GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SUI1 - Translation initiation factor SUI1
Pfam: PF01253 (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: 83
Sequences: 1052
Seq/Len: 12.67
HH_delta: 0.096 (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
39_E77_K0.775953.890
7_I26_L0.504672.530
71_K75_V0.377881.894
10_R24_S0.361321.811
22_I59_E0.351291.761
72_D76_E0.34521.730
66_H69_E0.331481.662
37_A50_V0.325551.632
35_E39_E0.321111.610
16_G19_F0.305451.531
49_S61_Q0.299191.500
73_L77_K0.297551.492
9_I71_K0.295611.482
29_F32_D0.291951.463
30_G34_K0.283241.420
37_A60_I0.281141.409
28_L32_D0.274671.377
41_K48_G0.269361.350
43_K73_L0.263881.323
13_K17_R0.262041.314
39_E73_L0.251631.261
7_I81_P0.240121.204
10_R22_I0.238991.198
23_V70_I0.237791.192
39_E43_K0.236861.187
46_C66_H0.234921.178
43_K76_E0.23461.176
44_F62_I0.229381.150
43_K69_E0.22451.125
42_K46_C0.219341.099
46_C62_I0.217151.088
31_I36_L0.216851.087
21_T66_H0.209071.048
40_L74_L0.207321.039
40_L44_F0.205241.029
14_R19_F0.199921.002
23_V29_F0.197270.989
18_K65_D0.196030.983
38_K42_K0.194080.973
47_G58_E0.190130.953
21_T72_D0.190080.953
75_V81_P0.189930.952
5_P12_E0.187780.941
47_G61_Q0.187740.941
21_T70_I0.184760.926
30_G46_C0.184330.924
33_L37_A0.176890.887
68_D72_D0.175150.878
21_T64_G0.173890.872
20_V45_A0.173240.868
26_L33_L0.172810.866
32_D35_E0.171850.861
19_F31_I0.169740.851
72_D75_V0.169080.848
12_E22_I0.168940.847
47_G63_Q0.166770.836
36_L40_L0.166720.836
44_F69_E0.164770.826
28_L61_Q0.16460.825
44_F66_H0.164250.823
36_L78_G0.163920.822
37_A56_K0.160220.803
24_S59_E0.158540.795
67_R78_G0.15840.794
71_K81_P0.158330.794
30_G33_L0.157340.789
23_V73_L0.156660.785
44_F73_L0.155590.780
24_S44_F0.154950.777
14_R17_R0.154920.777
8_H14_R0.153790.771
32_D46_C0.153190.768
18_K21_T0.152710.765
50_V70_I0.152570.765
68_D71_K0.151520.760
34_K42_K0.151290.758
49_S59_E0.15040.754
7_I16_G0.150280.753
49_S66_H0.150120.752
70_I76_E0.14840.744
42_K70_I0.147610.740
9_I35_E0.146690.735
4_P81_P0.146550.735
14_R70_I0.146140.733
48_G79_G0.145170.728
39_E42_K0.143880.721
9_I21_T0.143190.718
33_L70_I0.142050.712
22_I61_Q0.141540.709
35_E79_G0.139150.698
33_L68_D0.139050.697
13_K22_I0.138640.695
15_R25_G0.138210.693
18_K63_Q0.138070.692
40_L66_H0.137620.690
12_E21_T0.137270.688
48_G61_Q0.137080.687
43_K70_I0.136280.683
16_G61_Q0.135760.681
25_G44_F0.135490.679
74_L78_G0.134980.677
48_G56_K0.134860.676
16_G62_I0.134170.673
31_I80_I0.133930.671
9_I42_K0.13370.670
9_I60_I0.132980.667
31_I45_A0.132280.663
15_R20_V0.132080.662
63_Q79_G0.131950.661
43_K68_D0.131940.661
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
2oghA0.98899.80.096
2if1A0.98899.80.1
2xzmF0.98899.80.107
1d1rA0.927799.70.183
1neeA0.8795750.837
3cw2K0.891673.30.84
1k8bA0.578369.40.844
2d74B0.8795670.846
2g2kA0.951857.80.854
1gxuA0.831356.60.856

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