GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LpxB - Lipid-A-disaccharide synthetase
Pfam: PF02684 (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: CL0113
Length: 373
Sequences: 17273
Seq/Len: 46.31
HH_delta: 0.261 (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
188_A261_A1.773884.210
211_L331_A1.461463.468
220_Q246_S1.373473.260
136_H156_T1.254092.976
184_K220_Q1.233042.926
264_A275_A1.224422.906
207_E237_I1.188872.822
230_H235_E1.182882.807
29_E83_P1.14792.724
207_E327_P1.139322.704
20_A23_A1.116782.650
336_E343_K1.107952.630
209_A221_F1.101662.615
333_E336_E1.079122.561
211_L328_E1.046862.485
336_E340_N1.041432.472
264_A280_V1.033762.453
29_E81_E0.997522.367
344_R348_K0.989532.348
145_P149_K0.971122.305
329_N333_E0.955642.268
340_N343_K0.954022.264
253_E256_D0.914522.170
186_I222_V0.89652.128
186_I220_Q0.87422.075
185_P338_L0.870462.066
222_V248_V0.858792.038
327_P331_A0.854182.027
212_L335_L0.852992.024
326_T329_N0.838271.989
343_K346_K0.835661.983
335_L339_E0.832661.976
20_A24_R0.813861.932
224_P257_A0.797211.892
345_K349_E0.796041.889
186_I260_A0.785241.864
211_L327_P0.783681.860
142_P145_P0.768091.823
185_P262_D0.762241.809
238_L243_P0.744111.766
231_E235_E0.730181.733
341_P345_K0.720431.710
187_I334_L0.717021.702
208_A330_I0.715191.697
226_A230_H0.706351.676
329_N332_A0.697631.656
79_K105_R0.697451.655
210_K241_Y0.691851.642
323_E329_N0.686861.630
236_E240_E0.681191.617
187_I263_A0.676391.605
263_A334_L0.667261.584
341_P344_R0.65361.551
186_I262_D0.649371.541
229_V232_E0.634931.507
189_L201_L0.628371.491
237_I241_Y0.623541.480
42_G45_S0.622011.476
75_V104_K0.617771.466
203_P207_E0.605681.437
205_F265_L0.598081.419
142_P146_E0.597091.417
237_I240_E0.596021.415
77_R81_E0.594981.412
76_E80_E0.591171.403
212_L219_L0.590421.401
331_A335_L0.58641.392
200_R204_I0.577561.371
235_E239_A0.573031.360
332_A336_E0.570661.354
15_A19_R0.568841.350
204_I327_P0.568321.349
284_V321_I0.567171.346
283_V337_L0.563371.337
245_V249_I0.559821.329
275_A282_M0.55951.328
343_K347_Q0.554321.316
190_L254_S0.55241.311
146_E150_K0.551231.308
14_G89_I0.550241.306
205_F221_F0.548951.303
346_K349_E0.541151.284
258_M278_L0.540141.282
238_L247_I0.539941.281
261_A280_V0.537411.275
210_K214_K0.536871.274
254_S258_M0.530441.259
280_V348_K0.527161.251
203_P237_I0.526821.250
108_P135_D0.525561.247
139_V155_V0.521321.237
283_V333_E0.521271.237
211_L214_K0.51821.230
337_L347_Q0.517861.229
200_R203_P0.515931.224
75_V79_K0.514391.221
146_E149_K0.513961.220
29_E50_E0.509251.209
269_G272_T0.503431.195
320_L333_E0.503391.195
222_V257_A0.500451.188
187_I265_L0.500361.188
255_Y278_L0.499781.186
184_K218_D0.499741.186
75_V105_R0.497531.181
328_E332_A0.49631.178
222_V246_S0.493691.172
206_L238_L0.49271.169
86_V102_L0.492451.169
16_R19_R0.491261.166
207_E210_K0.490821.165
26_P84_D0.490061.163
181_D184_K0.489541.162
209_A219_L0.488511.159
72_R76_E0.485051.151
145_P157_Y0.484411.150
263_A337_L0.482241.145
149_K152_G0.479941.139
224_P248_V0.473851.125
204_I207_E0.47371.124
68_K72_R0.467331.109
259_A278_L0.465191.104
236_E239_A0.461881.096
195_K223_V0.46151.095
251_E257_A0.460371.093
138_L158_V0.460251.092
19_R22_K0.458921.089
140_I144_E0.457121.085
19_R23_A0.455651.081
188_A224_P0.454461.079
342_E345_K0.452241.073
22_K28_I0.451161.071
345_K348_K0.449611.067
103_K133_Y0.442341.050
188_A258_M0.43941.043
18_I30_F0.439381.043
139_V145_P0.437131.037
187_I221_F0.43651.036
212_L334_L0.434421.031
16_R20_A0.434361.031
