GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LacY_symp - LacY protonsugar symporter
Pfam: PF01306 (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: CL0015
Length: 412
Sequences: 41541
Seq/Len: 100.83
HH_delta: 0.113 (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
41_S44_E1.256262.828
107_A111_G1.058572.383
214_L218_K1.030492.320
287_G290_N1.019992.296
257_G260_M1.013062.281
288_A339_A1.007872.269
341_F349_L1.004972.263
298_I325_E0.964142.171
68_D347_A0.947922.134
182_L186_L0.921882.076
215_S218_K0.920312.072
280_P284_N0.916962.065
281_W285_R0.897542.021
94_V171_W0.877731.976
102_N106_G0.872441.964
383_L387_L0.858061.932
244_P248_A0.857881.932
342_D345_L0.857411.930
256_Q260_M0.848831.911
65_F69_K0.847731.909
123_P126_E0.843541.899
371_Y375_R0.834471.879
71_G74_K0.828461.865
347_A351_L0.824471.856
55_F59_A0.811631.827
73_K77_L0.776841.749
289_K293_L0.776061.747
64_G68_D0.773731.742
66_I70_L0.772391.739
271_L320_L0.756721.704
40_L44_E0.747421.683
70_L74_K0.744781.677
59_A62_V0.738031.662
70_L75_H0.733061.650
275_M278_F0.732171.648
171_W175_A0.731651.647
278_F281_W0.730171.644
42_G374_D0.726951.637
43_T374_D0.725881.634
111_G114_L0.72441.631
63_Y120_A0.724321.631
302_R325_E0.715221.610
302_R318_I0.711161.601
119_N123_P0.701881.580
313_W317_L0.700621.577
290_N294_L0.700421.577
135_R138_F0.693421.561
290_N293_L0.682221.536
311_N314_V0.674071.518
282_L286_I0.663971.495
361_G365_L0.661421.489
305_G318_I0.650711.465
168_I171_W0.643791.449
77_L185_L0.641431.444
66_I75_H0.635041.430
54_L363_I0.632241.423
126_E129_A0.627751.413
50_S367_P0.6271.412
275_M324_L0.625721.409
156_L160_I0.616751.389
286_I290_N0.616271.388
71_G75_H0.615741.386
307_G383_L0.613231.381
154_A158_A0.610511.375
300_A390_L0.609041.371
376_I380_H0.607661.368
297_V301_I0.607351.367
107_A110_G0.605561.363
271_L275_M0.604341.361
106_G110_G0.602341.356
370_G374_D0.595541.341
294_L298_I0.59291.335
62_V65_F0.591291.331
74_K77_L0.589321.327
68_D348_T0.588311.325
77_L181_L0.582991.313
211_K214_L0.581531.309
113_Y117_V0.579561.305
137_G284_N0.57811.302
274_L277_F0.575691.296
74_K78_W0.575621.296
68_D72_L0.574781.294
134_R137_G0.574141.293
43_T47_I0.573441.291
165_N168_I0.569751.283
259_Q263_Y0.569151.281
47_I51_A0.56881.281
277_F281_W0.568231.279
102_N107_A0.56331.268
55_F112_I0.561711.265
167_N170_F0.558251.257
286_I291_L0.557171.254
50_S363_I0.551331.241
274_L278_F0.548761.236
174_S178_I0.546711.231
140_Y144_R0.546511.230
105_L109_I0.54641.230
183_L187_L0.545771.229
372_L376_I0.543121.223
260_M263_Y0.541161.218
67_S72_L0.540261.216
171_W174_S0.538481.212
103_F107_A0.537141.209
47_I367_P0.537131.209
298_I302_R0.536161.207
139_E142_R0.534891.204
294_L297_V0.533391.201
97_P102_N0.531511.197
287_G291_L0.531221.196
41_S374_D0.530831.195
138_F142_R0.52971.193
142_R146_W0.52931.192
223_W227_L0.529021.191
111_G117_V0.527091.187
380_H383_L0.525071.182
293_L297_V0.5251.182
307_G386_G0.524541.181
220_R224_F0.524171.180
133_S136_N0.523961.180
