GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peripla_BP_6 - Periplasmic binding protein
Pfam: PF13458 (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: CL0144
Length: 343
Sequences: 8714
Seq/Len: 25.41
HH_delta: 0.082 (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
3_K44_E1.11733.810
30_D268_A1.014123.458
156_R169_E1.007643.436
137_K165_K0.85832.927
22_L26_E0.83182.836
263_E267_A0.82872.826
291_Q294_E0.817422.787
93_G110_N0.803042.738
48_Y63_K0.788282.688
72_A289_L0.772952.635
32_I290_A0.772792.635
159_L164_G0.764362.606
51_G56_Q0.743322.534
260_Q264_R0.742.523
57_A81_Q0.731032.493
170_I185_Q0.730812.492
31_E264_R0.72372.468
30_D34_A0.687212.343
291_Q295_R0.671722.290
259_K263_E0.661052.254
300_D303_A0.660712.253
73_V89_A0.636792.171
5_G64_L0.604132.060
156_R160_E0.592592.021
314_D319_P0.584821.994
266_R272_E0.582671.987
29_V286_A0.575531.962
26_E30_D0.569651.942
52_G78_S0.565071.927
312_K321_S0.559251.907
309_E327_H0.546631.864
48_Y60_A0.54581.861
136_K192_D0.54321.852
127_E131_K0.541861.848
7_L50_D0.539821.841
290_A294_E0.53841.836
7_L60_A0.537861.834
130_A162_A0.534011.821
303_A306_E0.529141.804
31_E283_Y0.527941.800
139_A168_G0.519811.772
127_E162_A0.515581.758
29_V45_L0.511691.745
158_A161_A0.510621.741
25_A286_A0.50751.730
307_A310_S0.500221.706
142_Y171_R0.495791.690
153_E157_K0.492791.680
261_F279_A0.489421.669
122_A126_A0.485891.657
93_G302_E0.48451.652
284_D315_G0.481341.641
286_A290_A0.479961.636
31_E287_R0.479511.635
305_R309_E0.47471.619
302_E306_E0.467691.595
63_K68_D0.460421.570
53_D56_Q0.458141.562
24_G282_G0.454341.549
23_R26_E0.450741.537
295_R307_A0.44831.529
291_Q311_L0.448011.528
32_I287_R0.445881.520
3_K46_V0.444071.514
112_F309_E0.441111.504
254_D259_K0.434591.482
306_E310_S0.430041.466
160_E165_K0.427641.458
23_R265_Y0.423841.445
31_E35_A0.41981.431
135_A193_V0.417111.422
260_Q263_E0.415891.418
28_A290_A0.409521.396
209_Q212_Q0.407931.391
157_K161_A0.401871.370
76_P85_V0.40051.366
172_Y198_G0.399991.364
139_A170_I0.398171.358
210_L215_L0.396781.353
135_A192_D0.395461.348
56_Q60_A0.395341.348
144_D149_R0.393831.343
6_V25_A0.393631.342
28_A286_A0.39341.341
61_A89_A0.391421.335
22_L47_V0.391341.334
110_N305_R0.391091.333
137_K190_G0.388221.324
65_I94_I0.387921.323
264_R267_A0.386911.319
9_P50_D0.386721.319
138_V193_V0.383491.308
48_Y68_D0.382841.305
183_V213_L0.38241.304
19_Q23_R0.377091.286
112_F305_R0.3721.268
56_Q59_Q0.37031.263
144_D173_P0.370151.262
123_A158_A0.369691.261
43_I290_A0.368711.257
95_P301_R0.368541.257
48_Y64_L0.368481.256
231_S234_Q0.367531.253
257_A314_D0.365421.246
26_E47_V0.362471.236
25_A74_V0.361251.232
139_A191_P0.361011.231
265_Y269_Y0.358481.222
149_R171_R0.358211.221
323_D326_D0.35821.221
23_R269_Y0.357811.220
183_V209_Q0.356281.215
61_A65_I0.35571.213
87_P91_E0.355541.212
46_V68_D0.352571.202
296_A307_A0.351551.199
137_K167_V0.348541.188
90_E109_P0.347071.183
183_V210_L0.345871.179
