GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Xan_ur_permease - Permease family
Pfam: PF00860 (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: 389
Sequences: 6739
Seq/Len: 17.32
HH_delta: 0.204 (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
97_L284_G0.826084.785
107_G274_L0.495032.867
196_I200_I0.474552.749
49_A279_G0.473272.741
101_I281_I0.452362.620
143_A164_A0.437942.537
104_I281_I0.433222.509
101_I105_L0.431792.501
104_I274_L0.425512.465
54_G316_G0.403722.338
51_L316_G0.399082.312
104_I277_G0.388112.248
166_L170_F0.382142.213
317_V321_L0.374482.169
51_L313_L0.365082.115
100_G281_I0.362392.099
166_L197_V0.341421.978
100_G280_T0.335141.941
88_G91_A0.331511.920
97_L281_I0.328841.905
189_I193_A0.326011.888
168_L346_V0.325311.884
309_R314_T0.321411.862
192_I196_I0.31451.822
45_V286_F0.314321.821
57_A278_L0.312431.810
44_L323_G0.304771.765
45_V291_T0.304081.761
156_G161_L0.30321.756
107_G277_G0.298331.728
170_F174_L0.296841.719
268_R271_R0.293131.698
47_G320_I0.289931.679
170_F193_A0.288211.669
27_A75_F0.286431.659
90_Q228_S0.285241.652
215_W327_K0.285121.652
167_T194_G0.28341.642
174_L189_I0.283371.641
207_S212_S0.280661.626
171_I343_P0.277391.607
91_A228_S0.274331.589
102_L238_L0.271181.571
171_I190_G0.271061.570
18_I43_F0.270941.569
162_G166_L0.269771.563
108_L274_L0.268761.557
66_G292_T0.262371.520
196_I199_A0.261851.517
313_L316_G0.2541.471
317_V320_I0.249991.448
197_V201_L0.24781.435
143_A168_L0.247341.433
47_G323_G0.246991.431
20_V23_L0.246911.430
170_F197_V0.246691.429
55_L313_L0.246671.429
61_L293_T0.246181.426
194_G339_V0.245771.424
297_N301_I0.245541.422
210_V213_A0.245131.420
282_L286_F0.244941.419
57_A60_R0.242721.406
94_G226_W0.242141.403
283_A288_T0.241551.399
314_T318_I0.240631.394
106_L241_A0.239131.385
281_I284_G0.236031.367
158_G162_G0.235731.365
354_S357_R0.233771.354
252_I272_G0.231941.343
99_S241_A0.231421.340
225_G228_S0.231241.339
51_L319_L0.229721.331
122_V126_A0.229581.330
206_F210_V0.229261.328
306_V311_V0.229061.327
195_W334_S0.228471.323
357_R361_W0.227761.319
157_D160_N0.225511.306
96_V290_P0.225091.304
193_A197_V0.224121.298
106_L245_M0.22361.295
52_L275_A0.223141.293
227_P230_D0.222721.290
98_I237_F0.22221.287
54_G313_L0.222181.287
48_I286_F0.220741.279
50_T319_L0.220181.275
105_L109_T0.217411.259
159_K162_G0.215321.247
298_A301_I0.214791.244
95_A233_A0.214421.242
94_G229_F0.212511.231
47_G51_L0.212081.228
255_V301_I0.211531.225
179_K351_I0.211161.223
99_S240_F0.209791.215
54_G312_G0.209281.212
178_L183_R0.207821.204
173_L177_F0.207041.199
162_G165_V0.204251.183
247_E292_T0.203951.181
207_S211_S0.203941.181
178_L182_L0.203851.181
215_W218_L0.202121.171
102_L241_A0.201891.169
187_I344_L0.199681.157
197_V200_I0.196481.138
167_T171_I0.195591.133
244_A290_P0.195381.132
