GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
tRNA-synt_2 - tRNA synthetases class II (D K and N)
Pfam: PF00152 (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: CL0040
Length: 335
Sequences: 6602
Seq/Len: 19.71
HH_delta: 0.082 (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
39_R138_E1.261044.307
34_E38_K1.038983.549
30_Q34_E1.032543.527
35_F138_E0.978333.342
37_D97_F0.93743.202
30_Q37_D0.871152.975
48_I103_F0.798992.729
31_A142_Y0.782372.672
85_L96_V0.7822.671
32_I120_L0.757752.588
31_A146_E0.74792.554
242_D245_G0.736942.517
33_R43_E0.697252.381
171_E175_I0.695692.376
141_K162_K0.679712.322
28_I315_V0.671322.293
24_I319_L0.65772.246
29_L311_L0.65652.242
264_Q305_G0.656172.241
127_A131_D0.637742.178
168_T227_D0.624822.134
129_Y248_E0.610592.086
273_R291_E0.594942.032
34_E146_E0.590852.018
168_T171_E0.588792.011
48_I100_G0.586722.004
165_P221_D0.581291.985
21_I321_L0.581181.985
170_E174_E0.57681.970
124_M127_A0.57581.967
273_R277_E0.574251.961
208_E212_P0.566231.934
32_I139_L0.557171.903
269_P273_R0.551051.882
34_E37_D0.548211.872
254_I259_I0.545431.863
137_E166_R0.543991.858
274_E278_E0.541281.849
134_D138_E0.535831.830
132_L305_G0.535611.829
122_W307_F0.530911.813
35_F139_L0.528991.807
35_F142_Y0.527241.801
89_L304_H0.525951.796
38_K142_Y0.518121.770
224_F252_L0.515931.762
35_F39_R0.514721.758
98_E121_E0.513211.753
277_E283_P0.507581.734
142_Y146_E0.499271.705
36_F120_L0.493241.685
26_S37_D0.488861.670
27_A30_Q0.486091.660
31_A143_I0.485411.658
239_P248_E0.482351.647
273_R283_P0.480571.641
140_I252_L0.480551.641
128_D131_D0.479631.638
134_D166_R0.47581.625
130_D166_R0.462861.581
64_D72_G0.45411.551
41_F124_M0.453431.549
278_E281_I0.45231.545
282_D285_E0.451341.542
167_I172_A0.449431.535
240_N248_E0.449331.535
23_R42_I0.44861.532
133_M166_R0.445661.522
171_E174_E0.438721.498
170_E246_V0.434931.486
20_S24_I0.434561.484
130_D134_D0.433681.481
269_P298_K0.433541.481
183_L221_D0.423491.446
45_D101_P0.415831.420
22_L329_P0.413361.412
44_V88_L0.411391.405
144_F318_L0.411281.405
271_E274_E0.408971.397
23_R27_A0.407441.392
31_A34_E0.406551.389
274_E277_E0.402511.375
102_C119_M0.395461.351
227_D239_P0.392141.339
273_R294_L0.3871.322
172_A225_I0.385951.318
43_E97_F0.385471.317
167_I225_I0.384821.314
124_M135_L0.383651.310
207_S211_E0.380871.301
165_P175_I0.379271.295
268_D271_E0.376041.284
165_P229_P0.372341.272
176_Y218_Y0.37081.266
20_S23_R0.361781.236
238_P268_D0.358461.224
32_I143_I0.357541.221
81_P102_C0.357321.220
238_P267_H0.352361.204
174_E178_G0.344751.178
164_F252_L0.342221.169
27_A37_D0.340421.163
127_A305_G0.338871.157
321_L326_D0.337461.153
95_R124_M0.337241.152
295_E298_K0.333431.139
321_L327_V0.3331.137
32_I311_L0.330871.130
295_E301_M0.327321.118
40_G95_R0.326541.115
230_A275_R0.325461.112
27_A146_E0.322681.102
31_A147_L0.322371.101
264_Q267_H0.321961.100
168_T226_T0.321711.099
140_I314_L0.319481.091
81_P119_M0.319411.091
236_Y241_D0.318461.088
25_R45_D0.317621.085
138_E142_Y0.317041.083
141_K161_P0.316911.082
133_M224_F0.316541.081
127_A132_L0.314871.075
24_I27_A0.311641.064
275_R278_E0.31091.062
310_G313_R0.310351.060
26_S30_Q0.309361.057
33_R97_F0.305931.045
137_E141_K0.304261.039
46_T98_E0.298541.020
22_L93_L0.295981.011
248_E264_Q0.294461.006
175_I218_Y0.293261.002
172_A175_I0.291330.995