284_D317_F0.345591.178
76_P82_A0.345461.178
289_L293_L0.340991.163
312_K319_P0.340431.161
21_F282_G0.340121.160
76_P96_Y0.338881.155
154_A157_K0.338871.155
97_I289_L0.338111.153
288_L308_L0.337591.151
62_R66_D0.336731.148
244_Y337_Q0.335781.145
23_R271_E0.33261.134
5_G70_V0.330721.128
149_R153_E0.330241.126
28_A287_R0.327581.117
64_L70_V0.326641.114
25_A45_L0.325811.111
137_K192_D0.325091.108
263_E266_R0.324541.107
10_L47_V0.321871.097
102_S118_D0.321641.097
127_E158_A0.320811.094
61_A73_V0.320321.092
130_A164_G0.319711.090
185_Q189_A0.318991.088
128_Y244_Y0.318841.087
282_G286_A0.318611.086
158_A162_A0.318291.085
256_P260_Q0.317981.084
142_Y152_A0.317481.082
141_V182_L0.317391.082
32_I43_I0.316751.080
175_G202_D0.316231.078
293_L304_V0.315651.076
138_V159_L0.314971.074
125_L195_V0.314591.073
6_V29_V0.311751.063
288_L322_F0.311091.061
287_R290_A0.310761.060
96_Y111_V0.309951.057
66_D92_A0.309221.054
187_K215_L0.308151.051
60_A63_K0.306871.046
32_I286_A0.306211.044
292_A308_L0.305611.042
159_L166_V0.305231.041
89_A96_Y0.305011.040
20_D276_S0.304991.040
29_V33_N0.304811.039
295_R311_L0.303791.036
26_E45_L0.303411.035
184_Q188_S0.302441.031
236_G240_L0.301181.027
50_D81_Q0.299781.022
7_L61_A0.299181.020
24_G28_A0.299091.020
126_A155_F0.298781.019
130_A136_K0.298031.016
79_S103_S0.297441.014
139_A186_L0.296861.012
24_G279_A0.294361.004
90_E108_S0.293040.999
209_Q213_L0.291810.995
82_A101_A0.291740.995
27_L31_E0.290040.989
303_A307_A0.289460.987
241_E339_K0.289120.986
139_A167_V0.287810.981
62_R88_I0.287420.980
152_A169_E0.286960.978
183_V215_L0.285860.975
11_S49_D0.284840.971
3_K70_V0.284570.970
98_S101_A0.283650.967
27_L264_R0.282870.964
141_V206_F0.281460.960
112_F308_L0.281370.959
86_A111_V0.280980.958
262_Q266_R0.280450.956
27_L265_Y0.27910.952
94_I301_R0.278380.949
298_S303_A0.277220.945
176_D182_L0.276760.944
157_K160_E0.273840.934
320_I323_D0.273670.933
152_A156_R0.273590.933
126_A159_L0.272890.930
142_Y169_E0.272220.928
155_F159_L0.27190.927
208_R212_Q0.270880.924
71_D301_R0.270560.923
82_A96_Y0.270130.921
140_I152_A0.269960.920
180_S209_Q0.269820.920
28_A32_I0.269540.919
109_P305_R0.268040.914
7_L85_V0.267950.914
272_E275_P0.267480.912
65_I88_I0.267130.911
168_G185_Q0.266890.910
76_P89_A0.26680.910
28_A283_Y0.266580.909
39_N294_E0.265910.907
74_V97_I0.265740.906
26_E268_A0.263610.899
65_I92_A0.26360.899
7_L76_P0.263350.898
131_K162_A0.262930.897
10_L22_L0.262490.895
145_D148_G0.262480.895
307_A311_L0.260420.888
151_L197_A0.260210.887
38_I290_A0.259760.886
173_P176_D0.259720.886
62_R91_E0.256960.876
264_R268_A0.256520.875
58_V62_R0.255720.872
27_L269_Y0.25570.872
33_N37_G0.255150.870
167_V191_P0.253750.865
31_E34_A0.253140.863
98_S111_V0.252960.863
38_I43_I0.252710.862
61_A85_V0.251430.857
258_V262_Q0.251430.857
292_A296_A0.251040.856
61_A88_I0.250030.853
6_V47_V0.249330.850
25_A282_G0.24870.848
3_K68_D0.247680.845
60_A64_L0.247340.843
287_R313_Y0.246290.840
