GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L23 - Ribosomal protein L23
Pfam: PF00276 (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: CL0221
Length: 91
Sequences: 1949
Seq/Len: 21.42
HH_delta: -0.023 (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
36_I53_T0.941183.137
29_P55_N0.775972.586
58_G72_D0.754622.515
6_K26_E0.716082.387
54_M77_I0.683242.277
22_Q77_I0.68152.271
56_Y73_Y0.667592.225
49_K81_K0.666062.220
53_T74_K0.658862.196
47_K81_K0.618352.061
5_K28_D0.571171.904
41_E47_K0.560571.868
4_I43_I0.536671.789
32_T35_E0.529071.763
60_K67_V0.525881.753
26_E73_Y0.510041.700
60_K69_K0.507761.692
47_K84_D0.504211.681
56_Y75_K0.500531.668
69_K72_D0.499751.666
38_E42_K0.488751.629
8_V26_E0.472931.576
19_N22_Q0.452851.509
40_I78_V0.446531.488
49_K79_T0.431221.437
35_E38_E0.429031.430
23_Y86_I0.426981.423
63_K66_F0.413161.377
53_T76_A0.409831.366
27_V36_I0.400091.334
34_T38_E0.398351.328
52_N79_T0.38261.275
21_N85_K0.361471.205
54_M75_K0.357091.190
34_T37_K0.354161.180
22_Q52_N0.351491.172
48_V81_K0.347711.159
29_P72_D0.332381.108
40_I48_V0.327631.092
46_V80_L0.310651.035
13_S24_T0.310391.035
48_V51_V0.30981.033
24_T77_I0.304011.013
2_D5_K0.301191.004
31_A39_A0.298380.995
63_K68_G0.287120.957
80_L84_D0.273610.912
8_V24_T0.271370.904
41_E48_V0.271160.904
55_N72_D0.270790.903
3_I39_A0.270580.902
26_E71_K0.270480.902
17_L85_K0.260430.868
7_P25_F0.25530.851
58_G70_T0.25460.849
16_L22_Q0.254520.848
27_V48_V0.249720.832
87_P90_E0.249630.832
10_T14_M0.24940.831
66_F71_K0.248650.829
31_A36_I0.243860.813
31_A76_A0.243710.812
58_G69_K0.242560.808
48_V78_V0.240020.800
62_R67_V0.239590.799
5_K26_E0.237510.792
37_K41_E0.237130.790
12_K15_K0.230290.768
49_K52_N0.230130.767
26_E75_K0.227110.757
39_A76_A0.226250.754
40_I43_I0.224910.750
57_P71_K0.221360.738
57_P72_D0.221230.737
22_Q79_T0.218620.729
60_K70_T0.218320.728
15_K19_N0.217930.726
23_Y89_F0.21670.722
14_M17_L0.215360.718
9_I14_M0.205850.686
5_K9_I0.204050.680
16_L24_T0.203740.679
16_L77_I0.199720.666
25_F40_I0.198550.662
64_G68_G0.195770.653
49_K82_E0.19550.652
25_F78_V0.195360.651
36_I76_A0.195350.651
36_I74_K0.194520.648
45_G84_D0.194480.648
49_K80_L0.194160.647
64_G67_V0.19270.642
21_N83_G0.190850.636
23_Y77_I0.187760.626
11_E31_A0.186710.622
3_I35_E0.185220.617
19_N69_K0.184530.615
57_P63_K0.184190.614
32_T38_E0.183660.612
81_K84_D0.182930.610
2_D79_T0.18130.604
16_L19_N0.179480.598
25_F33_K0.178620.595
45_G60_K0.17860.595
23_Y88_L0.17780.593
42_K45_G0.177680.592
39_A43_I0.177180.591
57_P73_Y0.176240.587
25_F86_I0.174770.583
19_N30_R0.174550.582
12_K16_L0.174540.582
66_F69_K0.17380.579
15_K18_E0.172640.575
8_V13_S0.17170.572
7_P76_A0.171460.571
82_E85_K0.171390.571
14_M89_F0.168530.562
59_K70_T0.168410.561
9_I39_A0.167590.559
28_D35_E0.167540.558
43_I76_A0.166380.555
46_V81_K0.166240.554
77_I85_K0.16470.549
10_T60_K0.163390.545
50_K67_V0.162970.543
80_L83_G0.162730.542
60_K73_Y0.161690.539
39_A51_V0.160760.536
31_A43_I0.16060.535
2_D10_T0.160040.533
12_K82_E0.15920.531
71_K74_K0.157820.526
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
3tveT0.989100-0.023
3j3wT0.989100-0.016
2zjrQ0.989100-0.014
3r8sT0.945199.90.014
3bboV0.857199.90.124
2zkrs0.857199.90.13
1vq8S0.857199.90.148
3u5eX0.857199.90.167
3j39X0.857199.90.167
3j3bX0.857199.90.17

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