GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S11 - Ribosomal protein S11
Pfam: PF00411 (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: CL0267
Length: 110
Sequences: 1127
Seq/Len: 10.25
HH_delta: -0.051 (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
2_I67_K0.538142.929
15_T23_V0.517342.816
65_R91_S0.491232.674
18_D22_N0.442012.406
27_S31_S0.418352.277
65_R90_V0.407482.218
27_S51_K0.400542.180
64_V87_L0.400372.179
53_A85_S0.363641.979
51_K55_K0.348131.895
3_I64_V0.333921.817
82_L87_L0.323351.760
16_L82_L0.318251.732
54_K57_K0.315661.718
24_L61_I0.313231.705
66_V82_L0.309811.686
1_G61_I0.306671.669
3_I16_L0.304271.656
32_L43_Y0.284981.551
67_K93_T0.280791.528
67_K91_S0.276391.504
6_K13_I0.274061.492
32_L47_Q0.271011.475
17_T21_G0.266511.451
24_L59_L0.262991.431
61_I87_L0.260761.419
9_F71_F0.255981.393
63_T90_V0.251081.367
10_N39_K0.248961.355
61_I64_V0.245041.334
67_K95_V0.244171.329
49_A53_A0.226361.232
12_T40_S0.226211.231
32_L51_K0.224541.222
14_V52_I0.223771.218
63_T88_K0.223481.216
52_I56_A0.222421.211
68_I79_L0.221531.206
37_A40_S0.212961.159
83_K89_I0.210611.146
55_K106_K0.208031.132
3_I82_L0.2061.121
64_V89_I0.199921.088
104_R110_R0.194341.058
54_K58_E0.194011.056
2_I61_I0.19131.041
74_G86_G0.191181.041
2_I19_L0.189621.032
52_I59_L0.188861.028
70_G107_K0.187441.020
27_S32_L0.182570.994
69_K77_A0.179350.976
19_L23_V0.176960.963
43_Y47_Q0.176440.960
57_K62_K0.176250.959
13_I21_G0.173030.942
34_F44_A0.172460.939
53_A56_A0.171730.935
8_S73_P0.169860.925
19_L73_P0.169610.923
20_K67_K0.167480.912
31_S51_K0.164320.894
4_H95_V0.163410.889
42_P81_A0.163110.888
67_K89_I0.162990.887
19_L84_K0.161340.878
7_S74_G0.160510.874
37_A47_Q0.159160.866
53_A82_L0.158770.864
24_L39_K0.157850.859
16_L52_I0.157010.855
38_R69_K0.15660.852
83_K91_S0.156310.851
100_H103_C0.156030.849
99_P103_C0.155540.847
13_I17_T0.155360.846
17_T23_V0.154870.843
53_A64_V0.154360.840
35_K47_Q0.151980.827
6_K73_P0.151650.825
65_R83_K0.150940.822
83_K88_K0.149530.814
54_K93_T0.148050.806
90_V93_T0.147990.805
29_A32_L0.147780.804
45_A50_E0.14750.803
35_K55_K0.147040.800
45_A74_G0.146650.798
13_I29_A0.145750.793
68_I78_A0.145430.792
55_K73_P0.145240.791
6_K66_V0.14480.788
55_K59_L0.14460.787
20_K89_I0.144570.787
10_N109_R0.143470.781
44_A104_R0.143410.781
13_I103_C0.143110.779
11_N100_H0.142960.778
16_L56_A0.142530.776
74_G96_T0.142430.775
36_G39_K0.141610.771
69_K97_P0.139980.762
64_V67_K0.139630.760
64_V82_L0.138940.756
25_F52_I0.138260.753
31_S69_K0.137920.751
4_H17_T0.13770.749
32_L63_T0.137650.749
25_F59_L0.13720.747
16_L61_I0.13670.744
50_E62_K0.136330.742
52_I106_K0.13630.742
28_S32_L0.136290.742
6_K55_K0.134810.734
75_R94_D0.134450.732
2_I65_R0.133510.727
16_L87_L0.133470.726
73_P89_I0.133250.725
6_K109_R0.132670.722
5_I66_V0.131730.717
55_K88_K0.131690.717
9_F50_E0.131650.717
22_N38_R0.130910.713
54_K67_K0.130020.708
59_L108_K0.129990.708
40_S55_K0.129920.707
5_I79_L0.129720.706
3_I53_A0.129460.705
81_A84_K0.129050.702
59_L73_P0.127730.695
4_H31_S0.126880.691
58_E71_F0.126680.689
99_P102_G0.126520.689
31_S35_K0.126490.688
10_N68_I0.125870.685
41_T44_A0.124870.680
99_P105_P0.124760.679
12_T31_S0.124490.678
20_K23_V0.124440.677
1_G56_A0.124190.676
49_A86_G0.12410.675
95_V106_K0.122990.669
31_S55_K0.122730.668
2_I31_S0.122320.666
49_A81_A0.122140.665
40_S63_T0.121870.663
63_T77_A0.121820.663
19_L91_S0.121350.660
51_K79_L0.120260.655
18_D21_G0.120090.654
66_V69_K0.119880.652
79_L83_K0.119510.650
4_H67_K0.119240.649
41_T68_I0.118720.646
104_R109_R0.118260.644
20_K65_R0.117820.641
64_V85_S0.117460.639
6_K106_K0.117290.638
47_Q50_E0.117120.637
44_A75_R0.117110.637
47_Q54_K0.116920.636
6_K20_K0.116280.633
67_K98_I0.116270.633
19_L88_K0.116250.633
15_T28_S0.115760.630
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
3r8nK1100-0.051
2vqeK1100-0.045
3bbnK1100-0.044
3u5cO1100-0.007
3j20M11000.004
2xzmK11000.031
3j21O0.918296.40.838
3r8sO0.809196.30.84
3v2dS0.7818960.844
1ovyA0.809195.60.849

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