223_F227_L0.246010.839
27_L30_D0.245040.836
168_G189_A0.244060.832
84_A87_P0.243430.830
145_D174_P0.243090.829
259_K262_Q0.242790.828
9_P18_G0.241740.824
130_A159_L0.240830.821
72_A95_P0.240560.820
36_G40_G0.240290.819
12_G18_G0.239590.817
280_A316_L0.239560.817
187_K213_L0.237950.811
172_Y202_D0.237580.810
143_P148_G0.237490.810
19_Q22_L0.236980.808
167_V189_A0.236950.808
294_E297_G0.236920.808
296_A303_A0.236720.807
2_I41_R0.236610.807
114_L285_A0.23560.803
114_L288_L0.235510.803
58_V88_I0.235410.803
152_A171_R0.235320.802
6_V45_L0.233920.798
184_Q213_L0.233640.797
74_V289_L0.233060.795
72_A304_V0.232660.793
4_I286_A0.232190.792
4_I72_A0.2320.791
256_P259_K0.231160.788
267_A270_G0.230970.788
59_Q62_R0.230630.786
187_K190_G0.229930.784
153_E156_R0.229150.781
122_A151_L0.229120.781
138_V164_G0.229120.781
2_I293_L0.228610.779
123_A127_E0.22750.776
257_A260_Q0.22740.775
112_F327_H0.227320.775
255_S258_V0.227190.775
52_G81_Q0.22690.774
206_F210_L0.226850.773
291_Q313_Y0.226360.772
61_A92_A0.225970.770
295_R310_S0.225220.768
144_D171_R0.224810.767
150_S153_E0.224760.766
126_A162_A0.224340.765
113_R328_Q0.224330.765
74_V285_A0.222840.760
4_I289_L0.220990.753
110_N302_E0.219940.750
306_E309_E0.218780.746
140_I166_V0.218370.745
21_F77_L0.218280.744
37_G42_K0.216930.740
155_F195_V0.216840.739
288_L313_Y0.216330.738
183_V187_K0.216170.737
70_V73_V0.215690.735
183_V206_F0.215380.734
3_K69_G0.215320.734
223_F226_S0.21470.732
233_Q237_G0.214510.731
5_G48_Y0.214240.730
55_A59_Q0.213030.726
287_R291_Q0.212590.725
38_I41_R0.212570.725
229_D233_Q0.212530.725
186_L191_P0.212510.725
78_S81_Q0.212460.724
71_D299_L0.211630.722
196_L206_F0.211330.721
7_L89_A0.209870.716
115_S281_Q0.209220.713
187_K217_P0.208510.711
12_G15_A0.208470.711
50_D57_A0.207970.709
205_A209_Q0.206960.706
129_L223_F0.206880.705
284_D316_L0.206870.705
185_Q188_S0.206390.704
139_A189_A0.206210.703
266_R270_G0.205620.701
102_S115_S0.205370.700
50_D76_P0.203290.693
236_G239_A0.202660.691
249_W258_V0.202570.691
313_Y320_I0.202230.690
7_L64_L0.202220.690
261_F275_P0.2020.689
211_R216_K0.201870.688
140_I156_R0.201860.688
95_P304_V0.201150.686
31_E260_Q0.201030.685
57_A84_A0.200120.682
109_P306_E0.199280.679
62_R92_A0.198790.678
129_L222_L0.198750.678
2_I5_G0.198610.677
138_V155_F0.198180.676
86_A108_S0.198090.675
180_S213_L0.197280.673
112_F322_F0.197220.672
261_F265_Y0.196750.671
178_D209_Q0.196720.671
126_A164_G0.196220.669
128_Y133_L0.196090.669
207_L211_R0.195860.668
205_A208_R0.195810.668
179_F209_Q0.19540.666
43_I286_A0.195170.665
17_Y77_L0.194580.663
85_V89_A0.194120.662
46_V70_V0.193910.661
46_V64_L0.193590.660
27_L268_A0.19190.654
65_I73_V0.191550.653
97_I114_L0.191080.652
65_I89_A0.1910.651
83_E87_P0.190210.649
33_N42_K0.190.648
44_E47_V0.189460.646
9_P77_L0.189450.646
36_G39_N0.189010.644
24_G27_L0.188750.644
88_I91_E0.18860.643
10_L18_G0.188330.642
242_G337_Q0.18820.642
156_R166_V0.18790.641
315_G318_G0.18790.641
