GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L18p - Ribosomal L18pL5e family
Pfam: PF00861 (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: 119
Sequences: 1827
Seq/Len: 15.35
HH_delta: 0.003 (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
75_L78_E0.952073.193
91_K118_E0.917213.076
90_A118_E0.902993.028
78_E82_K0.814922.733
70_V107_A0.785762.635
69_N72_A0.756242.536
85_L90_A0.737332.473
81_A115_G0.735162.465
79_L83_R0.696452.336
82_K86_E0.684382.295
26_L37_A0.679892.280
55_S83_R0.589831.978
10_K97_G0.550231.845
112_A117_L0.536721.800
39_I84_A0.532731.787
31_S36_Y0.516191.731
39_I80_L0.512381.718
74_Y114_E0.485651.629
37_A80_L0.484151.624
74_Y111_G0.468891.572
37_A108_L0.459851.542
111_G115_G0.459191.540
35_I108_L0.44881.505
41_D44_K0.421051.412
7_R11_L0.405351.359
74_Y78_E0.400891.344
24_P42_D0.400871.344
27_V40_I0.400481.343
82_K85_L0.400011.341
5_R9_R0.389521.306
92_V119_F0.379461.273
39_I89_I0.37211.248
3_K7_R0.36891.237
30_R104_R0.367271.232
53_T72_A0.36481.223
46_G87_K0.360371.209
6_R99_Y0.355181.191
34_H54_L0.352771.183
11_L15_R0.3521.180
39_I92_V0.347231.164
81_A111_G0.345241.158
51_A79_L0.343041.150
26_L112_A0.336481.128
19_G24_P0.331621.112
15_R18_K0.330831.109
51_A83_R0.320991.076
108_L111_G0.315881.059
79_L88_G0.310831.042
79_L82_K0.302971.016
71_E74_Y0.301621.011
40_I49_A0.298991.003
78_E114_E0.293720.985
55_S79_L0.293690.985
32_N68_K0.29260.981
21_A44_K0.291420.977
75_L79_L0.288350.967
68_K72_A0.285850.959
21_A43_S0.283140.950
26_L80_L0.28010.939
80_L112_A0.27970.938
2_K10_K0.278410.934
27_V97_G0.276980.929
34_H53_T0.276020.926
57_E60_K0.275030.922
71_E75_L0.2750.922
109_A113_R0.273690.918
58_L79_L0.2690.902
61_Y75_L0.268790.901
77_G108_L0.268450.900
70_V74_Y0.268430.900
106_K110_D0.263450.883
18_K43_S0.263110.882
19_G22_E0.261240.876
28_V108_L0.257580.864
4_R11_L0.253880.851
3_K6_R0.253470.850
7_R10_K0.251930.845
16_K19_G0.251770.844
57_E83_R0.251550.844
29_F99_Y0.248320.833
51_A55_S0.247970.832
112_A119_F0.247350.829
58_L75_L0.245620.824
15_R19_G0.244350.819
35_I105_V0.24030.806
27_V99_Y0.238960.801
69_N104_R0.238830.801
76_V108_L0.238770.801
29_F36_Y0.237610.797
80_L108_L0.235320.789
10_K20_T0.234670.787
9_R34_H0.232080.778
78_E111_G0.230870.774
18_K22_E0.229480.770
4_R33_K0.229250.769
36_Y102_H0.226130.758
5_R32_N0.223680.750
83_R87_K0.222620.747
80_L117_L0.222310.746
4_R7_R0.221780.744
11_L16_K0.220660.740
48_L89_I0.220560.740
30_R97_G0.219830.737
85_L115_G0.219460.736
76_V80_L0.218680.733
108_L119_F0.217040.728
77_G111_G0.216160.725
3_K99_Y0.215250.722
49_A83_R0.214690.720
23_R91_K0.214110.718
35_I73_A0.211170.708
61_Y67_T0.210930.707
56_K60_K0.20990.704
3_K11_L0.209880.704
103_G109_A0.209390.702
22_E91_K0.208280.698
35_I76_V0.208080.698
26_L92_V0.204330.685
72_A104_R0.203910.684
34_H56_K0.201590.676
25_R95_D0.201540.676
10_K13_I0.1980.664
77_G112_A0.197920.664
6_R9_R0.197490.662
11_L18_K0.195930.657
84_A89_I0.19580.657
9_R12_R0.19520.655
34_H68_K0.194730.653
3_K10_K0.194670.653
94_F109_A0.192580.646
58_L72_A0.192490.646
94_F103_G0.192490.646
29_F32_N0.192230.645
2_K32_N0.190460.639
16_K20_T0.189980.637
36_Y99_Y0.188930.634
45_G48_L0.187280.628
55_S76_V0.186920.627
13_I20_T0.18620.624
7_R15_R0.185460.622
11_L27_V0.185330.622
2_K7_R0.185130.621
40_I45_G0.184640.619
11_L72_A0.184340.618
19_G42_D0.183570.616
7_R70_V0.182740.613
77_G81_A0.18270.613
2_K5_R0.182030.610
54_L72_A0.181360.608
2_K8_R0.180850.606
10_K27_V0.179670.603
36_Y106_K0.179570.602
81_A112_A0.179380.602
68_K71_E0.179190.601
80_L84_A0.178560.599
53_T76_V0.178310.598
2_K9_R0.178060.597
84_A117_L0.178060.597
55_S58_L0.176420.592
83_R86_E0.175670.589
18_K91_K0.175490.589
2_K6_R0.173650.582
42_D47_T0.173440.582
103_G113_R0.173230.581
95_D103_G0.172610.579
24_P41_D0.171640.576
96_R103_G0.171060.574
5_R15_R0.170310.571
58_L93_V0.170110.570
9_R13_I0.169020.567
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
3bboQ11000.003
3r8sO0.97481000.035
1ovyA0.96641000.051
3v2dS0.93281000.064
1vq8N0.98321000.098
2zjrL0.93281000.099
3j21O0.99161000.116
2zkrn0.98321000.188
3u5eD0.983299.90.256
4a17M0.983299.90.257

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