GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
polyprenyl_synt - Polyprenyl synthetase
Pfam: PF00348 (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. )
Length: 260
Sequences: 4798
Seq/Len: 18.45
HH_delta: 0.051 (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
25_A35_A0.8423.330
164_D167_Q0.803143.176
60_D70_K0.782363.094
155_Q172_R0.759163.002
134_T137_E0.730852.890
151_A172_R0.689672.727
155_Q168_I0.643022.543
143_R176_R0.632242.500
73_G76_I0.621872.459
194_D197_E0.610082.413
61_L66_P0.589972.333
151_A176_R0.555882.198
201_P204_S0.551562.181
173_E177_H0.514872.036
169_E173_E0.500991.981
228_E232_E0.494261.955
119_E122_Q0.493351.951
193_G198_L0.48851.932
158_A171_L0.484751.917
87_L90_E0.472391.868
217_H221_R0.464771.838
154_C175_G0.460791.822
52_H81_G0.449991.780
140_E144_L0.442021.748
225_E228_E0.435381.722
51_I68_V0.431551.707
24_A171_L0.429031.697
37_P94_R0.425321.682
24_A28_L0.422281.670
135_E217_H0.415181.642
204_S208_E0.411821.629
163_A167_Q0.409751.620
38_L156_L0.406671.608
24_A154_C0.397031.570
52_H82_D0.392021.550
152_L156_L0.382171.511
227_R231_Q0.381921.510
189_L198_L0.380991.507
109_E155_Q0.380081.503
8_Y68_V0.375931.487
56_I79_L0.375841.486
6_R10_L0.37111.468
12_G15_R0.36841.457
28_L157_G0.365171.444
55_I74_N0.364551.442
59_S204_S0.362731.434
28_L161_A0.359261.421
157_G161_A0.359171.420
223_R226_L0.347721.375
22_L39_A0.34641.370
15_R18_P0.346271.369
188_L219_L0.345071.365
191_L214_P0.340831.348
76_I123_A0.340741.348
23_L26_E0.337891.336
20_L154_C0.33691.332
229_L232_E0.336581.331
170_A174_F0.332131.313
151_A155_Q0.331121.309
149_L153_A0.328811.300
143_R180_I0.328271.298
138_Y142_I0.326751.292
25_A30_G0.323711.280
142_I180_I0.320411.267
192_F223_R0.319521.264
195_E202_V0.31871.260
21_V42_V0.316231.251
69_H74_N0.313261.239
217_H220_E0.308891.222
103_R106_R0.308191.219
28_L167_Q0.307741.217
165_E169_E0.306411.212
124_L140_E0.30411.203
224_E228_E0.301821.194
195_E201_P0.300061.187
106_R156_L0.299411.184
11_R65_K0.299271.184
121_G125_D0.297131.175
67_T70_K0.294721.166
167_Q170_A0.291231.152
158_A163_A0.28661.133
198_L202_V0.286441.133
139_L180_I0.286081.131
159_I168_I0.285851.130
58_N74_N0.285581.129
140_E143_R0.283951.123
118_G121_G0.28161.114
20_L178_L0.280611.110
51_I77_A0.28011.108
189_L193_G0.279421.105
77_A81_G0.278171.100
193_G197_E0.276321.093
128_N133_P0.276121.092
122_Q125_D0.275911.091
133_P137_E0.274231.085
151_A175_G0.27371.082
68_V72_F0.27361.082
177_H232_E0.273481.082
109_E159_I0.272761.079
200_K205_D0.272671.078
221_R224_E0.271731.075
40_A91_L0.270021.068
138_Y216_L0.267541.058
79_L82_D0.266821.055
22_L35_A0.264921.048
188_L192_F0.26481.047
41_A92_L0.264151.045
22_L36_I0.263151.041
8_Y47_A0.262561.038
