GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SBP_bac_3 - Bacterial extracellular solute-binding proteins family 3
Pfam: PF00497 (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: 225
Sequences: 37872
Seq/Len: 168.32
HH_delta: 0.001 (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
114_G153_I3.17083.730
148_L156_F2.248752.645
104_S107_D2.163432.545
35_R208_E2.066572.431
138_V147_A1.80732.126
53_M59_A1.767952.080
145_L166_L1.73952.046
86_P160_E1.720122.024
88_V160_E1.712342.014
103_K107_D1.683711.981
144_A156_F1.680381.977
32_I205_A1.674451.970
53_M58_K1.645691.936
80_D210_K1.60021.882
112_R135_I1.580331.859
140_S143_E1.572951.850
95_D111_K1.567591.844
84_S186_P1.561121.836
81_P84_S1.545191.818
122_A126_K1.534721.805
114_G144_A1.475331.736
91_V155_A1.445261.700
200_E204_K1.443241.698
31_A34_K1.434091.687
50_L62_I1.427541.679
31_A35_R1.425381.677
31_A208_E1.404371.652
165_Y169_R1.400321.647
45_M53_M1.398551.645
92_R151_G1.395611.642
149_L166_L1.368151.609
52_E56_N1.34121.578
160_E164_E1.340351.577
146_E150_S1.337921.574
55_E75_K1.32641.560
138_V144_A1.311791.543
158_V163_A1.301941.532
33_A40_I1.282761.509
90_V163_A1.26941.493
147_A152_R1.268361.492
146_E149_L1.231991.449
80_D207_R1.21471.429
199_L203_N1.214181.428
81_P186_P1.191411.402
112_R136_V1.186591.396
164_E168_K1.179571.388
149_L171_P1.177151.385
89_L155_A1.176831.384
192_R195_N1.17461.382
84_S184_P1.173321.380
174_N177_V1.171281.378
205_A208_E1.165311.371
70_P73_A1.153611.357
204_K207_R1.148341.351
166_L171_P1.142331.344
54_L62_I1.141811.343
32_I38_I1.14141.343
88_V174_N1.133021.333
76_F190_A1.128171.327
112_R134_N1.127251.326
30_R34_K1.119741.317
203_N207_R1.11421.311
91_V95_D1.114161.311
32_I36_L1.10181.296
122_A137_E1.089551.282
68_I73_A1.086221.278
61_I202_F1.048361.233
145_L149_L1.042891.227
26_V30_R1.037771.221
147_A153_I1.018011.198
92_R95_D1.013641.192
101_T173_E1.007181.185
89_L157_I0.98311.156
111_K155_A0.982331.156
204_K208_E0.972561.144
36_L204_K0.968161.139
45_M49_R0.963721.134
205_A209_L0.963641.134
166_L169_R0.956121.125
35_R205_A0.955791.124
109_K132_N0.947751.115
38_I201_I0.947421.115
43_V59_A0.941791.108
201_I205_A0.938161.104
207_R210_K0.933061.098
80_D203_N0.925831.089
113_I155_A0.922061.085
32_I208_E0.921811.084
117_R139_D0.920691.083
52_E55_E0.911651.072
105_L180_P0.903941.063
25_D82_Y0.903871.063
46_P49_R0.896631.055
63_I189_F0.892031.049
85_S161_S0.889331.046
49_R52_E0.887041.043
136_V147_A0.8851.041
167_L170_H0.882861.039
106_D109_K0.875461.030
143_E146_E0.86551.018
57_G192_R0.859921.012
81_P188_Y0.856861.008
123_D127_Q0.846230.995
201_I204_K0.84560.995
196_P199_L0.844730.994
199_L202_F0.839910.988
68_I188_Y0.835470.983
31_A209_L0.83350.981
95_D112_R0.818750.963
191_V199_L0.812950.956
117_R137_E0.8120.955
139_D143_E0.805440.947
173_E177_V0.803460.945
33_A135_I0.794830.935
53_M56_N0.788050.927
49_R53_M0.787320.926
79_S203_N0.786750.926
165_Y168_K0.785040.923
200_E203_N0.783480.922
77_D193_K0.778090.915
100_K107_D0.773150.910
206_I210_K0.769650.905
77_D199_L0.759750.894
43_V53_M0.7580.892
94_G151_G0.75430.887
125_L129_Y0.753870.887
86_P184_P0.748370.880
45_M50_L0.740210.871
196_P200_E0.738330.869
91_V175_I0.733310.863
33_A112_R0.729720.858
61_I191_V0.728950.858
55_E76_F0.725140.853
107_D110_G0.719240.846
