GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GntP_permease - GntP family permease
Pfam: PF02447 (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: CL0182
Length: 441
Sequences: 8925
Seq/Len: 20.24
HH_delta: 0.507 (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
130_R136_L0.633493.763
287_S290_E0.578873.438
326_D330_N0.545263.239
412_S415_Q0.531823.159
77_E290_E0.513253.049
373_A380_P0.473232.811
338_P341_L0.443042.632
396_H399_D0.437942.601
77_E293_K0.421452.503
242_G248_F0.415592.469
297_K300_K0.382282.271
73_K297_K0.375362.230
87_T91_K0.372862.215
415_Q418_K0.367932.185
29_L311_A0.366872.179
372_L383_L0.365522.171
82_E86_N0.355152.110
289_E293_K0.354062.103
414_K418_K0.353992.103
106_F186_M0.348452.070
296_E300_K0.341912.031
217_T220_K0.335441.992
226_G230_L0.331821.971
196_F200_R0.328071.949
327_A330_N0.327431.945
330_N333_S0.327171.943
330_N334_G0.325891.936
317_Q321_D0.32011.901
101_L191_P0.317461.886
347_A389_A0.31591.876
290_E293_K0.312711.857
327_A331_L0.312261.855
73_K298_A0.30921.837
195_R199_K0.303781.804
218_D221_K0.302571.797
292_M296_E0.300921.787
342_L346_I0.300891.787
323_G326_D0.296611.762
164_A171_L0.292791.739
86_N227_L0.29141.731
32_A314_A0.290171.724
336_G341_L0.288211.712
183_I187_L0.287941.710
105_G108_V0.283291.683
77_E297_K0.281661.673
137_L415_Q0.281041.669
395_S399_D0.281041.669
395_S398_N0.279851.662
289_E292_M0.277561.649
28_L312_G0.276981.645
166_A361_M0.276621.643
192_L196_F0.276191.641
222_L225_F0.273661.625
354_Q360_A0.272441.618
87_T225_F0.271251.611
348_A353_A0.268751.596
173_L381_V0.268421.594
160_P385_L0.26651.583
109_G115_D0.262481.559
169_A381_V0.261061.551
375_L378_V0.260341.546
49_S321_D0.258221.534
42_P45_E0.255881.520
219_E223_P0.250151.486
77_E294_W0.248991.479
369_A373_A0.248121.474
331_L335_S0.245991.461
48_K52_K0.245331.457
223_P226_G0.244411.452
193_Y197_I0.243681.447
101_L195_R0.243431.446
413_V417_L0.243171.444
170_D173_L0.24221.439
293_K297_K0.238161.415
112_V115_D0.236271.403
331_L334_G0.235481.399
154_V182_A0.235281.398
91_K221_K0.234731.394
377_G380_P0.233441.387
45_E48_K0.232851.383
329_A333_S0.229851.365
197_I200_R0.22891.360
342_L372_L0.228211.356
32_A318_V0.227141.349
182_A186_M0.226431.345
216_E220_K0.226211.344
197_I201_I0.225921.342
356_S359_V0.225521.340
288_R292_M0.225151.337
122_A126_F0.224971.336
319_L324_I0.224931.336
87_T90_K0.224581.334
89_L132_T0.223641.328
218_D222_L0.223141.325
293_K296_E0.220271.308
49_S317_Q0.218751.299
114_F117_G0.216951.289
224_S227_L0.21571.281
180_I184_P0.215351.279
94_E216_E0.215171.278
342_L375_L0.214751.276
22_L27_A0.21371.269
179_L183_I0.21161.257
144_A148_S0.211231.255
317_Q320_K0.211071.254
27_A31_V0.210891.253
79_G82_E0.210731.252
223_P227_L0.207841.235
164_A174_V0.207381.232
96_R199_K0.207161.230
406_K413_V0.207081.230
113_F116_V0.205121.218
237_I241_L0.204841.217
141_L419_T0.204061.212
302_A306_L0.20231.202
123_P127_S0.202251.201
316_G363_T0.201831.199
49_S52_K0.20111.194
69_A298_A0.199621.186
216_E221_K0.199391.184
222_L226_G0.199341.184
127_S131_K0.198341.178
86_N90_K0.198221.177
340_L347_A0.197671.174
167_L365_A0.197221.171
286_M294_W0.197121.171
386_A390_G0.197091.171
379_S382_L0.197081.171
225_F229_L0.196991.170
73_K77_E0.196611.168
177_Y181_V0.195881.163
94_E221_K0.195771.163
