V0.249731.040
326_I329_I0.248461.035
335_F338_A0.247481.030
315_N320_R0.247021.029
371_L374_R0.246291.026
338_A341_V0.245971.024
67_R72_D0.245821.024
130_I134_I0.245271.021
68_R72_D0.245191.021
69_S72_D0.244641.019
246_G249_G0.244451.018
303_F312_S0.244091.016
315_N319_S0.243831.015
111_S276_R0.243481.014
102_L287_Y0.242491.010
144_L149_Y0.241711.006
67_R70_Y0.2411.004
8_A214_I0.240931.003
344_F347_I0.24031.001
74_A367_L0.240131.000
314_K321_W0.238910.995
109_L280_V0.238680.994
13_I16_I0.23860.994
18_G21_I0.238280.992
159_F163_V0.238050.991
166_V169_I0.237960.991
106_G128_I0.237270.988
7_S152_I0.237240.988
143_N146_S0.237010.987
361_F364_P0.236750.986
324_Y328_I0.236720.986
50_T208_H0.236710.986
153_L157_S0.236190.983
158_I161_F0.236110.983
282_S286_S0.235830.982
317_P320_R0.23540.980
318_S322_L0.235140.979
164_I168_Y0.23390.974
314_K317_P0.233790.973
328_I332_L0.233440.972
177_P180_V0.233160.971
365_A369_L0.232930.970
70_Y73_L0.232750.969
137_P140_F0.232210.967
313_P321_W0.232140.967
367_L372_F0.231570.964
291_L295_R0.231270.963
41_V45_L0.231190.963
26_Y29_A0.231180.963
312_S315_N0.230250.959
363_L367_L0.229410.955
56_R60_A0.229310.955
86_V363_L0.229280.955
313_P316_T0.229160.954
151_S154_G0.229070.954
262_L266_P0.226870.945
166_V170_I0.226150.942
180_V183_P0.226020.941
191_F195_F0.225580.939
98_C102_L0.225330.938
146_S154_G0.225210.938
95_F99_V0.225180.938
319_S324_Y0.225020.937
260_N267_N0.224320.934
41_V48_Y0.223640.931
338_A342_P0.223380.930
335_F339_I0.223150.929
15_S289_L0.222990.929
9_F13_I0.222950.928
187_P194_F0.222080.925
98_C291_L0.2210.920
263_L267_N0.220710.919
299_E314_K0.220610.919
85_F89_C0.220080.916
55_V59_N0.21980.915
17_I20_G0.219470.914
331_V334_S0.219170.913
9_F230_V0.218830.911
155_L159_F0.217780.907
147_L150_L0.21720.904
7_S148_R0.216710.902
58_A212_P0.216580.902
369_L374_R0.215820.899
91_F95_F0.215190.896
103_I338_A0.214650.894
316_T319_S0.213970.891
150_L153_L0.213750.890
72_D300_N0.213270.888
124_R128_I0.212870.886
57_A73_L0.212590.885
136_L328_I0.211210.879
143_N151_S0.210980.879
142_K146_S0.210910.878
250_Y253_F0.210590.877
270_V273_I0.210560.877
260_N263_L0.210310.876
369_L372_F0.210130.875
333_L336_L0.209670.873
332_L336_L0.209530.872
367_L374_R0.209050.870
110_S114_P0.208940.870
105_I280_V0.208940.870
74_A82_G0.208290.867
9_F12_L0.208170.867
91_F327_R0.208150.867
359_I363_L0.206170.858
55_V58_A0.204270.851
27_A36_G0.203940.849
14_N17_I0.203730.848
87_D297_S0.203710.848
103_I107_D0.203490.847
58_A73_L0.202930.845
37_I247_I0.202150.842
94_L290_Q0.201970.841
130_I133_L0.201930.841
265_L269_D0.201760.840
194_F198_F0.20110.837
95_F333_L0.200940.837
127_W130_I0.20040.834
27_A200_I0.200170.833
149_Y152_I0.199570.831
321_W329_I0.19940.830
11_N214_I0.198270.826
102_L132_A0.198120.825
266_P269_D0.197980.824