155_Q159_I0.262541.038
105_L108_L0.26011.029
7_Y65_K0.259631.027
49_S149_L0.257441.018
31_D34_K0.256731.015
148_S151_A0.256691.015
44_L91_L0.256411.014
44_L87_L0.256021.012
166_E170_A0.255061.009
169_E172_R0.253911.004
38_L160_L0.253271.002
176_R180_I0.252240.998
129_E211_P0.251280.994
135_E139_L0.250590.991
228_E231_Q0.249780.988
154_C174_F0.249540.987
139_L143_R0.249240.986
36_I40_A0.2490.985
141_I210_K0.247910.980
195_E198_L0.247750.980
158_A168_I0.247690.980
18_P47_A0.246140.973
182_F186_D0.244420.967
222_A226_L0.243620.963
185_R188_L0.243620.963
55_I78_I0.243240.962
46_H49_S0.242150.958
156_L160_L0.241360.955
30_G35_A0.240480.951
24_A27_A0.23720.938
7_Y72_F0.236530.935
25_A161_A0.236050.934
124_L141_I0.235840.933
146_T150_F0.235570.932
198_L201_P0.230710.912
66_P71_K0.229980.910
135_E220_E0.229740.909
10_L65_K0.229420.907
66_P70_K0.228920.905
90_E113_E0.226310.895
53_D57_D0.225240.891
184_I188_L0.225150.890
227_R230_L0.224730.889
5_A84_L0.224090.886
185_R226_L0.223440.884
17_R182_F0.221940.878
224_E227_R0.221560.876
177_H180_I0.221560.876
38_L92_L0.22060.872
7_Y71_K0.219670.869
116_I121_G0.217890.862
154_C171_L0.21780.861
105_L109_E0.217620.861
229_L233_A0.217340.860
138_Y184_I0.217180.859
150_F178_L0.216640.857
35_A160_L0.215750.853
17_R46_H0.214660.849
26_E32_P0.214640.849
5_A83_Y0.214370.848
96_G106_R0.214340.848
21_V35_A0.21390.846
89_F92_L0.213750.845
128_N141_I0.213440.844
124_L128_N0.212870.842
209_G215_V0.212210.839
141_I211_P0.210480.832
225_E229_L0.209550.829
191_L206_L0.209350.828
213_L217_H0.209310.828
190_D198_L0.208870.826
128_N132_D0.208490.825
111_F118_G0.207550.821
8_Y51_I0.207520.821
155_Q169_E0.207460.820
103_R168_I0.206760.818
146_T182_F0.20660.817
121_G124_L0.206420.816
174_F178_L0.206360.816
144_L148_S0.205270.812
186_D189_L0.205240.812
173_E176_R0.204550.809
190_D204_S0.203780.806
42_V153_A0.202950.803
46_H149_L0.20260.801
21_V39_A0.201980.799
61_L195_E0.201450.797
226_L233_A0.200930.795
83_Y120_I0.200760.794
193_G202_V0.19950.789
128_N137_E0.199380.788
147_G176_R0.199030.787
206_L215_V0.198110.783
60_D69_H0.197290.780
54_D62_R0.196750.778
24_A174_F0.19590.775
188_L223_R0.194950.771
17_R50_L0.194310.768
21_V153_A0.19360.766
224_E231_Q0.193260.764
223_R227_R0.193240.764
54_D57_D0.192810.763
14_K182_F0.19220.760
163_A168_I0.191970.759
83_Y116_I0.190520.753
102_E106_R0.190420.753
68_V71_K0.188520.746
186_D200_K0.18730.741
17_R146_T0.186960.739
56_I122_Q0.186440.737
45_I86_A0.186180.736
230_L234_Y0.186170.736
172_R176_R0.18610.736
165_E168_I0.185270.733
86_A119_E0.184960.731
21_V157_G0.184620.730
48_A85_L0.184440.729
138_Y213_L0.184030.728
143_R147_G0.182690.722
170_A173_E0.182570.722
125_D141_I0.182350.721
