GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SBP_bac_8 - Bacterial extracellular solute-binding protein
Pfam: PF13416 (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: 281
Sequences: 15492
Seq/Len: 55.13
HH_delta: 0.18 (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
101_K209_G1.9323.838
117_E121_K1.679193.336
7_E13_K1.497512.975
60_E233_P1.491482.963
102_D207_D1.473512.928
10_T240_E1.463052.907
5_E244_F1.417732.817
161_E165_E1.390362.762
164_K168_D1.347462.677
116_L165_E1.335352.653
247_S250_G1.326162.635
232_N235_A1.306492.596
61_D83_K1.259522.502
99_Y209_G1.235032.454
120_K169_N1.228892.442
5_E8_K1.218552.421
4_K8_K1.187312.359
111_T114_E1.155052.295
5_E9_E1.14312.271
5_E253_E1.113692.213
240_E243_K1.085922.157
12_I235_A1.08172.149
154_E158_E1.071242.128
59_L225_A1.066282.118
6_F240_E1.058922.104
165_E169_N1.03382.054
103_L189_A1.02332.033
3_V241_F0.97961.946
101_K105_K0.976311.940
114_E117_E0.97631.940
7_E10_T0.967591.922
158_E161_E0.963921.915
252_A256_E0.955121.898
4_K7_E0.950891.889
104_L190_M0.928851.845
117_E120_K0.924441.837
99_Y211_A0.919011.826
3_V7_E0.910861.810
27_K31_A0.890941.770
23_D26_Q0.888211.765
230_S233_P0.885951.760
248_P252_A0.883511.755
6_F12_I0.871521.732
79_T84_L0.870221.729
9_E247_S0.850951.691
63_D83_K0.848651.686
6_F10_T0.841.669
226_I242_L0.827991.645
110_K114_E0.825741.641
100_N103_L0.825291.640
86_G223_G0.822311.634
20_P23_D0.816971.623
182_L187_K0.81541.620
116_L166_L0.81231.614
101_K207_D0.80881.607
161_E164_K0.790681.571
157_V161_E0.790651.571
102_D106_K0.787171.564
162_F165_E0.785171.560
250_G253_E0.776871.543
109_P114_E0.769521.529
116_L120_K0.764211.518
175_S178_D0.749861.490
3_V14_V0.747241.485
6_F241_F0.746851.484
96_G210_V0.745691.482
162_F166_L0.743451.477
12_I240_E0.740961.472
70_D266_D0.740821.472
3_V16_I0.738441.467
72_P76_E0.737921.466
60_E228_K0.733471.457
233_P239_W0.724031.438
113_D116_L0.721771.434
248_P264_N0.721391.433
239_W243_K0.718611.428
224_F242_L0.717991.426
248_P266_D0.716491.423
155_N158_E0.706831.404
65_L239_W0.705881.402
235_A240_E0.704741.400
253_E256_E0.701621.394
61_D84_L0.696351.383
253_E257_A0.688921.369
6_F244_F0.680391.352
244_F250_G0.669531.330
122_L189_A0.667771.327
227_P230_S0.666471.324
230_S238_A0.662561.316
29_Q56_Q0.661161.314
226_I239_W0.660651.313
116_L169_N0.653031.297
165_E168_D0.641461.274
181_Q185_S0.637931.267
154_E157_V0.633621.259
143_G146_S0.633231.258
97_L211_A0.631911.255
116_L162_F0.628491.249
182_L188_V0.627551.247
57_G228_K0.626611.245
226_I238_A0.626061.244
54_A85_Y0.624331.240
113_D117_E0.621011.234
264_N267_V0.62051.233
249_E252_A0.619071.230
53_L59_L0.609231.210
183_F208_F0.608751.209
76_E79_T0.60851.209
78_F223_G0.60541.203
97_L190_M0.605061.202
73_D76_E0.604191.200
32_L37_A0.604041.200
66_E69_D0.603811.200
127_G188_V0.600591.193
234_E240_E0.600481.193
125_K189_A0.594271.181
5_E249_E0.593941.180
9_E249_E0.590761.174
103_L122_L0.589691.172
120_K124_G0.580961.154
226_I230_S0.577991.148
104_L122_L0.576951.146
241_F245_L0.576941.146
14_V241_F0.575571.144
111_T215_D0.573771.140
252_A267_V0.568081.129
