GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
tRNA-synt_1g - tRNA synthetases class I (M)
Pfam: PF09334 (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: CL0039
Length: 391
Sequences: 5745
Seq/Len: 14.69
HH_delta: 0.044 (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
32_L37_H1.398546.419
326_E332_R0.851393.907
27_V355_A0.83693.841
193_D197_E0.75573.468
105_K109_D0.733793.368
197_E201_S0.731773.358
123_C126_C0.709893.258
123_C172_C0.699723.211
55_A58_K0.688243.159
344_E368_W0.676363.104
106_R109_D0.65172.991
115_K182_E0.650262.984
102_E106_R0.59762.743
187_K190_K0.589792.707
126_C172_C0.587592.697
106_R110_N0.569362.613
75_K79_E0.550572.527
33_R84_S0.54822.516
117_E180_E0.544022.497
119_E180_E0.527692.422
13_D73_K0.513122.355
200_E219_K0.512392.352
32_L35_R0.508422.333
117_E182_E0.50832.333
200_E215_R0.505262.319
200_E211_R0.504432.315
197_E200_E0.500062.295
80_A343_E0.495682.275
38_D275_W0.493472.265
29_A39_V0.493082.263
196_R215_R0.48242.214
123_C169_C0.480582.206
38_D274_K0.463392.127
169_C172_C0.461552.118
196_R219_K0.456162.094
96_H257_T0.449742.064
31_Y35_R0.447822.055
72_A76_E0.445772.046
112_Y191_F0.439152.015
189_S193_D0.428951.969
194_Q197_E0.426721.958
126_C169_C0.420271.929
87_R95_R0.406261.865
72_A75_K0.405581.861
208_P211_R0.398451.829
94_D98_E0.39741.824
62_D65_E0.396331.819
187_K224_D0.393591.806
211_R215_R0.39221.800
22_Y78_L0.391171.795
121_W178_V0.372081.708
59_Q69_K0.370211.699
125_S172_C0.365361.677
341_L350_L0.364641.674
25_A287_F0.362841.665
61_I69_K0.362271.663
215_R219_K0.359341.649
212_E216_N0.357571.641
340_D343_E0.355561.632
192_R196_R0.350271.608
194_Q308_G0.34921.603
22_Y83_I0.34911.602
21_P318_H0.34691.592
73_K76_E0.342511.572
297_A315_I0.339561.558
125_S174_S0.339091.556
64_E68_D0.335951.542
322_T365_D0.333591.531
198_W201_S0.329131.511
296_H300_W0.327951.505
98_E263_A0.327091.501
293_I317_V0.316581.453
76_E80_A0.315571.448
340_D344_E0.315461.448
194_Q305_L0.315031.446
69_K73_K0.313861.440
110_N308_G0.313371.438
47_E92_T0.307561.412
42_V258_A0.307511.411
66_F70_Y0.306921.409
113_I227_I0.306881.408
79_E85_Y0.305661.403
339_D343_E0.305441.402
284_I313_R0.304381.397
87_R93_D0.301051.382
29_A33_R0.296681.362
68_D72_A0.295861.358
247_V251_A0.292541.343
366_F371_F0.291821.339
251_A255_Y0.288081.322
29_A84_S0.286551.315
119_E178_V0.285891.312
6_P21_P0.285521.310
49_G53_E0.285281.309
169_C174_S0.285121.309
55_A59_Q0.284361.305
80_A339_D0.283681.302
216_N219_K0.28131.291
131_P134_F0.280641.288
190_K193_D0.277781.275
337_W340_D0.277721.275
78_L83_I0.273771.256
94_D97_K0.27311.253
28_L32_L0.272471.251
71_S75_K0.271111.244
249_F303_M0.268141.231
98_E101_Q0.267871.229
148_R151_Q0.266811.225
33_R39_V0.266211.222
8_P22_Y0.265711.219
124_P177_E0.264541.214
344_E372_I0.262951.207
112_Y190_K0.262721.206
97_K236_P0.262371.204
76_E79_E0.261751.201
310_P313_R0.261181.199
12_G18_H0.259371.190
247_V250_D0.257591.182
206_P314_R0.257281.181
270_E273_K0.255791.174
71_S90_R0.255011.170
369_E372_I0.253371.163
196_R218_L0.253351.163
100_V245_I0.252071.157
121_W135_V0.252061.157
124_P174_S0.251141.153