125_D210_K0.181980.720
177_H229_L0.181810.719
49_S115_L0.18160.718
146_T186_D0.181550.718
153_A157_G0.181390.717
204_S207_K0.181070.716
7_Y68_V0.179450.710
110_L155_Q0.179220.709
226_L230_L0.17880.707
68_V73_G0.176940.700
168_I172_R0.176650.699
91_L94_R0.176610.698
5_A80_A0.176140.697
65_K71_K0.174950.692
61_L201_P0.174590.690
141_I144_L0.174340.689
64_G69_H0.173450.686
34_K95_L0.17270.683
38_L106_R0.172540.682
11_R47_A0.172480.682
214_P222_A0.171980.680
221_R225_E0.171380.678
91_L95_L0.170230.673
11_R15_R0.169590.671
125_D129_E0.169490.670
28_L163_A0.169380.670
136_E140_E0.169210.669
57_D62_R0.168810.668
59_S190_D0.16880.668
135_E213_L0.168750.667
166_E169_E0.168690.667
185_R192_F0.168580.667
13_G17_R0.168180.665
83_Y87_L0.168140.665
112_I119_E0.16730.662
46_H50_L0.167090.661
231_Q235_G0.166890.660
49_S118_G0.166430.658
86_A89_F0.166290.658
80_A83_Y0.165660.655
109_E172_R0.165390.654
77_A80_A0.165340.654
135_E216_L0.165220.653
48_A56_I0.16520.653
56_I74_N0.165050.653
69_H72_F0.164760.652
147_G180_I0.164660.651
137_E140_E0.16460.651
15_R19_L0.164320.650
9_I44_L0.164180.649
48_A86_A0.164160.649
46_H146_T0.164020.649
164_D169_E0.163930.648
34_K160_L0.16360.647
75_A126_L0.163360.646
48_A119_E0.162190.641
124_L144_L0.162080.641
121_G141_I0.162040.641
59_S69_H0.161850.640
138_Y214_P0.161640.639
90_E112_I0.160850.636
38_L157_G0.160260.634
58_N69_H0.159460.631
142_I213_L0.159340.630
190_D203_G0.159030.629
126_L129_E0.158880.628
51_I72_F0.158620.627
21_V25_A0.15850.627
14_K50_L0.157180.622
107_I156_L0.157170.622
199_G205_D0.157090.621
54_D145_K0.156830.620
42_V152_L0.156340.618
37_P40_A0.155940.617
87_L91_L0.155910.617
31_D166_E0.155880.616
54_D187_D0.155170.614
108_L111_F0.154970.613
8_Y11_R0.154710.612
190_D201_P0.154490.611
93_A108_L0.1540.609
28_L164_D0.152410.603
116_I120_I0.152280.602
33_E37_P0.151960.601
115_L119_E0.151840.600
145_K183_Q0.151830.600
72_F80_A0.151550.599
230_L233_A0.151420.599
79_L88_A0.151050.597
82_D85_L0.150710.596
133_P211_P0.150530.595
214_P217_H0.150040.593
123_A127_A0.149930.593
60_D67_T0.149630.592
30_G157_G0.149130.590
122_Q126_L0.148830.589
39_A43_E0.148790.588
59_S67_T0.148270.586
49_S153_A0.148150.586
220_E224_E0.147950.585
53_D145_K0.147860.585
63_R186_D0.147710.584
145_K187_D0.14760.584
19_L22_L0.147590.584
106_R110_L0.147440.583
82_D88_A0.147410.583
103_R165_E0.147230.582
101_S166_E0.14720.582
114_A117_E0.147020.581
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
1wy0A0.99231000.051
3nf2A0.98461000.057
4jxyA0.97311000.059
4dhdA0.97691000.061
3mzvA0.97311000.063
3oyrA0.97311000.063
3lk5A0.99231000.064
1wmwA0.98081000.066
3lmdA0.96541000.07
3rmgA0.96921000.073

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