97_S100_A0.197660.823
17_I238_C0.197220.821
50_T365_A0.197080.821
26_Y345_G0.19670.819
369_L373_K0.196460.818
37_I41_V0.195650.815
260_N266_P0.195460.814
230_V234_S0.195360.813
66_G72_D0.195180.813
352_G355_F0.194560.810
163_V166_V0.194430.810
31_S34_V0.194360.809
95_F327_R0.19420.809
364_P367_L0.194120.808
144_L148_R0.193980.808
320_R325_L0.193810.807
67_R76_R0.193810.807
296_N300_N0.193720.807
365_A368_Y0.193240.805
136_L139_S0.193050.804
21_I25_P0.192720.802
154_G285_L0.192530.802
19_A23_S0.191940.799
4_S8_A0.191390.797
344_F352_G0.190930.795
105_I283_L0.190910.795
68_R76_R0.19090.795
290_Q294_A0.190530.793
98_C287_Y0.190120.792
231_L234_S0.189910.791
165_V248_F0.189910.791
151_S158_I0.189460.789
257_V260_N0.189320.788
47_S50_T0.189220.788
132_A136_L0.189080.787
336_L339_I0.189030.787
38_I41_V0.188980.787
258_Q264_N0.188940.787
217_E221_P0.188860.786
349_S354_L0.188840.786
97_S290_Q0.188480.785
196_S200_I0.188040.783
279_L283_L0.1880.783
75_R79_G0.187870.782
26_Y30_Q0.187760.782
5_W223_K0.187620.781
264_N267_N0.187170.779
322_L325_L0.186990.779
148_R151_S0.186890.778
108_S279_L0.186790.778
345_G348_I0.186760.778
169_I175_G0.186570.777
108_S280_V0.186540.777
318_S324_Y0.186210.775
66_G70_Y0.186050.775
69_S73_L0.185930.774
259_G263_L0.185460.772
90_I94_L0.185360.772
217_E299_E0.185340.772
13_I241_I0.185260.771
364_P370_K0.185160.771
14_N288_P0.185040.770
162_I165_V0.184890.770
72_D76_R0.184580.769
147_L151_S0.184580.769
337_I341_V0.184060.766
38_I42_L0.184050.766
137_P141_L0.184010.766
19_A101_Y0.183730.765
18_G242_Y0.183610.765
109_L113_I0.183560.764
200_I204_A0.183470.764
112_L277_I0.183220.763
11_N14_N0.182220.759
143_N154_G0.182180.759
74_A77_A0.181820.757
261_I265_L0.181690.757
154_G161_F0.181440.756
146_S151_S0.181370.755
98_C294_A0.180930.753
312_S324_Y0.18080.753
333_L337_I0.180230.750
169_I173_G0.180220.750
165_V168_Y0.180070.750
170_I174_P0.179980.749
6_F146_S0.179720.748
353_A361_F0.179640.748
157_S161_F0.179620.748
325_L328_I0.179550.748
51_M55_V0.179120.746
110_S124_R0.179010.745
346_D352_G0.178990.745
47_S51_M0.178960.745
129_I132_A0.178660.744
323_R326_I0.178660.744
358_F362_I0.17860.744
164_I167_I0.178330.743
21_I245_F0.178080.742
318_S323_R0.177890.741
52_Y56_R0.177830.740
178_S181_P0.177480.739
171_S176_E0.177170.738
58_A215_Q0.176390.734
237_I241_I0.176360.734
81_K84_W0.176340.734
68_R73_L0.176230.734
14_N289_L0.175770.732
258_Q262_L0.175650.731
105_I108_S0.175570.731
30_Q196_S0.175550.731
174_P177_P0.175520.731
344_F353_A0.17530.730
249_G261_I0.175210.730
218_M230_V0.174810.728
339_I343_N0.1740.725
102_L106_G0.173910.724
107_D110_S0.17390.724
248_F252_A0.173790.724
212_P215_Q0.173630.723
115_S126_V0.173440.722
248_F251_L0.173440.722
37_I40_L0.173250.721
317_P322_L0.173190.721
96_G351_V0.173120.721
