GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HGTP_anticodon - Anticodon binding domain
Pfam: PF03129 (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: CL0458
Length: 94
Sequences: 7982
Seq/Len: 84.91
HH_delta: -0.017 (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
68_T81_T1.793462.424
83_S86_E1.52942.067
22_A26_R1.458951.972
24_K88_I1.411961.908
3_V48_A1.380741.866
17_Y20_E1.366321.847
80_E90_Y1.365491.846
62_K66_N1.310471.771
14_I61_E1.308241.768
20_E24_K1.28931.743
68_T83_S1.261281.705
86_E89_E1.246421.685
22_A32_V1.226021.657
22_A34_L1.209951.635
28_A92_K1.20971.635
73_D76_T1.190991.610
1_Q31_R1.091011.475
24_K84_L1.083411.464
61_E65_E1.076921.456
20_E67_G1.075281.453
40_S43_K1.048171.417
37_S47_Y1.047271.415
60_G63_E0.998181.349
4_I22_A0.998161.349
13_E61_E0.991851.341
66_N81_T0.958861.296
6_P44_Q0.955141.291
70_T81_T0.948481.282
4_I18_A0.947391.280
17_Y64_L0.887961.200
41_L45_I0.87831.187
17_Y59_I0.871281.178
24_K28_A0.858271.160
67_G85_E0.851561.151
28_A88_I0.848841.147
24_K85_E0.845731.143
88_I92_K0.841691.138
55_F71_V0.837121.131
86_E90_Y0.835181.129
62_K65_E0.833891.127
70_T79_Q0.826321.117
6_P18_A0.824711.115
71_V90_Y0.822011.111
3_V53_I0.807931.092
8_G61_E0.798471.079
49_D56_I0.788381.066
19_Q22_A0.785611.062
19_Q23_N0.785511.062
55_F73_D0.78121.056
48_A53_I0.781121.056
2_V25_L0.760671.028
23_N27_K0.756741.023
13_E65_E0.753871.019
43_K46_K0.73981.000
2_V57_I0.735980.995
7_V41_L0.732890.991
89_E92_K0.719420.972
56_I74_R0.718680.971
57_I87_L0.71440.966
14_I64_L0.692820.936
82_V90_Y0.688790.931
39_K43_K0.684180.925
84_L88_I0.679220.918
17_Y84_L0.677080.915
2_V30_I0.668130.903
35_D44_Q0.667080.902
19_Q36_D0.653060.883
3_V33_E0.652720.882
15_I19_Q0.647770.876
30_I92_K0.643360.870
67_G84_L0.630830.853
2_V32_V0.630830.853
71_V87_L0.628940.850
62_K81_T0.626110.846
5_I41_L0.625940.846
5_I56_I0.622350.841
43_K47_Y0.619820.838
69_V84_L0.618590.836
24_K27_K0.605930.819
21_L84_L0.604330.817
16_E20_E0.603290.815
8_G13_E0.592360.801
23_N26_R0.590350.798
49_D52_G0.589790.797
17_Y67_G0.580020.784
3_V51_L0.577030.780
55_F91_L0.573980.776
49_D74_R0.572320.774
9_K15_I0.570870.772
40_S44_Q0.567420.767
19_Q34_L0.565910.765
48_A56_I0.561510.759
20_E23_N0.555960.751
17_Y63_E0.539520.729
18_A59_I0.537820.727
33_E53_I0.53390.722
6_P15_I0.531920.719
8_G14_I0.531410.718
1_Q30_I0.524650.709
71_V82_V0.520430.703
9_K13_E0.517860.700
45_I58_I0.516530.698
30_I91_L0.515350.697
45_I49_D0.502330.679
57_I71_V0.499350.675
16_E19_Q0.49920.675
39_K47_Y0.494940.669
46_K50_K0.493030.666
6_P34_L0.492540.666
73_D80_E0.491950.665
13_E16_E0.487250.659
67_G83_S0.483510.654
2_V91_L0.475970.643
5_I44_Q0.473960.641
20_E84_L0.462870.626
18_A34_L0.461220.623
24_K67_G0.460990.623
58_I72_K0.454670.615
87_L92_K0.453270.613
26_R32_V0.448060.606
15_I36_D0.440210.595
47_Y51_L0.438490.593
4_I57_I0.437010.591
25_L30_I0.432290.584
69_V87_L0.431250.583
28_A89_E0.420950.569
21_L69_V0.420390.568
35_D47_Y0.416040.562
58_I70_T0.415070.561
63_E66_N0.41010.554
82_V87_L0.408760.552
57_I69_V0.402080.543
31_R53_I0.400210.541
49_D75_D0.394210.533
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
4g85A0.968199.6-0.017
4g84A0.968199.6-0.013
1qf6A0.968199.6-0.009
3uh0A199.6-0.007
1evlA0.968199.60.002
1nyrA0.968199.60.008
2zt5A0.989499.60.012
4hvcA199.60.023
2i4lA0.978799.50.028
2j3lA0.978799.50.028

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