120_L311_L0.290670.993
36_F122_W0.290410.992
28_I143_I0.289480.989
242_D246_V0.287320.981
137_E164_F0.287040.980
81_P84_Y0.286680.979
252_L260_A0.286640.979
29_L45_D0.282960.966
31_A35_F0.282030.963
202_V206_L0.281920.963
273_R298_K0.277620.948
83_L121_E0.276780.945
48_I101_P0.275350.940
101_P118_T0.274620.938
145_K159_D0.274550.938
238_P271_E0.274490.938
41_F95_R0.273780.935
34_E142_Y0.271080.926
301_M304_H0.269910.922
275_R279_Q0.269840.922
24_I147_L0.267160.913
39_R135_L0.266490.910
21_I326_D0.264930.905
167_I175_I0.263810.901
112_R257_G0.263620.900
270_E274_E0.263390.900
309_L314_L0.263110.899
233_S237_K0.26290.898
291_E295_E0.261620.894
167_I219_F0.261060.892
36_F139_L0.26070.890
227_D248_E0.259840.887
173_F206_L0.258670.884
236_Y263_S0.257580.880
251_D261_N0.256550.876
27_A31_A0.255590.873
21_I319_L0.252980.864
81_P100_G0.252850.864
137_E163_P0.252740.863
83_L292_W0.252720.863
139_L143_I0.252560.863
90_A301_M0.251560.859
177_G201_E0.251330.858
28_I311_L0.250730.856
111_R322_K0.249870.853
133_M137_E0.249850.853
138_E162_K0.248290.848
257_G317_L0.24790.847
143_I146_E0.247260.845
50_T84_Y0.247230.844
138_E141_K0.24650.842
170_E202_V0.246340.841
61_F105_N0.245390.838
111_R323_N0.244680.836
215_V253_Y0.24380.833
118_T312_E0.240080.820
136_I309_L0.240080.820
25_R312_E0.239240.817
295_E299_Y0.238860.816
269_P294_L0.238110.813
316_M324_I0.236890.809
133_M136_I0.236810.809
144_F160_L0.236720.809
203_G207_S0.236450.808
276_F290_D0.234870.802
229_P232_Q0.234530.801
270_E273_R0.234450.801
266_E271_E0.233940.799
164_F222_P0.23330.797
24_I28_I0.232790.795
52_S78_T0.230470.787
162_K229_P0.230340.787
28_I318_L0.229140.783
266_E275_R0.228370.780
24_I148_L0.226560.774
129_Y227_D0.225450.770
95_R125_A0.225140.769
258_E310_G0.224530.767
26_S43_E0.224240.766
83_L98_E0.223830.765
129_Y133_M0.223310.763
129_Y264_Q0.22230.759
230_A238_P0.221910.758
200_F204_R0.221510.757
99_I311_L0.220980.755
237_K240_N0.219520.750
239_P246_V0.219090.748
208_E211_E0.218750.747
44_V93_L0.218530.746
32_I36_F0.217370.742
143_I147_L0.216920.741
132_L307_F0.216690.740
277_E282_D0.216260.739
71_F105_N0.215120.735
239_P271_E0.215050.735
35_F38_K0.214180.732
85_L98_E0.21390.731
163_P166_R0.213870.730
178_G203_G0.213550.729
229_P235_F0.213290.729
141_K145_K0.212950.727
166_R226_T0.212850.727
142_Y145_K0.21250.726
185_F207_S0.212490.726
172_A176_Y0.210870.720
35_F135_L0.208920.714
136_I307_F0.208120.711
38_K146_E0.207860.710
207_S232_Q0.207240.708
173_F177_G0.205840.703
177_G214_L0.205580.702
172_A178_G0.204880.700
321_L324_I0.204480.698
26_S42_I0.204330.698
174_E177_G0.204120.697
237_K248_E0.204050.697
114_L328_I0.203720.696
161_P165_P0.203570.695
272_L276_F0.202540.692
209_E212_P0.202170.691
215_V219_F0.201920.690
128_D264_Q0.20190.690
22_L44_V0.201550.688
222_P254_I0.201320.688
88_L329_P0.20090.686
291_E294_L0.200580.685
147_L318_L0.198230.677
158_I220_T0.197110.673
141_K163_P0.197060.673
164_F223_V0.195610.668
183_L223_V0.195570.668
230_A245_G0.195230.667
26_S97_F0.194930.666
141_K164_F0.194320.664
124_M132_L0.193580.661
122_W136_I0.192620.658
167_I223_V0.192430.657
175_I178_G0.192260.657
207_S210_V0.190460.651
259_I314_L0.189540.647
145_K148_L0.189510.647
39_R134_D0.189460.647
49_L63_V0.188820.645
258_E313_R0.18830.643
82_Q265_R0.187950.642
