GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
IF3_C - Translation initiation factor IF-3 C-terminal domain
Pfam: PF00707 (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: 88
Sequences: 1335
Seq/Len: 15.17
HH_delta: -0.041 (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
18_L62_E1.105214.043
61_E64_K0.804492.943
24_Q27_K0.787952.883
15_E19_E0.732472.680
26_K65_D0.689752.523
67_G84_L0.590322.160
26_K30_E0.579442.120
26_K66_V0.577852.114
53_E57_E0.545211.995
70_E85_S0.536421.963
25_A59_I0.534641.956
25_A37_V0.518031.895
54_E57_E0.483121.768
48_H51_L0.478721.751
22_L62_E0.463331.695
22_L59_I0.456931.672
64_K87_K0.402941.474
57_E72_K0.394881.445
57_E60_I0.383911.405
56_L82_M0.37671.378
29_L67_G0.365991.339
40_R79_Q0.356431.304
25_A35_V0.352741.291
16_H19_E0.351571.286
41_F52_G0.350161.281
41_F80_M0.34361.257
37_V59_I0.33691.233
30_E66_V0.333161.219
19_E22_L0.328331.201
25_A63_L0.325781.192
71_K83_I0.319651.169
12_N45_E0.315951.156
69_V82_M0.314581.151
22_L26_K0.293181.073
18_L22_L0.289931.061
58_R62_E0.289111.058
46_M49_P0.282271.033
29_L63_L0.278181.018
34_K83_I0.272890.998
18_L58_R0.26930.985
10_S45_E0.269040.984
20_T24_Q0.268610.983
8_R40_R0.267950.980
13_I20_T0.263560.964
68_K87_K0.259930.951
51_L54_E0.259790.950
57_E61_E0.258060.944
63_L67_G0.256450.938
16_H63_L0.254680.932
60_I72_K0.254370.931
50_E54_E0.254230.930
13_I55_V0.252780.925
73_P77_G0.245940.900
53_E75_M0.244030.893
16_H20_T0.241830.885
39_I56_L0.241110.882
55_V58_R0.237470.869
60_I82_M0.235580.862
10_S42_R0.234480.858
35_V63_L0.232870.852
46_M78_K0.227640.833
11_P21_K0.224630.822
68_K72_K0.223290.817
6_E38_V0.220070.805
14_D24_Q0.219320.802
8_R11_P0.215570.789
14_D32_G0.215420.788
7_I37_V0.214720.786
3_K33_H0.214090.783
15_E54_E0.213330.780
27_K31_K0.212910.779
7_I25_A0.207710.760
27_K35_V0.205470.752
23_K26_K0.204790.749
31_K72_K0.201950.739
60_I64_K0.200170.732
8_R38_V0.200060.732
9_F13_I0.197630.723
39_I53_E0.194040.710
9_F37_V0.193310.707
23_K31_K0.192780.705
28_F41_F0.188650.690
56_L78_K0.187060.684
10_S40_R0.186290.682
56_L60_I0.182620.668
10_S13_I0.182370.667
4_V87_K0.182140.666
4_V83_I0.180980.662
16_H25_A0.177730.650
12_N51_L0.177290.649
53_E63_L0.176520.646
70_E83_I0.175780.643
13_I35_V0.174070.637
21_K70_E0.172910.633
29_L86_P0.172750.632
53_E72_K0.172110.630
51_L55_V0.171860.629
8_R56_L0.170940.625
39_I55_V0.17080.625
19_E23_K0.168620.617
60_I69_V0.168390.616
52_G86_P0.167860.614
6_E36_K0.16680.610
9_F18_L0.166720.610
9_F16_H0.166260.608
57_E73_P0.165790.607
36_K70_E0.165040.604
21_K52_G0.164930.603
54_E61_E0.163640.599
42_R45_E0.163470.598
30_E33_H0.163010.596
72_K75_M0.162490.594
36_K44_R0.161820.592
19_E62_E0.160130.586
9_F55_V0.159310.583
38_V48_H0.158890.581
29_L66_V0.158710.581
72_K87_K0.158530.580
54_E58_R0.158380.579
2_V81_S0.156610.573
47_A78_K0.15560.569
53_E80_M0.155260.568
47_A50_E0.154830.566
5_K17_D0.15460.566
34_K41_F0.154140.564
33_H48_H0.154070.564
10_S18_L0.153870.563
34_K70_E0.153510.562
39_I49_P0.152360.557
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
2m71A199.9-0.041
1tigA199.9-0.032
2ifeA199.9-0.024
1i96V0.977399.9-0.019
2crqA0.988699.90.012
1ew4A0.522712.30.899
4b89A111.90.9
4jqfA0.88647.20.909
4hs5A0.511470.909
2ln3A0.86366.80.91

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