GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
tRNA-synt_1_2 - Leucyl-tRNA synthetase Domain 2
Pfam: PF13603 (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: 185
Sequences: 4502
Seq/Len: 24.34
HH_delta: 0.088 (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
171_L179_K1.451933.930
168_F183_K1.215843.291
172_S175_E1.178283.190
167_E183_K1.098482.974
17_K97_K1.087592.944
88_Y97_K0.968382.621
11_E24_E0.916222.480
96_K137_K0.874762.368
13_D24_E0.856222.318
84_F88_Y0.827982.241
13_D22_K0.811982.198
179_K182_K0.791422.142
45_H108_M0.749252.028
36_V98_I0.732941.984
23_I114_A0.716021.938
46_P81_E0.691111.871
15_K22_K0.687391.861
129_A134_L0.653521.769
40_A117_G0.640221.733
39_I89_A0.633731.716
105_Y128_F0.632381.712
23_I39_I0.632111.711
39_I114_A0.622061.684
101_Y128_F0.616911.670
171_L176_A0.616541.669
174_K177_R0.612241.657
10_A181_I0.577011.562
105_Y117_G0.573011.551
93_L183_K0.572481.550
40_A103_A0.559651.515
173_S177_R0.55791.510
90_I97_K0.556441.506
178_E182_K0.550081.489
124_R127_E0.547631.482
123_E127_E0.536291.452
46_P108_M0.530421.436
91_H94_T0.528211.430
126_F130_K0.527181.427
121_H139_V0.527071.427
61_F65_C0.519971.408
12_I33_I0.519721.407
138_Q163_I0.513411.390
85_T102_V0.513061.389
37_T137_K0.504171.365
12_I184_L0.495291.341
14_F36_V0.490761.329
38_F101_Y0.48861.323
166_G169_N0.485261.314
55_N59_Q0.474911.286
63_E67_K0.467181.265
30_P177_R0.464921.259
171_L175_E0.448931.215
120_A136_I0.448821.215
168_F180_I0.447671.212
42_S45_H0.447591.212
41_L100_I0.443221.200
141_K161_I0.440711.193
15_K90_I0.439291.189
54_N57_E0.437061.183
182_K185_E0.437011.183
56_P60_E0.436771.182
25_V39_I0.432751.171
41_L114_A0.423551.147
106_V115_V0.422781.144
46_P55_N0.422171.143
57_E60_E0.418081.132
41_L102_V0.414481.122
168_F179_K0.413711.120
12_I25_V0.412041.115
64_K67_K0.410021.110
23_I100_I0.405431.098
89_A100_I0.405141.097
161_I172_S0.399761.082
60_E64_K0.39311.064
130_K136_I0.392821.063
36_V115_V0.388151.051
179_K183_K0.385611.044
123_E126_F0.384371.041
175_E178_E0.37761.022
52_A55_N0.375431.016
64_K81_E0.373251.010
164_N169_N0.370721.004
69_K72_E0.368870.999
25_V114_A0.366920.993
17_K88_Y0.362320.981
60_E63_E0.362040.980
49_K62_I0.360890.977
23_I41_L0.35970.974
163_I169_N0.356210.964
103_A128_F0.355440.962
17_K90_I0.354630.960
12_I27_T0.352830.955
126_F136_I0.352070.953
34_F167_E0.347530.941
43_P102_V0.346070.937
21_E50_K0.343110.929
63_E66_K0.342650.928
161_I175_E0.335550.908
39_I98_I0.333970.904
46_P79_E0.333390.903
33_I184_L0.331270.897
162_L173_S0.328740.890
42_S106_V0.328070.888
58_L83_V0.325120.880
36_V116_M0.323430.876
38_F129_A0.322620.873
40_A128_F0.320960.869
30_P180_I0.314280.851
56_P59_Q0.313320.848
165_S169_N0.311940.844
37_T134_L0.310730.841
175_E179_K0.309520.838
59_Q63_E0.30690.831
85_T132_Y0.306510.830
30_P181_I0.3040.823
51_L87_L0.303230.821
90_I167_E0.30190.817
58_L62_I0.301360.816
