GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
tRNA-synt_2b - tRNA synthetase class II core domain (G H P S and T)
Pfam: PF00587 (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: 173
Sequences: 11008
Seq/Len: 63.63
HH_delta: 0.073 (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
30_S34_E1.25482.582
12_E136_E1.18672.442
12_E140_K1.18112.430
71_F86_L1.170692.409
135_K139_E1.170122.408
136_E140_K1.095362.254
8_F140_K1.060282.182
10_R21_E1.054752.170
85_K129_E1.035132.130
12_E16_K1.002822.063
126_E129_E0.9892.035
17_F136_E0.944191.943
30_S56_E0.935751.925
31_E34_E0.928191.910
22_V70_L0.907221.867
116_I126_E0.906061.864
88_Q113_E0.895371.842
3_N6_E0.882471.816
13_F112_D0.838761.726
125_E129_E0.826151.700
26_I93_F0.818071.683
3_N21_E0.810941.669
135_K148_I0.79911.644
7_R11_E0.796481.639
132_E136_E0.772231.589
14_V87_Y0.767611.579
11_E140_K0.762551.569
9_I137_I0.754791.553
91_T108_E0.731381.505
12_E17_F0.72911.500
150_L162_Y0.719091.480
35_K72_K0.714491.470
3_N7_R0.714311.470
118_C126_E0.713891.469
30_S58_C0.712781.467
26_I91_T0.685621.411
124_E128_E0.683181.406
77_S80_R0.672791.384
135_K146_Y0.665371.369
139_E146_Y0.656611.351
4_A8_F0.652471.342
136_E139_E0.652211.342
50_K54_D0.651561.341
3_N10_R0.644031.325
12_E137_I0.642421.322
28_I66_G0.642061.321
22_V86_L0.626351.289
48_K58_C0.616661.269
9_I112_D0.614551.264
22_V67_I0.610661.256
85_K116_I0.609561.254
160_A163_E0.608961.253
127_F162_Y0.607381.250
142_G145_P0.591151.216
34_E40_D0.589861.214
6_E10_R0.588461.211
60_R90_G0.583581.201
16_K140_K0.581871.197
85_K126_E0.581411.196
11_E16_K0.579211.192
6_E89_I0.572861.179
6_E23_D0.570111.173
7_R10_R0.566331.165
50_K56_E0.56421.161
132_E135_K0.552941.138
19_F85_K0.549381.130
24_T66_G0.546471.124
17_F133_L0.540071.111
94_R109_F0.53821.107
19_F133_L0.537851.107
46_M58_C0.534261.099
3_N14_V0.533931.099
102_G105_R0.531531.094
39_W58_C0.531031.093
48_K56_E0.529831.090
21_E87_Y0.528331.087
151_S163_E0.523081.076
124_E161_K0.521951.074
63_S113_E0.514571.059
28_I69_S0.5121.053
128_E132_E0.505421.040
9_I13_F0.502731.034
20_Q84_L0.498611.026
19_F114_M0.496491.022
16_K136_E0.489831.008
26_I108_E0.484080.996
63_S90_G0.468530.964
10_R14_V0.467410.962
67_I88_Q0.467020.961
71_F117_F0.464710.956
10_R87_Y0.462710.952
8_F12_E0.462440.951
63_S88_Q0.459460.945
29_P32_V0.456270.939
13_F87_Y0.4540.934
23_D91_T0.452480.931
153_S162_Y0.451030.928
91_T110_T0.450260.926
77_S81_D0.449090.924
153_S156_L0.447810.921
5_L141_L0.444850.915
55_E95_N0.442990.911
10_R89_I0.441220.908
71_F84_L0.439620.905
131_L148_I0.439570.904
96_E105_R0.439090.903
155_E160_A0.435740.897
19_F116_I0.431910.889
129_E133_L0.431750.888
89_I112_D0.431520.888
59_L93_F0.430670.886
116_I133_L0.425660.876
129_E132_E0.425410.875
24_T70_L0.424880.874
63_S92_C0.421430.867