175_A179_I0.523851.179
75_H78_W0.523791.179
295_A328_L0.523761.179
86_L90_F0.519021.169
178_I182_L0.51811.166
167_N171_W0.517671.166
230_I361_G0.517041.164
263_Y267_V0.514261.158
371_Y374_D0.511441.151
281_W284_N0.510611.150
345_L348_T0.508891.146
144_R147_G0.507251.142
61_P65_F0.506241.140
81_A84_L0.502481.131
82_I117_V0.501491.129
293_L296_G0.501221.128
313_W316_S0.501141.128
317_L321_L0.500921.128
348_T351_L0.499361.124
343_K346_S0.496431.118
120_A124_L0.495181.115
184_L188_K0.494911.114
111_G115_G0.494831.114
270_F274_L0.490531.104
130_E133_S0.490141.104
46_G50_S0.489621.102
384_I388_I0.488051.099
64_G347_A0.486881.096
217_F223_W0.485191.092
143_A146_W0.483671.089
384_I387_L0.483421.088
335_K339_A0.482911.087
380_H384_I0.480461.082
300_A304_I0.478791.078
125_S128_Y0.4771.074
107_A113_Y0.476441.073
44_E47_I0.474281.068
222_F226_V0.472581.064
317_L320_L0.47181.062
234_A238_V0.471581.062
89_P92_I0.470451.059
141_G144_R0.467841.053
127_A131_R0.466991.051
191_V194_Q0.464651.046
367_P371_Y0.464531.046
188_K191_V0.464281.045
249_S252_Q0.464051.045
278_F282_L0.461691.039
379_Q383_L0.461331.039
295_A329_L0.459921.036
51_A55_F0.458981.033
72_L131_R0.458831.033
40_L45_I0.458711.033
245_I249_S0.456581.028
163_N259_Q0.45571.026
282_L291_L0.455611.026
111_G119_N0.454931.024
186_L189_P0.453011.020
234_A365_L0.452171.018
57_L363_I0.452121.018
221_N224_F0.451561.017
291_L294_L0.451231.016
124_L127_A0.449611.012
231_G235_I0.447921.008
67_S347_A0.444951.002
51_A108_I0.442440.996
164_I168_I0.441420.994
46_G370_G0.440340.991
297_V300_A0.439510.990
314_V317_L0.439280.989
360_I364_I0.439070.989
104_W107_A0.436870.984
67_S124_L0.43680.983
104_W108_I0.436230.982
142_R145_M0.436080.982
300_A386_G0.43470.979
65_F348_T0.431950.973
301_I305_G0.43190.972
304_I308_F0.429140.966
304_I386_G0.427720.963
314_V318_I0.424510.956
215_S344_R0.424130.955
102_N105_L0.423030.952
115_G119_N0.422770.952
101_S106_G0.42110.948
220_R223_W0.419180.944
331_V335_K0.418980.943
153_I156_L0.418910.943
106_G111_G0.418390.942
373_Y378_F0.418050.941
169_I173_A0.416730.938
173_A176_A0.41550.935
53_S366_S0.415260.935
47_I50_S0.414980.934
102_N108_I0.413840.932
229_V233_A0.413770.932
226_V357_A0.410320.924
316_S320_L0.410040.923
78_W82_I0.409680.922
140_Y143_A0.40890.921
219_M223_W0.408520.920
268_Q272_E0.408110.919
283_I287_G0.406770.916
74_K190_D0.40650.915
302_R322_H0.405030.912
211_K215_S0.404250.910
118_F123_P0.403240.908
97_P106_G0.402740.907
63_Y66_I0.401760.905
166_P170_F0.400910.903
117_V121_G0.400140.901
327_P331_V0.399930.900
309_A314_V0.399490.899
321_L325_E0.39910.899
267_V271_L0.398550.897
59_A116_L0.397970.896
81_A181_L0.396930.894
168_I172_I0.396360.892
109_I113_Y0.395320.890
72_L190_D0.393720.886
58_L61_P0.393550.886
284_N288_A0.393480.886
368_L371_Y0.392370.883
170_F174_S0.392120.883
386_G390_L0.391950.882
295_A325_E0.391370.881
110_G113_Y0.390140.878
141_G145_M0.389910.878
299_M389_V0.389760.878
266_S270_F0.389610.877
128_Y132_V0.389280.876
101_S104_W0.388510.875
