GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L5_C - ribosomal L5P family C-terminus
Pfam: PF00673 (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: 95
Sequences: 1353
Seq/Len: 14.24
HH_delta: -0.055 (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
46_S72_T1.011924.290
85_L89_S0.69942.965
25_L28_I0.698122.959
49_I54_L0.69432.943
20_L47_F0.644412.732
18_D22_T0.62812.663
79_T82_E0.578832.454
17_L73_I0.530592.249
59_E62_P0.529772.246
34_L92_I0.516972.191
85_L88_K0.509452.160
14_Y90_F0.502522.130
41_N80_P0.461281.955
64_P67_F0.44921.904
40_D44_N0.395271.676
52_H67_F0.392261.663
53_I60_Y0.383061.624
53_I66_I0.375191.590
17_L21_I0.374941.589
5_K70_D0.366821.555
25_L34_L0.361971.534
84_R88_K0.350291.485
15_E19_K0.329191.395
36_A84_R0.300981.276
75_T83_A0.288661.224
8_L16_F0.285151.209
60_Y67_F0.281661.194
24_V49_I0.281211.192
34_L47_F0.278531.181
73_I92_I0.270821.148
51_E66_I0.269451.142
86_L90_F0.261271.108
36_A95_Y0.257471.091
38_S70_D0.252451.070
5_K72_T0.242951.030
62_P65_G0.241031.022
1_P95_Y0.240811.021
11_K15_E0.236591.003
86_L93_P0.234220.993
38_S45_F0.232640.986
81_K84_R0.232120.984
33_G86_L0.228970.971
78_K82_E0.227660.965
42_S80_P0.224290.951
21_I90_F0.223770.949
4_C15_E0.222980.945
48_G68_G0.221790.940
52_H63_F0.221130.937
43_G48_G0.218790.927
10_G34_L0.217090.920
86_L91_G0.21240.900
15_E18_D0.210930.894
60_Y65_G0.206660.876
25_L47_F0.2050.869
38_S50_K0.203990.865
38_S47_F0.202780.860
89_S95_Y0.202740.859
53_I62_P0.19890.843
49_I69_M0.197470.837
35_K38_S0.197160.836
40_D43_G0.197080.835
67_F70_D0.197080.835
39_F45_F0.196930.835
39_F44_N0.191680.813
2_I29_K0.189350.803
60_Y66_I0.18710.793
19_K24_V0.186740.792
11_K14_Y0.184990.784
29_K95_Y0.183230.777
42_S81_K0.182430.773
49_I70_D0.18080.766
33_G55_F0.18050.765
38_S56_P0.179660.762
29_K89_S0.178750.758
35_K92_I0.178280.756
24_V54_L0.178250.756
22_T36_A0.176640.749
33_G93_P0.174990.742
77_A83_A0.174550.740
2_I15_E0.174410.739
3_G8_L0.173780.737
47_F56_P0.173530.736
24_V28_I0.173180.734
47_F74_V0.172520.731
20_L25_L0.17120.726
72_T89_S0.168430.714
87_L93_P0.165940.703
2_I74_V0.165420.701
18_D32_K0.165220.700
27_R33_G0.165090.700
24_V70_D0.163610.694
51_E61_D0.161220.683
81_K85_L0.160910.682
17_L90_F0.160740.681
14_Y22_T0.160540.681
41_N75_T0.159220.675
34_L65_G0.158080.670
60_Y64_P0.156740.664
4_C67_F0.155710.660
37_S64_P0.155580.660
34_L45_F0.154340.654
49_I71_I0.154180.654
59_E95_Y0.153650.651
16_F55_F0.15260.647
6_V37_S0.152490.646
3_G16_F0.152120.645
81_K88_K0.151620.643
75_T86_L0.151390.642
41_N87_L0.151090.640
64_P95_Y0.15010.636
79_T83_A0.149580.634
42_S78_K0.149310.633
41_N82_E0.149120.632
61_D68_G0.148660.630
59_E84_R0.148630.630
77_A82_E0.148550.630
19_K57_E0.148340.629
2_I65_G0.147790.626
75_T82_E0.147150.624
80_P84_R0.147090.624
16_F71_I0.147020.623
8_L13_M0.14660.621
32_K92_I0.146440.621
11_K37_S0.145820.618
22_T25_L0.145710.618
21_I95_Y0.142970.606
19_K23_I0.142670.605
5_K60_Y0.142330.603
25_L52_H0.141410.599
11_K64_P0.140770.597
45_F92_I0.140720.597
76_T82_E0.140640.596
29_K64_P0.140220.594
23_I53_I0.139790.593
8_L93_P0.139660.592
16_F20_L0.139540.592
11_K36_A0.138830.589
40_D94_F0.138590.587
80_P83_A0.138340.586
65_G85_L0.138160.586
50_K54_L0.138120.585
9_R30_D0.138040.585
74_V91_G0.137420.583
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
3bboH1100-0.055
1iq4A1100-0.048
1mjiA1100-0.047
3r8sF1100-0.047
3j21E0.926399.90.227
3j3bJ0.915899.90.233
3iz5E0.915899.90.241
4a17D0.915899.90.243
2zkrd0.915899.90.245
1vq8D0.905399.90.25

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