142_N337_S0.194261.125
195_W335_I0.193781.122
248_S252_I0.193321.120
205_D208_P0.193091.118
195_W198_A0.192551.115
91_A230_D0.192121.113
43_F47_G0.192041.112
200_I203_V0.191351.108
214_P217_S0.19111.107
105_L108_L0.191031.107
248_S276_D0.189641.098
208_P334_S0.188781.093
107_G270_R0.187771.088
163_L198_A0.187671.087
188_L192_I0.187391.085
202_G205_D0.187121.084
163_L203_V0.187121.084
98_I234_I0.186481.080
161_L164_A0.186411.080
190_G194_G0.186211.079
17_I21_V0.18551.074
23_L27_A0.184491.069
294_Y297_N0.183081.060
168_L342_G0.182091.055
248_S293_T0.181991.054
220_S223_P0.181991.054
50_T316_G0.181281.050
257_R358_N0.181171.049
72_I76_M0.180991.048
247_E251_T0.180791.047
67_P70_A0.180351.045
108_L111_L0.178891.036
165_V169_L0.178141.032
251_T295_S0.177891.030
48_I282_L0.177691.029
179_K347_L0.177391.028
258_I302_A0.175691.018
24_I27_A0.174941.013
249_I255_V0.174861.013
255_V298_A0.174551.011
297_N300_G0.174351.010
171_I194_G0.174251.009
53_Q65_P0.173911.007
336_P339_V0.173241.003
62_P318_I0.172811.001
96_V284_G0.17261.000
156_G159_K0.17250.999
249_I293_T0.172240.998
310_R313_L0.170550.988
90_Q223_P0.170550.988
85_G88_G0.170510.988
208_P211_S0.170170.986
90_Q93_L0.169720.983
142_N341_G0.169470.982
189_I192_I0.168650.977
52_L282_L0.16840.975
166_L193_A0.168030.973
325_S329_A0.167970.973
279_G282_L0.167860.972
121_P125_G0.166610.965
74_A77_I0.166330.963
46_S64_V0.165620.959
59_H272_G0.165140.957
195_W204_V0.164950.955
300_G304_T0.164810.955
301_I311_V0.163530.947
170_F194_G0.163520.947
64_V312_G0.162340.940
103_F241_A0.162340.940
93_L284_G0.161020.933
125_G355_G0.160790.931
50_T64_V0.160490.930
136_A345_L0.159730.925
282_L285_L0.1590.921
232_G235_L0.158910.920
211_S217_S0.158780.920
168_L172_L0.158390.917
327_K330_P0.158080.916
72_I75_F0.158040.915
63_L255_V0.157320.911
188_L336_P0.157270.911
174_L190_G0.156140.904
125_G358_N0.155880.903
129_L359_I0.155640.902
21_V42_T0.155630.901
326_P330_P0.155550.901
95_A236_T0.155290.899
157_D168_L0.155250.899
318_I322_F0.155220.899
59_H268_R0.155190.899
76_M79_I0.155020.898
274_L278_L0.154960.898
310_R314_T0.154420.894
277_G281_I0.153970.892
278_L282_L0.153530.889
42_T289_S0.153040.886
353_M357_R0.152690.884
99_S244_A0.152460.883
194_G198_A0.152210.882
198_A203_V0.151720.879
172_L346_V0.151360.877
213_A327_K0.151220.876
211_S214_P0.151050.875
308_S311_V0.150590.872
58_G61_L0.150470.872
21_V24_I0.150390.871
216_F219_P0.149920.868
174_L193_A0.149420.865
19_I23_L0.149240.864
217_S220_S0.149020.863
168_L171_I0.147950.857
137_P141_K0.147750.856
275_A278_L0.147740.856
215_W219_P0.147250.853
104_I108_L0.146990.851
103_F244_A0.146690.850
199_A334_S0.146660.850
94_G98_I0.146620.849
126_A130_L0.146610.849
89_L93_L0.146180.847
277_G280_T0.146120.846
281_I285_L0.146030.846
212_S215_W0.1460.846
298_A302_A0.145830.845
