GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Trp_Tyr_perm - Tryptophantyrosine permease family
Pfam: PF03222 (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: 394
Sequences: 15140
Seq/Len: 38.43
HH_delta: 0.295 (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
72_E80_G0.604682.894
359_V363_R0.566782.713
215_K219_K0.558592.673
273_W277_L0.504382.414
72_E77_K0.496462.376
361_K364_K0.484952.321
164_L238_S0.476612.281
133_G137_F0.472582.262
125_L330_L0.4572.187
358_M362_A0.447542.142
294_Y298_F0.431132.063
151_F155_I0.42932.055
219_K223_I0.427392.045
310_N313_G0.424452.031
313_G316_K0.4171.996
311_S314_R0.413491.979
44_W229_L0.409191.958
212_G215_K0.407931.952
216_K219_K0.407571.951
179_S182_D0.39821.906
13_A227_I0.391151.872
131_F290_F0.386611.850
75_L79_G0.385351.844
162_V166_P0.380251.820
210_L216_K0.377911.809
247_Q267_N0.369051.766
155_I159_I0.368191.762
119_S122_L0.36811.762
171_S175_D0.36311.738
318_W321_T0.359161.719
263_S267_N0.356261.705
316_K319_L0.356161.705
244_P247_Q0.354411.696
213_D216_K0.353991.694
35_P186_I0.353061.690
310_N314_R0.351041.680
226_L230_V0.347471.663
122_L126_L0.346711.659
125_L129_I0.346151.657
45_P49_Y0.344351.648
121_W125_L0.327731.568
263_S266_A0.326281.562
212_G216_K0.325031.556
311_S316_K0.321891.541
312_S316_K0.320351.533
92_Y96_V0.318861.526
347_I352_G0.318231.523
158_I162_V0.31741.519
145_I149_L0.315881.512
359_V362_A0.312521.496
61_T73_K0.312381.495
28_T36_S0.312241.494
77_K81_I0.312171.494
144_R147_R0.312151.494
132_G136_Y0.308691.477
71_A83_I0.306191.465
349_I352_G0.30371.453
347_I350_L0.303581.453
171_S174_L0.301171.441
140_K144_R0.298421.428
58_S70_M0.295971.416
222_I226_L0.295921.416
319_L322_F0.293511.405
318_W322_F0.293451.404
172_N175_D0.292581.400
154_I158_I0.291791.396
310_N316_K0.289611.386
118_L122_L0.287991.378
358_M363_R0.287711.377
276_I280_I0.285411.366
118_L121_W0.283161.355
352_G355_P0.282081.350
106_L123_S0.281981.350
230_V234_L0.278821.334
71_A79_G0.277651.329
102_G127_F0.276991.326
34_L38_I0.276361.323
315_L318_W0.275261.317
313_G317_T0.273151.307
294_Y297_L0.270461.294
350_L353_I0.270311.294
143_D147_R0.269161.288
129_I133_G0.268541.285
76_G79_G0.268471.285
159_I163_Y0.267171.279
356_A360_W0.26651.275
41_L233_L0.265071.269
295_L299_D0.263091.259
37_L41_L0.260971.249
75_L361_K0.259491.242
130_I287_A0.258491.237
65_S69_S0.25771.233
14_G150_V0.257561.233
127_F131_F0.25691.229
311_S315_L0.256851.229
302_A306_K0.254111.216
355_P358_M0.252481.208
81_I85_I0.252441.208
266_A275_S0.251391.203
142_V146_N0.251111.202
27_A31_A0.250641.200
15_T292_G0.249191.193
133_G136_Y0.248411.189
356_A359_V0.248231.188
312_S315_L0.246951.182
182_D185_Y0.246551.180
12_I224_G0.244921.172
52_L222_I0.244341.169
241_G244_P0.2431.163
99_I290_F0.241961.158
134_I138_G0.239871.148
39_L189_A0.239661.147
123_S126_L0.238911.143
16_A228_P0.23751.137
159_I162_V0.2371.134
219_K222_I0.236631.132
121_W332_F0.236251.131
310_N315_L0.236111.130
131_F135_V0.236051.130
23_A27_A0.235421.127
316_K320_L0.235181.126
