GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SBP_bac_5 - Bacterial extracellular solute-binding proteins family 5 Middle
Pfam: PF00496 (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: CL0177
Length: 374
Sequences: 9874
Seq/Len: 26.4
HH_delta: 0.078 (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
125_K136_E1.881994.722
219_A278_K1.533953.849
71_P77_V1.49443.749
231_E235_K1.471043.691
72_D75_T1.468853.685
271_K274_E1.455413.652
69_E77_V1.449833.638
26_D74_Y1.421193.566
123_K136_E1.319433.310
42_V46_E1.292693.243
9_S23_T1.23043.087
226_Y271_K1.167842.930
42_V70_A1.15692.903
224_L318_L1.140082.860
213_P216_S1.133922.845
274_E278_K1.106012.775
229_D232_A1.10132.763
39_E70_A1.069832.684
218_K222_Q1.068872.682
12_E23_T1.066282.675
295_P324_K1.020542.560
219_A275_L1.016842.551
36_L119_T1.011382.537
219_A222_Q0.993442.492
69_E79_T0.980762.461
319_K324_K0.97282.441
19_T77_V0.970642.435
21_T77_V0.954352.394
14_S18_K0.931932.338
31_S138_N0.919912.308
134_V151_R0.918522.304
19_T79_T0.917612.302
29_K35_P0.91252.289
13_V20_Y0.907582.277
45_F78_F0.88962.232
29_K140_D0.882012.213
23_T75_T0.873782.192
123_K139_P0.861482.161
28_L36_L0.858022.153
295_P326_E0.848252.128
66_D81_K0.837192.100
8_E26_D0.835762.097
37_T40_D0.834072.093
41_V76_V0.812092.037
128_S131_Q0.812052.037
166_A171_E0.808322.028
212_N346_D0.807132.025
9_S12_E0.801152.010
122_Y149_I0.79712.000
297_I326_E0.789841.982
222_Q271_K0.770641.933
11_W22_F0.747911.876
126_S134_V0.74591.871
208_F347_M0.736441.848
27_G35_P0.724571.818
136_E151_R0.723171.814
315_Q319_K0.713031.789
39_E73_D0.711471.785
168_Q185_Q0.70931.780
126_S132_R0.708321.777
8_E23_T0.705551.770
39_E42_V0.705071.769
67_S79_T0.704591.768
125_K151_R0.694151.742
34_E100_H0.688771.728
228_I314_L0.68751.725
268_D271_K0.686611.723
132_R153_E0.67581.696
137_R150_D0.672821.688
128_S132_R0.670241.682
37_T73_D0.670231.682
297_I328_K0.669971.681
224_L323_I0.668471.677
273_R277_E0.665521.670
338_K342_A0.663131.664
14_S19_T0.656941.648
157_I166_A0.649921.631
14_S21_T0.641751.610
227_A321_I0.640131.606
215_F224_L0.633541.590
339_R344_D0.63231.586
38_A70_A0.630821.583
8_E25_R0.623231.564
231_E244_P0.612951.538
134_V153_E0.610711.532
220_V279_A0.608321.526
277_E282_K0.605291.519
270_E273_R0.598791.502
21_T75_T0.591711.485
78_F87_F0.585011.468
28_L119_T0.583831.465
25_R28_L0.579581.454
220_V276_L0.579151.453
275_L278_K0.56911.428
135_L154_L0.563311.413
31_S123_K0.561521.409
32_D100_H0.560071.405
234_V244_P0.555381.393
317_Q320_K0.553821.389
184_D187_K0.55141.383
166_A172_I0.550771.382
23_T74_Y0.548161.375
35_P74_Y0.544521.366
71_P75_T0.543071.363
70_A73_D0.532831.337
215_F296_L0.528821.327
274_E277_E0.525191.318
308_K312_E0.524831.317
331_D335_T0.522421.311
66_D79_T0.515571.294
125_K134_V0.51551.293
162_S166_A0.50881.277
4_P11_W0.508211.275
313_A317_Q0.508121.275
20_Y87_F0.507981.274
29_K138_N0.507211.273
14_S17_G0.504141.265
137_R147_P0.501221.258
42_V68_I0.501121.257
31_S140_D0.48671.221
222_Q275_L0.484581.216
273_R283_K0.481431.208
6_L119_T0.48141.208
269_P273_R0.478461.200