189_F192_R0.716540.843
102_I107_D0.709710.835
198_L202_F0.702180.826
69_T74_K0.70130.825
29_L42_F0.70050.824
30_R42_F0.700030.823
191_V202_F0.699950.823
127_Q131_S0.696780.820
159_D162_T0.695030.818
79_S188_Y0.685710.807
33_A36_L0.68240.803
30_R33_A0.678740.798
141_P158_V0.678240.798
73_A77_D0.677290.797
148_L153_I0.676420.796
95_D100_K0.675940.795
27_D30_R0.675490.795
61_I189_F0.674250.793
124_Y128_Q0.671020.789
36_L205_A0.667960.786
93_K173_E0.657950.774
197_E201_I0.657350.773
195_N198_L0.65660.772
32_I204_K0.655640.771
123_D126_K0.652020.767
163_A166_L0.651530.766
31_A205_A0.6460.760
160_E174_N0.645290.759
51_L55_E0.642870.756
129_Y133_I0.637120.749
114_G138_V0.636020.748
62_I190_A0.631220.743
30_R152_R0.616120.725
170_H173_E0.607980.715
163_A167_L0.606250.713
141_P159_D0.604560.711
27_D31_A0.604020.711
85_S159_D0.603410.710
77_D191_V0.603010.709
45_M59_A0.601810.708
28_L208_E0.601580.708
138_V143_E0.600280.706
51_L76_F0.598670.704
30_R150_S0.596210.701
115_V137_E0.593660.698
80_D191_V0.59320.698
143_E147_A0.592960.698
90_V167_L0.588260.692
149_L170_H0.588040.692
203_N206_I0.585570.689
189_F206_I0.581080.684
29_L40_I0.576330.678
116_V144_A0.576280.678
62_I66_L0.575610.677
43_V58_K0.574690.676
55_E58_K0.572590.674
73_A76_F0.571880.673
167_L174_N0.571770.673
85_S160_E0.566780.667
80_D206_I0.566420.666
108_L155_A0.56040.659
113_I133_I0.558070.656
188_Y191_V0.557040.655
114_G148_L0.555480.653
124_Y127_Q0.553810.651
199_L205_A0.553140.651
77_D196_P0.552220.650
90_V156_F0.551980.649
35_R209_L0.546810.643
33_A39_K0.545330.642
181_P184_P0.543760.640
77_D80_D0.542340.638
69_T73_A0.541530.637
36_L201_I0.538460.633
54_L57_G0.534030.628
186_P189_F0.53010.624
77_D195_N0.528660.622
171_P174_N0.528540.622
70_P74_K0.527110.620
116_V141_P0.525570.618
92_R149_L0.521730.614
90_V158_V0.520680.613
87_Y121_Y0.520280.612
75_K193_K0.520040.612
158_V162_T0.519110.611
142_E146_E0.513630.604
37_G40_I0.510760.601
95_D102_I0.50970.600
197_E200_E0.508440.598
27_D150_S0.504630.594
89_L125_L0.501770.590
114_G147_A0.498630.587
202_F208_E0.496860.584
87_Y157_I0.493780.581
50_L59_A0.490310.577
86_P181_P0.487920.574
85_S185_S0.487570.574
87_Y159_D0.486840.573
93_K171_P0.486390.572
202_F205_A0.48530.571
127_Q130_P0.484170.570
23_G142_E0.483210.568
86_P182_I0.481440.566
144_A147_A0.480480.565
198_L201_I0.479780.564
115_V135_I0.476330.560
88_V91_V0.476280.560
29_L63_I0.474730.558
59_A62_I0.473340.557
54_L59_A0.472710.556
172_L175_I0.470880.554
93_K174_N0.469530.552
44_P143_E0.469160.552
126_K129_Y0.468990.552
29_L33_A0.468970.552
120_S123_D0.467730.550
191_V195_N0.467180.550
95_D155_A0.466890.549
116_V119_S0.465640.548
125_L157_I0.463970.546
115_V122_A0.462060.544
153_I156_F0.461460.543
54_L192_R0.457140.538
121_Y124_Y0.454070.534
54_L76_F0.446550.525
87_Y185_S0.445840.524
100_K103_K0.443940.522
93_K172_L0.442920.521
41_E137_E0.441650.520
179_P182_I0.440980.519
141_P162_T0.436840.514
83_Y187_V0.436110.513
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
4gvoA0.977899.90.001
4h5gA0.982299.90.009
3kzgA0.973399.90.016
3hv1A0.977899.90.019
3vv5A0.968999.90.026
3k4uA0.982299.90.029
4f3pA0.968999.90.035
3kbrA0.977899.90.039
3h7mA0.973399.90.04
3i6vA0.942299.90.041

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