GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Phosphonate-bd - ABC transporter phosphonate periplasmic substrate-binding protein
Pfam: PF12974 (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: 243
Sequences: 23504
Seq/Len: 96.72
HH_delta: 0.076 (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
109_A158_A2.563643.659
26_Q216_S2.143513.060
99_S102_D1.932392.758
149_V161_A1.701722.429
152_A157_K1.661392.372
98_T102_D1.616952.308
22_Y25_K1.563292.232
224_K228_D1.560082.227
225_A229_A1.538372.196
22_Y222_E1.478772.111
208_Q212_D1.45472.077
143_V152_A1.444462.062
222_E225_A1.426082.036
215_L219_K1.418672.025
204_P208_Q1.412482.016
44_E48_S1.390531.985
207_R211_R1.37461.962
22_Y26_Q1.337651.909
212_D216_S1.333021.903
45_A51_I1.316951.880
26_Q213_A1.29461.848
36_A45_A1.262351.802
213_A216_S1.260311.799
21_D25_K1.23831.768
21_D24_S1.211581.729
26_Q220_D1.207741.724
145_S148_A1.185111.692
163_I168_F1.172411.674
24_S31_V1.155221.649
221_P225_A1.151691.644
209_R213_A1.146671.637
22_Y217_L1.127091.609
92_R95_S1.126721.608
45_A50_E1.10521.578
103_L160_A1.096831.566
62_V65_R1.091231.558
27_L213_A1.072931.532
107_R141_V1.062871.517
211_R215_L1.043651.490
106_K159_D1.038181.482
123_R126_L1.020191.456
90_V168_F0.999351.427
226_I229_A0.998281.425
152_A158_A0.997621.424
88_V184_V0.996821.423
98_T183_R0.992631.417
23_L213_A0.989031.412
92_R156_G0.97871.397
209_R212_D0.976011.393
225_A228_D0.966831.380
107_R139_K0.959671.370
24_S30_P0.954481.362
107_R159_D0.949511.355
94_D183_R0.945851.350
108_V160_A0.945321.349
169_E173_A0.937361.338
86_R165_S0.923861.319
198_A207_R0.918551.311
198_A210_L0.918061.310
53_L210_L0.911751.301
91_V160_A0.906891.295
44_E47_R0.903871.290
53_L198_A0.899731.284
110_F140_Q0.883451.261
126_L133_D0.883381.261
226_I230_F0.881471.258
124_Y129_E0.87941.255
153_L161_A0.875331.249
18_P21_D0.874531.248
165_S169_E0.87341.247
93_A183_R0.861551.230
61_Y64_A0.859871.227
91_V95_S0.850831.215
151_E155_N0.844631.206
144_G148_A0.838911.197
18_P229_A0.836841.195
218_S223_G0.836571.194
119_Y123_R0.836291.194
221_P224_K0.819241.169
41_E45_A0.814741.163
75_T215_L0.806631.151
43_I47_R0.803091.146
109_A149_V0.801581.144
204_P207_R0.794681.134
91_V183_R0.788261.125
203_P206_L0.786741.123
151_E154_L0.784381.120
93_A181_Q0.774431.105
42_F54_A0.768531.097
60_P65_R0.767151.095
212_D215_L0.763261.090
46_L54_A0.757151.081
96_P183_R0.756711.080
143_V149_V0.755541.078
148_A151_E0.754651.077
18_P226_I0.751891.073
60_P195_P0.749781.070
41_E44_E0.746811.066
220_D223_G0.745831.065
22_Y220_D0.740211.057
208_Q211_R0.738721.054
154_L181_Q0.738341.054
153_L158_A0.730821.043
18_P230_F0.728991.041
26_Q217_L0.717911.025
21_D33_L0.705071.006
213_A217_L0.699860.999
222_E226_I0.692860.989
199_S203_P0.692410.988
205_E209_R0.691520.987
216_S219_K0.68920.984
20_A33_L0.687880.982
23_L27_L0.687650.982
71_E204_P0.677530.967
89_I160_A0.673310.961
26_Q222_E0.67240.960
54_A197_V0.66620.951
74_A77_V0.665190.950
223_G227_L0.662860.946
170_R174_E0.659440.941
23_L214_L0.653690.933
88_V165_S0.651680.930
171_L174_E0.649480.927
18_P223_G0.647170.924
71_E198_A0.647060.924
170_R173_A0.643290.918
147_D151_E0.640980.915
55_F196_L0.639640.913
24_S27_L0.639010.912
217_L220_D0.636860.909
73_L198_A0.636010.908
20_A24_S0.631040.901
91_V185_L0.630540.900
206_L209_R0.627980.896
36_A51_I0.626870.895
125_E130_A0.621450.887
205_E208_Q0.617930.882
216_S220_D0.616360.880
97_I103_L0.614380.877
34_V45_A0.612280.874
94_D156_G0.612170.874
89_I162_A0.609870.871
22_Y226_I0.606630.866
56_M197_V0.60160.859