249_E253_E0.566311.125
43_V227_P0.562111.117
51_P55_E0.556021.105
60_E230_S0.553971.101
103_L106_K0.545451.084
89_F224_F0.53971.072
30_S34_S0.537761.068
61_D85_Y0.512631.018
178_D181_Q0.511091.015
234_E239_W0.507891.009
100_N207_D0.505021.003
64_D239_W0.504281.002
54_A80_Y0.497180.988
60_E239_W0.496990.987
107_A121_K0.493840.981
5_E250_G0.493310.980
6_F235_A0.490950.975
99_Y108_P0.490630.975
98_Y193_G0.490390.974
26_Q30_S0.488880.971
52_Q56_Q0.48540.964
103_L107_A0.483830.961
27_K30_S0.480890.955
2_L250_G0.480130.954
67_N243_K0.477630.949
200_N203_K0.476460.947
107_A122_L0.475850.945
32_L58_L0.473040.940
179_A191_I0.47290.940
42_V238_A0.472310.938
193_G197_S0.471640.937
7_E11_G0.469050.932
110_K214_K0.465380.925
19_F27_K0.462630.919
241_F244_F0.461530.917
25_Q49_W0.45970.913
43_V225_A0.456980.908
238_A242_L0.454270.903
86_G225_A0.447960.890
54_A59_L0.446210.887
115_L190_M0.446210.887
120_K171_Y0.443880.882
61_D64_D0.441430.877
2_L5_E0.439270.873
7_E14_V0.439150.872
224_F245_L0.436140.867
9_E244_F0.432450.859
35_G229_N0.431560.857
243_K247_S0.430640.856
153_S157_V0.427030.848
112_W116_L0.425680.846
158_E162_F0.424570.844
231_K234_E0.424350.843
25_Q53_L0.421850.838
78_F84_L0.418770.832
45_P225_A0.412680.820
181_Q184_A0.410410.815
108_P114_E0.408270.811
67_N70_D0.406870.808
168_D171_Y0.405370.805
92_G220_G0.40440.803
70_D264_N0.40250.800
37_A227_P0.402230.799
60_E226_I0.402050.799
99_Y104_L0.40070.796
152_T157_V0.400020.795
31_A36_N0.399260.793
177_D180_R0.398710.792
72_P265_K0.398650.792
100_N206_P0.396990.789
153_S156_F0.394710.784
79_T82_G0.394580.784
59_L85_Y0.393860.783
7_E12_I0.390890.777
60_E227_P0.390320.775
54_A57_G0.389490.774
26_Q29_Q0.389240.773
160_L164_K0.388150.771
120_K123_K0.38760.770
230_S235_A0.385970.767
42_V242_L0.383490.762
121_K125_K0.377050.749
25_Q52_Q0.374630.744
25_Q29_Q0.373560.742
50_I86_G0.372560.740
123_K171_Y0.370630.736
62_L242_L0.369480.734
3_V13_K0.365810.727
11_G240_E0.365150.725
164_K167_Y0.364610.724
66_E243_K0.362530.720
197_S200_N0.360980.717
177_D181_Q0.360690.717
54_A81_D0.36020.716
226_I233_P0.359620.714
145_K149_D0.357560.710
174_G178_D0.356450.708
122_L190_M0.355730.707
62_L239_W0.351970.699
251_Q263_V0.351110.698
182_L185_S0.346620.689
112_W213_P0.344740.685
63_D84_L0.342090.680
29_Q52_Q0.341640.679
138_W141_I0.34090.677
2_L244_F0.335910.667
98_Y198_I0.335730.667
92_G222_N0.332040.660
106_K121_K0.331980.660
102_D105_K0.330930.657
239_W242_L0.330430.656
152_T155_N0.330220.656
137_Q140_L0.328890.653
109_P190_M0.328650.653
42_V241_F0.327980.652
99_Y190_M0.326890.649
87_V246_T0.326380.648
49_W52_Q0.325590.647
17_Q27_K0.325350.646
230_S234_E0.32470.645
104_L189_A0.324560.645
159_A163_L0.323610.643
102_D186_G0.323250.642
120_K165_E0.322730.641
60_E229_N0.322490.641
46_D49_W0.322090.640
255_A262_P0.321980.640
62_L226_I0.321480.639
115_L128_F0.321430.639
60_E64_D0.321340.638
180_R193_G0.320820.637
142_A162_F0.318330.632
137_Q141_I0.317740.631
152_T156_F0.316490.629
28_L43_V0.316360.629
198_I202_Q0.315550.627
108_P211_A0.314350.625
231_K235_A0.313270.622
