GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
tRNA-synt_1b - tRNA synthetases class I (W and Y)
Pfam: PF00579 (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: 292
Sequences: 4093
Seq/Len: 14.02
HH_delta: 0.121 (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
213_S216_E0.863064.126
7_R38_K0.666813.188
277_G281_K0.640863.064
38_K85_E0.601382.875
272_G277_G0.533572.551
147_L151_D0.510242.439
97_E100_W0.504142.410
40_I85_E0.503972.409
263_E266_L0.481192.300
9_Y42_L0.475052.271
87_F91_D0.46412.219
268_D284_A0.463022.214
263_E267_A0.459712.198
14_P48_A0.458032.190
163_I184_G0.457572.188
218_R222_K0.443532.120
17_D214_P0.437462.091
108_L135_F0.434962.079
170_A182_P0.425572.035
7_R40_I0.411781.969
276_P279_L0.408441.953
212_D220_K0.407261.947
9_Y44_A0.401481.919
229_D239_R0.393151.880
264_E268_D0.391481.872
285_E289_E0.38991.864
269_Y282_A0.386971.850
279_L282_A0.383591.834
160_R184_G0.378051.807
112_N135_F0.376361.799
191_P234_R0.373861.787
233_P251_E0.37051.771
146_L170_A0.366481.752
63_S67_Y0.349251.670
272_G280_K0.348181.665
284_A288_N0.347641.662
266_L270_V0.345741.653
265_L269_Y0.343041.640
79_L84_T0.340921.630
281_K285_E0.338111.616
80_D83_K0.337021.611
171_R181_K0.334651.600
87_F148_L0.331991.587
212_D216_E0.330741.581
10_T25_P0.32711.564
160_R186_T0.322561.542
218_R284_A0.317521.518
249_R253_F0.317161.516
45_D90_S0.316411.513
132_L136_S0.31641.513
252_A256_N0.316051.511
222_K281_K0.315471.508
81_P84_T0.313321.498
272_G278_D0.305491.460
251_E255_G0.304611.456
244_P248_E0.303771.452
12_I26_I0.299191.430
46_L93_P0.297311.421
268_D280_K0.297291.421
150_A174_N0.296441.417
54_S60_K0.292791.400
142_A166_A0.292341.398
233_P237_K0.292031.396
221_I287_L0.290991.391
146_L173_F0.290541.389
28_K31_W0.287671.375
209_F212_D0.286881.372
149_K174_N0.286841.371
217_I288_N0.281561.346
286_A289_E0.281351.345
14_P43_I0.279481.336
111_L132_L0.278511.331
152_L185_L0.277081.325
278_D281_K0.276611.322
214_P288_N0.275831.319
248_E251_E0.275811.319
167_R182_P0.2751.315
285_E288_N0.27471.313
267_A270_V0.273221.306
146_L150_A0.27251.303
35_A83_K0.271161.296
108_L172_K0.27011.291
278_D282_A0.269371.288
27_M31_W0.269161.287
189_L192_G0.266891.276
12_I18_L0.266491.274
267_A271_S0.265511.269
243_S246_L0.265251.268
121_K125_K0.265051.267
12_I25_P0.264031.262
6_F37_F0.2641.262
93_P96_M0.26231.254
8_V32_L0.262151.253
64_R68_N0.260291.244
63_S66_E0.255841.223
33_Q84_T0.254451.216
109_F165_L0.252271.206
10_T154_P0.250321.197
66_E69_I0.248711.189
40_I87_F0.247441.183
32_L185_L0.245111.172
8_V29_L0.242631.160
43_I69_I0.241181.153
27_M290_F0.240551.150
113_R116_R0.23881.142
60_K63_S0.236341.130
99_W103_S0.235731.127
59_R62_R0.234611.122
264_E288_N0.232031.109
142_A165_L0.230821.104
220_K224_A0.230671.103
12_I22_H0.229461.097
65_A88_R0.22881.094
264_E267_A0.227381.087
256_N268_D0.227261.086
49_L64_R0.226011.081
45_D91_D0.225361.077
12_I74_I0.22471.074
90_S94_E0.224561.074
62_R66_E0.224561.074
29_L41_I0.224021.071
262_L266_L0.223561.069
192_G196_Q0.222731.065
9_Y150_A0.221231.058
33_Q80_D0.220281.053
108_L112_N0.219011.047
242_I269_Y0.218131.043
229_D232_N0.216641.036
246_L249_R0.215471.030
9_Y40_I0.215231.029
95_H148_L0.214641.026
