GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TonB_dep_Rec - TonB dependent receptor
Pfam: PF00593 (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: CL0193
Length: 277
Sequences: 15207
Seq/Len: 54.9
HH_delta: 0.108 (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
15_L67_F2.20424.420
21_Y61_D2.191824.395
236_S273_G1.89133.793
23_R61_D1.745233.500
221_L243_F1.61563.240
15_L69_Y1.503653.015
238_G271_Y1.400492.808
11_P17_L1.302682.612
18_R66_G1.254182.515
247_Y265_G1.229852.466
233_L274_L1.167752.342
234_S275_R1.113372.233
233_L276_Y1.084652.175
194_S226_S1.071852.149
226_S234_S1.033042.072
69_Y78_L1.031942.069
199_Y219_T1.03112.068
228_R234_S1.026952.059
237_L270_F1.016112.038
18_R68_K1.010462.026
84_Y116_G1.009182.024
12_T15_L0.998422.002
239_V270_F0.997762.001
239_V242_L0.990541.986
2_P23_R0.990021.985
239_V268_R0.980071.965
21_Y63_Y0.97581.957
223_L242_L0.969331.944
18_R81_T0.901061.807
62_N85_N0.897451.800
5_G20_S0.894931.795
23_R59_T0.890261.785
2_P6_L0.883911.773
26_R58_E0.882921.771
235_L274_L0.847921.700
229_F235_L0.843871.692
64_E81_T0.843111.691
17_L67_F0.832871.670
65_L82_Y0.829881.664
204_S214_K0.820521.645
84_Y113_G0.816731.638
220_L247_Y0.806861.618
70_S77_S0.795961.596
63_Y86_D0.783081.570
234_S277_K0.771711.548
19_A63_Y0.767881.540
222_D240_N0.755721.515
58_E87_I0.753291.511
24_G60_S0.750251.504
229_F233_L0.742191.488
68_K79_S0.737991.480
196_S224_S0.734851.474
240_N269_T0.732291.468
201_Y219_T0.715871.436
198_S222_D0.696581.397
59_T89_N0.692181.388
199_Y221_L0.691891.387
224_S236_S0.688971.382
11_P67_F0.684761.373
63_Y84_Y0.681841.367
56_K89_N0.672631.349
76_L124_I0.660161.324
236_S275_R0.658221.320
220_L265_G0.652641.309
71_F78_L0.649881.303
272_L276_Y0.648571.301
228_R277_K0.64431.292
58_E90_L0.634591.273
116_G119_E0.631091.266
17_L65_L0.628211.260
26_R32_E0.622981.249
240_N271_Y0.621161.246
10_K16_S0.620981.245
16_S68_K0.611971.227
6_L11_P0.611061.225
131_S134_S0.60661.216
87_I90_L0.606111.215
15_L19_A0.604661.213
19_A65_L0.601981.207
119_E122_N0.601051.205
221_L242_L0.598481.200
3_R20_S0.597421.198
237_L272_L0.595291.194
242_L268_R0.590381.184
230_N233_L0.581291.166
29_S55_L0.580581.164
67_F80_A0.57261.148
201_Y204_S0.571351.146
114_G117_G0.569431.142
244_D267_G0.568761.141
1_S25_F0.566631.136
226_S236_S0.565811.135
14_N69_Y0.564651.132
60_S87_I0.561871.127
225_A239_V0.551271.105
60_S85_N0.550961.105
235_L272_L0.550231.103
233_L237_L0.546131.095
117_G120_E0.545731.094
137_S140_F0.545471.094
201_Y217_S0.542561.088
197_Y221_L0.540021.083
71_F76_L0.535841.075
72_F76_L0.534161.071
59_T88_K0.533151.069
69_Y72_F0.528571.060
180_N183_Y0.527631.058
266_P269_T0.526671.056
132_F135_S0.526661.056
135_S138_F0.523531.050
224_S238_G0.521571.046
126_F130_S0.519921.043
216_P245_K0.518911.041
79_S121_G0.517691.038
