GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
tRNA-synt_1c - tRNA synthetases class I (E and Q) catalytic domain
Pfam: PF00749 (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: 314
Sequences: 4912
Seq/Len: 15.64
HH_delta: 0.018 (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
87_K91_K1.104344.375
86_E90_D1.029744.079
159_R165_R0.956813.790
99_C126_C0.887453.516
50_P54_D0.887113.514
54_D58_E0.768713.045
53_Y73_Y0.705322.794
98_F144_A0.664772.633
115_G120_P0.6572.603
196_H225_W0.621642.463
83_E87_K0.584922.317
80_I197_L0.581362.303
122_Y126_C0.568782.253
114_A118_H0.566292.243
202_H229_P0.544292.156
220_Y230_Y0.542112.148
135_R139_A0.513342.034
73_Y76_D0.50612.005
140_K143_P0.500011.981
86_E132_E0.483521.915
79_E83_E0.481791.909
157_A167_I0.478951.897
57_L61_R0.474021.878
133_E138_L0.473981.878
163_R207_E0.468081.854
89_I94_A0.467491.852
38_L57_L0.466031.846
79_E180_R0.462941.834
85_A146_I0.461651.829
128_E133_E0.458251.815
19_A63_L0.455161.803
61_R66_E0.455161.803
100_S103_E0.450631.785
156_I170_P0.449371.780
13_Y55_A0.449111.779
148_L222_A0.441841.750
221_E227_P0.43981.742
61_R67_W0.438731.738
157_A165_R0.438351.736
217_I227_P0.438331.736
94_A146_I0.436461.729
95_Y175_D0.435241.724
85_A179_R0.431071.708
58_E61_R0.427061.692
87_K90_D0.426171.688
110_A114_A0.425561.686
106_A110_A0.416871.651
80_I84_A0.414891.644
89_I146_I0.414881.644
28_F32_Y0.411621.631
93_K222_A0.410281.625
84_A197_L0.405631.607
99_C107_A0.399561.583
148_L218_L0.399441.582
14_L18_H0.396681.571
41_E191_V0.391921.553
80_I83_E0.388731.540
188_H216_Q0.386341.530
84_A223_L0.381791.512
134_M138_L0.375291.487
166_I210_L0.367791.457
30_R68_D0.364461.444
6_F18_H0.363731.441
158_F210_L0.363581.440
107_A123_P0.361611.432
81_Y194_D0.358971.422
155_P167_I0.356181.411
124_G127_R0.355631.409
130_T133_E0.354231.403
162_V231_A0.352861.398
83_E86_E0.352771.397
89_I96_P0.351781.394
91_K224_G0.347431.376
251_K255_L0.347241.376
82_Q86_E0.34371.362
62_W259_R0.342991.359
28_F202_H0.339631.345
96_P146_I0.339551.345
98_F138_L0.337261.336
161_L229_P0.335521.329
150_V218_L0.335261.328
159_R229_P0.329851.307
4_T25_N0.329461.305
57_L71_P0.327521.297
257_D260_E0.327491.297
82_Q179_R0.326661.294
209_L212_S0.324591.286
238_N248_K0.324021.284
49_R52_F0.323911.283
136_A140_K0.323491.281
79_E82_Q0.322971.279
103_E123_P0.321931.275
155_P169_D0.316591.254
96_P144_A0.315361.249
188_H212_S0.314441.246
132_E136_A0.314311.245
103_E125_T0.311971.236
129_L134_M0.310111.228
54_D57_L0.30871.223
26_Y30_R0.304811.207
77_R80_I0.302921.200
141_G168_F0.301571.195
35_K68_D0.299031.185
153_E171_S0.297251.178
133_E139_A0.296161.173
129_L139_A0.296131.173
58_E256_G0.295871.172
217_I221_E0.294111.165
37_I70_G0.290521.151
94_A178_I0.285991.133
84_A193_V0.282591.119
85_A89_I0.2821.117
192_V219_L0.281831.116
74_Q190_A0.279331.107
27_L273_A0.277621.100
23_L65_L0.277261.098
244_L250_A0.276151.094
96_P138_L0.274051.086
20_R237_L0.273561.084
87_K224_G0.272041.078
78_L184_Y0.271191.074
133_E136_A0.26911.066
99_C125_T0.269071.066
170_P179_R0.267991.062
176_F215_R0.267031.058
88_L93_K0.265641.052
98_F143_P0.263171.043
86_E89_I0.262791.041
