GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L5 - Ribosomal protein L5
Pfam: PF00281 (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: 56
Sequences: 1462
Seq/Len: 26.11
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
13_I37_T1.22883.952
34_E40_K0.925752.977
34_E41_P0.779562.507
30_K43_I0.652252.098
15_I29_A0.64812.084
46_A49_S0.643382.069
31_K35_Q0.621031.997
9_E12_V0.590041.898
17_V29_A0.576071.853
15_I33_L0.543981.750
22_D52_N0.535171.721
17_V25_V0.514111.653
28_K32_E0.491231.580
3_M15_I0.434911.399
2_V5_V0.406251.307
30_K34_E0.400371.288
31_K34_E0.390711.257
21_G28_K0.384921.238
8_I11_I0.377321.214
21_G26_L0.366211.178
15_I32_E0.36181.164
17_V26_L0.335021.077
21_G52_N0.323221.040
44_T50_I0.316481.018
11_I48_K0.313141.007
27_E31_K0.312051.004
15_I49_S0.303460.976
14_N41_P0.299640.964
21_G55_I0.292640.941
26_L55_I0.281650.906
11_I54_K0.280370.902
18_G56_R0.279920.900
16_G53_F0.268020.862
19_E25_V0.264880.852
22_D28_K0.264090.849
37_T42_V0.263930.849
26_L43_I0.261290.840
42_V53_F0.260570.838
11_I28_K0.259910.836
30_K41_P0.258080.830
46_A55_I0.255670.822
48_K52_N0.253740.816
1_N22_D0.249350.802
22_D47_K0.248880.800
36_I51_A0.241230.776
41_P46_A0.241070.775
18_G49_S0.238720.768
2_V25_V0.236860.762
28_K31_K0.236150.759
20_A29_A0.236130.759
39_Q53_F0.231220.744
29_A32_E0.230260.741
31_K45_K0.22890.736
27_E32_E0.226010.727
50_I55_I0.213190.686
39_Q51_A0.212550.684
1_N19_E0.210420.677
19_E23_D0.206710.665
5_V54_K0.206450.664
1_N4_Q0.201880.649
13_I33_L0.19780.636
1_N5_V0.195020.627
8_I34_E0.189420.609
18_G24_K0.188960.608
14_N31_K0.187340.603
50_I53_F0.18250.587
26_L45_K0.182350.586
23_D27_E0.180170.579
12_V41_P0.179240.576
10_K55_I0.178660.575
40_K43_I0.178010.573
3_M21_G0.176280.567
24_K33_L0.174320.561
17_V20_A0.174170.560
24_K30_K0.170640.549
45_K48_K0.167860.540
9_E13_I0.164720.530
25_V28_K0.164490.529
6_P40_K0.164230.528
30_K45_K0.162770.523
9_E14_N0.162070.521
21_G27_E0.160970.518
48_K51_A0.160810.517
43_I50_I0.159910.514
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
4a17D0.964399.6-0.036
3j3bJ0.964399.6-0.036
3iz5E0.964399.6-0.033
3r8sF199.6-0.022
3zf7L0.964399.6-0.018
3bboH199.6-0.018
1iq4A199.6-0.015
1mjiA199.6-0.015
3j21E0.964399.6-0.012
2zkrd0.964399.6-0.007

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