GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L21p - Ribosomal prokaryotic L21 protein
Pfam: PF00829 (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: 96
Sequences: 1594
Seq/Len: 16.6
HH_delta: -0.04 (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
28_E31_D1.144263.763
6_E37_K1.119723.682
68_K92_P0.972833.199
73_I86_K0.932973.068
27_A63_V0.928483.053
15_E18_D0.862542.836
34_E58_K0.856712.817
21_D95_R0.729072.398
32_K60_E0.720722.370
78_K83_Y0.630472.073
35_L96_I0.618832.035
22_V96_I0.603871.986
19_V95_R0.590241.941
77_K80_R0.589531.939
40_L47_T0.571891.881
35_L61_A0.555881.828
61_A96_I0.549021.805
34_E60_E0.54541.794
7_I22_V0.517131.701
6_E53_Y0.504041.658
10_K23_E0.484471.593
65_E95_R0.476741.568
40_L49_I0.476731.568
67_G93_Y0.459541.511
27_A31_D0.449981.480
7_I23_E0.42721.405
5_I35_L0.419921.381
75_F86_K0.416521.370
74_V87_Q0.403491.327
75_F84_R0.402181.323
42_G45_D0.400991.319
21_D69_G0.395971.302
19_V64_L0.394891.299
54_L57_A0.378571.245
63_V94_T0.377611.242
76_K83_Y0.376121.237
49_I52_P0.360811.187
37_K53_Y0.354171.165
7_I12_Y0.350941.154
29_V65_E0.340641.120
43_S46_F0.330071.085
65_E93_Y0.324961.069
77_K84_R0.324491.067
21_D65_E0.313371.031
74_V83_Y0.310671.022
50_G53_Y0.30811.013
71_K90_R0.304061.000
52_P56_G0.302520.995
67_G95_R0.295580.972
21_D67_G0.294720.969
69_G93_Y0.291340.958
24_R92_P0.290240.954
78_K82_R0.289460.952
50_G54_L0.277830.914
14_V61_A0.272840.897
5_I14_V0.268810.884
20_I96_I0.26680.877
41_I54_L0.265560.873
74_V82_R0.264940.871
8_G23_E0.264620.870
41_I57_A0.264230.869
12_Y20_I0.264190.869
32_K62_T0.262620.864
67_G92_P0.25720.846
71_K88_G0.256010.842
4_I8_G0.241130.793
23_E91_Q0.239160.786
83_Y87_Q0.238920.786
5_I59_V0.237210.780
23_E93_Y0.235910.776
74_V84_R0.233860.769
43_S47_T0.226090.743
14_V18_D0.223510.735
82_R85_R0.22270.732
12_Y18_D0.221270.728
12_Y15_E0.219970.723
24_R66_H0.217980.717
20_I61_A0.216680.713
77_K83_Y0.216470.712
19_V65_E0.216150.711
23_E89_H0.212870.700
77_K81_K0.209710.690
39_L52_P0.207950.684
72_I87_Q0.203060.668
25_L66_H0.199380.656
37_K52_P0.194620.640
3_A11_Q0.188250.619
30_G62_T0.187360.616
16_E19_V0.1860.612
25_L94_T0.181830.598
78_K81_K0.179670.591
38_V52_P0.1780.585
11_Q71_K0.177780.585
7_I10_K0.173980.572
66_H92_P0.173460.570
77_K82_R0.171570.564
69_G95_R0.171510.564
53_Y56_G0.171210.563
29_V60_E0.171090.563
1_M20_I0.170670.561
48_L54_L0.170250.560
11_Q39_L0.169740.558
42_G46_F0.168370.554
51_R54_L0.168080.553
11_Q88_G0.167220.550
33_I61_A0.167110.550
4_I95_R0.166030.546
73_I76_K0.165160.543
66_H94_T0.161060.530
38_V59_V0.158750.522
2_Y43_S0.158490.521
29_V92_P0.158370.521
73_I87_Q0.15750.518
22_V25_L0.156710.515
19_V53_Y0.15670.515
88_G91_Q0.156620.515
15_E20_I0.156170.514
2_Y47_T0.156040.513
7_I25_L0.155830.512
60_E64_L0.154790.509
93_Y96_I0.154320.507
26_D66_H0.152910.503
7_I13_K0.152850.503
1_M30_G0.152680.502
79_R83_Y0.15220.501
50_G56_G0.151650.499
2_Y13_K0.151260.497
79_R86_K0.151180.497
16_E81_K0.151070.497
45_D55_E0.150430.495
16_E51_R0.149860.493
73_I78_K0.149840.493
73_I84_R0.149260.491
76_K82_R0.148660.489
45_D48_L0.148620.489
42_G68_K0.14860.489
14_V20_I0.148090.487
28_E38_V0.147580.485
21_D64_L0.147250.484
8_G13_K0.146170.481
24_R91_Q0.145840.480
57_A75_F0.145630.479
5_I9_G0.14540.478
5_I22_V0.145370.478
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
3bboT1100-0.04
3r8sR1100-0.025
3j3wR0.9896100-0.008
3v2dV0.97921000.001
2zjrO0.96881000.016
2xhaA0.87546.40.903
2lnvA0.604234.80.91
2wg5A0.604221.50.918
2y4xA0.583319.10.92
3pjyA0.333314.90.923

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