148_A152_A0.59860.854
196_L214_L0.597140.852
124_Y128_R0.593980.848
20_A31_V0.58830.840
71_E200_P0.581810.831
74_A211_R0.580820.829
123_R128_R0.580070.828
112_D144_G0.579820.828
92_R159_D0.577240.824
43_I54_A0.576420.823
142_F152_A0.576380.823
109_A143_V0.575490.821
49_G199_S0.575410.821
97_I102_D0.573940.819
46_L51_I0.572360.817
23_L217_L0.571240.815
37_D41_E0.569150.812
29_V209_R0.568710.812
63_Q66_Q0.56240.803
74_A214_L0.5620.802
21_D226_I0.558910.798
71_E207_R0.548870.783
75_T211_R0.546920.781
64_A68_A0.540940.772
19_L214_L0.54080.772
47_R68_A0.536710.766
112_D142_F0.534170.762
111_P114_S0.533740.762
217_L223_G0.531660.759
42_F45_A0.530060.757
28_G31_V0.529380.756
45_A48_S0.527740.753
150_L154_L0.523920.748
47_R67_R0.521840.745
218_S221_P0.519620.742
154_L171_L0.518670.740
126_L132_L0.517590.739
172_E184_V0.516990.738
164_P167_A0.512680.732
152_A155_N0.510640.729
74_A215_L0.51050.729
101_A130_A0.510430.729
117_S142_F0.507990.725
40_A44_E0.506020.722
27_L31_V0.501350.716
149_V152_A0.496880.709
27_L209_R0.496360.709
59_L63_Q0.496290.708
47_R70_V0.491640.702
64_A67_R0.487840.696
87_S91_V0.487070.695
217_L222_E0.486140.694
63_Q67_R0.485620.693
122_P162_A0.483110.690
60_P63_Q0.480950.687
120_L124_Y0.46950.670
188_S191_Y0.468530.669
22_Y213_A0.467510.667
54_A58_P0.465480.664
89_I103_L0.464260.663
196_L199_S0.464220.663
62_V68_A0.463290.661
49_G52_D0.463060.661
42_F51_I0.46080.658
87_S164_P0.45920.655
39_Y42_F0.458310.654
49_G201_D0.453290.647
73_L207_R0.45260.646
23_L210_L0.452350.646
19_L223_G0.451880.645
90_V182_L0.451070.644
27_L30_P0.44920.641
36_A42_F0.448520.640
153_L182_L0.448050.640
27_L210_L0.446480.637
88_V91_V0.445850.636
20_A23_L0.445360.636
112_D140_Q0.444350.634
18_P22_Y0.443290.633
58_P61_Y0.438430.626
20_A55_F0.436940.624
90_V184_V0.433770.619
217_L221_P0.433050.618
141_V152_A0.432260.617
203_P207_R0.431410.616
224_K227_L0.429650.613
106_K160_A0.428240.611
65_R68_A0.427050.610
150_L163_I0.425640.608
23_L29_V0.424180.605
121_I124_Y0.422440.603
73_L76_P0.419980.599
211_R214_L0.419570.599
85_Y166_D0.419180.598
111_P158_A0.418940.598
88_V168_F0.418560.597
86_R187_T0.416830.595
146_H163_I0.415760.593
40_A65_R0.415680.593
101_A104_K0.415550.593
163_I167_A0.415080.593
215_L218_S0.41450.592
87_S116_T0.414370.591
110_F142_F0.414130.591
75_T218_S0.413090.590
166_D170_R0.412960.589
34_V51_I0.410340.586
57_G163_I0.40730.581
203_P208_Q0.406520.580
92_R181_Q0.406150.580
150_L153_L0.404570.578
71_E197_V0.404490.577
153_L159_D0.403560.576
223_G226_I0.403440.576
95_S159_D0.399680.571
109_A159_D0.399310.570
150_L182_L0.398260.568
69_G200_P0.3980.568
219_K224_K0.397980.568
110_F122_P0.395790.565
36_A50_E0.394530.563
169_E172_E0.393250.561
72_P207_R0.391150.558
89_I100_L0.390830.558
53_L196_L0.389750.556
70_V73_L0.388250.554
107_R158_A0.38820.554
91_V97_I0.387950.554
207_R210_L0.387340.553
57_G60_P0.387110.553
90_V161_A0.386570.552
91_V96_P0.386340.551
126_L130_A0.385790.551
125_E129_E0.385540.550
93_A96_P0.385410.550
145_S163_I0.382660.546
55_F76_P0.378320.540
189_P192_P0.37750.539
156_G159_D0.376330.537
95_S106_K0.376270.537
36_A41_E0.375080.535
218_S224_K0.374190.534
172_E175_G0.370160.528
128_R133_D0.368670.526
72_P201_D0.366270.523
107_R111_P0.366160.523
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
3p7iA0.991899.90.076
3n5lA0.995999.90.084
3kzgA0.897199.90.217
2ieeA0.89399.90.221
4h5gA0.884899.90.236
3hv1A0.934299.90.238
3h7mA0.872499.90.25
3delB0.89399.90.25
4eq9A0.921899.90.251
2yjpA0.897199.90.253

Page generated in 0.0212 seconds.