318_L325_V0.476441.195
136_E139_P0.474941.192
234_V242_A0.473871.189
315_Q327_I0.47371.188
332_F337_D0.470891.181
23_T26_D0.464571.166
22_F78_F0.464551.166
270_E274_E0.463861.164
30_W40_D0.463281.162
227_A318_L0.462821.161
31_S124_L0.462771.161
269_P321_I0.460711.156
233_I310_I0.460491.155
212_N216_S0.46021.155
232_A317_Q0.458751.151
35_P73_D0.458671.151
38_A71_P0.457971.149
132_R155_R0.456891.146
207_A348_A0.456151.144
328_K339_R0.455871.144
68_I76_V0.454881.141
316_E320_K0.450611.131
40_D43_F0.448081.124
168_Q189_D0.445011.116
12_E21_T0.441381.107
238_F242_A0.440681.106
21_T71_P0.43961.103
8_E74_Y0.433751.088
314_L318_L0.42911.077
225_A230_R0.427031.071
123_K138_N0.423671.063
84_F90_L0.420211.054
186_L192_L0.420181.054
40_D44_S0.419281.052
137_R146_R0.417241.047
193_S196_Y0.414791.041
208_F224_L0.413741.038
25_R142_W0.412281.034
257_D260_F0.41061.030
219_A279_A0.407741.023
315_Q325_V0.40771.023
271_K275_L0.404151.014
189_D192_L0.403031.011
46_E50_D0.401971.009
31_S117_I0.401391.007
80_L87_F0.398621.000
20_Y88_L0.398441.000
46_E49_A0.396310.994
101_S104_K0.394960.991
23_T72_D0.390940.981
22_F88_L0.389680.978
282_K285_D0.38910.976
296_L347_M0.388990.976
31_S118_G0.38390.963
38_A76_V0.383810.963
311_A327_I0.381350.957
272_A321_I0.379840.953
39_E43_F0.379130.951
157_I172_I0.378860.951
6_L28_L0.377080.946
304_D307_W0.375330.942
184_D188_S0.374580.940
13_V17_G0.373490.937
222_Q226_Y0.368130.924
228_I233_I0.367820.923
340_L348_A0.367770.923
229_D317_Q0.366430.919
167_L192_L0.364610.915
38_A42_V0.363540.912
42_V76_V0.362810.910
87_F91_L0.362760.910
165_A168_Q0.361890.908
7_A22_F0.360640.905
206_L314_L0.360130.904
235_K240_G0.358790.900
6_L41_V0.355690.892
300_Y329_P0.353870.888
20_Y80_L0.353210.886
230_R244_P0.352020.883
96_P99_V0.350340.879
159_D162_S0.349160.876
172_I175_I0.349110.876
164_V168_Q0.344270.864
39_E99_V0.343590.862
46_E70_A0.343530.862
316_E319_K0.342250.859
68_I78_F0.34120.856
202_G353_S0.339940.853
164_V186_L0.337640.847
184_D239_G0.337620.847
70_A77_V0.336920.845
335_T339_R0.335480.842
232_A236_N0.334680.840
32_D117_I0.333810.838
46_E68_I0.331590.832
318_L347_M0.32910.826
70_A76_V0.327550.822
112_D116_P0.32710.821
298_I325_V0.326680.820
24_L36_L0.326650.820
182_D185_Q0.326390.819
314_L325_V0.326230.818
281_Y284_S0.323470.812
40_D101_S0.322740.810
36_L44_S0.322370.809
360_Y364_Y0.321230.806
26_D35_P0.32090.805
6_L36_L0.319690.802
223_A276_L0.317630.797
18_K82_E0.316250.793
224_L347_M0.314910.790
243_T251_P0.314680.790
332_F350_S0.314550.789
331_D334_D0.314310.789
305_P308_K0.313540.787
11_W88_L0.311680.782
281_Y285_D0.310240.778
64_S84_F0.310.778
217_D279_A0.309110.776
269_P320_K0.309010.775
226_Y275_L0.308790.775
167_L175_I0.307950.773
65_I68_I0.307630.772
36_L98_P0.307150.771
175_I178_V0.30650.769
267_Y320_K0.305940.768
18_K66_D0.305910.768
135_L152_I0.305040.765
16_D19_T0.30490.765
206_L347_M0.30350.761
102_A106_E0.302790.760
187_K197_S0.301710.757
106_E109_Y0.30160.757
355_D361_S0.30130.756
139_P150_D0.301230.756
34_E40_D0.301190.756
275_L279_A0.299750.752
312_E327_I0.299010.750
