GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Autoind_synth - Autoinducer synthetase
Pfam: PF00765 (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: CL0257
Length: 182
Sequences: 8035
Seq/Len: 44.15
HH_delta: 0.191 (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
122_V150_W1.496623.382
122_V171_I1.213112.741
19_R99_D1.176512.658
57_V102_R1.163542.629
115_M147_R1.125942.544
135_G145_L1.089292.461
60_A121_M1.032242.332
58_G98_V1.005772.273
49_V56_V0.996722.252
115_M148_A0.985572.227
120_G123_E0.978452.211
50_A113_V0.944512.134
62_L121_M0.866621.958
142_E146_R0.851831.925
132_H170_L0.848271.917
143_R146_R0.810351.831
122_V133_I0.799491.806
52_D57_V0.794931.796
55_R101_D0.794781.796
141_M145_L0.769971.740
12_E15_R0.766191.731
119_L148_A0.740171.672
5_L13_M0.737741.667
154_R157_P0.727091.643
142_E169_L0.700351.582
48_L120_G0.68671.552
118_L148_A0.685851.550
98_V113_V0.682451.542
124_F128_N0.681711.540
115_M119_L0.676511.529
52_D105_S0.665851.504
120_G124_F0.659411.490
51_L54_G0.657771.486
113_V116_E0.657681.486
124_F127_S0.647951.464
102_R105_S0.64161.450
55_R99_D0.63581.437
51_L56_V0.632671.430
12_E16_L0.632251.429
6_S9_L0.628081.419
91_W130_I0.605141.367
47_Y61_R0.588471.330
105_S113_V0.579321.309
60_A117_L0.561271.268
91_W125_A0.558531.262
146_R154_R0.557781.260
9_L51_L0.556721.258
52_D102_R0.555951.256
116_E120_G0.554091.252
50_A117_L0.55091.245
144_I148_A0.547311.237
123_E127_S0.544921.231
5_L49_V0.544171.230
125_A133_I0.537021.213
16_L56_V0.536481.212
93_L118_L0.536051.211
137_V141_M0.532161.202
12_E56_V0.520521.176
5_L9_L0.517791.170
11_E15_R0.513461.160
116_E119_L0.511061.155
62_L125_A0.510921.154
99_D102_R0.505871.143
90_V132_H0.505091.141
134_V170_L0.50481.141
112_P115_M0.50311.137
92_E134_V0.494921.118
114_T144_I0.492511.113
55_R102_R0.488221.103
157_P165_R0.488171.103
20_V97_C0.488041.103
12_E55_R0.469491.061
17_R59_C0.468751.059
15_R19_R0.462871.046
142_E167_V0.456481.031
118_L150_W0.453041.024
16_L97_C0.451261.020
50_A58_G0.446921.010
18_H22_V0.440070.994
96_F118_L0.438190.990
13_M59_C0.437610.989
100_P103_R0.431370.975
19_R100_P0.424810.960
48_L124_F0.419960.949
126_L171_I0.416420.941
36_E40_Y0.414470.936
90_V134_V0.408050.922
4_E124_F0.397280.898
119_L123_E0.388430.878
103_R140_A0.388360.878
59_C97_C0.383790.867
46_V124_F0.382410.864
135_G141_M0.382230.864
154_R167_V0.381570.862
123_E126_L0.381020.861
14_F18_H0.379620.858
17_R97_C0.376420.851
89_D131_R0.375260.848
21_F97_C0.37280.842
93_L135_G0.368890.834
17_R21_F0.36690.829
137_V142_E0.364340.823
98_V117_L0.362570.819
37_I41_D0.36050.815
57_V113_V0.357370.807
10_L14_F0.357030.807
122_V148_A0.355070.802
92_E136_V0.352580.797
146_R169_L0.351230.794
5_L47_Y0.35090.793
141_M144_I0.350760.793
58_G117_L0.34620.782
143_R147_R0.345710.781
118_L145_L0.345050.780
125_A130_I0.344950.779
52_D55_R0.343840.777
58_G113_V0.334310.755
19_R23_D0.330430.747
133_I150_W0.328820.743
118_L144_I0.328640.743
50_A57_V0.328620.743
98_V114_T0.326460.738
12_E51_L0.325660.736
21_F24_R0.324320.733
12_E99_D0.322420.729
36_E39_Q0.322390.728
138_D141_M0.320610.724
50_A116_E0.318790.720
114_T145_L0.315170.712
32_E36_E0.313210.708
138_D164_E0.312640.706
35_M39_Q0.309050.698
104_R140_A0.308940.698
19_R22_V0.307960.696
7_R41_D0.30580.691
22_V26_G0.302380.683
15_R99_D0.299870.678
35_M40_Y0.299320.676
146_R151_P0.296450.670
91_W133_I0.29560.668
145_L169_L0.294320.665
136_V166_V0.293850.664
157_P167_V0.292750.661
7_R10_L0.29160.659
16_L99_D0.29150.659
19_R101_D0.290910.657
34_G38_D0.289340.654
160_S165_R0.28820.651
159_R166_V0.287690.650
38_D42_D0.286710.648
122_V126_L0.28580.646
125_A129_G0.285140.644
48_L121_M0.284980.644
96_F145_L0.280540.634
159_R162_G0.273810.619
34_G37_I0.272150.615
13_M49_V0.271460.613
93_L133_I0.271410.613
13_M56_V0.26890.608
17_R36_E0.268760.607
57_V99_D0.268710.607
4_E48_L0.268350.606
10_L40_Y0.266770.603
38_D41_D0.266550.602
62_L91_W0.265490.600
21_F25_L0.265160.599
145_L150_W0.260550.589
16_L20_V0.25990.587
134_V168_A0.259570.587
126_L131_R0.257520.582
168_A171_I0.25510.576
9_L56_V0.253590.573
61_R94_S0.24990.565
60_A93_L0.249660.564
167_V170_L0.249630.564
31_C34_G0.248670.562
151_P170_L0.248080.561
126_L129_G0.245570.555
156_G159_R0.242770.549
117_L120_G0.24240.548
27_W136_V0.241670.546
23_D92_E0.24040.543
98_V104_R0.240240.543
161_I166_V0.238080.538
116_E123_E0.237760.537
154_R158_P0.237670.537
93_L150_W0.237270.536
139_P143_R0.236990.535
11_E14_F0.234520.530
165_R168_A0.234250.529
64_P91_W0.233950.529
64_P128_N0.233520.528
16_L59_C0.231250.523
155_L168_A0.231220.522
94_S134_V0.230610.521
142_E154_R0.230030.520
135_G169_L0.229880.519
137_V145_L0.229840.519
27_W94_S0.226910.513
23_D100_P0.22680.512
21_F145_L0.226510.512
63_L94_S0.224740.508
134_V137_V0.224560.507
137_V166_V0.223990.506
98_V103_R0.22320.504
154_R159_R0.222390.502
7_R40_Y0.222370.502
158_P169_L0.222370.502
104_R113_V0.221410.500
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
1ro5A0.96799.90.191
1kzfA0.950599.80.232
3p2hA0.97899.80.24
3efaA0.774799.70.333
4e2aA0.835299.70.336
2g0bA0.923199.70.35
2x7bA0.829799.70.351
1kuxA0.917699.70.356
1xebA0.774799.70.363
1tiqA0.884699.70.367

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