212_D217_I0.214091.024
132_L139_L0.213981.023
54_S59_R0.21381.022
268_D272_G0.212721.017
18_L74_I0.212321.015
210_L290_F0.211571.011
250_L283_L0.210981.009
269_Y272_G0.209881.003
242_I265_L0.209361.001
42_L87_F0.209241.000
195_G241_F0.207440.992
215_E218_R0.206780.989
282_A286_A0.205620.983
31_W35_A0.204730.979
242_I246_L0.204410.977
283_L286_A0.204290.977
146_L182_P0.202290.967
25_P187_S0.201120.962
280_K287_L0.199250.953
196_Q203_D0.199020.951
93_P97_E0.198850.951
280_K284_A0.19840.949
41_I79_L0.197760.945
59_R63_S0.197140.942
218_R288_N0.197040.942
235_L238_G0.196370.939
252_A255_G0.195860.936
249_R252_A0.195290.934
171_R175_Y0.194420.929
45_D88_R0.194380.929
109_F113_R0.194050.928
103_S136_S0.193940.927
265_L268_D0.193390.925
256_N264_E0.19280.922
240_P270_V0.19260.921
29_L32_L0.19150.916
282_A285_E0.191150.914
28_K187_S0.190070.909
146_L174_N0.189650.907
107_R110_S0.189540.906
279_L283_L0.189130.904
218_R285_E0.189060.904
32_L152_L0.188430.901
26_I77_L0.187810.898
220_K271_S0.187790.898
281_K284_A0.187440.896
250_L253_F0.18710.894
257_D264_E0.186970.894
74_I86_I0.186350.891
96_M100_W0.184950.884
98_L101_F0.184280.881
42_L148_L0.183510.877
189_L193_L0.183220.876
88_R91_D0.182510.873
12_I16_G0.18050.863
264_E284_A0.179520.858
235_L243_S0.17950.858
246_L265_L0.178630.854
170_A174_N0.178490.853
231_E235_L0.177940.851
102_L139_L0.176940.846
247_I266_L0.176880.846
228_P231_E0.176660.845
113_R168_D0.176040.842
110_S129_G0.176030.842
22_H27_M0.17590.841
60_K64_R0.175430.839
268_D281_K0.174830.836
149_K176_K0.17480.836
46_L96_M0.174170.833
53_P58_E0.174080.832
98_L140_L0.173980.832
18_L26_I0.173960.832
62_R70_N0.172590.825
247_I265_L0.172510.825
22_H25_P0.172360.824
191_P203_D0.172110.823
208_I221_I0.17130.819
18_L68_N0.171270.819
95_H147_L0.171110.818
10_T22_H0.170690.816
6_F151_D0.170630.816
217_I291_L0.17030.814
103_S132_L0.169650.811
286_A290_F0.169180.809
71_D88_R0.169090.808
139_L169_L0.168960.808
237_K251_E0.168650.806
106_A169_L0.168610.806
284_A287_L0.167010.798
99_W136_S0.166820.798
76_A86_I0.166530.796
42_L144_D0.166490.796
6_F152_L0.165950.793
172_K176_K0.165820.793
275_H278_D0.164860.788
214_P218_R0.164380.786
233_P254_H0.164290.785
93_P140_L0.164060.784
204_P207_A0.163810.783
190_L193_L0.16330.781
93_P143_A0.163290.781
78_G81_P0.162980.779
145_I166_A0.162920.779
58_E61_I0.16290.779
168_D171_R0.162880.779
110_S113_R0.16260.777
41_I75_L0.162040.775
199_M202_S0.161760.773
247_I251_E0.161730.773
231_E234_R0.161540.772
256_N265_L0.161440.772
108_L117_F0.160650.768
239_R266_L0.160470.767
100_W104_D0.159380.762
192_G195_G0.158210.756
216_E219_K0.156740.749
85_E88_R0.156290.747
221_I284_A0.155880.745
250_L254_H0.155260.742
253_F290_F0.155050.741
102_L140_L0.154630.739
215_E286_A0.154130.737
239_R270_V0.154090.737
22_H26_I0.154040.736
253_F257_D0.153510.734
198_K202_S0.152690.730
240_P269_Y0.152450.729
19_H210_L0.152170.727
142_A169_L0.152030.727
137_Y144_D0.151650.725
248_E252_A0.151430.724
194_D205_N0.150730.721
106_A109_F0.150420.719
102_L169_L0.150050.717
28_K154_P0.149860.716
240_P243_S0.149480.715
234_R243_S0.149320.714
237_K244_P0.149310.714
254_H286_A0.148810.711
115_L119_D0.148790.711
29_L39_V0.148640.711
