GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
BenE - Benzoate membrane transport protein
Pfam: PF03594 (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: 378
Sequences: 5567
Seq/Len: 14.73
HH_delta: 0.336 (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
95_L255_A0.780484.770
54_T250_A0.560773.427
99_A103_L0.519543.175
99_A252_L0.510343.119
56_I292_G0.485732.969
102_L252_L0.473922.896
59_S289_V0.462632.827
176_A180_L0.418192.556
282_S287_A0.408052.494
141_L148_V0.406052.482
88_A202_E0.401892.456
105_G245_T0.389722.382
56_I289_V0.38792.371
102_L248_G0.37082.266
293_V297_L0.361472.209
52_G296_L0.361042.207
169_A173_A0.35632.178
102_L245_T0.341662.088
172_V176_A0.336772.058
67_V291_A0.328142.005
98_G251_S0.325171.987
290_A294_F0.32441.983
98_G252_L0.3221.968
204_S207_A0.318311.945
86_S89_E0.317691.942
106_V245_T0.30971.893
111_G241_N0.30631.872
105_G248_G0.299241.829
66_I269_A0.29371.795
92_G205_W0.289051.767
53_L253_L0.288961.766
50_G257_F0.285111.742
95_L252_L0.282681.728
52_G292_G0.28071.716
103_L107_T0.278851.704
130_L133_F0.272941.668
146_L150_P0.272811.667
174_G316_L0.265331.622
239_P242_P0.265311.621
57_L246_V0.264491.616
92_G208_L0.264241.615
96_V208_L0.263231.609
120_P124_A0.261331.597
72_T75_A0.259641.587
89_E202_E0.259121.584
253_L257_F0.258111.577
205_W208_L0.250131.529
130_L137_A0.248651.520
146_L149_G0.248311.518
177_V181_T0.237611.452
176_A179_A0.237211.450
175_V311_A0.235871.442
35_A87_F0.234541.433
173_A177_V0.233711.428
223_Q226_P0.230151.407
94_F255_A0.229941.405
52_G56_I0.228521.397
55_S292_G0.22811.394
153_A157_L0.224511.372
98_G248_G0.218881.338
254_A259_G0.21371.306
230_V269_A0.212441.298
231_L238_P0.211391.292
232_R236_Y0.210181.285
203_F256_P0.208721.276
49_L299_G0.208441.274
73_P76_A0.208331.273
111_G115_R0.208081.272
169_A172_V0.206781.264
252_L255_A0.205471.256
158_A162_S0.204171.248
69_A73_P0.20361.244
57_L61_R0.201151.229
177_V180_L0.201081.229
154_V173_A0.200121.223
286_I290_A0.199281.218
57_L249_L0.198831.215
327_G331_G0.198681.214
167_V322_G0.198191.211
92_G203_F0.196991.204
53_L257_F0.196941.204
250_A253_L0.194711.190
71_S74_G0.19411.186
140_A314_P0.192351.176
290_A293_V0.191011.167
206_S210_S0.190491.164
89_E204_S0.188081.149
50_G262_V0.187871.148
175_V312_L0.187831.148
324_A327_G0.186771.141
186_P189_L0.18531.132
174_G178_A0.185041.131
60_L289_V0.184851.130
253_L256_P0.184211.126
64_M243_L0.184061.125
175_V178_A0.181631.110
245_T249_L0.181481.109
213_L216_F0.180761.105
223_Q227_G0.179661.098
249_L253_L0.177821.087
148_V177_V0.175511.073
179_A311_A0.175231.071
289_V293_V0.175071.070
181_T184_L0.174611.067
227_G269_A0.173631.061
157_L329_L0.17351.060
107_T110_F0.173441.060
135_L139_T0.173261.059
48_Y292_G0.172231.053
224_N228_I0.171971.051
215_L219_T0.171751.050
130_L136_A0.171331.047
101_I220_M0.171041.045
98_G255_A0.170421.042
50_G254_A0.170381.041
175_V184_L0.170191.040
73_P78_L0.169471.036
151_M170_A0.168291.029
180_L183_Q0.167351.023
56_I296_L0.166831.020
108_G112_R0.166331.017
33_A43_W0.166271.016
69_A72_T0.166111.015
60_L63_R0.16491.008
104_L216_F0.164321.004
49_L257_F0.164091.003
127_A130_L0.162130.991
70_W74_G0.160980.984
224_N231_L0.160540.981
147_L177_V0.160420.980
291_A298_F0.160150.979
51_M55_S0.159480.975
324_A330_G0.158120.966
104_L110_F0.157980.966
223_Q231_L0.157920.965
129_V226_P0.157540.963
133_F137_A0.157430.962
149_G153_A0.157340.962
