GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S10 - Ribosomal protein S10pS20e
Pfam: PF00338 (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: 97
Sequences: 1003
Seq/Len: 10.34
HH_delta: -0.032 (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
2_R70_Q0.628943.683
48_R56_S0.580323.398
45_T59_Q0.516353.024
42_K64_T0.479392.807
27_L78_L0.358252.098
45_T57_R0.319591.871
37_L68_L0.313061.833
47_L50_P0.304071.781
47_L51_H0.301751.767
56_S60_F0.278641.632
7_S86_Q0.265061.552
48_R60_F0.260691.527
10_K14_E0.256521.502
51_H57_R0.256351.501
18_K22_K0.255421.496
49_S53_D0.251511.473
39_T65_H0.248891.457
47_L56_S0.239951.405
7_S13_L0.235411.379
32_S69_I0.234461.373
80_D84_Y0.230981.353
49_S52_V0.230741.351
32_S72_K0.22671.328
22_K26_N0.224741.316
42_K45_T0.222621.304
49_S55_K0.222451.303
14_E67_R0.221551.297
51_H54_K0.219681.286
12_L76_S0.215761.263
44_F49_S0.213641.251
23_L26_N0.211931.241
52_V55_K0.208331.220
47_L52_V0.206771.211
41_K63_R0.197781.158
54_K57_R0.197561.157
36_P67_R0.192611.128
19_F84_Y0.192351.126
25_K31_V0.189221.108
11_K73_N0.188271.102
35_I66_K0.185741.088
48_R58_E0.1781.042
58_E61_E0.176771.035
49_S56_S0.176391.033
22_K55_K0.176381.033
75_N81_K0.175191.026
14_E36_P0.172351.009
30_K73_N0.170420.998
38_P66_K0.168840.989
25_K30_K0.167860.983
34_P67_R0.160490.940
6_K9_D0.156520.917
47_L55_K0.155360.910
81_K93_I0.154930.907
44_F53_D0.154620.905
40_K66_K0.154510.905
31_V69_I0.15330.898
50_P53_D0.152020.890
52_V56_S0.151970.890
6_K94_E0.15020.880
53_D57_R0.149860.878
83_L89_E0.149610.876
23_L83_L0.147390.863
15_S18_K0.14660.858
22_K29_I0.146460.858
20_I82_L0.144630.847
17_V31_V0.144630.847
21_H25_K0.142980.837
49_S54_K0.142650.835
44_F52_V0.142540.835
43_R59_Q0.141960.831
79_A85_I0.141340.828
22_K30_K0.140330.822
20_I36_P0.140320.822
11_K72_K0.140250.821
83_L94_E0.139830.819
86_Q92_Q0.139710.818
17_V96_K0.138820.813
15_S72_K0.138780.813
19_F43_R0.137890.807
18_K62_I0.137590.806
60_F76_S0.137430.805
47_L54_K0.136450.799
27_L82_L0.135820.795
34_P70_Q0.135440.793
77_E88_P0.135430.793
15_S22_K0.135010.791
19_F25_K0.13410.785
40_K43_R0.132830.778
80_D86_Q0.132070.773
22_K25_K0.131440.770
4_K66_K0.130620.765
37_L91_V0.129980.761
4_K73_N0.129860.760
4_K68_L0.129710.760
20_I23_L0.128270.751
44_F50_P0.126450.740
20_I88_P0.126330.740
79_A82_L0.125370.734
1_I13_L0.124940.732
7_S10_K0.124840.731
40_K62_I0.124370.728
15_S30_K0.123970.726
73_N76_S0.122960.720
32_S88_P0.122430.717
52_V57_R0.122060.715
38_P65_H0.122020.715
17_V21_H0.121650.712
18_K75_N0.121430.711
70_Q94_E0.121390.711
76_S83_L0.120970.708
38_P68_L0.120720.707
17_V40_K0.119520.700
75_N78_L0.119040.697
47_L57_R0.118980.697
27_L84_Y0.118960.697
26_N30_K0.118070.691
12_L93_I0.117790.690
9_D89_E0.11750.688
88_P93_I0.116270.681
45_T60_F0.115680.677
24_A90_G0.115330.675
34_P68_L0.11520.675
23_L85_I0.11520.675
49_S57_R0.114850.673
51_H56_S0.114490.670
39_T63_R0.114090.668
54_K59_Q0.113420.664
83_L87_L0.113390.664
87_L93_I0.113280.663
55_K90_G0.112560.659
49_S61_E0.112360.658
86_Q89_E0.111820.655
26_N76_S0.111030.650
74_L81_K0.110570.647
26_N62_I0.109850.643
10_K79_A0.109680.642
32_S79_A0.109590.642
46_V55_K0.109520.641
31_V48_R0.109160.639
3_I25_K0.108920.638
38_P90_G0.108910.638
71_I95_I0.10870.637
3_I11_K0.108490.635
10_K39_T0.108090.633
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
3r8nJ199.9-0.032
3bbnJ199.9-0.028
2vqeJ199.9-0.024
3j20L0.989799.9-0.007
3iz6J0.989799.9-0.002
3u5cU0.989799.9-0.001
3j3aU0.989799.90.003
2xzmJ0.989799.90.004
2zkqj0.989799.90.024
3zeyQ0.989799.90.047

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