GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LysR_substrate - LysR substrate binding domain
Pfam: PF03466 (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: 209
Sequences: 47233
Seq/Len: 226
HH_delta: -0.019 (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
11_G56_L2.702682.896
7_T38_E2.614322.801
73_E205_R2.568022.751
9_R38_E2.399542.571
7_T36_R2.376332.546
97_T100_D2.332922.500
77_E182_P2.269632.432
146_V153_A2.222192.381
74_P77_E2.170692.326
88_H104_Y2.117262.269
79_P157_D2.117162.268
74_P182_P2.092062.242
27_E203_L2.060362.208
143_L163_E1.98862.131
81_V157_D1.976272.117
107_I151_G1.971342.112
147_A168_E1.940892.080
50_A56_L1.874532.008
50_A55_E1.830911.962
49_E53_S1.751971.877
105_P133_V1.749061.874
147_A163_E1.703471.825
18_S140_E1.639091.756
28_F200_F1.630381.747
47_L59_A1.573121.686
116_R120_D1.560951.672
28_F35_I1.546441.657
72_S184_Y1.512281.620
27_E31_R1.508021.616
42_G46_E1.490231.597
144_S147_A1.490231.597
27_E30_E1.445031.548
84_V172_L1.436211.539
199_W202_D1.419311.521
93_K100_D1.414831.516
71_E189_K1.401391.502
71_E187_W1.395681.495
107_I142_I1.387461.487
9_R40_R1.387451.487
96_I100_D1.38051.479
201_I205_R1.378571.477
81_V171_F1.368611.466
77_E180_P1.368561.466
31_R203_L1.347641.444
185_L201_I1.346021.442
26_A30_E1.320871.415
104_Y152_I1.320651.415
73_E187_W1.311071.405
136_V145_L1.30551.399
187_W201_I1.299841.393
5_R34_N1.285951.378
84_V88_H1.275871.367
86_P170_V1.272871.364
144_S148_S1.267571.358
202_D205_R1.264351.355
52_R69_G1.255231.345
86_P168_E1.253511.343
84_V152_I1.253421.343
161_Q165_E1.240741.329
198_Q202_D1.239121.328
193_L197_I1.238471.327
61_T186_V1.220771.308
29_R105_P1.213441.300
163_E168_E1.212981.300
94_K170_V1.202871.289
42_G50_A1.202761.289
51_L59_A1.19881.284
136_V142_I1.196611.282
138_S141_S1.189741.275
58_L197_I1.170161.254
28_F32_H1.166271.250
142_I153_A1.164331.248
74_P184_Y1.160191.243
85_S149_G1.158761.242
58_L185_L1.157481.240
188_R191_R1.14931.231
78_E158_S1.147021.229
63_G184_Y1.138561.220
29_R133_V1.136791.218
28_F203_L1.11271.192
162_D166_S1.108311.187
26_A148_S1.108261.187
157_D161_Q1.098311.177
40_R50_A1.091771.170
32_H199_W1.087191.165
73_E201_I1.084351.162
72_S186_V1.056121.132
143_L147_A1.051691.127
10_I58_L1.051311.126
23_P148_S1.048251.123
8_L200_F1.044041.119
17_A41_E1.032661.106
203_L206_E1.019771.093
83_V160_A1.01951.092
6_G35_I1.016581.089
88_H91_A1.014271.087
123_L128_F1.011621.084
31_R206_E1.004551.076
11_G61_T0.997461.069
38_E135_E0.982751.053
82_L152_I0.978771.049
105_P131_N0.963561.032
194_S197_I0.962831.032
95_P175_P0.948731.017
85_S88_H0.94321.011
99_E102_A0.941871.009
145_L150_D0.939021.006
157_D171_F0.936751.004
195_P199_W0.935831.003
24_L204_L0.919420.985
70_L186_V0.912540.978
24_L203_L0.90580.971
84_V90_L0.90270.967
42_G47_L0.901950.966
11_G59_A0.89460.959
4_E32_H0.889040.953
52_R67_P0.888530.952
88_H105_P0.884650.948
100_D103_D0.879540.942
172_L175_P0.872020.934
71_E74_P0.871690.934
164_L167_G0.860710.922
105_P132_I0.856780.918
87_D91_A0.854750.916
116_R135_E0.845560.906
46_E49_E0.843060.903
14_P138_S0.837390.897
163_E166_S0.837030.897
122_W126_H0.832060.892
40_R56_L0.827230.886
83_V171_F0.824080.883
12_A17_A0.818220.877
28_F199_W0.816210.875
49_E52_R0.811690.870
193_L198_Q0.810250.868
29_R150_D0.807920.866
9_R57_D0.807330.865
134_I145_L0.8040.861
108_L132_I0.801450.859
160_A163_E0.798860.856
145_L151_G0.794880.852
91_A170_V0.794740.852
26_A150_D0.793750.850
8_L58_L0.790520.847
63_G182_P0.789410.846
23_P26_A0.782990.839
57_D197_I0.780390.836
109_L142_I0.777460.833
90_L94_K0.775480.831
48_I52_R0.773970.829
54_G188_R0.772830.828