71_S77_F0.299260.810
100_I114_A0.294950.798
138_Q141_K0.293530.795
11_E64_K0.293370.794
84_F87_L0.292440.792
42_S104_N0.289240.783
89_A98_I0.288420.781
141_K163_I0.286990.777
93_L180_I0.286650.776
37_T135_P0.286120.775
162_L168_F0.285450.773
127_E131_K0.285230.772
59_Q79_E0.2850.772
90_I95_G0.283480.767
71_S76_D0.280880.760
58_L61_F0.279960.758
117_G129_A0.279660.757
117_G128_F0.279630.757
62_I66_K0.27790.752
80_K83_V0.276490.748
12_I30_P0.274920.744
41_L48_V0.272820.739
105_Y110_Y0.272140.737
140_I160_G0.27190.736
46_P76_D0.271760.736
180_I184_L0.270870.733
37_T96_K0.270660.733
68_I71_S0.270090.731
93_L184_L0.269540.730
38_F117_G0.268550.727
140_I162_L0.266570.722
48_V76_D0.265710.719
96_K135_P0.265570.719
128_F132_Y0.261750.709
176_A180_I0.259730.703
35_G162_L0.25830.699
120_A139_V0.257510.697
16_I19_S0.254920.690
61_F81_E0.254470.689
37_T129_A0.254350.689
15_K20_N0.252490.684
107_L110_Y0.252190.683
10_A30_P0.251940.682
103_A127_E0.2510.679
34_F183_K0.250610.678
62_I65_C0.249750.676
40_A105_Y0.248840.674
48_V55_N0.248050.671
55_N79_E0.246840.668
140_I173_S0.244850.663
119_P129_A0.243990.660
81_E102_V0.240580.651
27_T32_T0.237750.644
40_A101_Y0.237320.642
103_A117_G0.23720.642
49_K59_Q0.232680.630
116_M122_D0.232530.629
26_F177_R0.22840.618
177_R181_I0.228250.618
19_S50_K0.227840.617
76_D79_E0.226180.612
44_E83_V0.225530.611
42_S102_V0.223410.605
61_F64_K0.223340.605
38_F134_L0.223020.604
120_A137_K0.222960.604
61_F104_N0.222840.603
16_I21_E0.222670.603
16_I89_A0.221560.600
167_E179_K0.220370.597
127_E130_K0.219910.595
35_G139_V0.218060.590
29_R122_D0.216730.587
45_H107_L0.216480.586
54_N58_L0.215210.583
36_V118_V0.215090.582
47_L50_K0.212710.576
86_G89_A0.212570.575
17_K22_K0.210850.571
168_F171_L0.209990.568
105_Y124_R0.209730.568
175_E182_K0.209650.568
139_V163_I0.209210.566
89_A92_P0.207810.563
39_I109_D0.207430.562
31_D177_R0.207210.561
33_I116_M0.20670.560
14_F98_I0.206240.558
39_I115_V0.206140.558
178_E181_I0.205940.557
162_L177_R0.205310.556
81_E132_Y0.204370.553
52_A56_P0.204170.553
116_M124_R0.204010.552
10_A33_I0.20370.551
89_A114_A0.203160.550
16_I87_L0.20280.549
31_D34_F0.202450.548
102_V132_Y0.202090.547
99_P132_Y0.201910.547
28_T122_D0.201780.546
161_I173_S0.201640.546
174_K178_E0.200810.544
42_S108_M0.200220.542
30_P33_I0.199940.541
130_K133_N0.199480.540
126_F138_Q0.199110.539
34_F93_L0.198960.539
99_P102_V0.198890.538
11_E112_T0.198720.538
56_P66_K0.197840.536
11_E26_F0.197050.533
26_F31_D0.19680.533
54_N84_F0.19640.532
81_E104_N0.195570.529
37_T98_I0.195160.528
24_E112_T0.195110.528
13_D55_N0.194980.528
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
4arcA0.99461000.088
2v0cA0.99461000.114
3o0aA0.95681000.133
2ajgA0.99461000.192
1wnyA0.86491000.214
1ffyA0.90271000.248
2wfdA0.9731000.275
1wz2A0.98381000.286
1ileA0.88111000.292
1wkbA0.98381000.295

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