GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S9 - Ribosomal protein S9S16
Pfam: PF00380 (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: 121
Sequences: 1602
Seq/Len: 13.24
HH_delta: -0.011 (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
109_R115_K0.978013.916
75_A95_L0.67872.717
56_A70_I0.677142.711
102_V111_K0.641382.568
79_V95_L0.617382.472
27_E36_R0.598812.397
10_V73_A0.572212.291
109_R116_P0.569562.280
111_K114_K0.553412.216
33_P36_R0.542632.173
18_K25_P0.5412.166
87_P91_K0.522922.094
43_L54_I0.516512.068
13_K55_F0.477041.910
18_K53_D0.437321.751
17_G53_D0.436491.748
110_K116_P0.430131.722
25_P28_E0.429861.721
52_F81_F0.428431.715
45_L92_A0.421361.687
2_K76_R0.419561.680
26_L36_R0.414041.658
41_E71_R0.410581.644
79_V86_K0.402711.612
110_K114_K0.3771.509
38_K41_E0.36591.465
41_E94_L0.365511.463
26_L39_I0.361681.448
15_G53_D0.358621.436
48_T85_L0.354071.418
58_V70_I0.350411.403
40_L49_L0.346911.389
5_T101_R0.340561.364
68_G71_R0.336431.347
103_E106_K0.336141.346
19_I39_I0.323941.297
24_K28_E0.318631.276
31_P36_R0.316311.266
48_T52_F0.312411.251
30_F70_I0.312021.249
90_K95_L0.30381.216
88_E91_K0.297381.191
16_S53_D0.29561.184
9_R57_N0.295161.182
2_K101_R0.294871.181
86_K90_K0.294831.180
44_E49_L0.293641.176
11_W57_N0.286911.149
12_L77_A0.284531.139
23_G57_N0.282461.131
20_R55_F0.282231.130
46_T85_L0.28111.125
64_S68_G0.279591.119
102_V105_K0.276591.107
110_K115_K0.269621.079
3_R68_G0.267791.072
48_T51_K0.263331.054
110_K118_W0.262311.050
111_K115_K0.25921.038
75_A79_V0.257211.030
37_E41_E0.250881.004
6_A65_G0.248410.995
35_L63_I0.247150.990
105_K108_G0.246680.988
81_F85_L0.245780.984
45_L88_E0.244990.981
48_T82_N0.240540.963
12_L54_I0.23790.952
46_T89_L0.237520.951
34_Y37_E0.236830.948
8_A58_V0.230050.921
14_P51_K0.221910.888
31_P39_I0.218820.876
73_A97_R0.218690.876
1_G7_I0.216910.868
43_L48_T0.213280.854
102_V114_K0.212570.851
32_N35_L0.212410.850
86_K95_L0.209280.838
12_L52_F0.206550.827
107_P119_S0.205910.824
111_K116_P0.205550.823
32_N37_E0.204720.820
39_I42_P0.203630.815
6_A36_R0.20080.804
12_L74_I0.199860.800
39_I67_A0.19930.798
40_L43_L0.199010.797
61_G65_G0.198920.796
107_P116_P0.197550.791
33_P37_E0.197030.789
38_K68_G0.194350.778
11_W76_R0.193470.775
8_A21_I0.193460.775
114_K118_W0.193120.773
31_P63_I0.192940.772
82_N85_L0.192430.770
33_P40_L0.188390.754
20_R23_G0.187930.752
2_K7_I0.186750.748
72_L97_R0.18630.746
117_Q121_R0.184290.738
8_A70_I0.184240.738
20_R25_P0.182850.732
32_N63_I0.182360.730
29_Y104_R0.182330.730
27_E31_P0.181040.725
30_F104_R0.177730.712
27_E40_L0.177080.709
36_R40_L0.176760.708
79_V85_L0.176710.708
107_P118_W0.176580.707
37_E44_E0.176030.705
35_L64_S0.175910.704
113_R121_R0.174410.698
33_P63_I0.174140.697
23_G59_K0.174130.697
11_W56_A0.173720.696
36_R39_I0.173130.693
93_G96_T0.172110.689
38_K45_L0.171790.688
109_R114_K0.17140.686
13_K53_D0.171380.686
43_L50_G0.170810.684
6_A61_G0.169270.678
35_L38_K0.167730.672
43_L52_F0.164570.659
38_K71_R0.164530.659
47_G88_E0.163330.654
51_K82_N0.162810.652
46_T52_F0.161690.647
44_E47_G0.160890.644
26_L31_P0.160850.644
110_K119_S0.159780.640
31_P70_I0.159670.639
13_K16_S0.159620.639
72_L75_A0.159580.639
32_N41_E0.159030.637
30_F39_I0.159020.637
2_K72_L0.158980.637
21_I25_P0.158630.635
30_F64_S0.158580.635
7_I107_P0.158490.635
21_I30_F0.158180.633
60_G66_Q0.157550.631
10_V54_I0.156290.626
15_G22_N0.154720.619
93_G104_R0.154710.619
105_K110_K0.154390.618
38_K94_L0.153960.616
88_E92_A0.153220.613
14_P84_S0.153130.613
16_S37_E0.152350.610
71_R94_L0.151740.608
90_K96_T0.151630.607
48_T73_A0.151580.607
1_G9_R0.151090.605
111_K119_S0.151010.605
13_K19_I0.150610.603
7_I59_K0.150540.603
50_G101_R0.150420.602
9_R97_R0.149870.600
44_E88_E0.148080.593
34_Y107_P0.14720.589
65_G68_G0.147090.589
52_F78_L0.146590.587
51_K91_K0.146430.586
61_G66_Q0.146040.585
40_L44_E0.145440.582
3_R77_A0.145120.581
102_V110_K0.144620.579
6_A69_A0.144580.579
51_K80_K0.144280.578
34_Y38_K0.143940.576
73_A78_L0.143140.573
26_L101_R0.143090.573
4_K8_A0.142850.572
95_L107_P0.142330.570
38_K67_A0.14080.564
40_L50_G0.140410.562
2_K24_K0.140260.562
19_I52_F0.139420.558
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
2vqeI1100-0.011
3r8nI1100-0.01
3bbnI1100-0.003
2xzmI0.99171000.022
2zkqi0.99171000.022
3iz6I0.99171000.03
3u5cQ0.99171000.032
3j3aQ0.99171000.032
3j20K0.99171000.045
3zeyK0.99171000.077

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