GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L2 - Ribosomal Proteins L2 RNA binding domain
Pfam: PF00181 (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: CL0021
Length: 77
Sequences: 1653
Seq/Len: 21.47
HH_delta: -0.086 (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
38_I54_K1.271983.824
35_G53_V0.985672.963
70_K73_D0.946412.845
3_N9_T0.878152.640
54_K60_K0.787672.368
29_N61_R0.77682.335
31_G77_S0.718272.159
30_K57_D0.676782.035
69_M75_I0.661771.989
36_I74_I0.635221.910
39_D71_V0.630951.897
34_K56_E0.614861.848
66_P69_M0.596631.794
10_S13_R0.592921.782
34_K74_I0.583571.754
37_V69_M0.553241.663
51_A65_A0.539911.623
56_E74_I0.503181.513
34_K76_E0.493491.484
36_I54_K0.482221.450
30_K59_E0.463991.395
38_I60_K0.445611.340
36_I56_E0.432141.299
8_I12_H0.416461.252
51_A69_M0.410631.234
43_D46_R0.399891.202
47_S65_A0.398161.197
35_G55_Y0.380041.142
33_I56_E0.374361.125
49_P67_E0.369751.112
39_D49_P0.363911.094
63_I66_P0.360571.084
17_H20_R0.331540.997
53_V75_I0.322860.971
39_D52_L0.322150.968
10_S49_P0.318770.958
40_I51_A0.3180.956
39_D60_K0.314650.946
52_L62_Y0.314280.945
5_S20_R0.313840.943
2_R62_Y0.306760.922
32_N76_E0.302860.910
49_P73_D0.300590.904
19_R45_N0.298520.897
20_R67_E0.289520.870
8_I13_R0.284520.855
20_R49_P0.284030.854
53_V61_R0.282920.851
15_G62_Y0.281130.845
7_R65_A0.275720.829
13_R19_R0.272850.820
30_K33_I0.269280.810
39_D51_A0.269010.809
36_I72_G0.26380.793
41_E45_N0.263430.792
2_R6_G0.261820.787
15_G18_K0.259990.782
24_I50_I0.259540.780
48_A65_A0.25940.780
7_R12_H0.258510.777
39_D54_K0.258510.777
37_V53_V0.254650.766
19_R50_I0.252980.761
37_V51_A0.251370.756
52_L60_K0.251190.755
7_R13_R0.248930.748
7_R47_S0.247880.745
20_R39_D0.247640.744
29_N68_G0.242760.730
3_N7_R0.238510.717
55_Y77_S0.235080.707
40_I71_V0.232260.698
55_Y58_G0.231710.697
10_S65_A0.230580.693
56_E76_E0.229690.691
41_E50_I0.229030.689
41_E62_Y0.224860.676
4_N23_I0.224420.675
40_I49_P0.218070.656
21_Y45_N0.215890.649
12_H31_G0.215380.647
67_E70_K0.214870.646
22_R43_D0.214840.646
49_P54_K0.21060.633
31_G47_S0.210250.632
1_G6_G0.208630.627
15_G44_P0.207610.624
16_G19_R0.206130.620
53_V56_E0.20510.617
5_S8_I0.202770.610
21_Y24_I0.202660.609
29_N67_E0.202030.607
14_G43_D0.201870.607
5_S9_T0.201780.607
33_I59_E0.199680.600
63_I75_I0.198610.597
28_R63_I0.198480.597
5_S10_S0.196430.591
22_R25_D0.193190.581
23_I27_K0.190970.574
53_V63_I0.187870.565
3_N6_G0.187370.563
43_D64_I0.186940.562
39_D50_I0.186380.560
14_G50_I0.183050.550
40_I65_A0.182630.549
49_P68_G0.180930.544
17_H67_E0.179970.541
4_N10_S0.179660.540
20_R76_E0.179490.540
38_I51_A0.178980.538
15_G45_N0.178370.536
40_I60_K0.177210.533
58_G62_Y0.175720.528
11_R52_L0.175610.528
22_R44_P0.172640.519
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
3j3wC199.9-0.086
3r8sC199.9-0.085
3v2dD199.9-0.081
3bboE199.9-0.076
3jywB0.97499.90.079
3iz5B0.97499.90.087
3j3bA0.97499.90.087
4a17A0.97499.90.092
3j21B0.96199.90.107
1vq8A0.935199.80.16

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