140_F328_I0.173050.721
210_N293_P0.172890.720
127_W131_F0.17280.720
350_L353_A0.172470.718
192_S195_F0.172440.718
285_L288_P0.172440.718
90_I210_N0.17240.718
105_I109_L0.172240.717
340_F343_N0.172220.717
100_A203_F0.172140.717
71_G75_R0.172050.716
66_G69_S0.1720.716
135_V138_L0.171980.716
17_I22_L0.171860.716
83_K87_D0.17180.715
18_G203_F0.17180.715
285_L289_L0.17170.715
193_G196_S0.17170.715
136_L140_F0.171670.715
204_A242_Y0.171620.715
238_C242_Y0.17160.715
316_T320_R0.171470.714
313_P317_P0.171440.714
245_F248_F0.171410.714
161_F278_L0.171050.712
161_F165_V0.170980.712
355_F360_S0.170920.712
237_I240_I0.170730.711
78_F367_L0.170680.711
312_S316_T0.170630.710
152_I155_L0.170310.709
122_I127_W0.170160.709
36_G39_L0.169870.707
291_L294_A0.169850.707
195_F199_G0.169740.707
171_S174_P0.16960.706
175_G179_G0.169480.706
4_S142_K0.169380.705
350_L355_F0.169340.705
10_F15_S0.169160.704
169_I252_A0.168880.703
34_V186_W0.168820.703
312_S326_I0.168750.703
206_S209_P0.168660.702
166_V244_L0.168560.702
69_S74_A0.16850.702
177_P183_P0.168440.701
177_P182_S0.168440.701
321_W328_I0.168250.701
113_I127_W0.168250.701
51_M235_M0.167820.699
14_N285_L0.167740.698
189_I193_G0.16770.698
72_D75_R0.167610.698
142_K145_K0.167350.697
339_I342_P0.167320.697
43_V47_S0.166770.694
73_L367_L0.166690.694
163_V168_Y0.166630.694
43_V202_I0.166530.693
12_L15_S0.166520.693
96_G99_V0.166010.691
368_Y371_L0.165950.691
178_S183_P0.165930.691
177_P181_P0.165780.690
101_Y104_I0.165550.689
297_S301_L0.165540.689
346_D353_A0.165470.689
144_L151_S0.165410.689
92_I96_G0.165260.688
247_I251_L0.165230.688
31_S197_A0.165180.688
44_A48_Y0.165070.687
362_I366_L0.165030.687
154_G158_I0.164420.685
264_N268_D0.164340.684
20_G203_F0.163690.682
179_G185_V0.163640.681
316_T321_W0.16330.680
79_G83_K0.163290.680
20_G204_A0.162890.678
348_I355_F0.162810.678
93_Y97_S0.162490.677
197_A201_I0.162240.676
300_N304_K0.162090.675
289_L292_F0.162010.675
332_L335_F0.161940.674
16_I234_S0.161920.674
146_S150_L0.16190.674
317_P324_Y0.161890.674
365_A370_K0.161840.674
98_C331_V0.161810.674
97_S206_S0.16180.674
11_N151_S0.161740.673
319_S323_R0.161370.672
13_I155_L0.16130.672
95_F294_A0.161290.672
33_W37_I0.160830.670
347_I351_V0.16070.669
23_S200_I0.16040.668
113_I277_I0.160240.667
37_I49_Y0.159990.666
89_C93_Y0.159920.666
100_A347_I0.159840.666
19_A203_F0.159780.665
155_L158_I0.159710.665
240_I243_L0.159490.664
329_I332_L0.159460.664
122_I130_I0.159450.664
94_L98_C0.159370.664
198_F202_I0.159190.663
208_H234_S0.159150.663
20_G242_Y0.159040.662
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
3l1lA0.95111000.322
3giaA0.9341000.374
4djkA0.96091000.394
3dh4A0.926799.60.638
2jlnA0.943899.60.651
2xq2A0.929199.60.651
2a65A0.95698.30.81
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