319_L327_V0.18720.639
29_L99_I0.186630.637
39_R142_Y0.186510.637
79_Q82_Q0.186460.637
45_D312_E0.185310.633
140_I309_L0.184840.631
262_G307_F0.184630.631
230_A247_A0.184530.630
29_L120_L0.184370.630
78_T98_E0.183910.628
174_E180_K0.18380.628
63_V105_N0.183620.627
293_Y297_L0.183610.627
94_E125_A0.18360.627
148_L157_N0.183080.625
249_R261_N0.183010.625
127_A135_L0.182920.625
117_F310_G0.182820.624
184_R208_E0.182650.624
68_G71_F0.182250.622
133_M226_T0.181740.621
211_E215_V0.181540.620
177_G205_L0.181460.620
30_Q42_I0.180910.618
132_L135_L0.180020.615
167_I176_Y0.179990.615
204_R207_S0.179380.613
29_L315_V0.179050.612
161_P221_D0.17880.611
281_I290_D0.178620.610
123_E251_D0.178240.609
272_L297_L0.178020.608
84_Y102_C0.177930.608
143_I314_L0.176990.605
111_R257_G0.176190.602
252_L309_L0.175640.600
257_G323_N0.175590.600
223_V253_Y0.175570.600
297_L300_G0.175320.599
135_L138_E0.175280.599
22_L26_S0.174740.597
127_A264_Q0.17470.597
198_L205_L0.174620.596
122_W132_L0.174560.596
233_S236_Y0.174470.596
128_D303_P0.17440.596
131_D134_D0.174230.595
227_D246_V0.17370.593
124_M131_D0.173650.593
322_K326_D0.173620.593
271_E275_R0.173060.591
55_E82_Q0.172310.589
136_I140_I0.171670.586
48_I81_P0.171610.586
250_F262_G0.171520.586
204_R208_E0.170810.583
132_L250_F0.170760.583
266_E272_L0.170530.582
228_Y232_Q0.170480.582
89_L125_A0.169880.580
83_L102_C0.16960.579
162_K221_D0.168640.576
240_N246_V0.168610.576
134_D162_K0.168520.576
117_F313_R0.168410.575
169_Y207_S0.167730.573
45_D118_T0.167480.572
128_D248_E0.166910.570
255_P317_L0.166710.569
23_R26_S0.166420.568
36_F97_F0.166060.567
122_W135_L0.166060.567
53_T102_C0.165750.566
49_L77_L0.165670.566
215_V218_Y0.165480.565
237_K267_H0.165360.565
145_K157_N0.165310.565
227_D240_N0.165110.564
104_R310_G0.164970.563
123_E265_R0.164510.562
42_I93_L0.16370.559
176_Y214_L0.163240.558
87_R296_A0.162510.555
140_I164_F0.162390.555
231_E275_R0.161940.553
205_L209_E0.160620.549
25_R118_T0.160430.548
281_I285_E0.160270.547
26_S33_R0.160130.547
24_I315_V0.159880.546
130_D133_M0.159840.546
141_K160_L0.15920.544
169_Y173_F0.159110.543
33_R99_I0.15910.543
102_C121_E0.158630.542
233_S249_R0.158540.542
225_I253_Y0.157970.540
85_L89_L0.157750.539
278_E282_D0.157560.538
25_R315_V0.157310.537
159_D162_K0.156270.534
316_M319_L0.15550.531
122_W309_L0.154880.529
101_P116_E0.154850.529
28_I32_I0.154810.529
241_D245_G0.154640.528
315_V319_L0.154480.528
285_E290_D0.15430.527
58_A61_F0.154130.526
277_E281_I0.153870.526
205_L208_E0.153850.525
239_P242_D0.153730.525
214_L223_V0.153040.523
36_F39_R0.152540.521
204_R282_D0.152420.521
224_F250_F0.151670.518
309_L324_I0.151440.517
108_S111_R0.151380.517
104_R313_R0.151370.517
106_E112_R0.151320.517
85_L121_E0.151230.517
136_I252_L0.151220.517
23_R30_Q0.150610.514
87_R292_W0.150260.513
292_W295_E0.150230.513
208_E215_V0.150010.512
33_R46_T0.149870.512
71_F108_S0.149710.511
198_L201_E0.149350.510
267_H301_M0.148640.508
52_S62_S0.148590.508
316_M327_V0.148560.507
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
3nemA0.92241000.082
3m4pA0.93131000.089
2xgtA0.93431000.1
3i7fA0.93131000.101
1wydA0.91941000.104
4j15A0.93431000.107
4ex5A0.98211000.108
1e1oA0.98211000.108
3a74A0.98211000.11
3bjuA0.98211000.11

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