GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L7Ae - Ribosomal protein L7AeL30eS12eGadd45 family
Pfam: PF01248 (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: CL0101
Length: 95
Sequences: 1880
Seq/Len: 19.79
HH_delta: 0.03 (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
32_A84_A1.166565.151
66_S69_E0.551712.436
26_A84_A0.522422.307
35_V54_C0.444541.963
18_K80_V0.4141.828
40_D67_K0.412671.822
24_L53_L0.393561.738
46_I63_F0.371781.642
35_V50_L0.364091.608
39_E65_P0.336381.485
8_K12_K0.326171.440
23_V84_A0.322541.424
36_I83_L0.320691.416
15_R87_D0.315351.392
76_K80_V0.308141.361
36_I62_V0.306341.353
25_K29_K0.303361.339
11_R16_L0.294821.302
54_C61_Y0.286041.263
22_E25_K0.285121.259
9_L12_K0.284321.255
50_L82_A0.281661.244
23_V82_A0.276261.220
21_K25_K0.276061.219
23_V35_V0.273291.207
34_L62_V0.261211.153
17_V22_E0.259211.145
11_R14_G0.257741.138
26_A86_K0.256511.133
53_L56_E0.249531.102
43_P51_P0.248041.095
44_D48_K0.246461.088
21_K24_L0.244951.082
67_K71_G0.243481.075
17_V86_K0.242131.069
32_A35_V0.238381.053
24_L50_L0.235861.041
47_K52_A0.232121.025
39_E66_S0.228851.010
56_E64_V0.228751.010
52_A56_E0.22641.000
73_A83_L0.221840.980
33_K87_D0.220260.973
51_P63_F0.218440.965
17_V84_A0.218180.963
27_L54_C0.216420.956
50_L67_K0.21580.953
38_A71_G0.213570.943
11_R74_C0.21170.935
33_K86_K0.209330.924
43_P46_I0.208980.923
34_L85_I0.208150.919
51_P55_E0.204990.905
46_I61_Y0.203650.899
24_L28_K0.201790.891
39_E63_F0.201690.891
18_K22_E0.201550.890
29_K57_K0.201280.889
51_P61_Y0.201060.888
54_C57_K0.200970.887
53_L57_K0.199890.883
26_A31_K0.196860.869
27_L32_A0.195810.865
52_A55_E0.193150.853
35_V84_A0.191990.848
32_A68_E0.186070.822
40_D45_S0.185530.819
26_A32_A0.182050.804
71_G78_R0.180730.798
24_L48_K0.180280.796
41_C67_K0.178550.788
72_R77_K0.177530.784
28_K57_K0.176050.777
18_K76_K0.174450.770
22_E50_L0.174170.769
27_L59_I0.173980.768
16_L36_I0.173730.767
45_S48_K0.172050.760
59_I63_F0.171940.759
33_K88_A0.171610.758
67_K81_S0.167980.742
12_K83_L0.167340.739
74_C83_L0.165220.730
30_G57_K0.164710.727
68_E74_C0.163870.724
37_L46_I0.163560.722
27_L63_F0.162760.719
22_E80_V0.162420.717
43_P47_K0.160480.709
22_E26_A0.159910.706
32_A86_K0.158430.700
69_E72_R0.157430.695
28_K67_K0.155590.687
18_K62_V0.154950.684
39_E83_L0.154540.682
21_K28_K0.154330.681
65_P69_E0.154190.681
17_V27_L0.153910.680
11_R67_K0.153630.678
9_L13_A0.153570.678
38_A67_K0.153280.677
41_C46_I0.153120.676
71_G81_S0.15190.671
20_I47_K0.151330.668
41_C77_K0.150160.663
16_L74_C0.149030.658
39_E56_E0.148750.657
31_K87_D0.14870.657
9_L16_L0.147650.652
42_S47_K0.147390.651
40_D85_I0.147340.651
39_E64_V0.14680.648
23_V30_G0.146520.647
16_L73_A0.145970.645
36_I39_E0.145430.642
13_A69_E0.144220.637
11_R23_V0.144120.636
41_C45_S0.143260.633
33_K74_C0.143130.632
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
3u5ec0.989599.80.03
3iz5f0.989599.80.031
2lbwA199.80.032
4a18G0.989599.80.034
3v7qA0.978999.80.034
3on1A0.978999.80.035
1vq8F199.80.045
2fc3A199.80.047
1rlgA199.80.048
3o85A199.80.054

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