35_I196_A0.770570.826
52_R55_E0.76990.825
52_R70_L0.76460.819
123_L130_P0.763330.818
87_D149_G0.763080.818
90_L104_Y0.762840.817
117_D120_D0.762170.817
56_L59_A0.760020.814
21_L24_L0.75450.808
121_R125_E0.754310.808
69_G189_K0.750730.804
83_V155_L0.745260.799
60_I185_L0.744860.798
31_R199_W0.740860.794
160_A164_L0.739730.793
46_E50_A0.735590.788
162_D165_E0.735410.788
58_L200_F0.733280.786
99_E126_H0.732570.785
139_F156_P0.732290.785
79_P178_P0.731280.784
120_D124_R0.730070.782
195_P198_Q0.726530.778
202_D206_E0.725980.778
82_L154_I0.724540.776
41_E137_D0.713040.764
199_W203_L0.712640.764
106_L130_P0.710010.761
9_R56_L0.705560.756
156_P159_L0.699860.750
147_A166_S0.699470.749
32_H35_I0.699030.749
79_P173_P0.694730.744
87_D170_V0.694510.744
13_S16_F0.693750.743
79_P180_P0.692150.742
84_V170_V0.690890.740
6_G196_A0.686830.736
110_S135_E0.685320.734
93_K96_I0.68390.733
83_V164_L0.683810.733
187_W198_Q0.680220.729
11_G47_L0.67940.728
136_V141_S0.675880.724
51_L54_G0.673390.721
16_F20_L0.67110.719
23_P27_E0.670220.718
43_D46_E0.66570.713
36_R131_N0.665370.713
122_W125_E0.664660.712
8_L196_A0.663970.711
102_A128_F0.659680.707
78_E181_R0.658560.706
119_L122_W0.655520.702
97_T175_P0.651770.698
140_E144_S0.650390.697
83_V153_A0.649670.696
85_S150_D0.645930.692
121_R124_R0.643680.690
78_E156_P0.642110.688
50_A53_S0.638830.684
191_R194_S0.637870.683
118_Q121_R0.636920.682
14_P41_E0.634730.680
12_A21_L0.633810.679
110_S137_D0.631480.677
88_H152_I0.628340.673
26_A29_R0.622890.667
173_P176_D0.619660.664
60_I75_L0.61160.655
71_E190_D0.60840.652
11_G40_R0.604770.648
58_L201_I0.603180.646
141_S144_S0.601130.644
82_L106_L0.598210.641
193_L201_I0.597060.640
20_L24_L0.594580.637
22_P26_A0.594470.637
119_L123_L0.5940.636
29_R32_H0.593840.636
10_I37_I0.593540.636
197_I201_I0.590280.632
10_I200_F0.58830.630
18_S144_S0.587650.630
6_G32_H0.585570.627
196_A199_W0.584160.626
6_G34_N0.583930.626
99_E128_F0.583020.625
141_S145_L0.582890.625
175_P178_P0.5820.624
51_L70_L0.578630.620
23_P144_S0.574830.616
54_G191_R0.567230.608
12_A39_I0.566640.607
58_L187_W0.566130.607
193_L196_A0.566070.607
198_Q201_I0.56490.605
71_E192_P0.562590.603
4_E7_T0.561760.602
200_F204_L0.560850.601
106_L152_I0.559580.600
60_I204_L0.557850.598
109_L139_F0.557190.597
142_I146_V0.555190.595
90_L93_K0.554460.594
18_S138_S0.553740.593
117_D121_R0.553620.593
41_E138_S0.55190.591
76_G183_I0.55040.590
167_G171_F0.550160.589
143_L155_L0.547130.586
25_L37_I0.546530.586
78_E183_I0.543230.582
27_E206_E0.54260.581
36_R135_E0.541340.580
86_P167_G0.540150.579
123_L127_G0.537680.576
59_A186_V0.537640.576
107_I145_L0.537450.576
14_P43_D0.536310.575
80_L154_I0.534230.572
51_L186_V0.533870.572
146_V155_L0.531030.569
107_I146_V0.529510.567
13_S62_F0.52550.563
101_L106_L0.525050.563
82_L101_L0.524980.562
5_R36_R0.523520.561
95_P100_D0.522150.559
123_L126_H0.521760.559
11_G42_G0.520460.558
62_F181_R0.520430.558
75_L185_L0.519310.556
170_V173_P0.518310.555
40_R137_D0.517040.554
164_L171_F0.515360.552
109_L113_S0.515130.552
168_E171_F0.513070.550
62_F78_E0.510950.547
107_I136_V0.510860.547
111_P135_E0.507740.544
146_V169_L0.505790.542
8_L35_I0.501070.537
88_H93_K0.500590.536
171_F174_L0.500550.536
8_L197_I0.499440.535
4_E199_W0.496680.532
19_S140_E0.494750.530
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
4ab5A0.995299.9-0.019
3ho7A199.9-0.017
1i6aA0.995299.9-0.009
2y7pA0.995299.9-0.003
3oxnA0.990499.9-0.002
2hxrA0.985699.90.005
3jv9A0.985699.90.008
3fzvA0.995299.90.009
2esnA0.995299.90.011
3fxqA0.990499.90.014

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