31_Y77_R0.432291.026
98_L102_L0.430891.023
145_P155_V0.430361.021
134_V137_L0.42871.017
25_D28_I0.42781.015
190_L224_P0.425271.009
239_A244_D0.422791.003
323_E326_T0.421741.001
185_P219_L0.420820.999
342_E346_K0.420320.998
281_P337_L0.419690.996
210_K213_K0.419310.995
78_I83_P0.416570.989
140_I160_H0.414010.983
208_A331_A0.413730.982
265_L334_L0.413190.981
267_A285_A0.411260.976
42_G46_L0.410420.974
224_P251_E0.409340.971
185_P218_D0.408290.969
279_G349_E0.408190.969
286_Y323_E0.406670.965
279_G348_K0.406440.965
208_A327_P0.403040.957
18_I22_K0.401070.952
267_A330_I0.400240.950
232_E236_E0.399010.947
69_R73_K0.396290.941
158_V161_P0.395820.939
283_V334_L0.395450.939
255_Y259_A0.395330.938
111_V138_L0.39530.938
256_D259_A0.39470.937
188_A257_A0.393720.934
204_I325_A0.3910.928
213_K244_D0.388010.921
276_A348_K0.387690.920
332_A335_L0.387610.920
207_E211_L0.382810.909
190_L258_M0.382130.907
227_P230_H0.380790.904
222_V260_A0.379510.901
212_L338_L0.378890.899
89_I113_Y0.374680.889
285_A322_Q0.373410.886
258_M271_A0.373230.886
163_L167_K0.372760.885
71_F75_V0.371680.882
22_K25_D0.370480.879
275_A280_V0.369750.878
324_D329_N0.367470.872
141_F144_E0.36690.871
337_L343_K0.366490.870
263_A338_L0.365780.868
142_P157_Y0.365310.867
321_I324_D0.364430.865
207_E241_Y0.362880.861
272_T282_M0.362160.860
181_D220_Q0.361020.857
100_K104_K0.360970.857
87_I113_Y0.359770.854
238_L241_Y0.359340.853
256_D260_A0.355810.844
222_V261_A0.355330.843
156_T159_G0.354830.842
186_I261_A0.353270.838
201_L223_V0.352950.838
87_I111_V0.352920.838
269_G273_L0.352890.838
268_S284_V0.352320.836
337_L344_R0.351050.833
263_A283_V0.35030.831
212_L331_A0.349740.830
86_V107_I0.348640.827
283_V322_Q0.347210.824
210_K243_P0.346370.822
219_L338_L0.344580.818
185_P263_A0.344060.817
102_L105_R0.343440.815
21_L28_I0.341560.811
263_A344_R0.340460.808
276_A282_M0.339490.806
139_V148_Y0.338810.804
22_K26_P0.338320.803
157_Y160_H0.338040.802
258_M280_V0.337130.800
140_I270_T0.335270.796
101_K105_R0.335010.795
189_L267_A0.33390.792
103_K135_D0.333750.792
322_Q333_E0.333220.791
266_A271_A0.327680.778
266_A272_T0.326910.776
72_R80_E0.325490.772
234_I237_I0.322780.766
208_A212_L0.321460.763
275_A284_V0.321440.763
268_S274_E0.321360.763
271_A275_A0.321160.762
18_I43_V0.320430.760
186_I189_L0.319730.759
185_P341_P0.319450.758
29_E77_R0.316450.751
185_P220_Q0.316320.751
191_P194_R0.315650.749
187_I219_L0.3150.748
328_E331_A0.314940.747
206_L243_P0.314190.746
258_M275_A0.312980.743
21_L26_P0.312610.742
77_R80_E0.311410.739
251_E254_S0.309790.735
73_K76_E0.309580.735
262_D344_R0.309520.735
182_P185_P0.309420.734
204_I208_A0.307030.729
257_A260_A0.307020.729
264_A271_A0.306610.728
248_V257_A0.3040.721
258_M264_A0.303780.721
111_V115_I0.303750.721
29_E48_D0.303030.719
281_P344_R0.302990.719
187_I190_L0.302930.719
204_I330_I0.302860.719
190_L271_A0.301990.717
18_I28_I0.301640.716
230_H234_I0.301480.716
266_A275_A0.301290.715
234_I247_I0.300990.714
255_Y258_M0.300610.713
19_R41_A0.300440.713
143_F146_E0.300080.712
268_S271_A0.299070.710
336_E339_E0.29890.709
13_H270_T0.298290.708
322_Q325_A0.296830.704
147_F150_K0.296590.704
205_F267_A0.296270.703
331_A334_L0.296140.703
325_A329_N0.295410.701
103_K106_G0.294290.698
340_N344_R0.291410.692
17_L89_I0.290930.690
272_T284_V0.290150.689
225_V249_I0.289740.688
73_K77_R0.289310.687
189_L264_A0.287890.683
88_L134_V0.286650.680
105_R108_P0.285870.678
172_R262_D0.285110.677
340_N346_K0.284470.675
191_P201_L0.28440.675
46_L49_M0.284230.675