144_R148_V0.234021.120
122_L125_L0.233671.118
357_L361_K0.233521.118
78_K82_V0.233441.117
132_G322_F0.233371.117
48_Y222_I0.232791.114
49_Y53_L0.230761.104
100_S104_S0.228641.094
273_W276_I0.22851.094
35_P179_S0.227481.089
186_I190_L0.227061.087
327_I331_L0.226151.082
146_N288_T0.225811.081
37_L40_L0.225031.077
272_P276_I0.224571.075
107_S111_G0.224391.074
53_L356_A0.223341.069
280_I284_F0.222941.067
285_A288_T0.222751.066
58_S204_P0.222431.065
327_I330_L0.222331.064
357_L362_A0.221781.061
57_V70_M0.22151.060
357_L360_W0.221421.060
101_G104_S0.221141.058
69_S73_K0.220871.057
294_Y299_D0.219191.049
170_P173_L0.219051.048
126_L130_I0.218761.047
109_L276_I0.21871.047
295_L298_F0.218641.046
108_S279_S0.21791.043
277_L281_F0.217891.043
309_N312_S0.217241.040
183_W186_I0.216791.038
360_W364_K0.216341.035
128_T132_G0.215191.030
63_E69_S0.21411.025
218_R221_I0.213581.022
360_W363_R0.213041.020
66_S69_S0.212091.015
285_A289_S0.212021.015
215_K218_R0.2121.015
88_L92_Y0.211911.014
21_M25_P0.21011.006
68_T84_G0.209541.003
33_F36_S0.209241.001
149_L288_T0.208951.000
209_Y299_D0.208861.000
64_G70_M0.208220.997
212_G219_K0.207810.995
63_E73_K0.207480.993
185_Y188_P0.20720.992
42_I45_P0.206930.990
359_V364_K0.206740.989
141_A145_I0.206730.989
168_W241_G0.206630.989
297_L301_L0.206550.989
55_A59_L0.206050.986
143_D146_N0.205640.984
38_I42_I0.205630.984
266_A272_P0.205550.984
245_R249_A0.205160.982
336_F340_L0.204950.981
323_L327_I0.204730.980
32_G35_P0.204710.980
51_G221_I0.20470.980
201_N205_S0.204620.979
37_L237_F0.203420.974
347_I351_L0.202960.971
229_L233_L0.202950.971
314_R317_T0.202670.970
50_S200_H0.202480.969
161_V164_L0.202450.969
358_M361_K0.20240.969
99_I128_T0.201180.963
213_D218_R0.201020.962
17_I20_G0.200620.960
228_P232_Y0.199740.956
56_E59_L0.19930.954
152_G156_S0.198890.952
346_G350_L0.198510.950
91_L94_L0.198310.949
41_L45_P0.198170.948
94_L97_A0.197560.945
223_I226_L0.197280.944
315_L319_L0.196950.943
236_V240_L0.196790.942
353_I357_L0.196770.942
304_L307_L0.196750.942
137_F141_A0.19670.941
161_V234_L0.196610.941
48_Y51_G0.196120.939
44_W197_F0.195720.937
88_L301_L0.195480.936
314_R318_W0.194620.931
317_T321_T0.194560.931
56_E60_N0.194420.930
139_T143_D0.194120.929
130_I133_G0.193940.928
12_I16_A0.193660.927
107_S120_P0.192890.923
23_A336_F0.19220.920
18_G21_M0.191880.918
354_L358_M0.191580.917
21_M235_W0.191450.916
160_L164_L0.191220.915
75_L357_L0.190570.912
135_V291_L0.190440.911
303_D307_L0.190030.909
82_V86_S0.189860.909
89_F93_A0.189680.908
326_L330_L0.189420.907
104_S107_S0.189310.906
244_P267_N0.188320.901
93_A96_V0.188250.901
125_L128_T0.188240.901
187_L191_P0.187790.899
293_V297_L0.187040.895
109_L280_I0.186780.894
104_S108_S0.186690.893
179_S183_W0.186380.892
31_A35_P0.186240.891
106_L110_L0.186220.891
291_L294_Y0.18590.890
169_N172_N0.185720.889
75_L358_M0.185210.886
38_I41_L0.185190.886
48_Y52_L0.184250.882
95_L99_I0.18380.880
198_G201_N0.183320.877
238_S242_S0.183240.877
206_L295_L0.183120.876
288_T291_L0.183080.876
69_S72_E0.183050.876