272_G276_A0.194861.157
217_T221_K0.19381.151
163_A384_V0.193461.149
138_Y142_P0.192571.144
76_E82_E0.192361.143
337_I341_L0.19191.140
191_P195_R0.191311.136
70_M273_V0.188551.120
411_L416_T0.188481.120
271_I275_I0.188231.118
70_M298_A0.187281.112
166_A365_A0.186911.110
360_A364_A0.186671.109
340_L344_F0.185381.101
29_L314_A0.185131.100
365_A369_A0.184991.099
109_G150_T0.183491.090
140_A411_L0.182771.086
112_V401_G0.182461.084
347_A386_A0.181671.079
113_F117_G0.181051.075
22_L26_L0.180741.074
173_L176_L0.180031.069
54_F306_L0.179931.069
82_E285_G0.178311.059
344_F348_A0.177741.056
361_M365_A0.177681.055
54_F310_G0.177651.055
346_I368_V0.176891.051
28_L315_F0.176881.051
79_G83_R0.176881.051
25_F311_A0.176151.046
52_K56_S0.173431.030
88_L92_F0.173311.029
70_M295_L0.172961.027
50_I311_A0.172961.027
117_G147_L0.171941.021
135_S201_I0.170921.015
118_F122_A0.170721.014
143_L147_L0.169751.008
192_L195_R0.169351.006
139_L142_P0.169251.005
360_A390_G0.168611.002
219_E222_L0.168571.001
406_K416_T0.168060.998
198_S202_P0.167780.997
323_G327_A0.167530.995
73_K76_E0.167060.992
92_F95_K0.166890.991
225_F228_S0.166720.990
284_R287_S0.166420.988
343_A347_A0.166020.986
177_Y385_L0.165720.984
219_E226_G0.16520.981
228_S231_P0.164820.979
31_V34_I0.164290.976
34_I38_L0.163290.970
136_L415_Q0.163260.970
129_A139_L0.163210.969
45_E49_S0.161860.961
196_F199_K0.161690.960
372_L378_V0.16150.959
91_K94_E0.161070.957
86_N220_K0.1610.956
23_H27_A0.16040.953
172_G176_L0.160150.951
30_I34_I0.160060.951
67_L269_L0.160020.950
378_V382_L0.159390.947
341_L344_F0.159010.944
307_L310_G0.157860.938
371_L374_S0.156950.932
86_N131_K0.156860.932
115_D400_S0.156690.931
344_F347_A0.155760.925
120_I123_P0.155660.925
103_I143_L0.155610.924
340_L378_V0.155560.924
220_K223_P0.155020.921
100_A194_G0.155020.921
230_L282_R0.154980.921
286_M290_E0.15490.920
71_I273_V0.154840.920
367_I371_L0.154730.919
365_A387_I0.154440.917
167_L369_A0.1540.915
90_K94_E0.153610.912
416_T419_T0.153560.912
122_A408_F0.153040.909
126_F409_F0.15280.908
405_V411_L0.152230.904
104_T194_G0.151880.902
160_P178_G0.151340.899
108_V112_V0.151050.897
184_P188_I0.151020.897
386_A393_F0.150940.897
83_R87_T0.150870.896
35_V38_L0.15080.896
112_V117_G0.150470.894
159_G361_M0.150.891
38_L41_M0.149970.891
174_V384_V0.149730.889
139_L389_A0.149480.888
94_E215_E0.148260.881
30_I33_L0.148070.880
190_G194_G0.147850.878
169_A380_P0.147830.878
300_K304_M0.147160.874
404_L408_F0.146920.873
107_I110_I0.146850.872
394_F399_D0.146820.872
221_K224_S0.146540.870
320_K325_G0.146250.869
115_D150_T0.146080.868
346_I372_L0.146030.867
47_V50_I0.145960.867
226_G229_L0.14580.866
414_K417_L0.145390.864
110_I114_F0.145180.862
74_L277_L0.14480.860
50_I314_A0.144240.857
108_V144_A0.144110.856
72_G325_G0.143840.854
326_D329_A0.143840.854
221_K225_F0.143760.854
359_V363_T0.143010.849
336_G342_L0.142750.848
43_P46_I0.142720.848
295_L299_L0.142590.847
233_L236_I0.142130.844
220_K224_S0.142080.844
231_P283_R0.14130.839
85_A311_A0.141140.838
23_H26_L0.140940.837
105_G121_L0.140830.836
154_V157_T0.140510.835
90_K224_S0.140150.832
272_G275_I0.139940.831
82_E131_K0.139660.830
233_L237_I0.13960.829
312_G359_V0.13960.829
83_R285_G0.139320.828
162_A358_T0.13890.825
285_G290_E0.138810.824
318_V322_S0.138730.824