103_E107_A0.262011.038
126_C129_L0.260651.033
21_T25_N0.259771.029
37_I200_I0.25941.028
258_Y268_T0.25611.015
204_I231_A0.254831.009
122_Y125_T0.253871.006
135_R138_L0.251980.998
192_V220_Y0.250170.991
148_L178_I0.249310.988
209_L216_Q0.249260.987
84_A225_W0.248910.986
58_E62_W0.248630.985
97_C126_C0.247460.980
106_A109_E0.245370.972
97_C104_L0.243180.963
48_C51_E0.243170.963
37_I72_Y0.242660.961
196_H226_P0.241870.958
83_E90_D0.24120.956
21_T206_G0.240490.953
6_F56_I0.238720.946
53_Y57_L0.235260.932
115_G118_H0.233410.925
158_F217_I0.233370.924
257_D261_W0.232880.923
48_C52_F0.23230.920
242_K248_K0.231130.916
84_A87_K0.230780.914
51_E54_D0.230680.914
28_F204_I0.230620.914
256_G260_E0.230210.912
55_A58_E0.228390.905
107_A125_T0.227380.901
161_L231_A0.226250.896
238_N242_K0.225450.893
96_P134_M0.2250.891
85_A94_A0.223920.887
196_H220_Y0.223540.886
115_G152_M0.223420.885
89_I130_T0.223070.884
72_Y198_M0.222560.882
36_F65_L0.222060.880
156_I217_I0.221090.876
50_P53_Y0.22090.875
136_A139_A0.219910.871
103_E126_C0.219050.868
103_E106_A0.218650.866
188_H209_L0.217840.863
45_P48_C0.216190.856
67_W70_G0.215490.854
81_Y190_A0.213930.847
95_Y149_K0.213880.847
251_K257_D0.213270.845
221_E228_P0.213050.844
30_R66_E0.212970.844
91_K222_A0.212950.844
218_L222_A0.21260.842
45_P184_Y0.211960.840
40_I53_Y0.211710.839
58_E259_R0.211660.838
169_D172_D0.210180.833
107_A114_A0.209420.830
220_Y227_P0.209280.829
60_L65_L0.208610.826
193_V223_L0.208430.826
90_D93_K0.207960.824
189_F192_V0.207820.823
123_P126_C0.206470.818
72_Y77_R0.206210.817
57_L67_W0.205610.815
53_Y175_D0.204810.811
45_P78_L0.204640.811
69_Y199_G0.204260.809
264_P267_A0.203550.806
99_C122_Y0.202420.802
78_L82_Q0.202070.800
188_H191_V0.201770.799
148_L219_L0.201760.799
26_Y66_E0.201490.798
24_L233_L0.201220.797
74_Q194_D0.201190.797
99_C104_L0.199550.791
101_R105_K0.199210.789
109_E113_G0.198560.787
13_Y256_G0.197610.783
98_F142_G0.196540.779
6_F22_A0.196180.777
72_Y80_I0.196010.776
128_E139_A0.195090.773
45_P75_S0.195010.773
37_I69_Y0.195010.773
134_M142_G0.194030.769
135_R183_G0.193790.768
240_D248_K0.193070.765
35_K70_G0.192640.763
130_T134_M0.192440.762
127_R149_K0.191870.760
220_Y228_P0.19120.757
80_I87_K0.190910.756
105_K109_E0.190130.753
4_T274_R0.189440.750
132_E135_R0.188630.747
251_K261_W0.188330.746
156_I218_L0.188160.745
22_A60_L0.187690.744
140_K168_F0.187360.742
128_E138_L0.186990.741
210_L233_L0.186220.738
6_F14_L0.183490.727
128_E149_K0.183130.725
121_R124_G0.183060.725
69_Y72_Y0.182560.723
150_V173_L0.181940.721
124_G149_K0.180410.715
55_A59_D0.180020.713
77_R81_Y0.179340.710
110_A113_G0.179250.710
4_T28_F0.178850.709
59_D256_G0.178410.707
250_A257_D0.178250.706
87_K225_W0.178070.705
157_A212_S0.177980.705
4_T36_F0.177530.703
26_Y36_F0.177070.701
168_F172_D0.176030.697
161_L202_H0.175650.696
220_Y225_W0.175580.696
170_P218_L0.175130.694
99_C139_A0.173990.689
119_R172_D0.173970.689
139_A143_P0.172630.684
150_V176_F0.17260.684
26_Y65_L0.172580.684
46_E49_R0.171640.680
62_W256_G0.171440.679
148_L176_F0.171110.678
34_G201_T0.169330.671
60_L67_W0.168710.668
98_F140_K0.168640.668
212_S215_R0.167810.665
158_F214_P0.167550.664