53_S57_L0.388310.874
103_F106_G0.388260.874
154_A159_G0.387280.872
334_F338_T0.387040.871
52_G56_A0.386680.871
102_N111_G0.382290.861
121_G124_L0.381730.859
305_G308_F0.381710.859
83_L87_F0.381490.859
101_S105_L0.381330.859
364_I368_L0.381150.858
150_G154_A0.380660.857
277_F280_P0.380090.856
363_I367_P0.379560.855
116_L120_A0.379030.853
53_S362_I0.37880.853
186_L190_D0.37790.851
261_Y265_W0.377810.851
181_L185_L0.377230.849
143_A147_G0.376850.848
157_L160_I0.376830.848
42_G373_Y0.37580.846
156_L159_G0.374480.843
110_G114_L0.374170.842
223_W226_V0.373320.841
219_M340_H0.373320.841
280_P283_I0.372450.839
85_L89_P0.371350.836
58_L62_V0.371340.836
159_G262_G0.370870.835
137_G140_Y0.36990.833
328_L332_A0.369820.833
77_L80_I0.369790.833
75_H79_F0.369730.832
57_L360_I0.369120.831
57_L356_F0.369060.831
182_L185_L0.368480.830
155_S265_W0.367550.828
127_A130_E0.367150.827
158_A162_F0.366920.826
151_F154_A0.366680.826
132_V135_R0.366360.825
63_Y116_L0.366290.825
54_L57_L0.366090.824
118_F122_V0.36560.823
173_A177_A0.365320.823
279_S282_L0.365110.822
185_L189_P0.364540.821
43_T371_Y0.36440.820
57_L359_Q0.363570.819
56_A359_Q0.362590.816
88_G91_F0.361970.815
133_S139_E0.361130.813
180_L184_L0.36080.812
43_T367_P0.360330.811
128_Y131_R0.359130.809
108_I111_G0.358920.808
359_Q363_I0.358890.808
224_F228_F0.358590.807
78_W81_A0.35820.806
382_Y386_G0.357090.804
121_G125_S0.356120.802
208_V211_K0.355160.800
235_I239_F0.35380.797
372_L384_I0.353790.797
279_S328_L0.353350.796
114_L119_N0.353080.795
148_S151_F0.35170.792
136_N140_Y0.35160.792
136_N139_E0.351480.791
172_I175_A0.351450.791
105_L111_G0.349470.787
346_S350_Y0.349270.786
132_V136_N0.348710.785
369_A381_T0.348570.785
304_I307_G0.348270.784
368_L385_M0.347860.783
362_I366_S0.346880.781
272_E276_M0.346550.780
127_A132_V0.345680.778
106_G109_I0.344910.777
216_L219_M0.344570.776
180_L183_L0.344280.775
348_T352_V0.3440.775
323_A327_P0.343680.774
79_F120_A0.34290.772
375_R379_Q0.342470.771
60_Q359_Q0.342330.771
252_Q258_N0.341640.769
282_L285_R0.341450.769
272_E327_P0.340630.767
356_F360_I0.340180.766
383_L386_G0.340120.766
232_V236_Y0.340.766
139_E143_A0.339850.765
281_W286_I0.339530.764
284_N287_G0.33930.764
114_L118_F0.339050.763
172_I176_A0.338470.762
113_Y119_N0.337330.759
183_L186_L0.337230.759
129_A133_S0.337080.759
331_V334_F0.336670.758
82_I86_L0.336530.758
94_V97_P0.336280.757
260_M264_L0.335950.756
152_A155_S0.335180.755
386_G389_V0.334930.754
129_A134_R0.333770.751
145_M148_S0.333710.751
76_L79_F0.332990.750
150_G156_L0.332860.749
215_S219_M0.332450.749
146_W150_G0.33220.748
364_I367_P0.332060.748
234_A237_D0.331980.747
104_W109_I0.331130.746
246_Y249_S0.330730.745
162_F169_I0.330670.744
271_L274_L0.330210.743
97_P101_S0.328960.741
59_A63_Y0.328790.740
50_S53_S0.328530.740
84_L88_G0.327780.738
381_T385_M0.326710.736
262_G266_S0.326620.735
189_P192_P0.326040.734
248_A252_Q0.325580.733
80_I83_L0.325570.733
55_F58_L0.325090.732
263_Y266_S0.324880.731
105_L108_I0.32470.731