65_P276_D0.145540.843
53_Q275_A0.145520.843
230_D233_A0.145310.842
49_A291_T0.145080.840
98_I233_A0.144740.838
21_V67_P0.144720.838
179_K186_A0.144430.837
190_G342_G0.144350.836
66_G294_Y0.143980.834
224_F285_L0.143890.833
195_W199_A0.143810.833
21_V70_A0.143790.833
18_I325_S0.143780.833
259_A302_A0.14360.832
161_L165_V0.143280.830
102_L234_I0.142870.828
353_M356_I0.142310.824
244_A248_S0.142310.824
103_F277_G0.142290.824
163_L201_L0.14220.824
157_D161_L0.14170.821
99_S281_I0.141630.820
18_I46_S0.141580.820
129_L132_G0.141490.820
100_G277_G0.141080.817
140_L144_G0.140610.814
177_F181_F0.140470.814
97_L285_L0.14040.813
244_A292_T0.140390.813
131_I295_S0.140180.812
170_F190_G0.14010.812
110_G273_L0.140040.811
319_L323_G0.139610.809
251_T294_Y0.139310.807
62_P312_G0.138220.801
200_I204_V0.137480.796
42_T46_S0.137470.796
318_I325_S0.137280.795
210_V216_F0.137220.795
43_F46_S0.137190.795
111_L114_R0.136990.793
100_G284_G0.136910.793
147_W155_V0.136610.791
45_V288_T0.136390.790
171_I175_S0.136140.789
95_A237_F0.136070.788
166_L201_L0.1360.788
63_L300_G0.135790.787
143_A345_L0.134820.781
215_W220_S0.134510.779
22_P25_L0.13430.778
252_I276_D0.134060.777
104_I278_L0.134010.776
227_P231_P0.133830.775
94_G233_A0.133760.775
43_F332_F0.133660.774
164_A342_G0.133480.773
192_I195_W0.133470.773
107_G273_L0.133260.772
297_N304_T0.132940.770
106_L111_L0.132710.769
211_S328_F0.132650.768
146_I156_G0.132640.768
110_G270_R0.132190.766
45_V283_A0.132170.766
133_L352_M0.131890.764
348_F352_M0.131430.761
91_A94_G0.131420.761
301_I304_T0.131040.759
167_T339_V0.130870.758
162_G197_V0.130790.758
160_N338_P0.130710.757
208_P212_S0.13070.757
139_G346_V0.130580.756
66_G297_N0.130120.754
231_P234_I0.130070.753
218_L223_P0.129820.752
41_A45_V0.129820.752
354_S358_N0.129640.751
198_A204_V0.129480.750
302_A328_F0.129440.750
51_L55_L0.12930.749
51_L320_I0.129220.748
58_G66_G0.128840.746
313_L317_V0.12880.746
185_G189_I0.128790.746
69_F72_I0.12850.744
51_L54_G0.128450.744
348_F351_I0.128420.744
167_T198_A0.128270.743
61_L272_G0.128240.743
87_Y91_A0.128230.743
187_I343_P0.128210.743
173_L176_L0.128130.742
103_F245_M0.128120.742
280_T293_T0.127990.741
92_A95_A0.127930.741
174_L178_L0.127530.739
143_A165_V0.127370.738
46_S50_T0.127250.737
132_G139_G0.127070.736
257_R361_W0.127010.736
199_A203_V0.126840.735
311_V316_G0.126750.734
25_L28_A0.126530.733
213_A227_P0.126490.733
211_S215_W0.12620.731
92_A96_V0.126050.730
201_L204_V0.1260.730
68_S71_F0.125880.729
159_K163_L0.125730.728
19_I335_I0.125720.728
129_L356_I0.125680.728
40_S326_P0.125620.728
90_Q225_G0.12560.728
116_R119_F0.125520.727
174_L197_V0.125520.727
103_F107_G0.12540.726
72_I77_I0.125160.725
144_G155_V0.125020.724
159_K203_V0.124660.722
177_F180_G0.124140.719
80_G85_G0.123920.718
328_F339_V0.123910.718