238_D241_E0.186250.635
211_R239_A0.186110.635
145_D149_R0.185970.634
207_L210_L0.185530.633
128_Y132_K0.185390.632
118_D147_Y0.185130.631
231_S235_L0.184890.630
39_N42_K0.184020.627
159_L162_A0.183980.627
129_L133_L0.183330.625
194_V210_L0.183160.625
14_F78_S0.182880.624
128_Y335_I0.182620.623
97_I285_A0.181840.620
129_L193_V0.181550.619
82_A98_S0.181220.618
178_D181_A0.180680.616
35_A294_E0.180460.615
247_S336_V0.180180.614
36_G41_R0.179940.614
26_E29_V0.179720.613
27_L283_Y0.179310.611
176_D179_F0.179140.611
129_L135_A0.178990.610
124_A333_V0.178880.610
17_Y278_Y0.178360.608
28_A31_E0.178330.608
23_R27_L0.178320.608
166_V169_E0.178240.608
58_V84_A0.178130.607
71_D94_I0.178090.607
323_D327_H0.177910.607
170_I182_L0.177770.606
71_D304_V0.177030.604
88_I92_A0.176840.603
257_A287_R0.176620.602
299_L303_A0.176470.602
240_L243_V0.176350.601
123_A161_A0.176130.601
34_A37_G0.176120.601
32_I38_I0.17560.599
296_A304_V0.175470.598
126_A130_A0.175190.597
145_D199_D0.174460.595
275_P279_A0.174190.594
102_S147_Y0.173970.593
144_D148_G0.173910.593
121_Q147_Y0.173520.592
222_L226_S0.173480.592
198_G206_F0.173380.591
37_G40_G0.173340.591
71_D300_D0.172820.589
2_I299_L0.17280.589
37_G41_R0.172530.588
99_P282_G0.172450.588
3_K71_D0.172360.588
289_L304_V0.172170.587
118_D121_Q0.171470.585
265_Y275_P0.171320.584
104_P119_S0.170410.581
61_A76_P0.169390.578
211_R238_D0.169280.577
57_A61_A0.169020.576
326_D329_A0.168710.575
141_V172_Y0.168640.575
180_S212_Q0.168560.575
231_S237_G0.16770.572
5_G73_V0.167650.572
59_Q63_K0.167220.570
126_A158_A0.16710.570
269_Y275_P0.166770.569
125_L246_V0.166490.568
25_A29_V0.166360.567
6_V22_L0.166310.567
155_F164_G0.16630.567
82_A111_V0.166020.566
142_Y149_R0.165980.566
292_A304_V0.165910.566
140_I155_F0.165270.564
280_A284_D0.16510.563
151_L155_F0.165040.563
265_Y270_G0.164570.561
90_E110_N0.164040.559
233_Q236_G0.163820.559
146_P149_R0.163690.558
95_P305_R0.163150.556
194_V215_L0.162970.556
266_R271_E0.162930.556
173_P182_L0.162610.554
288_L291_Q0.16250.554
9_P52_G0.162380.554
248_P251_P0.162010.552
33_N36_G0.16160.551
127_E130_A0.16120.550
109_P302_E0.161140.549
240_L338_V0.160510.547
125_L129_L0.159870.545
125_L335_I0.159170.543
74_V99_P0.158460.540
284_D287_R0.158450.540
293_L296_A0.158290.540
146_P150_S0.158240.540
87_P90_E0.15820.539
140_I169_E0.157760.538
2_I71_D0.157420.537
95_P110_N0.15710.536
323_D328_Q0.157010.535
108_S111_V0.156740.534
147_Y151_L0.156370.533
207_L240_L0.156290.533
228_D231_S0.155850.531
304_V307_A0.154760.528
95_P112_F0.154480.527
255_S259_K0.154470.527
151_L224_G0.154120.525
97_I308_L0.153860.525
297_G300_D0.153560.524
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
4f06A0.98831000.082
4gnrA0.97081000.114
3i45A0.98541000.114
3lkbA0.98251000.118
3h5lA0.98541000.12
3n0wA0.97671000.125
3ipcA0.97961000.128
3i09A0.97381000.129
3td9A0.97081000.134
3eafA0.98831000.135

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