GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L13 - Ribosomal protein L13
Pfam: PF00572 (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: 128
Sequences: 1776
Seq/Len: 13.88
HH_delta: -0.041 (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
18_I42_V0.942933.239
56_R76_K0.911573.131
11_L50_L0.804822.764
50_L75_A0.768962.641
82_D85_R0.766272.632
7_K47_K0.753262.587
61_Y72_N0.693752.383
59_V72_N0.663812.280
39_H109_K0.591942.033
111_Y118_H0.574281.972
16_S20_K0.568661.953
55_W75_A0.564991.940
111_Y117_P0.564871.940
87_L91_V0.542431.863
61_Y70_L0.534771.837
85_R88_K0.522281.794
55_W79_H0.510311.753
73_P78_L0.504651.733
21_L40_V0.49981.717
79_H86_I0.499431.715
74_T77_G0.498611.712
4_I18_I0.498031.711
21_L26_H0.495161.701
45_A110_V0.49041.684
8_G49_V0.486731.672
46_E113_G0.477821.641
18_I91_V0.477721.641
6_A42_V0.475281.632
53_K57_Q0.467641.606
21_L126_L0.464421.595
43_I114_E0.458441.575
22_L108_L0.45691.569
15_A90_A0.456611.568
59_V74_T0.452031.553
53_K56_R0.445041.529
77_G81_K0.440441.513
103_E106_K0.436051.498
3_V43_I0.434651.493
9_Q127_E0.430781.480
73_P81_K0.425081.460
27_K38_D0.410021.408
60_Y75_A0.408211.402
23_L30_Y0.393161.350
7_K114_E0.390751.342
11_L48_I0.380511.307
88_K105_L0.380351.306
75_A79_H0.369721.270
9_Q17_K0.369531.269
6_A14_L0.369421.269
17_K20_K0.368811.267
36_C107_R0.36621.258
29_T36_C0.360631.239
75_A86_I0.348391.197
62_R73_P0.345311.186
46_E112_P0.3451.185
92_R105_L0.339071.165
18_I87_L0.3371.157
2_Y126_L0.33581.153
95_L105_L0.332651.143
7_K10_I0.332611.142
95_L101_G0.330691.136
85_R89_R0.325571.118
64_T71_K0.323191.110
55_W86_I0.319621.098
89_R92_R0.314631.081
73_P77_G0.313031.075
99_K102_R0.310461.066
115_P119_A0.308111.058
84_S112_P0.299161.027
3_V41_V0.291081.000
14_L87_L0.289420.994
91_V108_L0.289180.993
14_L18_I0.287660.988
17_K126_L0.287520.988
20_K26_H0.283030.972
55_W76_K0.276620.950
10_I49_V0.266880.917
95_L104_A0.264180.907
83_P112_P0.260590.895
78_L89_R0.260270.894
109_K117_P0.257840.886
93_G97_K0.256250.880
39_H107_R0.253950.872
101_G104_A0.252760.868
45_A83_P0.250460.860
31_T34_V0.24360.837
2_Y21_L0.242840.834
73_P82_D0.241820.831
5_D44_N0.23830.818
77_G80_E0.236940.814
104_A107_R0.233720.803
23_L104_A0.233420.802
86_I90_A0.227990.783
6_A48_I0.22480.772
45_A87_L0.224710.772
64_T69_G0.219810.755
78_L82_D0.21790.748
84_S88_K0.216950.745
17_K21_L0.216540.744
2_Y26_H0.215140.739
35_D107_R0.213710.734
62_R71_K0.213520.733
63_H68_G0.21230.729
26_H38_D0.211090.725
89_R93_G0.208610.716
11_L90_A0.207670.713
2_Y9_Q0.207040.711
4_I14_L0.20560.706
120_A123_P0.205460.706
41_V117_P0.204870.704
88_K106_K0.204340.702
2_Y40_V0.2030.697
51_T54_K0.201420.692
76_K80_E0.20060.689
14_L85_R0.198680.682
88_K110_V0.198490.682
2_Y39_H0.198140.681
118_H121_Q0.198030.680
12_G94_M0.196450.675
76_K79_H0.195130.670
119_A125_V0.194890.669
73_P80_E0.193320.664
87_L110_V0.192160.660
66_Y69_G0.190790.655
78_L93_G0.190490.654
9_Q14_L0.18990.652
105_L110_V0.189680.651
10_I51_T0.189570.651
4_I42_V0.187760.645
4_I29_T0.186960.642
29_T73_P0.186530.641
101_G105_L0.184820.635
23_L93_G0.184190.633
116_H120_A0.184120.632
62_R81_K0.180260.619
48_I87_L0.180110.619
23_L31_T0.17920.615
92_R101_G0.178950.615
64_T67_P0.178480.613
34_V104_A0.177330.609
41_V124_V0.174530.599
63_H69_G0.171880.590
97_K101_G0.171120.588
39_H117_P0.168870.580
14_L48_I0.168730.580
3_V114_E0.168380.578
4_I16_S0.162710.559
43_I46_E0.162250.557
28_P124_V0.162070.557
46_E83_P0.161430.554
103_E107_R0.16020.550
92_R97_K0.160110.550
7_K125_V0.160090.550
82_D89_R0.159930.549
59_V70_L0.159190.547
54_K116_H0.158750.545
56_R119_A0.158340.544
54_K69_G0.158120.543
72_N76_K0.158030.543
11_L75_A0.157890.542
68_G71_K0.157780.542
122_K125_V0.156470.537
88_K101_G0.155250.533
37_G40_V0.15510.533
27_K36_C0.155040.532
50_L55_W0.15490.532
18_I40_V0.154710.531
36_C39_H0.154320.530
79_H82_D0.154310.530
13_R16_S0.153450.527
110_V121_Q0.151950.522
15_A109_K0.15120.519
48_I84_S0.150950.518
46_E115_P0.150820.518
2_Y107_R0.150190.516
60_Y101_G0.149930.515
44_N47_K0.147780.508
2_Y124_V0.146850.504
54_K58_K0.146510.503
26_H126_L0.146050.502
98_N101_G0.14490.498
15_A87_L0.143620.493
27_K35_D0.143010.491
7_K49_V0.142880.491
7_K15_A0.14270.490
45_A88_K0.14260.490
60_Y86_I0.141780.487
27_K37_G0.14090.484
19_A23_L0.13950.479
45_A112_P0.139330.479
79_H84_S0.138970.477
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
3bboL1100-0.041
3f1fN1100-0.036
3v2dN1100-0.035
3r8sJ1100-0.035
2zjrG1100-0.034
3j3wJ1100-0.034
2ftcH1100-0.03
1j3aA0.89841000.145
4a17I0.90621000.185
1vq8J0.85161000.2

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