71_F115_H0.42120.867
32_V69_S0.420980.866
8_F11_E0.420390.865
60_R63_S0.419690.864
47_F95_N0.416290.857
32_V72_K0.414950.854
125_E128_E0.411250.846
27_L57_Y0.410280.844
36_S45_E0.408160.840
27_L49_V0.407170.838
8_F141_L0.40710.838
116_I130_L0.40680.837
61_P65_P0.405650.835
30_S48_K0.403610.830
69_S73_N0.403460.830
33_W46_M0.40280.829
114_M133_L0.401280.826
128_E131_L0.400850.825
17_F129_E0.399850.823
51_D56_E0.393580.810
7_R14_V0.393420.809
131_L135_K0.390170.803
14_V21_E0.38790.798
131_L150_L0.387490.797
68_Y117_F0.386280.795
134_Y138_L0.385120.792
96_E109_F0.383640.789
4_A7_R0.379830.782
31_E72_K0.37870.779
103_L106_L0.378160.778
22_V88_Q0.377190.776
23_D110_T0.376910.775
6_E110_T0.37680.775
51_D55_E0.376190.774
43_S48_K0.373770.769
62_T65_P0.369770.761
17_F85_K0.369350.760
81_D84_L0.358380.737
133_L136_E0.353290.727
34_E39_W0.34230.704
29_P55_E0.341290.702
131_L162_Y0.341110.702
30_S39_W0.338190.696
41_N45_E0.332220.684
27_L93_F0.331720.683
96_E107_R0.330840.681
69_S72_K0.329160.677
68_Y115_H0.327510.674
24_T88_Q0.327330.673
119_T124_E0.325050.669
26_I59_L0.324890.668
114_M130_L0.324820.668
86_L115_H0.323270.665
17_F132_E0.322390.663
116_I129_E0.321270.661
67_I86_L0.318950.656
157_G161_K0.318480.655
156_L159_Y0.317770.654
11_E14_V0.315480.649
43_S58_C0.313640.645
64_E113_E0.313270.645
74_E81_D0.312490.643
156_L160_A0.305640.629
37_G65_P0.302660.623
124_E127_F0.301060.619
101_R104_F0.299290.616
124_E162_Y0.297090.611
152_S155_E0.294750.606
46_M61_P0.294490.606
159_Y162_Y0.293960.605
72_K75_I0.293490.604
139_E148_I0.293080.603
89_I110_T0.292660.602
109_F113_E0.289380.595
27_L59_L0.287590.592
92_C111_M0.287020.591
26_I90_G0.286470.589
70_L74_E0.286290.589
50_K57_Y0.284750.586
67_I115_H0.284260.585
127_F131_L0.284020.584
105_R109_F0.283440.583
76_R84_L0.281830.580
31_E35_K0.279760.576
155_E159_Y0.27810.572
13_F114_M0.277850.572
150_L156_L0.275840.568
36_S42_F0.273910.564
13_F137_I0.273290.562
26_I60_R0.270810.557
42_F45_E0.270090.556
119_T123_S0.269580.555
74_E86_L0.2690.553
30_S43_S0.268710.553
93_F108_E0.266270.548
76_R81_D0.265810.547
159_Y163_E0.264880.545
68_Y72_K0.263940.543
19_F126_E0.263890.543
63_S66_G0.263750.543
49_V58_C0.262150.539
120_P126_E0.260190.535
138_L146_Y0.258370.532
42_F61_P0.257680.530
23_D26_I0.257270.529
4_A11_E0.256070.527
23_D89_I0.255730.526
138_L143_L0.254880.524
12_E133_L0.25460.524
8_F137_I0.253910.522
64_E111_M0.253050.521
119_T125_E0.252910.520
67_I113_E0.251810.518
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
3vbbA0.98271000.073
3lssA0.97691000.083
3errA0.96531000.083
1wleA0.982799.90.097
1sesA0.965399.90.109
3qneA0.982799.90.11
2dq0A0.965399.90.116
2dq3A0.965399.90.127
1qf6A0.953899.90.145
1nyrA0.982799.90.152

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