GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Arg_tRNA_synt_N - Arginyl tRNA synthetase N terminal domain
Pfam: PF03485 (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. )
Length: 85
Sequences: 2223
Seq/Len: 26.15
HH_delta: 0.042 (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
52_N55_E1.390074.411
58_E62_E1.146673.639
72_K84_F1.143983.630
61_A81_I0.859312.727
51_K59_E0.852822.706
54_R77_G0.762862.421
51_K55_E0.751812.386
55_E58_E0.54211.720
37_Y85_L0.535861.700
26_I37_Y0.502221.594
54_R58_E0.476211.511
4_K8_S0.458021.453
9_E13_K0.453251.438
39_T42_A0.449691.427
7_I83_F0.443711.408
5_K9_E0.431621.370
13_K63_K0.429871.364
31_N34_F0.425811.351
51_K56_I0.42271.341
30_P34_F0.415021.317
42_A60_I0.407531.293
29_P38_Q0.404761.284
8_S12_K0.389691.237
5_K8_S0.377281.197
75_V81_I0.36611.162
14_A63_K0.361051.146
74_E84_F0.360051.143
59_E62_E0.355521.128
10_A13_K0.353831.123
7_I39_T0.347391.102
73_V83_F0.344471.093
6_A67_S0.336641.068
3_L37_Y0.325471.033
70_I83_F0.317921.009
54_R76_A0.316491.004
62_E65_E0.311720.989
61_A75_V0.311610.989
59_E63_K0.310950.987
64_L73_V0.305240.969
54_R75_V0.29980.951
38_Q41_I0.297180.943
10_A14_A0.291860.926
9_E18_D0.290790.923
61_A65_E0.289110.917
57_A75_V0.2880.914
65_E72_K0.286550.909
55_E59_E0.286390.909
49_L56_I0.284210.902
29_P35_G0.282160.895
13_K20_E0.281810.894
6_A10_A0.281370.893
45_L56_I0.278540.884
54_R78_P0.276710.878
9_E12_K0.276470.877
30_P38_Q0.270890.860
56_I59_E0.270880.860
12_K19_L0.268320.851
6_A9_E0.265470.842
41_I60_I0.262210.832
43_F78_P0.261980.831
11_L41_I0.258910.822
3_L15_F0.257890.818
66_K70_I0.252440.801
61_A73_V0.252150.800
43_F80_F0.251690.799
29_P34_F0.25150.798
27_E38_Q0.246430.782
38_Q82_N0.240670.764
46_A56_I0.239040.759
7_I41_I0.238410.757
40_N44_R0.237870.755
45_L48_K0.23380.742
78_P82_N0.233030.739
41_I45_L0.232860.739
15_F44_R0.229410.728
9_E66_K0.227440.722
47_K80_F0.226840.720
75_V79_G0.226120.718
4_K23_E0.224560.713
10_A15_F0.224150.711
40_N80_F0.222760.707
60_I69_I0.222010.704
46_A49_L0.221810.704
3_L10_A0.219960.698
50_K56_I0.218430.693
32_P35_G0.217460.690
14_A37_Y0.215850.685
28_K37_Y0.214870.682
25_Q44_R0.214370.680
43_F79_G0.211640.672
52_N56_I0.209290.664
11_L15_F0.209160.664
5_K12_K0.207370.658
4_K37_Y0.207110.657
9_E65_E0.20420.648
37_Y79_G0.202430.642
11_L45_L0.20170.640
14_A18_D0.2010.638
19_L23_E0.200570.636
46_A53_P0.197520.627
27_E39_T0.197220.626
26_I44_R0.197090.625
70_I73_V0.196590.624
38_Q80_F0.196050.622
56_I60_I0.195960.622
12_K15_F0.195130.619
10_A68_P0.193920.615
27_E30_P0.192570.611
53_P57_A0.192340.610
42_A57_A0.190040.603
62_E71_E0.189580.602
30_P35_G0.188990.600
45_L50_K0.18870.599
11_L36_D0.188150.597
25_Q41_I0.186540.592
40_N47_K0.18630.591
21_E83_F0.186210.591
26_I85_L0.186090.591
42_A45_L0.185940.590
44_R48_K0.18560.589
46_A78_P0.183940.584
40_N43_F0.183320.582
12_K18_D0.182640.580
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
3gdzA0.976599.70.042
2zueA0.976599.60.104
1iq0A0.929499.60.141
1f7uA0.964799.50.183
3ej9A0.694129.50.849
2bb6A0.882425.20.854
2pmvA0.870621.80.858
3r8nC0.917613.10.871
3i1mC0.917613.10.871
1iioA0.811.80.874

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