268_D271_S0.148560.710
104_D133_G0.148380.709
209_F220_K0.148080.708
78_G220_K0.148030.708
7_R149_K0.147830.707
175_Y181_K0.147470.705
103_S131_S0.147280.704
215_E219_K0.147120.703
38_K83_K0.146910.702
10_T29_L0.146280.699
40_I148_L0.146240.699
243_S247_I0.146080.698
269_Y276_P0.145970.698
59_R267_A0.145970.698
243_S269_Y0.145940.698
11_G19_H0.145780.697
7_R85_E0.14560.696
256_N262_L0.145380.695
233_P266_L0.144860.693
69_I86_I0.143490.686
219_K223_K0.143350.685
174_N182_P0.14320.685
76_A84_T0.143030.684
87_F92_W0.142630.682
254_H257_D0.142040.679
240_P266_L0.141890.678
250_L265_L0.141840.678
136_S139_L0.141120.675
10_T41_I0.14110.675
146_L169_L0.141030.674
137_Y140_L0.139850.669
164_E167_R0.139560.667
192_G205_N0.138940.664
11_G42_L0.138710.663
29_L74_I0.138070.660
23_L27_M0.137980.660
233_P238_G0.137940.659
203_D207_A0.137940.659
95_H100_W0.137910.659
216_E271_S0.137490.657
222_K277_G0.136640.653
110_S115_L0.136610.653
132_L135_F0.135860.650
13_D51_G0.135670.649
251_E254_H0.135530.648
108_L173_F0.135350.647
117_F164_E0.134560.643
105_V169_L0.134150.641
158_D198_K0.133990.641
238_G243_S0.133960.640
283_L287_L0.133240.637
269_Y279_L0.133120.636
288_N291_L0.13250.633
241_F269_Y0.132310.633
110_S131_S0.132280.632
125_K128_E0.132150.632
170_A181_K0.132060.631
15_T53_P0.131940.631
20_L224_A0.131740.630
173_F182_P0.131450.628
279_L287_L0.131310.628
71_D211_D0.130950.626
18_L71_D0.130930.626
122_K126_N0.130710.625
31_W36_G0.130550.624
10_T280_K0.130390.623
42_L150_A0.130020.622
257_D263_E0.129070.617
25_P154_P0.128960.617
67_Y70_N0.128830.616
17_D67_Y0.128760.616
20_L210_L0.128610.615
138_P142_A0.128030.612
268_D282_A0.127970.612
37_F152_L0.127690.610
268_D277_G0.127370.609
243_S276_P0.127280.608
266_L269_Y0.127010.607
161_G164_E0.126680.606
119_D130_I0.126650.605
194_D228_P0.126530.605
107_R131_S0.126350.604
26_I75_L0.125920.602
98_L136_S0.125860.602
109_F112_N0.125510.600
229_D270_V0.125170.598
146_L149_K0.124790.597
93_P98_L0.124590.596
119_D138_P0.124560.595
241_F266_L0.124550.595
68_N74_I0.124540.595
210_L291_L0.124360.595
253_F265_L0.124340.594
287_L291_L0.124290.594
233_P248_E0.124040.593
27_M241_F0.123950.593
109_F115_L0.123670.591
36_G59_R0.123540.591
12_I29_L0.123180.589
236_L266_L0.123010.588
10_T140_L0.123010.588
232_N242_I0.122820.587
249_R255_G0.122820.587
137_Y141_Q0.122790.587
15_T207_A0.122740.587
170_A173_F0.12270.587
47_H140_L0.122570.586
154_P187_S0.122160.584
96_M99_W0.122150.584
265_L279_L0.122140.584
253_F286_A0.121830.582
99_W132_L0.12180.582
9_Y145_I0.121430.581
24_V190_L0.121390.580
193_L223_K0.121290.580
60_K66_E0.121290.580
114_M161_G0.121180.579
147_L150_A0.12090.578
220_K270_V0.120550.576
105_V143_A0.120270.575
157_I188_P0.119830.573
193_L230_R0.119670.572
44_A47_H0.119570.572
253_F258_D0.119570.572
168_D172_K0.11950.571
150_A173_F0.119310.570
116_R121_K0.119210.570
167_R183_A0.118980.569
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
2cyaA0.97951000.121
2cycA0.98631000.124
3prhA0.94521000.124
3tzlA0.93151000.125
3sz3A0.95211000.128
3vgjA0.97951000.131
3n9iA0.94861000.138
2el7A0.93841000.139
3p0jA0.96921000.143
1yi8B0.96581000.147

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