106_L283_F0.182730.875
16_A19_A0.182650.874
68_T80_G0.181750.870
28_T31_A0.181720.870
47_M51_G0.18110.867
67_L70_M0.180840.865
224_G228_P0.179930.861
100_S107_S0.179320.858
102_G286_I0.17860.855
192_V196_S0.178430.854
276_I279_S0.177950.852
54_L67_L0.17770.850
52_L56_E0.177620.850
282_A286_I0.177460.849
34_L37_L0.176990.847
135_V139_T0.176830.846
102_G283_F0.176790.846
326_L329_A0.176490.845
68_T72_E0.176410.844
146_N153_M0.176160.843
24_L33_F0.176020.842
68_T303_D0.175920.842
26_I29_A0.175830.841
302_A305_F0.175560.840
349_I353_I0.17530.839
154_I231_M0.17510.838
26_I337_L0.174960.837
179_S186_I0.174950.837
339_A342_Y0.174690.836
241_G245_R0.17450.835
353_I356_A0.173840.832
224_G227_I0.17350.830
95_L294_Y0.173260.829
173_L241_G0.173220.829
177_P180_P0.172960.828
67_L71_A0.172890.827
264_A267_N0.172610.826
348_A352_G0.172610.826
135_V138_G0.172410.825
98_Y290_F0.172410.825
298_F302_A0.17220.824
105_I109_L0.171580.821
13_A17_I0.171210.819
138_G141_A0.171140.819
26_I30_G0.171010.818
356_A361_K0.170640.817
101_G286_I0.17060.816
13_A16_A0.170560.816
107_S110_L0.170540.816
156_S281_F0.17050.816
166_P169_N0.170310.815
348_A351_L0.170290.815
330_L333_P0.17020.815
298_F301_L0.170090.814
211_G216_K0.169670.812
178_P182_D0.169590.812
91_L293_V0.169530.811
290_F293_V0.169460.811
10_L147_R0.169220.810
170_P174_L0.168930.808
61_T74_Y0.168410.806
180_P184_S0.16840.806
294_Y300_F0.16830.805
299_D302_A0.168260.805
72_E76_G0.168230.805
201_N296_G0.168190.805
346_G351_L0.168070.804
95_L290_F0.167810.803
225_S229_L0.167780.803
239_I243_L0.167550.802
14_G17_I0.167210.800
28_T33_F0.167170.800
124_S132_G0.16710.800
183_W187_L0.167030.799
90_L94_L0.16680.798
23_A192_V0.166740.798
153_M288_T0.166570.797
357_L363_R0.166560.797
105_I283_F0.166480.797
218_R222_I0.166420.796
230_V233_L0.166260.796
237_F241_G0.166090.795
98_Y289_S0.165890.794
259_S263_S0.165430.792
309_N313_G0.165390.792
55_A58_S0.165290.791
198_G343_A0.165070.790
52_L55_A0.164650.788
216_K220_A0.164420.787
329_A333_P0.164360.787
320_L323_L0.164210.786
299_D303_D0.164030.785
324_P328_F0.164030.785
354_L362_A0.164010.785
147_R151_F0.163930.785
153_M285_A0.163280.781
358_M364_K0.163250.781
11_L14_G0.163140.781
163_Y274_I0.162450.777
102_G105_I0.16240.777
11_L206_L0.162330.777
211_G214_P0.162260.777
83_I354_L0.161640.774
79_G82_V0.161510.773
78_K81_I0.161350.772
246_E249_A0.161160.771
236_V241_G0.161050.771
13_A231_M0.160880.770
20_G232_Y0.160460.768
181_S185_Y0.160360.767
18_G232_Y0.160310.767
282_A285_A0.160120.766
165_I238_S0.159990.766
71_A358_M0.159330.763
144_R149_L0.15920.762
224_G231_M0.159090.761
74_Y362_A0.159040.761
339_A343_A0.158960.761
107_S123_S0.158770.760
319_L323_L0.158720.760
295_L301_L0.158380.758
23_A26_I0.158210.757
47_M200_H0.157850.755
279_S282_A0.157790.755
71_A75_L0.157680.755
14_G291_L0.157350.753
126_L129_I0.157240.753
140_K143_D0.157230.752
90_L347_I0.15710.752
56_E363_R0.156910.751
24_L27_A0.156780.750
43_A194_V0.156580.749
35_P38_I0.156220.748
190_L194_V0.156110.747
