GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
eIF-1a - Translation initiation factor 1A IF-1
Pfam: PF01176 (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: CL0021
Length: 65
Sequences: 1585
Seq/Len: 24.38
HH_delta: -0.036 (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
8_R47_F0.848232.706
9_V42_I0.817552.608
10_T21_E0.800862.555
51_E63_I0.647542.066
6_I49_L0.623891.990
11_E19_E0.620341.979
8_R21_E0.613431.957
19_E29_L0.592481.890
21_E27_E0.583641.862
30_A60_G0.575421.836
49_L64_Y0.523931.671
19_E27_E0.506231.615
23_E47_F0.497691.588
7_G30_A0.472511.507
20_V30_A0.446941.426
6_I47_F0.440861.406
18_F62_I0.411641.313
7_G20_V0.401861.282
22_C28_R0.388661.240
30_A50_V0.360321.149
29_L59_K0.360051.149
28_R50_V0.357151.139
22_C50_V0.356571.138
18_F36_F0.355311.134
10_T27_E0.346951.107
21_E25_G0.33461.067
17_L31_R0.333121.063
17_L29_L0.33011.053
12_M44_R0.329181.050
32_I42_I0.298620.953
48_V62_I0.296070.945
9_V48_V0.293220.935
37_R45_G0.287150.916
13_L19_E0.283470.904
7_G60_G0.279110.890
26_E57_K0.278040.887
16_N37_R0.276570.882
12_M49_L0.275680.879
37_R44_R0.273660.873
28_R52_P0.269410.859
7_G48_V0.268090.855
54_P57_K0.263340.840
50_V60_G0.251570.803
24_D28_R0.248670.793
53_S61_R0.247920.791
34_G46_D0.246790.787
33_P61_R0.236460.754
38_K64_Y0.23610.753
20_V50_V0.23580.752
16_N44_R0.234860.749
45_G49_L0.234790.749
12_M18_F0.233680.745
38_K63_I0.233430.745
13_L29_L0.227060.724
6_I39_R0.225020.718
24_D58_V0.22290.711
22_C40_I0.222140.709
10_T25_G0.215320.687
15_N43_K0.214310.684
21_E26_E0.211650.675
27_E54_P0.207380.662
25_G58_V0.206790.660
49_L63_I0.203330.649
32_I39_R0.202650.646
6_I64_Y0.200940.641
51_E61_R0.198660.634
23_E27_E0.191760.612
52_P59_K0.19090.609
40_I64_Y0.190720.608
11_E16_N0.189670.605
31_R59_K0.189410.604
16_N34_G0.188220.600
15_N29_L0.185640.592
17_L32_I0.183780.586
6_I25_G0.183640.586
35_K40_I0.183250.585
46_D55_Y0.181850.580
51_E54_P0.180480.576
36_F41_W0.178390.569
36_F48_V0.177850.567
15_N44_R0.176830.564
13_L17_L0.175130.559
12_M15_N0.173930.555
15_N18_F0.173380.553
32_I41_W0.172630.551
10_T19_E0.172570.551
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
1d7qA199.6-0.036
1jt8A199.5-0.024
2dgyA199.5-0.022
2oqkA199.50.009
3i4oA199.40.043
1hr0W199.40.068
1ah9A199.40.082
1t9hA0.953898.40.401
2rcnA0.938598.40.406
2yv5A0.938598.10.447

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