GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Lip_A_acyltrans - Bacterial lipid A biosynthesis acyltransferase
Pfam: PF03279 (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: CL0228
Length: 295
Sequences: 2047
Seq/Len: 6.94
HH_delta: 0.885 (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
269_Q273_D0.436043.463
68_S71_E0.395833.144
108_E249_R0.367852.921
78_E284_E0.353752.809
106_E249_R0.342052.716
211_P269_Q0.339162.693
57_R76_I0.336382.671
60_L72_R0.334262.655
108_E251_E0.317512.522
43_R81_R0.307382.441
67_K71_E0.3072.438
273_D276_E0.303832.413
213_F276_E0.303142.407
57_R73_K0.302822.405
109_G112_H0.297032.359
112_H254_P0.289732.301
219_T272_N0.287172.281
187_A192_G0.283232.249
242_E249_R0.282122.240
66_E280_R0.277172.201
38_G84_G0.274582.181
114_E118_A0.271582.157
30_P33_L0.266982.120
110_E114_E0.263752.095
211_P216_P0.262772.087
148_A192_G0.255872.032
62_R215_R0.250831.992
64_F67_K0.244321.940
46_Y53_R0.241871.921
58_A61_R0.23951.902
61_R69_E0.238641.895
235_V252_I0.235021.866
55_R291_R0.23471.864
67_K75_L0.231251.836
153_P176_P0.2221.763
253_E274_R0.219861.746
74_K78_E0.214891.707
236_P253_E0.209861.667
263_D266_E0.206621.641
61_R72_R0.204051.620
116_A235_V0.203381.615
89_E241_R0.201391.599
115_A119_E0.200621.593
121_R233_P0.197891.572
67_K72_R0.197181.566
210_V269_Q0.195691.554
38_G42_G0.193791.539
265_E269_Q0.192591.529
208_V268_T0.192471.529
240_Y282_H0.188751.499
112_H115_A0.187381.488
111_E115_A0.186021.477
152_R155_K0.185371.472
275_L279_I0.184941.469
56_A76_I0.182971.453
161_R165_K0.182931.453
34_A88_A0.182571.450
71_E75_L0.180461.433
240_Y249_R0.177921.413
24_W28_L0.1761.398
236_P255_P0.17511.391
253_E277_E0.171921.365
56_A79_S0.170531.354
112_H235_V0.17051.354
274_R277_E0.169761.348
150_I184_L0.169111.343
288_W292_R0.168821.341
132_N286_W0.16791.333
173_E192_G0.167731.332
71_E74_K0.166951.326
46_Y77_R0.166871.325
123_V233_P0.165411.314
128_G275_L0.165321.313
39_R81_R0.164671.308
200_Q290_H0.164291.305
151_Y174_L0.163971.302
100_Q104_R0.162531.291
224_A268_T0.162051.287
124_I232_A0.160631.276
125_L237_V0.160631.276
241_R285_Q0.158051.255
63_A293_W0.157461.250
39_R85_R0.157141.248
211_P273_D0.156851.246
240_Y251_E0.154971.231
276_E280_R0.154731.229
198_G223_P0.153331.218
54_K58_A0.153151.216
40_F44_L0.152311.210
210_V272_N0.151071.200
213_F280_R0.151031.199
286_W293_W0.150971.199
164_N168_E0.150471.195
36_K39_R0.150181.193
290_H294_K0.14981.190
185_I189_K0.145551.156
32_K36_K0.145051.152
44_L48_L0.144831.150
134_E195_G0.143931.143
75_L284_E0.143691.141
209_F218_S0.143391.139
57_R61_R0.142981.135
154_Q160_D0.142111.129
133_W197_L0.141011.120
20_K162_L0.140711.117
209_F216_P0.140391.115
98_K102_K0.140251.114
236_P274_R0.139861.111
184_L194_V0.137151.089
43_R77_R0.136971.088
264_I268_T0.13661.085
84_G87_L0.13651.084
97_S100_Q0.136431.083
60_L67_K0.13611.081
50_K53_R0.136091.081
123_V193_I0.13451.068
32_K35_Y0.134171.066
114_E117_L0.133691.062
53_R57_R0.133171.058
50_K54_K0.133081.057
102_K142_R0.132561.053
52_R290_H0.132551.053
82_N85_R0.132031.049
274_R278_W0.131991.048
200_Q288_W0.131411.044
154_Q163_L0.129591.029
28_L33_L0.129491.028
36_K40_F0.129031.025
35_Y85_R0.128951.024
96_M100_Q0.128951.024
241_R248_Y0.128891.024
53_R80_F0.12881.023
270_R273_D0.127421.012
183_E186_R0.126271.003
200_Q287_F0.125710.998