29_E46_L0.283890.674
166_V278_L0.28380.674
196_S228_E0.283340.672
194_R198_I0.282520.671
129_K133_Y0.281720.669
50_E77_R0.281290.668
253_E257_A0.280320.665
72_R104_K0.279040.662
264_A282_M0.278570.661
139_V144_E0.278480.661
322_Q329_N0.278140.660
166_V255_Y0.27790.660
157_Y161_P0.277290.658
254_S257_A0.275950.655
66_K69_R0.275790.655
269_G274_E0.273690.650
208_A211_L0.273570.649
14_G30_F0.273180.648
344_R347_Q0.271750.645
320_L347_Q0.270890.643
263_A281_P0.270560.642
271_A274_E0.270540.642
204_I285_A0.270250.641
195_K201_L0.269950.641
287_K290_P0.269060.639
270_T274_E0.268230.637
29_E44_E0.267990.636
31_Y74_L0.266960.634
131_K137_L0.266420.632
223_V234_I0.266080.631
164_D167_K0.265890.631
128_K132_K0.265690.631
83_P107_I0.265180.629
112_I134_V0.264810.628
82_K107_I0.264010.627
31_Y83_P0.26370.626
206_L245_V0.261610.621
17_L87_I0.261510.621
199_K271_A0.261320.620
264_A267_A0.261140.620
167_K255_Y0.261120.620
265_L285_A0.260780.619
64_L68_K0.260190.618
206_L234_I0.259340.615
209_A213_K0.259110.615
280_V344_R0.259110.615
283_V320_L0.259050.615
209_A212_L0.258930.615
197_E203_P0.257550.611
200_R267_A0.256760.609
72_R75_V0.256640.609
189_L205_F0.256170.608
16_R161_P0.255860.607
337_L340_N0.255560.607
285_A324_D0.255260.606
133_Y136_H0.254590.604
101_K104_K0.254380.604
31_Y81_E0.253940.603
98_L101_K0.253850.602
187_I338_L0.253480.602
210_K240_E0.253340.601
129_K132_K0.252780.600
88_L113_Y0.252660.600
235_E238_L0.252590.599
71_F104_K0.252210.599
50_E53_S0.251950.598
259_A280_V0.251360.597
185_P189_L0.251290.596
29_E33_V0.249960.593
162_L277_L0.248130.589
281_P348_K0.247970.589
78_I102_L0.247220.587
195_K199_K0.247120.586
184_K260_A0.246940.586
153_V157_Y0.246940.586
160_H270_T0.24650.585
172_R260_A0.245580.583
265_L330_I0.244690.581
248_V251_E0.244650.581
325_A330_I0.242720.576
108_P111_V0.242020.574
333_E343_K0.241690.574
204_I326_T0.241270.573
320_L343_K0.241250.573
327_P330_I0.241090.572
21_L25_D0.240890.572
71_F74_L0.240820.572
326_T332_A0.24070.571
136_H154_P0.240170.570
65_P69_R0.239740.569
113_Y140_I0.238610.566
21_L87_I0.237410.563
76_E79_K0.236960.562
26_P29_E0.236430.561
231_E236_E0.236330.561
338_L341_P0.236220.561
199_K268_S0.23480.557
125_G128_K0.234660.557
136_H140_I0.234470.556
189_L223_V0.234180.556
226_A250_I0.234170.556
95_N98_L0.23380.555
66_K70_L0.233570.554
27_D83_P0.233020.553
206_L241_Y0.232890.553
104_K107_I0.232090.551
72_R79_K0.232010.551
284_V300_V0.231170.549
284_V299_L0.230630.547
239_A242_P0.229720.545
203_P206_L0.22860.543
337_L348_K0.227980.541
219_L262_D0.227480.540
183_D218_D0.227390.540
112_I115_I0.226730.538
130_I134_V0.22640.537
68_K76_E0.225560.535
185_P188_A0.225410.535
189_L209_A0.225170.534
79_K104_K0.225070.534
219_L335_L0.225060.534
234_I238_L0.224960.534
333_E337_L0.224760.533
232_E235_E0.22470.533
22_K27_D0.224630.533
17_L21_L0.223160.530
183_D220_Q0.222570.528
160_H273_L0.222430.528
201_L204_I0.222410.528
13_H16_R0.222280.528
85_V111_V0.221650.526
139_V157_Y0.221090.525
96_L99_A0.22040.523
13_H113_Y0.220380.523
87_I114_Y0.220270.523
290_P321_I0.220260.523
165_E255_Y0.220070.522
36_P40_A0.220020.522
320_L337_L0.220010.522
167_K278_L0.219550.521
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
2jjmA0.91961000.261
3froA0.91961000.261
2r60A0.92491000.267
3c48A0.9331000.279
3okpA0.90081000.283
2qzsA0.91691000.292
1rzuA0.91691000.295
2gekA0.90081000.297
2iw1A0.90881000.302
3s28A0.92491000.304

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