61_I65_E0.250351.149
342_L347_A0.249641.146
325_G365_D0.247421.136
114_Y187_K0.243921.119
28_L285_V0.242311.112
328_M334_N0.240811.105
26_D30_R0.238921.097
14_L18_H0.238771.096
53_E57_E0.23621.084
90_R93_D0.235041.079
193_D196_R0.234711.077
105_K108_Y0.2341.074
136_E170_K0.233251.071
114_Y224_D0.232751.068
186_F227_I0.231771.064
205_F293_I0.230281.057
255_Y276_W0.230241.057
368_W372_I0.229951.055
154_N157_R0.229191.052
157_R160_E0.228541.049
140_P153_E0.228341.048
16_L335_V0.227761.045
300_W304_L0.225621.035
203_P314_R0.225421.035
108_Y239_G0.22531.034
151_Q155_C0.225131.033
45_T71_S0.225121.033
59_Q66_F0.224231.029
65_E69_K0.223781.027
210_V213_I0.222791.023
13_D77_L0.221941.019
5_T41_F0.221211.015
70_Y73_K0.22111.015
198_W202_N0.219921.009
52_I63_P0.219031.005
345_Y368_W0.217640.999
353_Y370_D0.217060.996
150_D153_E0.216640.994
110_N306_A0.216310.993
151_Q156_G0.215890.991
246_Y251_A0.214920.986
299_Y303_M0.213030.978
156_G159_L0.212850.977
52_I56_A0.212330.974
50_S88_F0.211570.971
151_Q159_L0.210530.966
207_P213_I0.209680.962
118_Y185_F0.208820.958
78_L85_Y0.207780.954
342_L348_D0.206750.949
107_L306_A0.206490.948
68_D92_T0.206010.945
51_K54_T0.205990.945
23_L27_V0.205960.945
346_G349_A0.205950.945
125_S169_C0.205870.945
32_L39_V0.205470.943
25_A41_F0.2050.941
218_L296_H0.204380.938
330_K334_N0.204190.937
153_E156_G0.204160.937
42_V259_T0.203560.934
126_C174_S0.203430.934
65_E68_D0.202270.928
312_P315_I0.201970.927
23_L355_A0.201610.925
101_Q105_K0.201020.923
196_R200_E0.20050.920
61_I66_F0.199950.918
206_P213_I0.198850.913
271_E274_K0.198670.912
150_D157_R0.198030.909
288_I301_P0.197850.908
207_P211_R0.197640.907
137_G165_I0.197220.905
321_L364_S0.197160.905
183_N230_P0.196390.901
103_I253_I0.196130.900
173_G331_S0.195730.898
8_P21_P0.195420.897
151_Q154_N0.19440.892
116_R224_D0.193090.886
150_D156_G0.191890.881
370_D373_E0.190990.877
112_Y306_A0.189670.870
276_W304_L0.189540.870
288_I292_I0.188630.866
199_L215_R0.188260.864
123_C174_S0.188150.864
246_Y250_D0.187720.862
332_R335_V0.187440.860
5_T25_A0.187420.860
205_F315_I0.186240.855
231_L244_V0.18610.854
5_T85_Y0.185750.853
107_L110_N0.185690.852
21_P25_A0.184910.849
108_Y113_I0.184760.848
151_Q157_R0.184690.848
291_D320_F0.18430.846
47_E90_R0.184130.845
19_L81_L0.18380.844
293_I297_A0.183780.843
129_F226_S0.183420.842
209_R212_E0.183320.841
5_T78_L0.182740.839
152_C155_C0.182550.838
121_W176_P0.181890.835
5_T22_Y0.181780.834
285_V314_R0.181210.832
160_E163_E0.179910.826
139_C155_C0.179790.825
40_L275_W0.179580.824
80_A342_L0.179580.824
116_R185_F0.179080.822
300_W303_M0.178370.819
41_F85_Y0.17770.816
77_L339_D0.177530.815
168_V173_G0.177360.814
22_Y85_Y0.177250.813
269_P272_F0.176420.810
154_N159_L0.17620.809
183_N226_S0.1760.808
115_K184_Y0.175820.807
24_A287_F0.175120.804
341_L368_W0.174820.802
104_F108_Y0.174340.800
185_F226_S0.174250.800
50_S304_L0.173540.796
208_P212_E0.172880.793
321_L354_L0.172640.792
216_N220_E0.172170.790
101_Q236_P0.172160.790
149_G157_R0.171580.787
156_G160_E0.171080.785
75_K86_D0.170870.784
99_F102_E0.169560.778
141_Y157_R0.169250.777
269_P273_K0.16920.777