22_F91_L0.297040.745
318_L321_I0.296880.745
124_L127_Y0.296560.744
18_K83_P0.294020.738
217_D281_Y0.293450.736
41_V98_P0.292150.733
229_D267_Y0.292020.733
30_W34_E0.291640.732
44_S98_P0.291530.731
17_G21_T0.291090.730
330_V339_R0.289230.726
208_F215_F0.289110.725
30_W36_L0.288840.725
122_Y151_R0.288440.724
155_R166_A0.288370.723
38_A74_Y0.287840.722
165_A169_S0.287470.721
318_L323_I0.286870.720
11_W23_T0.286580.719
332_F336_Y0.285990.718
296_L299_L0.285710.717
30_W119_T0.285670.717
136_E150_D0.285040.715
220_V281_Y0.284350.713
312_E315_Q0.282930.710
127_Y133_I0.282180.708
157_I163_A0.281420.706
226_Y267_Y0.280310.703
179_P182_D0.279580.701
42_V69_E0.278820.700
108_D111_K0.278420.699
5_W142_W0.277550.696
352_W355_D0.276660.694
335_T338_K0.276630.694
210_T216_S0.275620.692
319_K325_V0.274890.690
28_L142_W0.274180.688
28_L74_Y0.274080.688
27_G74_Y0.274020.687
226_Y263_E0.2740.687
7_A11_W0.270870.680
137_R145_G0.270870.680
78_F91_L0.270090.678
309_A312_E0.269270.676
45_F91_L0.268450.674
204_Y307_W0.268230.673
30_W118_G0.266410.668
276_L279_A0.266350.668
107_D110_G0.266340.668
122_Y147_P0.266060.668
43_F47_R0.265610.666
228_I318_L0.265380.666
86_D358_D0.26460.664
30_W37_T0.264590.664
217_D220_V0.264430.663
30_W100_H0.263980.662
122_Y150_D0.263640.661
13_V88_L0.263280.661
208_F225_A0.262280.658
12_E15_D0.262070.658
300_Y327_I0.261840.657
18_K79_T0.260820.654
137_R149_I0.260730.654
276_L323_I0.260630.654
269_P276_L0.259970.652
233_I237_I0.258950.650
226_Y266_E0.258550.649
127_Y156_V0.25830.648
46_E67_S0.257610.646
212_N215_F0.257510.646
297_I346_D0.257220.645
131_Q155_R0.256540.644
305_P309_A0.256030.642
260_F263_E0.255620.641
160_A163_A0.255010.640
50_D53_Y0.254730.639
319_K323_I0.254090.637
94_P98_P0.2540.637
36_L74_Y0.25160.631
215_F347_M0.251040.630
336_Y348_A0.24920.625
137_R142_W0.249080.625
30_W44_S0.247760.622
299_L328_K0.247580.621
8_E28_L0.247240.620
211_N343_G0.247070.620
124_L133_I0.246790.619
167_L172_I0.24650.618
363_L367_F0.244740.614
122_Y137_R0.244550.614
296_L300_Y0.244320.613
330_V335_T0.243220.610
209_N346_D0.243120.610
277_E281_Y0.242460.608
149_I152_I0.242140.608
133_I156_V0.241690.606
300_Y311_A0.240930.604
276_L321_I0.240650.604
146_R150_D0.239970.602
183_I187_K0.239950.602
38_A72_D0.239070.600
296_L325_V0.238510.598
227_A269_P0.238090.597
123_K140_D0.238020.597
86_D89_Y0.237780.597
312_E316_E0.23490.589
310_I314_L0.234470.588
197_S241_Y0.232550.583
217_D278_K0.232230.583
227_A267_Y0.231380.581
285_D296_L0.231270.580
233_I313_A0.231070.580
212_N344_D0.230140.577
7_A24_L0.229440.576
45_F68_I0.229110.575
237_I313_A0.228310.573
301_T307_W0.228050.572
102_A105_A0.227820.572
277_E283_K0.227820.572
112_D115_N0.227280.570
161_D165_A0.226980.569
206_L349_L0.226660.569
86_D90_L0.226580.568
215_F220_V0.226090.567
4_P9_S0.225850.567
199_P243_T0.224690.564
181_S239_G0.22440.563
24_L28_L0.223870.562
234_V238_F0.223430.561
203_Y245_A0.222560.558
4_P7_A0.22160.556
64_S82_E0.221490.556
101_S105_A0.221320.555
67_S81_K0.221170.555
217_D280_G0.220580.553
355_D362_F0.219270.550
