GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L29 - Ribosomal L29 protein
Pfam: PF00831 (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: CL0346
Length: 58
Sequences: 1626
Seq/Len: 28.03
HH_delta: -0.09 (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
9_D58_R1.201812.844
15_K18_E1.194282.826
7_L15_K1.127132.667
8_S11_E0.979672.318
20_K52_L0.89852.126
5_R57_E0.897792.124
16_L51_I0.86482.046
14_E18_E0.83721.981
22_E40_R0.821991.945
12_L51_I0.800971.895
47_D50_R0.726161.718
21_K25_N0.718551.700
30_K41_I0.701821.661
54_V57_E0.656681.554
1_A54_V0.650051.538
40_R43_E0.589421.395
15_K19_L0.547381.295
13_Q17_E0.513121.214
13_Q55_L0.505781.197
9_D55_L0.504961.195
11_E14_E0.487351.153
42_R46_R0.478321.132
10_E14_E0.459651.088
19_L51_I0.452751.071
54_V58_R0.445431.054
17_E21_K0.442071.046
39_H43_E0.441931.046
29_Q34_Q0.426611.009
5_R54_V0.42010.994
2_K6_E0.417860.989
12_L58_R0.417230.987
40_R44_I0.41150.974
4_L54_V0.393980.932
52_L56_R0.392880.930
28_F31_A0.385190.911
10_E13_Q0.376350.890
43_E47_D0.362960.859
44_I48_I0.35950.851
19_L47_D0.354070.838
14_E17_E0.353910.837
24_F34_Q0.352580.834
9_D13_Q0.350520.829
26_L29_Q0.347880.823
3_E6_E0.343730.813
35_L41_I0.340110.805
24_F29_Q0.334830.792
4_L12_L0.327590.775
29_Q40_R0.327270.774
19_L44_I0.320040.757
38_P52_L0.311380.737
23_L45_R0.305350.722
30_K33_G0.302240.715
22_E44_I0.295680.700
1_A5_R0.293430.694
52_L55_L0.288410.682
16_L52_L0.284910.674
37_N40_R0.280680.664
19_L48_I0.275160.651
23_L41_I0.274160.649
20_K23_L0.271540.642
11_E22_E0.269640.638
26_L44_I0.266820.631
24_F32_T0.26570.629
23_L44_I0.26280.622
30_K56_R0.259660.614
16_L48_I0.259360.614
29_Q35_L0.259220.613
11_E15_K0.258320.611
20_K31_A0.256790.608
24_F28_F0.255230.604
29_Q32_T0.242480.574
22_E25_N0.241930.572
4_L16_L0.239950.568
17_E36_E0.237840.563
4_L51_I0.235130.556
46_R49_A0.233090.552
25_N29_Q0.232270.550
21_K24_F0.231480.548
22_E33_G0.231270.547
25_N33_G0.231070.547
22_E26_L0.228340.540
35_L38_P0.227520.538
24_F27_R0.226730.536
23_L48_I0.22130.524
27_R31_A0.21970.520
34_Q45_R0.215640.510
30_K35_L0.215010.509
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
3bboZ199.6-0.09
3iz5c199.6-0.061
3v2d2199.6-0.061
2zjrV199.6-0.054
3j3wX199.6-0.053
1r73A199.6-0.053
4a17U199.6-0.053
3r8sY199.6-0.052
3j39h199.6-0.049
3j21W199.6-0.048

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