135_L301_I0.123860.717
40_S241_A0.123780.717
128_V251_T0.123650.716
124_K253_V0.123480.715
312_G315_A0.123450.715
256_A259_A0.123190.714
22_P26_A0.122620.710
191_I249_I0.122240.708
126_A359_I0.121940.706
50_T315_A0.121910.706
162_G201_L0.121860.706
253_V257_R0.121810.706
164_A168_L0.12180.706
93_L96_V0.121640.705
248_S277_G0.121470.704
278_L281_I0.121420.703
167_T342_G0.121390.703
259_A307_A0.121190.702
216_F220_S0.121170.702
155_V158_G0.121110.702
298_A349_G0.121050.701
175_S179_K0.120780.700
345_L349_G0.120590.698
200_I205_D0.120150.696
296_E299_G0.120060.695
47_G319_L0.119810.694
199_A204_V0.119520.692
74_A79_I0.119350.691
175_S190_G0.119090.690
132_G198_A0.119010.689
115_L290_P0.118970.689
321_L327_K0.118870.689
314_T317_V0.118840.688
41_A286_F0.118540.687
248_S292_T0.118450.686
49_A65_P0.118440.686
226_W229_F0.11840.686
172_L342_G0.118330.685
193_A200_I0.117970.683
316_G320_I0.117970.683
256_A261_K0.117680.682
212_S216_F0.117560.681
141_K144_G0.117430.680
169_L173_L0.117290.679
127_V295_S0.117090.678
211_S216_F0.117050.678
186_A190_G0.116850.677
332_F335_I0.116720.676
115_L230_D0.116560.675
170_F178_L0.116550.675
86_G321_L0.116540.675
244_A280_T0.116390.674
168_L175_S0.1160.672
52_L278_L0.115970.672
85_G89_L0.115670.670
270_R274_L0.115650.670
160_N321_L0.115640.670
60_R65_P0.115580.669
53_Q276_D0.115510.669
68_S244_A0.115430.669
217_S326_P0.115340.668
235_L239_I0.115160.667
157_D164_A0.115150.667
57_A61_L0.115150.667
259_A262_D0.114960.666
181_F185_G0.11490.666
175_S347_L0.114890.665
74_A240_F0.114760.665
19_I332_F0.114420.663
131_I292_T0.114190.661
238_L245_M0.114140.661
103_F279_G0.114090.661
67_P72_I0.113970.660
178_L181_F0.113970.660
232_G236_T0.113860.660
220_S224_F0.113790.659
131_I294_Y0.113720.659
71_F240_F0.113670.658
60_R261_K0.113620.658
231_P235_L0.113550.658
252_I293_T0.113370.657
90_Q226_W0.113160.655
17_I296_E0.113150.655
335_I339_V0.112890.654
61_L261_K0.112520.652
357_R360_D0.112470.651
91_A223_P0.112250.650
180_G194_G0.112240.650
102_L281_I0.112230.650
67_P244_A0.112040.649
271_R274_L0.112030.649
46_S49_A0.111850.648
199_A206_F0.111710.647
355_G358_N0.111550.646
241_A245_M0.111510.646
254_A293_T0.111440.645
178_L189_I0.111320.645
160_N164_A0.111290.645
193_A196_I0.11110.644
158_G161_L0.110890.642
297_N302_A0.110790.642
106_L109_T0.110640.641
188_L195_W0.110560.640
63_L66_G0.110340.639
18_I39_I0.110240.639
272_G275_A0.110240.639
44_L47_G0.110210.638
218_L225_G0.109790.636
308_S314_T0.109730.636
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
3qe7A0.93831000.204
3qe7A0.519382.80.942
1btsA0.066850.10.954
4he8J0.426719.30.962
4j05A0.46271.70.977
3n2fG0.07971.50.977
4ib4A0.41391.30.978
1erfA0.06681.30.978
3arcX0.10031.30.978
2ls4A0.06681.20.978

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