177_V183_Q0.157180.961
248_G252_L0.156310.955
327_G330_G0.156250.955
181_T185_H0.156250.955
48_Y52_G0.155850.952
64_M237_Q0.155820.952
119_P123_S0.155730.952
223_Q261_A0.155560.951
123_S334_Q0.155280.949
70_W73_P0.154950.947
153_A170_A0.154760.946
168_L313_P0.154720.946
175_V179_A0.154660.945
223_Q269_A0.154350.943
72_T76_A0.154080.942
178_A183_Q0.153250.937
101_I248_G0.152790.934
31_Q37_P0.152770.934
185_H188_A0.152540.932
91_V255_A0.152360.931
47_L51_M0.151730.927
242_P245_T0.151480.926
247_T251_S0.151420.925
269_A272_C0.151350.925
48_Y51_M0.150920.922
71_S263_N0.150780.921
204_S208_L0.150340.919
147_L178_A0.15020.918
180_L184_L0.149720.915
298_F302_A0.149690.915
293_V296_L0.149440.913
142_Q147_L0.149420.913
90_A93_A0.149020.911
35_A260_H0.147990.904
147_L183_Q0.147950.904
108_G241_N0.147560.902
323_L327_G0.14750.901
35_A43_W0.147390.901
50_G54_T0.146670.896
102_L249_L0.146310.894
89_E93_A0.14580.891
64_M239_P0.145490.889
157_L160_R0.145220.888
141_L152_L0.14520.887
191_L194_A0.145180.887
313_P316_L0.144980.886
56_I60_L0.144310.882
223_Q263_N0.1440.880
90_A94_F0.143880.879
229_A232_R0.143780.879
150_P174_G0.143770.879
328_T331_G0.143180.875
246_V249_L0.143130.875
89_E207_A0.141990.868
129_V263_N0.141760.866
77_L218_V0.141090.862
283_R286_I0.141080.862
52_G55_S0.140770.860
77_L81_S0.140120.856
324_A328_T0.139970.855
201_P204_S0.139940.855
33_A82_L0.138470.846
329_L333_L0.137980.843
141_L226_P0.137730.842
153_A156_L0.137680.841
97_A219_T0.137570.841
94_F261_A0.137280.839
130_L134_G0.137030.837
178_A182_G0.137010.837
60_L288_A0.1370.837
185_H189_L0.136950.837
139_T142_Q0.136870.836
96_V207_A0.136670.835
49_L254_A0.136220.833
326_L329_L0.136220.833
324_A331_G0.136080.832
112_R115_R0.1360.831
151_M174_G0.135980.831
79_A97_A0.135770.830
88_A199_T0.135740.830
167_V302_A0.135660.829
105_G244_I0.135570.829
150_P153_A0.13550.828
175_V316_L0.135420.828
101_I247_T0.134970.825
73_P155_F0.134850.824
228_I243_L0.134840.824
150_P177_V0.134510.822
154_V174_G0.133780.818
233_A236_Y0.13350.816
161_F165_Y0.133340.815
152_L156_L0.133160.814
213_L217_I0.133010.813
167_V170_A0.132560.810
105_G241_N0.13220.808
180_L185_H0.132160.808
198_F201_P0.132010.807
252_L256_P0.131780.805
97_A252_L0.131750.805
248_G317_I0.131510.804
66_I97_A0.131320.803
124_A128_G0.131240.802
150_P154_V0.130930.800
229_A233_A0.130790.799
72_T133_F0.130750.799
54_T68_T0.130420.797
219_T226_P0.130340.797
38_A45_F0.130110.795
67_V70_W0.129990.794
148_V152_L0.129970.794
218_V224_N0.129950.794
104_L220_M0.129840.794
218_V226_P0.129730.793
152_L299_G0.129720.793
45_F196_P0.129280.790
147_L181_T0.129150.789
247_T263_N0.129120.789
101_I216_F0.128310.784
226_P230_V0.128130.783
335_T338_S0.128080.783
165_Y169_A0.128070.783
187_S190_Q0.128050.783
153_A177_V0.127610.780
170_A316_L0.127510.779
51_M312_L0.127360.778
159_R163_P0.126720.774
101_I219_T0.126190.771
323_L326_L0.125980.770
71_S325_L0.125680.768
150_P324_A0.125680.768
103_L106_V0.125660.768
32_A129_V0.125360.766
251_S261_A0.124850.763
87_F91_V0.12470.762
52_G299_G0.124660.762
110_F290_A0.12450.761
219_T224_N0.124230.759
217_I232_R0.124170.759
88_A91_V0.124090.758
220_M224_N0.123860.757
118_P322_G0.123660.756
91_V95_L0.123560.755
92_G207_A0.12330.754
169_A199_T0.123130.753
281_P284_R0.123070.752
170_A174_G0.1230.752
45_F49_L0.122920.751
68_T247_T0.122860.751
219_T263_N0.122780.750
114_M117_I0.122730.750