243_F246_K0.514441.032
117_G122_N0.511511.026
206_N214_K0.509181.021
55_L91_I0.508781.020
206_N211_N0.503041.009
130_S135_S0.502821.008
173_P177_P0.500711.004
84_Y114_G0.500061.003
118_E121_G0.492290.987
235_L239_V0.491790.986
11_P15_L0.491110.985
178_N181_F0.490360.983
219_T245_K0.4880.979
238_G273_G0.481110.965
205_R215_I0.479810.962
123_G126_F0.477060.957
127_N130_S0.476190.955
126_F132_F0.475760.954
232_N276_Y0.472170.947
130_S136_Y0.464830.932
1_S23_R0.463030.929
208_D211_N0.460480.923
126_F129_S0.455570.914
129_S135_S0.45470.912
130_S137_S0.452840.908
6_L9_Y0.450340.903
203_N206_N0.446680.896
166_N169_G0.445780.894
78_L82_Y0.4420.886
182_S185_W0.441810.886
191_N201_Y0.441270.885
173_P176_N0.439750.882
202_S218_Y0.43970.882
114_G119_E0.438180.879
168_S174_P0.43720.877
172_P176_N0.4360.874
174_P177_P0.435470.873
111_G114_G0.435450.873
170_N173_P0.435310.873
170_N177_P0.431820.866
177_P183_Y0.429720.862
223_L239_V0.428630.860
200_Q220_L0.42320.849
64_E83_F0.422860.848
131_S135_S0.422670.848
106_N109_N0.422270.847
80_A117_G0.418730.840
25_F57_P0.417380.837
177_P180_N0.415530.833
4_L9_Y0.414880.832
208_D212_S0.413410.829
28_P91_I0.410650.823
179_N183_Y0.41060.823
78_L122_N0.410580.823
80_A120_E0.409840.822
28_P55_L0.408550.819
80_A118_E0.405940.814
244_D268_R0.405540.813
128_A134_S0.404960.812
179_N182_S0.404090.810
172_P177_P0.402940.808
134_S137_S0.400410.803
90_L110_G0.397820.798
246_K264_P0.397620.797
202_S205_R0.396880.796
219_T243_F0.393470.789
136_Y175_S0.392460.787
63_Y67_F0.392270.787
3_R22_G0.388930.780
114_G118_E0.383960.770
80_A84_Y0.383480.769
119_E123_G0.38340.769
61_D86_D0.382860.768
130_S134_S0.380380.763
10_K13_D0.380.762
168_S172_P0.378650.759
4_L21_Y0.374690.751
218_Y247_Y0.373170.748
25_F59_T0.373120.748
134_S138_F0.372950.748
112_G117_G0.371610.745
132_F136_Y0.370680.743
172_P178_N0.368940.740
221_L225_A0.366660.735
200_Q222_D0.364610.731
227_Y230_N0.364070.730
178_N182_S0.363240.728
169_G172_P0.363080.728
177_P181_F0.362220.726
6_L19_A0.362150.726
131_S137_S0.359720.721
58_E91_I0.358790.719
241_N244_D0.35830.719
20_S62_N0.356980.716
169_G176_N0.356620.715
9_Y12_T0.355450.713
125_F128_A0.354810.712
132_F138_F0.351110.704
164_Y167_P0.350470.703
183_Y187_Y0.350450.703
172_P175_S0.350440.703
113_G117_G0.346370.695
136_Y139_N0.345970.694
19_A66_G0.34540.693
194_S197_Y0.345280.692
215_I218_Y0.342780.687
207_A213_E0.342560.687
171_G174_P0.342350.687
130_S140_F0.34230.686
114_G120_E0.341970.686
119_E124_I0.340330.682
131_S139_N0.339610.681
136_Y140_F0.339340.680
130_S133_N0.338530.679
132_F137_S0.33620.674
222_D242_L0.335290.672
192_Y195_Y0.335010.672
66_G81_T0.331580.665
18_R79_S0.331560.665
124_I127_N0.331190.664
163_S166_N0.331140.664
168_S171_G0.32960.661
61_D84_Y0.329080.660
113_G116_G0.327720.657
61_D88_K0.32690.656
248_Y264_P0.326860.655