89_L100_A0.138720.824
333_S374_S0.138690.824
274_L278_Y0.138670.824
160_P388_G0.138630.823
150_T400_S0.138550.823
281_G284_R0.13850.823
44_E48_K0.138350.822
405_V409_F0.138170.821
240_L244_V0.13810.820
241_L245_A0.137490.817
48_K51_T0.137420.816
76_E81_A0.137290.815
139_L148_S0.137270.815
354_Q364_A0.137140.815
342_L378_V0.136930.813
207_E345_L0.136350.810
229_L233_L0.136190.809
278_Y281_G0.136160.809
169_A384_V0.135930.807
295_L298_A0.13590.807
111_P115_D0.135840.807
72_G81_A0.135760.806
111_P114_F0.135720.806
116_V401_G0.135680.806
238_L275_I0.135360.804
33_L52_K0.135060.802
231_P235_P0.13480.801
130_R133_G0.134740.800
270_L273_V0.134730.800
369_A380_P0.134690.800
150_T154_V0.134650.800
291_V295_L0.134440.799
340_L343_A0.134280.798
402_F405_V0.13420.797
32_A311_A0.134090.796
100_A129_A0.134050.796
358_T362_I0.134040.796
147_L151_H0.133840.795
163_A365_A0.133420.792
115_D401_G0.133420.792
138_Y194_G0.133180.791
355_G396_H0.133070.790
411_L415_Q0.132890.789
303_G307_L0.132820.789
366_G370_P0.131790.783
90_K218_D0.131530.781
290_E294_W0.131450.781
136_L411_L0.131060.778
308_I312_G0.131030.778
160_P164_A0.130970.778
324_I327_A0.130870.777
143_L146_G0.130790.777
99_L191_P0.13070.776
310_G314_A0.130580.776
406_K417_L0.130230.774
25_F307_L0.130110.773
152_A357_A0.130060.773
62_G66_A0.130050.772
300_K303_G0.129990.772
343_A386_A0.129830.771
102_A186_M0.129780.771
378_V386_A0.129770.771
135_S138_Y0.129330.768
88_L91_K0.12930.768
121_L125_A0.129260.768
287_S294_W0.129260.768
181_V184_P0.129130.767
37_L43_P0.129090.767
200_R203_I0.128890.766
128_L132_T0.128870.765
368_V383_L0.128450.763
112_V116_V0.128440.763
29_L33_L0.12840.763
161_L175_I0.128350.762
167_L387_I0.128270.762
109_G182_A0.128180.761
235_P239_I0.128130.761
329_A332_L0.128120.761
85_A127_S0.128030.760
126_F129_A0.127960.760
360_A365_A0.127820.759
415_Q419_T0.127610.758
305_I308_I0.127490.757
145_A148_S0.127480.757
60_S64_V0.127390.757
74_L276_A0.127360.756
287_S292_M0.126830.753
109_G401_G0.12670.753
217_T223_P0.126660.752
333_S336_G0.126360.751
407_R410_G0.126340.750
362_I365_A0.126240.750
288_R291_V0.126120.749
145_A190_G0.126110.749
107_I146_G0.126070.749
128_L131_K0.125940.748
73_K294_W0.125690.747
277_L291_V0.125680.747
151_H357_A0.12560.746
357_A391_S0.125550.746
148_S394_F0.125520.746
368_V372_L0.125380.745
296_E299_L0.125260.744
335_S338_P0.125240.744
400_S404_L0.125130.743
394_F401_G0.124510.740
163_A169_A0.124450.739
404_L407_R0.124390.739
332_L371_L0.124120.737
114_F118_F0.123920.736
223_P289_E0.12330.732
109_G112_V0.123240.732
163_A361_M0.122940.730
177_Y180_I0.122750.729
54_F58_L0.122640.728
164_A169_A0.122610.728
141_L389_A0.122260.726
74_L273_V0.122240.726
394_F400_S0.12190.724
106_F117_G0.121890.724
54_F62_G0.121660.723
152_A391_S0.121390.721
80_A229_L0.121290.720
109_G117_G0.121060.719
70_M74_L0.120930.718
278_Y283_R0.120920.718
171_L174_V0.120890.718
151_H157_T0.120850.718
352_T394_F0.120810.718
113_F404_L0.120720.717
351_R360_A0.120640.717
399_D403_W0.120530.716
44_E47_V0.120360.715
347_A390_G0.120160.714
53_G57_T0.120030.713
412_S417_L0.119990.713
112_V122_A0.119940.712
339_P378_V0.119910.712
395_S401_G0.11970.711
78_S81_A0.119690.711
95_K98_P0.119650.711
278_Y282_R0.119550.710
187_L192_L0.11950.710
119_V404_L0.119450.710