211_S214_P0.167330.663
98_F103_E0.167160.662
100_S104_L0.166160.658
136_A143_P0.165840.657
163_R210_L0.165310.655
153_E156_I0.164920.653
21_T24_L0.164540.652
129_L133_E0.164540.652
185_P190_A0.164470.652
110_A118_H0.162720.645
30_R35_K0.162630.644
141_G144_A0.162620.644
21_T204_I0.162370.643
93_K96_P0.162240.643
5_R10_P0.161130.638
187_Y246_K0.160730.637
151_P175_D0.16040.635
5_R8_P0.160010.634
188_H192_V0.15960.632
13_Y51_E0.158970.630
37_I71_P0.158710.629
35_K69_Y0.158710.629
82_Q132_E0.158350.627
75_S184_Y0.15680.621
74_Q81_Y0.15540.616
213_T230_Y0.154980.614
19_A62_W0.154840.613
190_A194_D0.154230.611
8_P15_H0.154140.611
22_A67_W0.154010.610
23_L27_L0.153830.609
25_N28_F0.15320.607
163_R219_L0.152960.606
213_T217_I0.152530.604
143_P181_S0.152040.602
22_A65_L0.15190.602
39_R42_D0.151880.602
149_K152_M0.151770.601
180_R208_D0.151740.601
168_F214_P0.151370.600
14_L59_D0.151230.599
100_S142_G0.151210.599
187_Y191_V0.151040.598
61_R70_G0.150920.598
110_A153_E0.15090.598
263_D268_T0.150460.596
153_E170_P0.149710.593
138_L143_P0.14970.593
59_D270_N0.149460.592
72_Y197_L0.149310.591
56_I60_L0.149190.591
18_H268_T0.149160.591
99_C103_E0.149010.590
266_E269_L0.148930.590
212_S216_Q0.148880.590
32_Y202_H0.148810.590
189_F193_V0.148780.589
102_E106_A0.14860.589
18_H59_D0.148320.588
87_K93_K0.147950.586
78_L81_Y0.147870.586
4_T204_I0.147870.586
62_W260_E0.147570.585
138_L142_G0.147310.584
187_Y190_A0.14670.581
191_V204_I0.14610.579
90_D132_E0.146030.578
7_A10_P0.145740.577
85_A178_I0.145310.576
107_A110_A0.14530.576
98_F129_L0.144980.574
58_E270_N0.144660.573
219_L223_L0.144480.572
140_K144_A0.144420.572
202_H205_R0.144370.572
224_G228_P0.143940.570
193_V225_W0.143770.570
41_E198_M0.143680.569
213_T231_A0.143430.568
82_Q185_P0.143150.567
87_K223_L0.143040.567
84_A192_V0.142560.565
118_H121_R0.142480.564
20_R236_I0.142320.564
47_R51_E0.14230.564
63_L267_A0.14230.564
129_L144_A0.141780.562
128_E132_E0.141680.561
115_G119_R0.141630.561
40_I56_I0.140070.555
149_K175_D0.13950.553
35_K72_Y0.138970.551
245_S248_K0.138950.550
193_V197_L0.138450.548
238_N249_G0.138130.547
22_A36_F0.137840.546
14_L60_L0.137750.546
33_G224_G0.137620.545
44_D47_R0.137610.545
45_P73_Y0.137170.543
168_F210_L0.137010.543
84_A189_F0.136990.543
99_C114_A0.136260.540
130_T136_A0.135420.536
53_Y76_D0.135240.536
195_D200_I0.135220.536
121_R125_T0.134990.535
54_D61_R0.134450.533
158_F165_R0.134330.532
11_T247_R0.134160.531
18_H208_D0.133890.530
27_L65_L0.133780.530
44_D74_Q0.133680.530
102_E105_K0.13360.529
84_A219_L0.133540.529
38_L67_W0.13350.529
19_A60_L0.133390.528
221_E226_P0.133220.528
13_Y52_F0.13310.527
219_L228_P0.133050.527
40_I71_P0.132950.527
179_R184_Y0.132930.527
244_L251_K0.132630.525
55_A256_G0.132460.525
136_A141_G0.132090.523
121_R173_L0.132090.523
28_F161_L0.132070.523
193_V224_G0.132030.523
249_G267_A0.131840.522
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
4griA0.98731000.018
4g6zA0.98091000.042
2ja2A0.98091000.048
2cfoA0.98731000.049
1j09A0.96821000.062
3afhA0.92681000.095
3al0C0.92681000.113
2o5rA0.98411000.115
4h3sA0.98091000.181
1qtqA0.9651000.192

Page generated in 0.0455 seconds.