189_A193_L0.155960.746
234_L238_S0.155730.745
346_G352_G0.155690.745
210_L220_A0.155480.744
206_L210_L0.155060.742
293_V296_G0.155020.742
36_S236_V0.154890.741
94_L98_Y0.154770.741
231_M234_L0.154710.740
170_P175_D0.154610.740
221_I228_P0.154590.740
55_A207_V0.154080.737
346_G349_I0.154010.737
170_P241_G0.153850.736
57_V60_N0.15380.736
285_A292_G0.153630.735
20_G195_F0.153250.733
152_G155_I0.153040.732
44_W228_P0.152990.732
18_G22_L0.152920.732
98_Y101_G0.152820.731
313_G318_W0.152780.731
352_G357_L0.152770.731
157_F164_L0.152620.730
153_M289_S0.152270.729
137_F144_R0.151960.727
271_S277_L0.151940.727
207_V217_I0.151910.727
121_W124_S0.151660.726
188_P192_V0.151460.725
209_Y217_I0.15140.725
141_A144_R0.150890.722
94_L198_G0.150690.721
97_A340_L0.150650.721
129_I326_L0.150610.721
322_F325_P0.150470.720
214_P217_I0.150420.720
124_S127_F0.150130.719
128_T329_A0.149570.716
197_F201_N0.149490.715
338_I342_Y0.149450.715
304_L318_W0.149420.715
328_F332_F0.149380.715
51_G200_H0.149380.715
177_P182_D0.149340.715
66_S71_A0.149130.714
44_W48_Y0.14880.712
156_S278_G0.148650.711
150_V153_M0.148590.711
195_F347_I0.148580.711
77_K80_G0.148460.711
260_A264_A0.148450.710
352_G356_A0.148220.709
131_F294_Y0.147770.707
167_H170_P0.147660.707
76_G80_G0.147570.706
296_G300_F0.147070.704
15_T198_G0.146950.703
39_L42_I0.14680.703
329_A332_F0.146780.702
137_F140_K0.146610.702
43_A197_F0.146420.701
328_F334_N0.146390.701
75_L78_K0.146320.700
291_L301_L0.146140.699
127_F287_A0.145910.698
119_S123_S0.145860.698
172_N244_P0.145750.698
57_V61_T0.145580.697
351_L356_A0.145440.696
198_G347_I0.145160.695
65_S80_G0.145130.695
127_F290_F0.14510.694
81_I84_G0.145040.694
337_L342_Y0.144870.693
225_S228_P0.144780.693
52_L218_R0.144630.692
305_F322_F0.144450.691
65_S73_K0.144450.691
223_I227_I0.144440.691
74_Y358_M0.14440.691
169_N176_A0.14440.691
24_L236_V0.144290.691
19_A286_I0.1440.689
200_H204_P0.143990.689
66_S303_D0.14390.689
336_F339_A0.14380.688
335_G338_I0.143730.688
94_L293_V0.143370.686
351_L359_V0.143310.686
138_G145_I0.14320.685
134_I291_L0.143110.685
337_L341_G0.143080.685
340_L344_G0.142840.684
48_Y221_I0.14270.683
23_A33_F0.142650.683
289_S293_V0.142590.682
132_G135_V0.142170.680
266_A269_S0.141940.679
191_P194_V0.141220.676
91_L202_I0.140950.675
177_P181_S0.140860.674
10_L15_T0.140660.673
99_I131_F0.140620.673
350_L358_M0.140540.673
355_P359_V0.140490.672
66_S70_M0.140420.672
110_L118_L0.140220.671
236_V239_I0.140180.671
27_A192_V0.140120.671
104_S109_L0.140030.670
65_S70_M0.139930.670
340_L347_I0.139920.670
294_Y301_L0.139770.669
51_G225_S0.139460.667
357_L364_K0.139360.667
176_A179_S0.139310.667
316_K321_T0.139220.666
17_I21_M0.139160.666
65_S68_T0.139030.665
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
3l1lA0.96451000.295
3giaA0.95181000.349
4djkA0.96951000.395
2jlnA0.946799.70.619
3dh4A0.941699.50.681
2xq2A0.941699.50.683
2a65A0.989899.10.745
2wswA0.906197.70.844
4ainA0.964596.90.868
4humA0.741148.90.934

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