227_L230_L0.119360.709
126_F130_R0.119260.708
36_G41_M0.119120.708
144_A395_S0.118960.707
109_G244_V0.118640.705
86_N89_L0.118590.704
25_F32_A0.11850.704
159_G391_S0.11840.703
67_L399_D0.118190.702
363_T366_G0.118160.702
299_L303_G0.118040.701
83_R227_L0.117960.701
65_I398_N0.117860.700
369_A372_L0.11780.700
390_G395_S0.117750.699
65_I399_D0.117730.699
57_T63_I0.117660.699
69_A73_K0.117660.699
75_L80_A0.117420.697
153_L185_A0.117140.696
230_L234_L0.117070.695
173_L379_S0.116960.695
386_A389_A0.116830.694
36_G46_I0.116760.694
390_G396_H0.116740.693
402_F416_T0.116590.693
28_L291_V0.116490.692
195_R200_R0.11640.691
58_L64_V0.116170.690
292_M295_L0.116070.689
122_A125_A0.116060.689
357_A400_S0.115960.689
67_L398_N0.115830.688
140_A409_F0.115810.688
336_G339_P0.115710.687
116_V405_V0.115640.687
309_T319_L0.115430.686
49_S53_G0.115430.686
149_V185_A0.11540.685
116_V404_L0.115390.685
105_G144_A0.115340.685
150_T153_L0.115280.685
152_A155_P0.114970.683
142_P148_S0.114950.683
329_A371_L0.114920.683
36_G45_E0.114840.682
316_G323_G0.11480.682
167_L388_G0.114730.681
38_L43_P0.114710.681
51_T345_L0.114690.681
165_G168_G0.114650.681
30_I121_L0.114590.681
215_E220_K0.114580.681
52_K317_Q0.114430.680
281_G286_M0.114410.680
104_T146_G0.11410.678
413_V416_T0.113910.677
85_A125_A0.113850.676
394_F404_L0.113730.676
88_L406_K0.113670.675
196_F201_I0.113630.675
136_L140_A0.113610.675
176_L179_L0.113590.675
142_P146_G0.113490.674
122_A147_L0.113110.672
351_R364_A0.113060.672
316_G359_V0.11290.671
144_A405_V0.112850.670
35_V409_F0.112770.670
394_F397_V0.112470.668
216_E293_K0.112390.668
271_I276_A0.112350.667
113_F401_G0.112190.666
215_E218_D0.111980.665
385_L391_S0.111880.665
91_K225_F0.111870.664
146_G149_V0.111870.664
58_L62_G0.111770.664
322_S325_G0.111710.664
320_K326_D0.111690.663
146_G393_F0.111340.661
373_A378_V0.11130.661
35_V318_V0.111290.661
105_G148_S0.111260.661
148_S152_A0.111260.661
146_G150_T0.111230.661
328_I331_L0.11120.661
313_G358_T0.111160.660
240_L245_A0.111160.660
159_G357_A0.110970.659
125_A129_A0.110880.659
383_L415_Q0.110870.659
84_I316_G0.110820.658
32_A36_G0.110680.657
74_L294_W0.110610.657
67_L270_L0.110320.655
319_L325_G0.11030.655
393_F398_N0.11010.654
201_I419_T0.109770.652
134_K139_L0.109760.652
93_G99_L0.10960.651
204_P207_E0.109530.651
168_G335_S0.109490.650
50_I310_G0.109190.649
343_A378_V0.109180.649
144_A147_L0.109160.648
183_I334_G0.108970.647
375_L383_L0.108860.647
147_L394_F0.108850.647
322_S326_D0.108790.646
105_G399_D0.108790.646
335_S341_L0.108740.646
169_A173_L0.108730.646
178_G182_A0.108640.645
338_P367_I0.108550.645
348_A393_F0.108480.644
151_H156_P0.10830.643
350_L368_V0.108140.642
336_G375_L0.108130.642
342_L371_L0.108120.642
316_G320_K0.108010.642
378_V383_L0.107970.641
366_G369_A0.107930.641
298_A301_P0.107870.641
34_I288_R0.107470.638
61_I299_L0.107380.638
42_P46_I0.107160.637
37_L44_E0.106920.635
108_V389_A0.106860.635
99_L132_T0.106830.635
193_Y196_F0.106740.634
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
4f35D0.91381000.507
4f35D0.428698.80.83
2nq2A0.439929.80.955
3qe7A0.489824.80.957
4g1uA0.437620.60.958
3qnqA0.4603170.96
2m20A0.136115.80.961
3ne5A0.351512.10.962
2qi9A0.4286120.962
2a65A0.55339.90.964
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