148_A175_I0.12470.990
182_R185_I0.124370.988
200_Q292_R0.124040.985
242_E247_H0.123960.984
58_A215_R0.123890.984
69_E73_K0.123610.982
122_G188_L0.123610.982
115_A118_A0.123260.979
57_R72_R0.122740.975
270_R274_R0.12270.974
201_D209_F0.122250.971
253_E281_E0.12180.967
65_P72_R0.121750.967
238_F278_W0.121110.962
126_L198_G0.119940.953
63_A213_F0.11890.944
56_A289_F0.118040.937
273_D277_E0.117810.936
121_R231_G0.116940.929
186_R190_E0.116790.927
227_A234_V0.116630.926
29_L33_L0.115420.917
128_G198_G0.115140.914
228_R267_L0.114860.912
83_F289_F0.114720.911
282_H285_Q0.114630.910
107_I110_E0.114160.907
160_D164_N0.114010.905
267_L270_R0.113860.904
99_E102_K0.113090.898
243_P247_H0.113020.898
238_F274_R0.112940.897
223_P271_Y0.112710.895
113_L125_L0.112330.892
105_V139_A0.112070.890
173_E187_A0.111840.888
55_R59_N0.110590.878
210_V268_T0.110350.876
259_P267_L0.11030.876
40_F43_R0.109940.873
152_R288_W0.109910.873
207_G218_S0.10980.872
127_T195_G0.109510.870
29_L32_K0.109440.869
106_E247_H0.109240.868
25_L37_L0.109160.867
64_F72_R0.109030.866
115_A254_P0.108260.860
254_P277_E0.107980.858
111_E114_E0.107950.857
112_H116_A0.107230.852
62_R213_F0.106670.847
116_A120_G0.106550.846
31_L247_H0.106320.844
128_G271_Y0.105890.841
107_I113_L0.105820.840
122_G232_A0.105470.838
37_L40_F0.105140.835
182_R225_R0.104850.833
109_G254_P0.104750.832
59_N213_F0.104750.832
134_E200_Q0.104640.831
46_Y57_R0.104560.830
102_K143_R0.103980.826
201_D218_S0.103530.822
47_Y77_R0.103450.822
72_R157_P0.103110.819
53_R76_I0.102780.816
122_G194_V0.102710.816
49_I52_R0.102350.813
118_A121_R0.102140.811
120_G123_V0.102090.811
83_F287_F0.101870.809
208_V265_E0.101780.808
175_I187_A0.101420.805
124_I149_V0.10140.805
82_N89_E0.101370.805
217_A292_R0.101290.804
59_N279_I0.101070.803
248_Y294_K0.100990.802
151_Y160_D0.100710.800
55_R290_H0.100610.799
121_R257_D0.100480.798
127_T159_I0.100310.797
126_L271_Y0.100190.796
261_S267_L0.099980.794
18_L21_F0.099980.794
125_L193_I0.099960.794
253_E278_W0.09980.793
82_N285_Q0.099740.792
208_V269_Q0.099740.792
221_T225_R0.099560.791
148_A187_A0.099020.786
168_E173_E0.098780.784
156_N290_H0.098670.784
133_W195_G0.098260.780
131_G197_L0.09820.780
84_G135_L0.097830.777
119_E233_P0.097550.775
219_T288_W0.097510.774
212_F279_I0.09730.773
85_R89_E0.097120.771
34_A92_K0.096690.768
45_L74_K0.096560.767
35_Y39_R0.096280.765
183_E187_A0.096170.764
185_I229_K0.095930.762
24_W27_R0.095840.761
288_W294_K0.095310.757
83_F86_T0.095270.757
187_A194_V0.095270.757
128_G197_L0.095210.756
130_F285_Q0.095150.756
149_V174_L0.094820.753
233_P255_P0.094420.750
140_L155_K0.093950.746
130_F282_H0.093910.746
117_L191_G0.093820.745
58_A293_W0.093730.744
186_R205_K0.093610.743
23_I91_F0.093590.743
220_P223_P0.093390.742
137_G147_V0.093180.740
84_G88_A0.092950.738
32_K37_L0.092730.736
150_I222_G0.092590.735
33_L36_K0.092360.733
31_L151_Y0.092050.731
52_R80_F0.091990.731
251_E281_E0.091810.729
228_R264_I0.091340.725
116_A119_E0.091340.725
42_G46_Y0.090660.720
175_I183_E0.090620.720
79_S287_F0.090330.717
78_E81_R0.090240.717
256_L260_S0.089980.715
58_A62_R0.089810.713
110_E143_R0.089760.713
89_E132_N0.089750.713
155_K177_K0.089650.712
238_F281_E0.089280.709
217_A293_W0.089120.708
266_E269_Q0.088990.707
49_I290_H0.088590.704
158_Y162_L0.088570.703
55_R64_F0.088460.703
116_A233_P0.088370.702