263_E266_E0.21890.549
253_S256_Y0.217450.546
310_I313_A0.217260.545
103_N106_E0.217220.545
111_K115_N0.217090.545
15_D19_T0.216870.544
8_E36_L0.216720.544
304_D308_K0.216510.543
109_Y112_D0.215880.542
209_N345_F0.215510.541
144_G147_P0.215450.541
233_I314_L0.215170.540
24_L74_Y0.214540.538
281_Y323_I0.21360.536
6_L24_L0.213360.535
13_V16_D0.212770.534
44_S99_V0.212280.533
298_I349_L0.211610.531
137_R144_G0.21110.530
17_G83_P0.210880.529
36_L40_D0.209850.526
301_T304_D0.209820.526
104_K109_Y0.209470.526
30_W41_V0.208140.522
303_D308_K0.207290.520
116_P124_L0.207090.520
276_L281_Y0.206950.519
224_L296_L0.206680.519
303_D306_I0.206040.517
28_L31_S0.205980.517
204_Y310_I0.205750.516
311_A349_L0.205730.516
211_N216_S0.204890.514
276_L322_G0.204750.514
111_K114_K0.204630.513
313_A316_E0.20450.513
220_V224_L0.204340.513
44_S47_R0.203520.511
38_A77_V0.203340.510
356_Y360_Y0.203310.510
15_D21_T0.203170.510
36_L118_G0.202990.509
220_V275_L0.202920.509
155_R172_I0.202680.509
114_K129_P0.201740.506
214_P346_D0.201510.506
8_E24_L0.200850.504
226_Y274_E0.200240.502
308_K329_P0.20.502
204_Y351_G0.199580.501
105_A109_Y0.198430.498
241_Y244_P0.198390.498
40_D102_A0.198270.497
330_V336_Y0.19820.497
155_R171_E0.198140.497
295_P298_I0.198070.497
336_Y340_L0.197990.497
223_A272_A0.197590.496
356_Y361_S0.197530.496
337_D341_R0.197040.494
210_T213_P0.19670.494
325_V347_M0.19630.493
230_R246_N0.196250.492
41_V44_S0.196180.492
276_L280_G0.195870.491
46_E64_S0.195840.491
163_A172_I0.195510.491
48_L95_P0.19550.490
307_W349_L0.195350.490
185_Q188_S0.195180.490
166_A169_S0.194450.488
106_E110_G0.194340.488
266_E271_K0.194080.487
103_N107_D0.193360.485
164_V182_D0.193180.485
64_S81_K0.192730.484
345_F348_A0.192660.483
31_S119_T0.192090.482
37_T74_Y0.19190.481
298_I301_T0.191320.480
28_L41_V0.191040.479
257_D261_D0.190850.479
231_E234_V0.190620.478
232_A313_A0.190260.477
300_Y308_K0.189870.476
24_L38_A0.189230.475
56_P59_Y0.189050.474
65_I81_K0.188490.473
49_A81_K0.188290.472
306_I309_A0.188080.472
38_A75_T0.188060.472
253_S354_G0.187870.471
8_E12_E0.187020.469
9_S22_F0.186890.469
268_D274_E0.186740.469
245_A251_P0.186660.468
302_S307_W0.186160.467
181_S309_A0.185750.466
299_L330_V0.185630.466
223_A275_L0.185140.465
130_G156_V0.184850.464
302_S305_P0.184810.464
24_L41_V0.184790.464
337_D340_L0.184310.462
102_A107_D0.184150.462
218_K221_R0.18410.462
44_S48_L0.184080.462
2_L89_Y0.183980.462
13_V19_T0.183190.460
339_R342_A0.183160.460
138_N141_Y0.182160.457
183_I194_V0.181940.456
8_E11_W0.181120.454
234_V241_Y0.180960.454
334_D337_D0.180530.453
205_Y350_S0.180440.453
222_Q263_E0.180440.453
49_A67_S0.179450.450
19_T69_E0.179210.450
36_L41_V0.179070.449
4_P22_F0.178980.449
90_L356_Y0.178950.449
299_L339_R0.178820.449
13_V18_K0.178620.448
208_F323_I0.178080.447
44_S97_A0.177870.446
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
1uqwA0.95451000.078
1xocA0.97331000.079
3zs6A0.96521000.079
2nooA0.97331000.08
3o9pA0.96791000.081
3m8uA0.95991000.089
3tpaA0.95991000.09
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