GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UPF0020 - Putative RNA methylase family UPF0020
Pfam: PF01170 (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: CL0063
Length: 179
Sequences: 7758
Seq/Len: 43.34
HH_delta: 0.167 (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
108_D142_K1.206233.372
43_L66_G1.205863.371
68_D74_V1.02912.877
65_I107_V0.99672.786
37_C66_G0.978182.734
33_L67_S0.830362.321
37_C77_A0.802272.243
74_V92_F0.766452.142
71_P94_Q0.758762.121
81_L92_F0.708121.979
136_E139_R0.708031.979
77_A92_F0.69871.953
74_V94_Q0.692741.936
43_L64_I0.686521.919
31_V107_V0.640621.791
71_P75_R0.631581.765
67_S95_W0.589931.649
47_A64_I0.564631.578
136_E140_V0.561061.568
70_D73_A0.551331.541
32_V46_A0.551271.541
51_A89_Y0.54741.530
33_L107_V0.545121.524
65_I93_I0.543341.519
31_V108_D0.542541.517
74_V78_R0.532441.488
44_I80_N0.522441.460
110_I137_L0.522291.460
110_I141_L0.486651.360
75_R78_R0.484561.354
141_L145_A0.48241.348
141_L144_R0.481791.347
81_L90_I0.461151.289
65_I91_D0.460961.288
67_S93_I0.460421.287
144_R150_T0.45771.279
68_D73_A0.455691.274
18_A22_N0.453371.267
37_C43_L0.453181.267
27_R30_D0.45021.258
30_D109_A0.448791.254
81_L86_V0.446031.247
145_A149_T0.433451.212
31_V65_I0.430331.203
96_D99_E0.419341.172
68_D92_F0.412621.153
98_R132_Q0.409321.144
32_V111_V0.407331.139
35_P97_A0.398031.113
75_R79_E0.397161.110
106_S142_K0.396781.109
40_G77_A0.395041.104
37_C68_D0.393791.101
19_A23_L0.390121.090
82_K87_E0.384051.073
45_E48_L0.376831.053
47_A86_V0.374881.048
39_S73_A0.374131.046
22_N49_M0.372261.041
132_Q135_R0.372141.040
36_F112_T0.368481.030
30_D108_D0.368351.030
44_I81_L0.367891.028
95_W100_L0.36381.017
108_D144_R0.363081.015
127_E131_R0.358771.003
132_Q136_E0.358021.001
131_R135_R0.357410.999
66_G92_F0.354420.991
14_P18_A0.353790.989
66_G77_A0.352640.986
35_P137_L0.351360.982
109_A147_F0.347940.973
34_D38_G0.346220.968
133_F137_L0.342290.957
33_L140_V0.339870.950
135_R139_R0.338930.947
46_A111_V0.335520.938
45_E49_M0.334030.934
50_G53_I0.329560.921
126_L129_L0.328650.919
17_A21_L0.327860.916
34_D111_V0.325890.911
43_L47_A0.324760.908
79_E82_K0.324710.908
66_G90_I0.32070.896
128_K132_Q0.319590.893
72_K75_R0.312340.873
44_I86_V0.311560.871
128_K131_R0.306640.857
34_D66_G0.301950.844
34_D37_C0.298770.835
120_L152_N0.297840.833
152_N156_E0.297430.831
39_S80_N0.296360.828
76_G79_E0.294640.824
80_N84_A0.292730.818
147_F150_T0.292640.818
67_S100_L0.292490.818
137_L146_V0.292070.816
31_V54_P0.29070.813
20_L147_F0.290010.811
139_R143_P0.288580.807
79_E83_A0.287730.804
112_T137_L0.285860.799
42_I112_T0.284420.795
19_A22_N0.283040.791
35_P112_T0.282230.789
30_D144_R0.280670.785
41_T80_N0.280540.784
15_T19_A0.279680.782
38_G42_I0.277480.776
80_N83_A0.27640.773
48_L86_V0.275410.770
104_D139_R0.274790.768
78_R82_K0.272250.761
95_W99_E0.269690.754
101_P136_E0.268360.750
123_K128_K0.264940.741
20_L111_V0.26370.737
137_L141_L0.26320.736
18_A21_L0.260440.728
43_L92_F0.259890.726
47_A89_Y0.259880.726
37_C40_G0.259560.726
122_S125_D0.259380.725
100_L140_V0.259340.725
33_L65_I0.258150.722
20_L42_I0.256910.718
38_G73_A0.254830.712
145_A150_T0.254670.712
112_T133_F0.254460.711
150_T155_L0.253760.709
50_G64_I0.253750.709
47_A90_I0.252440.706
15_T18_A0.251880.704
91_D94_Q0.251650.703
154_E157_K0.251110.702
134_L137_L0.248180.694
33_L110_I0.247360.691
36_F41_T0.244080.682
41_T45_E0.243660.681
32_V109_A0.243580.681
123_K126_L0.242940.679
112_T148_L0.239540.670
48_L84_A0.233670.653
42_I111_V0.233150.652
129_L133_F0.23220.649
26_W32_V0.230780.645
20_L24_A0.228240.638
16_L20_L0.227690.636
86_V89_Y0.227640.636
36_F97_A0.226530.633
39_S42_I0.225630.631
71_P78_R0.224580.628
138_K143_P0.222530.622
46_A50_G0.222330.621
74_V77_A0.220460.616
119_R123_K0.220270.616
31_V106_S0.220190.615
43_L90_I0.219220.613
95_W98_R0.217140.607
106_S140_V0.216850.606
98_R129_L0.216250.604
22_N25_G0.216210.604
119_R124_K0.215260.602
144_R155_L0.214410.599
46_A64_I0.212430.594
29_G108_D0.211780.592
39_S76_G0.211110.590
36_F42_I0.210360.588
133_F147_F0.210360.588
50_G54_P0.210170.587
150_T153_R0.209790.586
68_D95_W0.209630.586
34_D129_L0.209280.585
18_A48_L0.20880.584
122_S128_K0.208290.582
44_I48_L0.207730.581
36_F67_S0.207350.580
32_V53_I0.206050.576
130_Y134_L0.205340.574
73_A76_G0.204830.573
26_W30_D0.203070.568
34_D40_G0.202590.566
137_L145_A0.202450.566
106_S143_P0.200870.561
97_A136_E0.20080.561
134_L149_T0.199550.558
20_L146_V0.199280.557
146_V150_T0.199170.557
150_T156_E0.199080.556
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
3ldgA0.988899.90.167
3k0bA0.988899.90.174
3v97A199.90.176
3tm4A0.944199.90.186
3lduA0.988899.90.189
3tmaA0.938599.90.205
3khkA0.972199.80.33
2okcA0.972199.80.34
2f8lA0.960999.80.345
3lkdA0.966599.80.348

Page generated in 0.055 seconds.