98_Y210_V0.312280.620
179_A188_V0.312040.620
107_A189_A0.311920.620
245_L250_G0.311740.619
123_K127_G0.311720.619
228_K233_P0.311380.619
23_D27_K0.309090.614
37_A229_N0.306650.609
129_P188_V0.306640.609
163_L167_Y0.303890.604
90_D222_N0.303160.602
29_Q33_A0.30120.598
122_L126_Y0.300090.596
166_L171_Y0.295810.588
92_G194_G0.295320.587
248_P267_V0.293320.583
167_Y170_G0.29120.579
167_Y172_F0.290490.577
233_P238_A0.290460.577
196_W260_Y0.290430.577
254_W258_T0.290390.577
71_I75_L0.290070.576
251_Q262_P0.289680.576
105_K207_D0.289410.575
146_S149_D0.286680.570
183_F191_I0.286140.568
139_A144_G0.285870.568
2_L253_E0.285820.568
251_Q255_A0.284870.566
97_L115_L0.283860.564
97_L192_I0.283040.562
111_T214_K0.281990.560
9_E240_E0.281830.560
39_D230_S0.281260.559
63_D239_W0.280390.557
104_L108_P0.279640.556
45_P53_L0.278520.553
107_A125_K0.276660.550
199_S203_K0.27660.550
60_E65_L0.275340.547
19_F24_Y0.274420.545
113_D165_E0.273580.544
243_K246_T0.27270.542
116_L171_Y0.272410.541
157_V160_L0.27170.540
180_R184_A0.271350.539
47_S221_G0.270850.538
72_P75_L0.27070.538
17_Q31_A0.269560.536
10_T14_V0.269020.534
53_L58_L0.268930.534
6_F14_V0.268770.534
75_L79_T0.268220.533
10_T235_A0.267610.532
65_L243_K0.267440.531
102_D206_P0.267220.531
75_L84_L0.266640.530
235_A239_W0.265440.527
123_K169_N0.265390.527
50_I225_A0.264790.526
44_W224_F0.264220.525
71_I246_T0.264030.525
93_T96_G0.263830.524
92_G95_Y0.262640.522
147_F150_D0.262310.521
74_A78_F0.262030.521
105_K108_P0.261970.520
178_D182_L0.261720.520
66_E239_W0.260940.518
176_G179_A0.260440.517
136_M140_L0.260190.517
98_Y208_F0.260020.517
184_A204_A0.259930.516
12_I244_F0.259820.516
229_N233_P0.259270.515
31_A38_P0.258910.514
2_L245_L0.258610.514
199_S202_Q0.2570.511
98_Y183_F0.256950.510
13_K16_I0.25690.510
145_K148_D0.256850.510
104_L109_P0.255160.507
110_K115_L0.252630.502
123_K170_G0.252430.502
100_N186_G0.251510.500
29_Q32_L0.251390.499
169_N172_F0.250150.497
29_Q53_L0.249850.496
28_L227_P0.248250.493
93_T195_S0.24770.492
66_E84_L0.247690.492
112_W162_F0.247540.492
139_A159_A0.246780.490
24_Y28_L0.245830.488
59_L227_P0.242970.483
240_E244_F0.242850.482
183_F188_V0.242570.482
21_S24_Y0.241730.480
65_L68_Y0.24160.480
107_A126_Y0.241160.479
196_W199_S0.240910.479
195_S261_L0.240530.478
50_I54_A0.239570.476
58_L227_P0.239470.476
100_N105_K0.239350.476
95_Y192_I0.238860.475
195_S198_I0.238270.473
37_A231_K0.234780.466
64_D67_N0.234680.466
232_N238_A0.234070.465
242_L246_T0.233630.464
95_Y194_G0.233530.464
29_Q58_L0.233010.463
106_K125_K0.232810.463
170_G173_Y0.232710.462
50_I59_L0.232690.462
92_G221_G0.231170.459
244_F247_S0.230980.459
39_D231_K0.230630.458
142_A158_E0.230010.457
92_G195_S0.229480.456
71_I263_V0.228530.454
250_G254_W0.228450.454
44_W89_F0.2280.453
79_T83_K0.227010.451
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
3uorA0.98221000.18
2zyoA0.97861000.188
2gh9A0.97151000.189
2ghaA0.97151000.19
2xd3A0.9681000.195
1eljA0.9681000.195
4dxbA0.9681000.197
3k01A0.97861000.207
4h1gA0.9681000.209
1eu8A0.98221000.214

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