GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L35p - Ribosomal protein L35
Pfam: PF01632 (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: 61
Sequences: 1277
Seq/Len: 20.93
HH_delta: -0.08 (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
7_K10_A1.343033.875
31_L34_K0.894062.580
25_R47_T0.840132.424
9_A13_F0.745392.151
15_V21_I0.680211.963
22_K48_L0.623941.800
53_D56_R0.61261.767
51_K54_V0.588521.698
6_H60_L0.583751.684
6_H9_A0.57221.651
39_R43_L0.563781.627
23_R49_V0.553231.596
16_T20_K0.551321.591
23_R47_T0.551.587
28_K44_R0.544921.572
50_H53_D0.530471.531
49_V57_I0.510331.472
21_I57_I0.50161.447
36_S39_R0.496331.432
20_K48_L0.478291.380
38_K42_R0.47241.363
22_K46_T0.450171.299
37_S40_K0.44161.274
31_L35_K0.43751.262
27_G39_R0.413371.193
24_K28_K0.399821.154
14_K22_K0.395241.140
41_R44_R0.379231.094
53_D57_I0.377681.090
54_V58_K0.377011.088
9_A60_L0.359781.038
32_L40_K0.358321.034
21_I58_K0.357181.031
5_T10_A0.349351.008
16_T48_L0.348231.005
37_S41_R0.338740.977
36_S40_K0.335860.969
15_V58_K0.335160.967
24_K29_R0.329070.949
24_K46_T0.316230.912
25_R43_L0.30990.894
32_L35_K0.308170.889
29_R32_L0.303160.875
55_K59_K0.296960.857
52_A55_K0.278980.805
28_K40_K0.276310.797
26_A53_D0.265320.765
37_S44_R0.26360.761
16_T19_G0.263520.760
39_R42_R0.259310.748
31_L39_R0.257370.743
5_T11_K0.256450.740
23_R26_A0.249110.719
25_R36_S0.247350.714
13_F21_I0.244910.707
15_V51_K0.244780.706
27_G35_K0.232680.671
56_R60_L0.232560.671
37_S59_K0.230590.665
56_R61_L0.228430.659
6_H33_T0.224260.647
13_F49_V0.222930.643
10_A15_V0.219350.633
28_K32_L0.21540.621
5_T9_A0.207360.598
23_R45_K0.206930.597
56_R59_K0.204030.589
1_P61_L0.203370.587
48_L54_V0.203090.586
1_P32_L0.201560.582
8_S11_K0.200990.580
29_R45_K0.200580.579
21_I49_V0.19750.570
50_H54_V0.19630.566
17_G20_K0.196140.566
33_T39_R0.194740.562
24_K31_L0.192250.555
35_K39_R0.191930.554
15_V22_K0.191680.553
26_A43_L0.191150.552
35_K43_L0.189030.545
3_M21_I0.188980.545
52_A56_R0.188960.545
51_K58_K0.188680.544
17_G48_L0.18770.542
54_V59_K0.187650.541
57_I60_L0.18730.540
16_T22_K0.186610.538
33_T37_S0.185950.537
22_K33_T0.183240.529
34_K39_R0.183040.528
18_S22_K0.18280.527
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
3bbo5199.7-0.08
2zjr3199.7-0.053
3r8s3199.7-0.053
3v2d8199.7-0.051
3taiA0.59029.50.867
3e7wA0.65574.20.886
3bbnT0.90162.90.894
3fceA0.65572.50.897
3ivrA0.65572.40.898
2pmvA0.36072.10.901

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