137_G149_V0.08830.701
122_G192_G0.088230.701
155_K290_H0.08820.700
200_Q220_P0.087770.697
215_R293_W0.087680.696
46_Y80_F0.087640.696
194_V226_L0.087610.696
220_P225_R0.087590.696
150_I180_G0.087530.695
115_A190_E0.087520.695
195_G200_Q0.08750.695
152_R202_P0.08750.695
213_F271_Y0.087450.694
214_G280_R0.087150.692
277_E280_R0.087090.692
181_I226_L0.086940.690
132_N293_W0.086870.690
136_A197_L0.086750.689
238_F253_E0.086690.688
224_A228_R0.086640.688
99_E103_K0.086590.688
90_F200_Q0.086360.686
41_L84_G0.086340.686
106_E242_E0.086110.684
202_P220_P0.086030.683
66_E70_A0.085960.683
196_L222_G0.085930.682
259_P262_E0.085590.680
79_S289_F0.085530.679
239_A243_P0.085410.678
152_R177_K0.085310.677
26_L108_E0.085220.677
82_N284_E0.085150.676
52_R55_R0.085110.676
221_T251_E0.085070.676
188_L226_L0.084780.673
231_G260_S0.084610.672
198_G272_N0.084520.671
124_I226_L0.08440.670
57_R60_L0.084120.668
188_L230_T0.084080.668
62_R293_W0.084070.668
59_N167_R0.084060.668
287_F290_H0.083750.665
210_V265_E0.083430.663
122_G233_P0.083350.662
151_Y202_P0.083290.661
122_G193_I0.083210.661
177_K290_H0.083170.660
86_T163_L0.083060.660
122_G220_P0.082870.658
26_L37_L0.082860.658
262_E267_L0.082770.657
201_D207_G0.082740.657
173_E183_E0.082520.655
54_K71_E0.082470.655
60_L75_L0.082450.655
242_E281_E0.082430.655
125_L185_I0.082420.655
131_G196_L0.082330.654
109_G115_A0.082220.653
70_A78_E0.082190.653
219_T292_R0.08190.650
107_I252_I0.081780.649
211_P219_T0.08150.647
112_H255_P0.081340.646
54_K211_P0.08130.646
277_E281_E0.08130.646
49_I80_F0.0810.643
25_L45_L0.0810.643
28_L123_V0.080920.643
102_K105_V0.08090.642
73_K77_R0.080850.642
208_V221_T0.080810.642
68_S243_P0.080560.640
113_L117_L0.080370.638
68_S72_R0.080360.638
35_Y38_G0.080280.638
184_L226_L0.080010.635
56_A60_L0.079980.635
236_P256_L0.079980.635
65_P71_E0.079770.633
94_P286_W0.079490.631
31_L35_Y0.079420.631
99_E143_R0.079410.631
271_Y275_L0.079370.630
59_N63_A0.079250.629
181_I185_I0.078990.627
227_A256_L0.078920.627
189_K230_T0.078820.626
272_N292_R0.078750.625
132_N200_Q0.078720.625
92_K133_W0.078710.625
47_Y73_K0.078660.625
108_E253_E0.078650.625
260_S270_R0.078410.623
160_D163_L0.078410.623
254_P257_D0.07840.623
77_R119_E0.078350.622
223_P227_A0.078110.620
133_W196_L0.0780.619
19_V223_P0.077980.619
140_L147_V0.077860.618
93_L195_G0.077820.618
83_F163_L0.077610.616
256_L259_P0.077570.616
201_D290_H0.07750.615
266_E270_R0.077470.615
17_W21_F0.077410.615
82_N132_N0.077410.615
150_I196_L0.077370.614
116_A123_V0.077330.614
173_E190_E0.077320.614
133_W159_I0.077250.613
42_G81_R0.076990.611
209_F219_T0.076840.610
89_E284_E0.076740.609
124_I229_K0.076560.608
248_Y285_Q0.076510.608
41_L45_L0.076450.607
202_P218_S0.076430.607
260_S263_D0.076210.605
84_G89_E0.07620.605
177_K200_Q0.07620.605
112_H236_P0.07620.605
74_K119_E0.076150.605
103_K115_A0.076070.604
27_R30_P0.076050.604
257_D264_I0.075980.603
31_L89_E0.075770.602
197_L286_W0.075760.602
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
1iuqA0.894997.90.885
2lpmA0.403467.60.949
3o85A0.383123.60.961
2jnbA0.450823.10.962
3on1A0.335619.10.963
3tqrA0.383114.90.965
1wgxA0.12212.70.966
2i3sB0.108512.40.966
3zkvA0.33912.30.966
3f6pA0.3831120.966
If you are interested in a protein containing this domain,
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