GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L30 - Ribosomal protein L30pL7e
Pfam: PF00327 (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: 52
Sequences: 1555
Seq/Len: 29.9
HH_delta: -0.047 (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
37_N42_R1.687363.651
5_T32_A1.437393.111
10_P21_L1.252552.711
15_P19_K1.200442.598
46_K49_K1.106172.394
17_V50_H0.98262.126
16_K47_K0.926052.004
3_F34_F0.915151.980
27_R31_Q0.908161.965
3_F32_A0.89251.931
6_R21_L0.892431.931
20_T44_M0.888171.922
35_V41_I0.828071.792
21_L48_V0.748561.620
48_V52_V0.68581.484
19_K22_K0.660261.429
4_V35_V0.633791.372
2_L37_N0.601621.302
28_K31_Q0.570931.235
23_A44_M0.563751.220
19_K23_A0.554681.200
23_A35_V0.51961.124
2_L42_R0.502791.088
13_A17_V0.459320.994
2_L45_L0.455460.986
14_P17_V0.43310.937
20_T47_K0.420390.910
10_P22_K0.419060.907
6_R10_P0.406250.879
36_K41_I0.402330.871
23_A40_S0.383590.830
7_I15_P0.353260.764
4_V33_V0.349070.755
38_T41_I0.343160.743
25_G33_V0.340840.738
15_P18_R0.329620.713
11_I18_R0.326690.707
21_L31_Q0.326620.707
15_P22_K0.322820.699
34_F50_H0.32070.694
8_R12_G0.30570.662
20_T23_A0.298240.645
6_R29_I0.295630.640
41_I44_M0.293810.636
35_V44_M0.293310.635
41_I45_L0.292470.633
23_A38_T0.289130.626
16_K20_T0.288210.624
22_K27_R0.286860.621
10_P18_R0.284950.617
36_K40_S0.282720.612
17_V47_K0.274860.595
10_P13_A0.271980.589
26_L29_I0.266410.577
4_V45_L0.253890.549
8_R11_I0.253450.548
10_P29_I0.252710.547
8_R13_A0.245560.531
24_L48_V0.241720.523
6_R31_Q0.240210.520
49_K52_V0.238240.516
33_V41_I0.234850.508
5_T33_V0.234160.507
5_T25_G0.228190.494
43_G47_K0.226850.491
42_R46_K0.226340.490
26_L33_V0.225870.489
16_K19_K0.225840.489
20_T35_V0.223130.483
2_L34_F0.214850.465
45_L52_V0.212230.459
20_T48_V0.210960.457
8_R43_G0.207830.450
36_K39_P0.207320.449
5_T51_L0.204530.443
22_K31_Q0.199240.431
7_I46_K0.198910.430
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
3iz5e199.5-0.047
3j3bF199.5-0.046
4a17V199.5-0.046
1vq8W199.5-0.046
3izce199.5-0.045
3j39F199.5-0.042
2zkrw199.5-0.04
3j21Y199.4-0.02
3j3vY199.4-0.002
3r8sZ199.4-0.001

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