225_L232_R0.122620.749
75_A78_L0.12260.749
226_P232_R0.12250.749
155_F170_A0.122460.748
59_S292_G0.122260.747
74_G77_L0.122060.746
219_T225_L0.121840.745
74_G324_A0.121620.743
218_V225_L0.121570.743
91_V254_A0.121110.740
248_G269_A0.120820.738
188_A311_A0.120560.737
52_G289_V0.120190.735
59_S246_V0.120060.734
88_A146_L0.120050.734
308_L311_A0.119970.733
61_R199_T0.119940.733
92_G96_V0.119130.728
82_L85_Y0.118750.726
68_T251_S0.118390.724
101_I105_G0.118270.723
150_P173_A0.118130.722
46_A50_G0.118070.722
172_V175_V0.118030.721
286_I289_V0.117970.721
51_M54_T0.117880.720
61_R64_M0.11770.719
232_R237_Q0.11760.719
288_A292_G0.117560.718
99_A249_L0.117310.717
91_V299_G0.117180.716
188_A191_L0.11710.716
88_A180_L0.116950.715
68_T246_V0.116870.714
123_S127_A0.116830.714
112_R118_P0.11680.714
186_P311_A0.116650.713
217_I221_A0.116630.713
154_V158_A0.116140.710
51_M69_A0.116080.709
157_L161_F0.116020.709
70_W75_A0.115710.707
185_H190_Q0.11560.706
97_A216_F0.115350.705
227_G230_V0.115290.705
37_P44_L0.115060.703
179_A183_Q0.115030.703
173_A176_A0.114990.703
224_N263_N0.114610.700
55_S289_V0.11460.700
115_R236_Y0.114590.700
50_G259_G0.114260.698
95_L256_P0.114220.698
216_F226_P0.11380.695
56_I59_S0.113670.695
129_V223_Q0.113550.694
71_S270_A0.11350.694
73_P130_L0.113460.693
325_L331_G0.113430.693
207_A210_S0.113160.692
136_A140_A0.112950.690
218_V221_A0.112950.690
53_L296_L0.112830.690
103_L112_R0.112740.689
252_L269_A0.11210.685
116_R121_I0.112090.685
134_G325_L0.111990.684
100_L213_L0.111760.683
192_S196_P0.111710.683
79_A168_L0.111640.682
154_V170_A0.111550.682
117_I157_L0.11150.681
138_F294_F0.11130.680
94_F121_I0.111210.680
131_L300_L0.110970.678
234_A238_P0.110720.677
197_V200_T0.110630.676
96_V99_A0.11060.676
117_I126_L0.110470.675
334_Q338_S0.110370.675
134_G323_L0.110360.674
100_L103_L0.110210.674
51_M262_V0.110150.673
54_T246_V0.109890.672
151_M316_L0.109850.671
259_G296_L0.109840.671
105_G125_M0.109710.670
167_V271_I0.109580.670
301_F312_L0.109570.670
95_L99_A0.109530.669
216_F219_T0.109510.669
178_A184_L0.109360.668
104_L151_M0.108790.665
246_V250_A0.108730.665
248_G251_S0.108680.664
155_F167_V0.108670.664
312_L316_L0.108450.663
219_T230_V0.108260.662
55_S67_V0.1080.660
211_L214_P0.107950.660
171_L316_L0.107720.658
45_F299_G0.107720.658
69_A75_A0.107540.657
231_L237_Q0.107220.655
189_L293_V0.107060.654
140_A318_A0.106630.652
58_L64_M0.106360.650
105_G111_G0.106310.650
82_L86_S0.106050.648
61_R242_P0.105770.646
56_I139_T0.105610.645
68_T166_A0.105510.645
153_A325_L0.10530.644
101_I262_V0.105160.643
153_A180_L0.104970.642
249_L252_L0.104910.641
130_L295_Y0.104860.641
181_T315_A0.104640.640
289_V292_G0.104540.639
322_G328_T0.104470.638
94_F247_T0.104440.638
53_L57_L0.10440.638
205_W209_V0.104220.637
91_V271_I0.104210.637
244_I263_N0.10410.636
214_P218_V0.104080.636
215_L226_P0.104070.636
74_G79_A0.103860.635
146_L189_L0.103830.635
285_Y288_A0.103760.634
225_L228_I0.103610.633
105_G214_P0.10360.633
44_L310_A0.103580.633
333_L337_F0.103550.633
92_G211_L0.103350.632
142_Q183_Q0.103280.631
126_L223_Q0.103010.630
48_Y309_F0.102970.629
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
3qe7A0.94441000.336
3qe7A0.513290.80.939
1btsA0.068810.20.969
2ksfA0.28318.60.97
3zuxA0.59265.80.972
4he8J0.3734.40.973
2jpnA0.071440.974
2vdaB0.07412.40.976
2nq2A0.80161.70.978
2k9jB0.11381.80.978

Page generated in 0.0261 seconds.