139_E146_W0.324270.730
300_A389_V0.323730.729
59_A119_N0.323670.729
160_I163_N0.323190.728
156_L266_S0.323180.728
122_V126_E0.323150.728
233_A237_D0.322960.727
86_L89_P0.322430.726
88_G92_I0.322150.725
302_R321_L0.32210.725
124_L128_Y0.321160.723
126_E130_E0.320250.721
372_L381_T0.320210.721
335_K338_T0.319530.719
215_S345_L0.319530.719
356_F359_Q0.319310.719
175_A178_I0.318450.717
229_V236_Y0.318380.717
111_G118_F0.318350.717
63_Y67_S0.31780.716
141_G146_W0.317690.715
238_V369_A0.317350.715
337_I341_F0.316750.713
227_L230_I0.316430.712
312_P316_S0.316210.712
151_F155_S0.315720.711
160_I164_I0.315670.711
152_A156_L0.315670.711
134_R138_F0.315320.710
226_V230_I0.31530.710
336_Y340_H0.314620.708
315_I319_K0.31380.707
218_K221_N0.313720.706
53_S56_A0.312650.704
120_A123_P0.312540.704
77_L81_A0.312530.704
60_Q63_Y0.312480.704
159_G162_F0.31210.703
233_A236_Y0.312080.703
372_L375_R0.311780.702
45_I49_F0.311690.702
87_F91_F0.311630.702
123_P127_A0.311380.701
137_G143_A0.31120.701
225_F228_F0.310660.699
286_I294_L0.310620.699
275_M279_S0.309770.697
60_Q351_L0.309340.696
176_A179_I0.308630.695
155_S159_G0.308230.694
235_I238_V0.308190.694
184_L187_L0.307740.693
169_I172_I0.307650.693
131_R134_R0.307550.692
161_L168_I0.307360.692
49_F366_S0.306960.691
216_L349_L0.306380.690
179_I183_L0.306090.689
47_I371_Y0.305810.689
283_I288_A0.305810.689
336_Y339_A0.305810.689
329_L333_A0.305770.688
61_P356_F0.305680.688
128_Y133_S0.305210.687
301_I304_I0.305140.687
129_A132_V0.304610.686
256_Q264_L0.304060.685
224_F227_L0.303970.684
248_A261_Y0.303920.684
299_M325_E0.303670.684
227_L231_G0.303520.683
42_G249_S0.303080.682
310_T314_V0.302760.682
131_R135_R0.302510.681
116_L119_N0.300710.677
60_Q355_Q0.30040.676
303_I307_G0.300390.676
260_M312_P0.299420.674
81_A85_L0.299050.673
378_F381_T0.298840.673
62_V66_I0.298750.673
91_F95_F0.298330.672
259_Q262_G0.298150.671
245_I248_A0.297750.670
205_K208_V0.297740.670
320_L324_L0.297670.670
310_T313_W0.297560.670
268_Q276_M0.297350.669
254_A257_G0.296290.667
48_I51_A0.2940.662
44_E48_I0.293890.662
368_L372_L0.293390.661
292_L333_A0.293090.660
252_Q255_G0.292360.658
355_Q358_K0.292280.658
296_G300_A0.290670.654
176_A180_L0.29040.654
73_K190_D0.290370.654
63_Y119_N0.289950.653
118_F121_G0.289520.652
46_G49_F0.289170.651
96_G102_N0.289080.651
267_V270_F0.288930.651
179_I182_L0.28870.650
214_L217_F0.288660.650
266_S269_V0.288310.649
318_I322_H0.287950.648
292_L296_G0.287530.647
190_D193_P0.286910.646
139_E144_R0.285110.642
381_T384_I0.284760.641
320_L323_A0.284520.641
56_A59_A0.284450.640
130_E134_R0.284110.640
217_F220_R0.283970.639
387_L390_L0.28360.639
87_F90_F0.283440.638
56_A60_Q0.282520.636
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
2cfqA11000.113
1pw4A0.97571000.239
4j05A0.9831000.243
3o7qA0.93931000.275
4apsA0.96841000.309
2gfpA0.89081000.328
4iu9B0.94171000.346
4jr9A0.92721000.348
2xutA0.97821000.382
4gc0A0.97571000.392

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