GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L12 - Ribosomal protein L7L12 C-terminal domain
Pfam: PF00542 (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: 68
Sequences: 1457
Seq/Len: 21.43
HH_delta: -0.065 (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
55_K59_E1.458832.847
7_K66_E1.445132.821
23_I54_I1.438832.808
8_S64_K1.328962.594
29_K33_K1.316972.570
7_K64_K1.286142.510
53_E57_K1.281462.501
58_L63_A1.275452.489
22_E57_K1.226892.395
19_E22_E1.114252.175
56_K60_A1.101152.149
12_K15_K1.065852.080
47_S50_E1.039482.029
5_V41_V0.944981.844
33_K37_S0.843261.646
15_K61_A0.792821.547
50_E53_E0.764681.492
43_K50_E0.744471.453
2_F48_K0.744351.453
20_V35_V0.701561.369
3_D45_G0.696011.358
55_K65_V0.661311.291
9_F36_D0.637021.243
37_S40_K0.608471.188
5_V66_E0.598771.169
48_K52_E0.585161.142
14_I17_I0.576031.124
19_E57_K0.575841.124
43_K54_I0.575421.123
49_E53_E0.54591.065
50_E54_I0.530941.036
19_E60_A0.526111.027
4_V51_A0.523061.021
14_I21_R0.519461.014
46_V67_L0.517411.010
3_D44_E0.508250.992
13_K35_V0.503680.983
1_E45_G0.500840.978
53_E56_K0.498550.973
33_K40_K0.496660.969
52_E56_K0.487640.952
41_V44_E0.486490.950
23_I57_K0.473560.924
17_I21_R0.466760.911
34_L40_K0.464930.907
49_E52_E0.452010.882
20_V42_I0.448260.875
8_S11_E0.439770.858
55_K67_L0.425390.830
46_V54_I0.422340.824
34_L42_I0.414420.809
52_E67_L0.402370.785
3_D41_V0.381580.745
6_L38_L0.374450.731
12_K61_A0.366070.714
21_R26_L0.358140.699
21_R27_G0.350670.684
35_V38_L0.350640.684
46_V50_E0.349840.683
24_T43_K0.349410.682
25_G43_K0.348450.680
56_K59_E0.338560.661
23_I58_L0.334470.653
59_E64_K0.331190.646
21_R24_T0.326010.636
16_V63_A0.325070.634
30_E33_K0.323920.632
5_V68_K0.318120.621
14_I19_E0.299090.584
59_E67_L0.297080.580
27_G30_E0.293730.573
3_D68_K0.290430.567
19_E23_I0.288730.564
4_V54_I0.284940.556
34_L41_V0.284720.556
6_L42_I0.284490.555
57_K60_A0.283770.554
22_E36_D0.279480.545
10_G15_K0.256620.501
7_K68_K0.253510.495
6_L9_F0.251550.491
47_S52_E0.248040.484
59_E65_V0.243060.474
3_D46_V0.233380.456
5_V15_K0.228570.446
10_G66_E0.227420.444
10_G13_K0.22550.440
13_K36_D0.221820.433
14_I18_K0.220710.431
6_L13_K0.220650.431
10_G16_V0.218810.427
7_K50_E0.218040.426
22_E45_G0.214630.419
15_K19_E0.214120.418
37_S41_V0.212670.415
24_T27_G0.21120.412
26_L34_L0.210920.412
1_E48_K0.209690.409
13_K20_V0.208210.406
5_V67_L0.205440.401
7_K38_L0.204270.399
10_G17_I0.203670.398
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
3sgfJ199.8-0.065
2ftcE199.8-0.053
1dd3A199.8-0.05
1ctfA199.8-0.035
2j01L0.985399.8-0.014
2zjq50.985399.8-0.011
4kcze0.941299.80.031
3avxA0.7580.10.805
1xb2B0.735376.90.811
1aipC0.720666.30.825

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