53_E232_D0.168650.774
352_Y356_R0.168390.773
16_L328_M0.167960.771
357_E364_S0.167930.771
150_D155_C0.167610.769
98_E102_E0.166820.766
276_W308_G0.166730.765
188_L222_L0.166620.765
328_M335_V0.16610.762
102_E105_K0.1650.757
82_N347_A0.164210.754
290_K320_F0.164210.754
270_E274_K0.164160.753
189_S192_R0.163620.751
165_I168_V0.163580.751
99_F260_G0.163460.750
206_P212_E0.163450.750
148_R156_G0.163340.750
21_P287_F0.163230.749
150_D159_L0.162970.748
8_P12_G0.162780.747
97_K101_Q0.162620.746
6_P22_Y0.16250.746
155_C159_L0.161980.743
68_D90_R0.161940.743
210_V317_V0.161820.743
254_G258_A0.161090.739
118_Y226_S0.160390.736
112_Y187_K0.160270.736
30_R84_S0.160140.735
324_D367_S0.160090.735
115_K240_D0.159530.732
150_D154_N0.15950.732
369_E373_E0.159450.732
286_H296_H0.159370.731
104_F237_V0.159230.731
228_S237_V0.158790.729
45_T75_K0.158690.728
19_L23_L0.157460.723
98_E273_K0.157450.723
54_T58_K0.157060.721
148_R159_L0.156740.719
120_G129_F0.156450.718
159_L162_E0.156340.718
205_F214_V0.156090.716
77_L337_W0.155910.716
122_Y129_F0.154940.711
52_I55_A0.154750.710
328_M336_I0.15470.710
294_R299_Y0.154540.709
296_H302_A0.15420.708
173_G332_R0.153810.706
356_R370_D0.153680.705
139_C148_R0.153380.704
148_R154_N0.153340.704
252_L255_Y0.153290.704
156_G163_E0.152470.700
50_S53_E0.152220.699
157_R162_E0.152180.698
316_V360_E0.152090.698
207_P210_V0.151460.695
148_R152_C0.151450.695
205_F317_V0.150660.691
188_L302_A0.149640.687
263_A269_P0.149160.685
148_R153_E0.148920.683
283_E286_H0.148770.683
189_S224_D0.14850.682
246_Y249_F0.148250.680
225_L229_R0.147810.678
341_L345_Y0.147630.678
230_P235_I0.147590.677
213_I216_N0.147570.677
345_Y372_I0.147380.676
209_R213_I0.147220.676
199_L205_F0.147030.675
82_N348_D0.1470.675
105_K239_G0.146820.674
154_N162_E0.146780.674
152_C160_E0.146690.673
290_K363_D0.146650.673
24_A318_H0.146610.673
107_L249_F0.146550.673
30_R33_R0.146370.672
24_A360_E0.146060.670
285_V316_V0.145810.669
72_A79_E0.145380.667
159_L163_E0.145320.667
22_Y25_A0.145220.666
296_H301_P0.144780.664
164_L168_V0.144540.663
107_L304_L0.144290.662
87_R261_Y0.144240.662
246_Y255_Y0.14410.661
243_Q304_L0.144050.661
227_I237_V0.144010.661
335_V338_P0.143780.660
148_R160_E0.142940.656
22_Y41_F0.142810.655
192_R222_L0.142770.655
309_L313_R0.142550.654
16_L336_I0.142530.654
184_Y240_D0.142330.653
247_V254_G0.142280.653
51_K171_I0.142010.652
251_A254_G0.141970.652
299_Y302_A0.141720.650
88_F304_L0.141680.650
305_L311_L0.141670.650
149_G152_C0.14150.649
243_Q251_A0.141370.649
247_V255_Y0.140940.647
158_P163_E0.140740.646
259_T271_E0.140720.646
341_L366_F0.140590.645
294_R298_I0.140350.644
249_F253_I0.13990.642
14_L74_F0.139420.640
203_P211_R0.139220.639
328_M333_G0.139210.639
128_R131_P0.1390.638
340_D368_W0.138970.638
14_L77_L0.138810.637
253_I257_T0.138770.637
272_F307_A0.138750.637
69_K72_A0.138720.637
46_D49_G0.138560.636
99_F262_L0.138270.635
357_E370_D0.138260.635
137_G167_P0.138220.634
24_A355_A0.138080.634
153_E159_L0.137750.632
141_Y240_D0.137680.632
4_T7_I0.137370.630
324_D368_W0.137070.629
336_I341_L0.137020.629
75_K85_Y0.136950.629
