GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S19 - Ribosomal protein S19
Pfam: PF00203 (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: 81
Sequences: 1281
Seq/Len: 15.81
HH_delta: -0.038 (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
10_L35_S0.946073.797
21_N45_K0.783673.145
51_N54_K0.675212.710
28_V48_G0.659282.646
20_L45_K0.63882.564
31_T69_L0.583932.343
47_I60_I0.475011.906
9_V39_L0.458331.839
67_H72_F0.441451.772
18_K41_E0.422681.696
32_H55_F0.421151.690
37_T68_K0.392511.575
15_K19_K0.357771.436
14_L18_K0.356761.432
8_F12_K0.342451.374
14_L39_L0.340251.365
19_K22_P0.336021.349
28_V54_K0.329541.323
53_K56_V0.320931.288
70_G75_T0.319881.284
33_S36_S0.319341.282
20_L25_K0.312761.255
56_V73_A0.311041.248
51_N73_A0.30731.233
16_K29_I0.304671.223
8_F36_S0.300171.205
50_Y64_M0.295761.187
5_K9_V0.288861.159
18_K22_P0.285061.144
46_T57_P0.275731.107
49_V60_I0.273051.096
39_L63_E0.266621.070
24_K27_K0.261881.051
53_K77_K0.259411.041
47_I57_P0.257461.033
51_N56_V0.253421.017
8_F33_S0.252741.014
48_G64_M0.251421.009
64_M67_H0.24740.993
20_L27_K0.245150.984
17_I47_I0.244890.983
1_R4_W0.240720.966
67_H71_E0.233340.936
41_E63_E0.232870.935
19_K23_S0.225140.904
6_G62_P0.224860.902
48_G57_P0.224540.901
42_M47_I0.224350.900
1_R7_P0.223180.896
19_K25_K0.221410.889
68_K74_P0.221210.888
12_K35_S0.217650.873
46_T58_I0.215830.866
41_E55_F0.214330.860
6_G76_R0.213510.857
44_G73_A0.211330.848
51_N63_E0.210970.847
30_K54_K0.210450.845
42_M64_M0.208960.839
50_Y59_K0.207930.834
19_K51_N0.207780.834
11_K63_E0.206230.828
39_L42_M0.205620.825
32_H36_S0.205510.825
14_L37_T0.205170.823
11_K15_K0.2050.823
17_I45_K0.204710.822
28_V57_P0.203980.819
50_Y63_E0.199170.799
75_T81_H0.198260.796
39_L51_N0.198160.795
28_V45_K0.198080.795
39_L43_V0.197470.792
47_I55_F0.19570.785
11_K28_V0.195680.785
66_G71_E0.188310.756
47_I79_V0.186660.749
41_E62_P0.186310.748
2_S5_K0.184860.742
4_W7_P0.181940.730
62_P76_R0.179710.721
12_K15_K0.177130.711
2_S6_G0.176960.710
19_K49_V0.176950.710
21_N25_K0.175510.704
13_L31_T0.175330.704
31_T40_P0.175320.704
48_G55_F0.175160.703
34_R44_G0.174770.701
1_R6_G0.172890.694
22_P63_E0.172240.691
10_L33_S0.17140.688
21_N61_T0.171330.688
17_I42_M0.171110.687
13_L69_L0.170940.686
35_S58_I0.170170.683
13_L36_S0.167680.673
22_P27_K0.167640.673
44_G60_I0.167150.671
25_K59_K0.166820.669
27_K63_E0.162520.652
14_L41_E0.16210.651
8_F13_L0.159790.641
30_K37_T0.15960.641
11_K23_S0.156650.629
54_K77_K0.156120.627
26_K59_K0.155240.623
19_K27_K0.154840.621
5_K8_F0.154530.620
4_W8_F0.154360.619
25_K48_G0.153780.617
30_K62_P0.153670.617
27_K30_K0.153340.615
21_N24_K0.153330.615
12_K16_K0.152950.614
57_P80_K0.152430.612
31_T59_K0.151690.609
20_L26_K0.150510.604
58_I73_A0.149010.598
68_K76_R0.148650.597
54_K79_V0.147770.593
34_R51_N0.147590.592
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
3bbnS1100-0.038
3a1pB1100-0.038
3i1mS1100-0.036
2xzmS1100-0.016
3r8nS0.9753100-0.01
3j20T11000.007
3iz6R199.90.118
3u5cP199.90.118
3zeyI199.90.123
3j3aP199.90.129

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