129_S132_F0.324720.651
117_G121_G0.323980.650
133_N137_S0.323770.649
10_K14_N0.323750.649
220_L240_N0.323450.649
181_F184_S0.323220.648
116_G120_E0.322270.646
116_G123_G0.321850.645
268_R272_L0.321580.645
110_G114_G0.321520.645
73_D76_L0.320330.642
76_L80_A0.319610.641
129_S133_N0.319560.641
113_G119_E0.318760.639
108_N114_G0.318620.639
125_F131_S0.318330.638
111_G117_G0.31750.637
119_E126_F0.317360.636
161_D164_Y0.317060.636
193_W227_Y0.316810.635
178_N183_Y0.31670.635
229_F274_L0.315830.633
173_P178_N0.315490.633
186_N189_W0.315090.632
58_E89_N0.315030.632
86_D114_G0.313760.629
22_G62_N0.313380.628
64_E68_K0.312970.628
120_E123_G0.312350.626
129_S134_S0.310590.623
67_F78_L0.309650.621
195_Y199_Y0.309110.620
69_Y79_S0.30790.617
169_G173_P0.307220.616
129_S137_S0.306820.615
168_S175_S0.306220.614
2_P21_Y0.305950.614
128_A131_S0.305940.614
234_S237_L0.305830.613
127_N137_S0.304460.611
3_R27_A0.304420.610
83_F139_N0.304230.610
12_T17_L0.303160.608
132_F139_N0.302810.607
32_E91_I0.302710.607
172_P180_N0.302140.606
190_S193_W0.300740.603
115_N119_E0.30040.602
216_P248_Y0.300130.602
114_G121_G0.299760.601
9_Y17_L0.299730.601
176_N179_N0.299020.600
166_N171_G0.298470.599
94_V97_S0.29650.595
77_S80_A0.29630.594
24_G27_A0.296120.594
191_N195_Y0.295740.593
114_G122_N0.295570.593
206_N212_S0.295510.593
240_N266_P0.295490.593
3_R24_G0.295460.592
16_S70_S0.29530.592
12_T69_Y0.295130.592
65_L69_Y0.294380.590
197_Y219_T0.294150.590
217_S245_K0.293150.588
26_R91_I0.292330.586
28_P58_E0.292160.586
110_G118_E0.292130.586
166_N173_P0.291430.584
136_Y174_P0.291120.584
169_G177_P0.291080.584
251_A262_G0.289860.581
94_V98_N0.289740.581
84_Y111_G0.289440.580
179_N184_S0.289230.580
1_S27_A0.289140.580
135_S139_N0.289080.580
4_L19_A0.288570.579
108_N111_G0.287510.577
199_Y203_N0.286870.575
15_L78_L0.28650.575
173_P179_N0.285550.573
215_I250_Y0.284180.570
184_S187_Y0.284140.570
28_P32_E0.28260.567
28_P33_L0.282590.567
68_K81_T0.282150.566
238_G270_F0.281680.565
113_G118_E0.281640.565
109_N114_G0.280860.563
215_I248_Y0.279180.560
110_G116_G0.277770.557
77_S123_G0.276860.555
79_S118_E0.27320.548
239_V244_D0.270570.543
131_S140_F0.270050.542
187_Y190_S0.269270.540
115_N118_E0.269010.539
183_Y186_N0.268530.538
122_N125_F0.267660.537
131_S138_F0.267360.536
198_S201_Y0.267330.536
2_P5_G0.266790.535
22_G64_E0.26610.534
239_V243_F0.265120.532
172_P182_S0.264810.531
15_L71_F0.264790.531
220_L243_F0.264230.530
185_W188_N0.264140.530
107_Q110_G0.263790.529
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
3efmA0.844899.90.108
4epaA0.866499.90.125
3fhhA0.866499.90.134
2hdiA0.888199.90.137
1fepA0.909799.90.142
4b7oA0.902599.90.143
3v8xA0.91799.90.149
2w16A0.837599.90.151
3qlbA0.844899.90.156
2gufA0.790699.90.164

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