195_L300_W0.136910.628
241_P304_L0.136870.628
122_Y127_E0.136280.625
336_I366_F0.136170.625
195_L198_W0.136150.625
152_C157_R0.136070.624
132_E135_V0.136010.624
107_L113_I0.135960.624
138_T166_N0.135760.623
95_R99_F0.135620.622
59_Q70_Y0.135510.622
13_D337_W0.135480.622
113_I184_Y0.135220.621
214_V297_A0.135080.620
128_R172_C0.134950.619
214_V218_L0.134930.619
295_F302_A0.134840.619
8_P17_G0.134690.618
59_Q62_D0.134650.618
319_G361_G0.134420.617
212_E215_R0.134410.617
246_Y252_L0.133690.614
20_Y364_S0.13360.613
18_H329_S0.133580.613
294_R297_A0.133480.613
107_L186_F0.133350.612
188_L191_F0.133290.612
6_P292_I0.132480.608
188_L192_R0.132140.606
10_P13_D0.131850.605
323_L335_V0.131580.604
4_T283_E0.131540.604
262_L269_P0.131490.603
16_L337_W0.131280.603
42_V88_F0.131280.603
248_W251_A0.13120.602
100_V103_I0.131170.602
255_Y258_A0.131150.602
23_L354_L0.130460.599
14_L81_L0.130440.599
156_G162_E0.130070.597
40_L87_R0.129960.596
202_N310_P0.129860.596
243_Q247_V0.129730.595
286_H292_I0.129480.594
141_Y152_C0.129270.593
206_P211_R0.129090.592
65_E243_Q0.129010.592
153_E163_E0.12880.591
297_A300_W0.128610.590
202_N205_F0.128240.589
51_K56_A0.128230.589
104_F113_I0.128130.588
206_P316_V0.128070.588
285_V288_I0.127970.587
139_C147_A0.127830.587
106_R111_G0.127820.587
121_W132_E0.127820.587
324_D369_E0.127820.587
199_L218_L0.127370.585
8_P15_H0.127250.584
225_L299_Y0.127180.584
330_K333_G0.126730.582
29_A41_F0.126560.581
341_L371_F0.126260.579
153_E157_R0.126190.579
319_G359_P0.126180.579
11_N291_D0.126090.579
324_D365_D0.12580.577
203_P208_P0.125630.577
227_I253_I0.125630.577
76_E339_D0.125550.576
14_L22_Y0.125520.576
338_P353_Y0.125190.575
147_A151_Q0.125040.574
323_L328_M0.124960.574
206_P210_V0.124860.573
18_H23_L0.124830.573
319_G360_E0.124490.571
253_I256_L0.124110.570
191_F195_L0.124010.569
364_S367_S0.123920.569
324_D332_R0.123810.568
198_W303_M0.123610.567
45_T74_F0.123460.567
272_F276_W0.123460.567
9_Y47_E0.123340.566
199_L202_N0.123320.566
15_H18_H0.123080.565
64_E67_C0.122870.564
13_D70_Y0.122860.564
14_L41_F0.122330.561
147_A150_D0.122320.561
259_T275_W0.122290.561
303_M306_A0.121890.559
190_K194_Q0.121750.559
129_F133_S0.121690.558
198_W310_P0.121680.558
4_T42_V0.121410.557
150_D160_E0.121070.556
344_E349_A0.121010.555
167_P178_V0.120710.554
118_Y181_E0.120620.554
89_I254_G0.120590.553
111_G187_K0.120480.553
155_C158_P0.12020.552
55_A69_K0.120180.552
126_C173_G0.120080.551
155_C160_E0.120050.551
68_D71_S0.11950.548
348_D351_R0.119490.548
130_L157_R0.119290.547
138_T141_Y0.11910.547
200_E203_P0.119080.547
125_S157_R0.119070.546
106_R307_A0.11880.545
98_E260_G0.118710.545
301_P304_L0.11870.545
141_Y163_E0.118660.545
28_L316_V0.118570.544
103_I307_A0.118490.544
139_C240_D0.118440.544
297_A312_P0.118410.543
296_H299_Y0.118360.543
113_I245_I0.11830.543
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
1rqgA0.99491000.044
3h99A0.99491000.11
1gaxA0.96421000.171
1ileA0.97191000.179
3kflA0.93611000.18
3u1fA0.94121000.189
1ffyA0.98471000.196
4dlpA0.9131000.203
2x1lA0.91561000.205
2d5bA0.90031000.217

Page generated in 0.0412 seconds.