GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RNA_ligase - RNA ligase
Pfam: PF09414 (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: CL0078
Length: 186
Sequences: 4654
Seq/Len: 25.02
HH_delta: 0.277 (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
5_V169_I0.841652.952
26_F49_Y0.824282.891
2_E172_E0.729232.557
117_L121_E0.687982.413
125_F129_L0.659512.313
19_D73_N0.652092.287
9_L81_V0.59422.084
16_I26_F0.592472.078
89_K92_Y0.56951.997
16_I56_L0.545011.911
78_G100_F0.533041.869
144_E147_D0.526431.846
120_D172_E0.522231.831
13_N77_Y0.520091.824
6_T170_K0.517321.814
125_F128_E0.508891.785
4_V119_W0.497851.746
118_S121_E0.495571.738
99_D132_K0.477591.675
121_E124_E0.472791.658
84_K163_I0.458871.609
147_D150_D0.458671.609
19_D24_V0.456351.600
4_V172_E0.446321.565
124_E128_E0.436871.532
20_N72_E0.436811.532
25_R33_L0.432751.518
14_F100_F0.427091.498
148_L169_I0.424721.490
120_D124_E0.421611.479
105_I125_F0.420241.474
173_D176_H0.410441.439
76_I102_V0.409281.435
122_V126_A0.407161.428
143_T147_D0.407021.427
85_P161_G0.402481.412
16_I100_F0.399451.401
146_D150_D0.392211.376
104_D122_V0.390241.369
14_F26_F0.390011.368
14_F49_Y0.382591.342
120_D139_R0.382191.340
142_F147_D0.377051.322
15_S106_Y0.374971.315
111_Q117_L0.373381.309
124_E127_E0.3731.308
83_A99_D0.372331.306
14_F80_L0.371581.303
9_L101_Y0.363791.276
72_E109_D0.362221.270
83_A86_S0.361681.268
119_W122_V0.359341.260
88_Q92_Y0.358471.257
15_S75_I0.357311.253
90_N94_L0.355731.248
86_S97_P0.354971.245
122_V174_E0.353571.240
14_F45_G0.352181.235
17_Y75_I0.347171.218
18_F21_D0.344341.208
108_I125_F0.342391.201
17_Y73_N0.342281.200
134_V162_N0.34121.197
4_V120_D0.331031.161
13_N104_D0.326681.146
17_Y25_R0.32471.139
81_V101_Y0.324311.137
120_D173_D0.323481.134
116_Y122_V0.322091.130
8_K79_E0.31811.116
52_Q80_L0.314641.103
158_S162_N0.309571.086
82_G96_P0.295021.035
4_V123_R0.29451.033
111_Q125_F0.292811.027
14_F28_S0.286071.003
2_E143_T0.285571.002
6_T123_R0.283120.993
12_T28_S0.281790.988
8_K165_E0.277550.973
7_E164_R0.273640.960
89_K93_Q0.273150.958
118_S122_V0.272880.957
82_G86_S0.27230.955
17_Y27_Q0.269710.946
15_S27_Q0.267440.938
5_V151_L0.266450.934
7_E151_L0.266220.934
8_K29_R0.263980.926
10_D29_R0.263440.924
11_G166_G0.262410.920
13_N80_L0.262220.920
81_V99_D0.261370.917
8_K11_G0.260220.913
118_S172_E0.255820.897
49_Y52_Q0.255660.897
145_L149_D0.254210.892
28_S45_G0.25380.890
73_N110_E0.253560.889
5_V148_L0.251270.881
157_P161_G0.250340.878
18_F24_V0.247990.870
29_R79_E0.245310.860
26_F50_W0.245240.860
2_E171_P0.244980.859
20_N73_N0.241380.847
49_Y80_L0.238580.837
3_V171_P0.238090.835
122_V125_F0.237190.832
55_W132_K0.236660.830
52_Q55_W0.230830.810
127_E137_L0.230240.807
146_D149_D0.229230.804
15_S104_D0.2290.803
26_F80_L0.227850.799
139_R172_E0.224250.786
105_I122_V0.224220.786
55_W99_D0.223760.785
15_S77_Y0.222990.782
88_Q93_Q0.218820.767
82_G165_E0.218640.767
51_A97_P0.216930.761
123_R137_L0.216030.758
86_S99_D0.215730.757
150_D158_S0.215340.755
124_E137_L0.214960.754
18_F74_I0.214920.754
12_T45_G0.210010.737
149_D157_P0.208950.733
2_E173_D0.208940.733
82_G98_K0.208720.732
13_N103_F0.208610.732
87_I90_N0.208090.730
119_W123_R0.207330.727
5_V142_F0.202810.711
13_N176_H0.199640.700
123_R126_A0.199610.700
116_Y125_F0.199570.700
70_L73_N0.198560.696
101_Y162_N0.198550.696
19_D25_R0.19830.695
119_W174_E0.198180.695
74_I129_L0.197940.694
120_D135_P0.197150.691
31_H45_G0.196840.690
151_L167_I0.195620.686
46_D53_A0.195550.686
79_E165_E0.194970.684
9_L134_V0.194170.681
27_Q30_S0.193450.678
7_E136_V0.192460.675
157_P160_E0.192180.674
24_V56_L0.192020.673
84_K161_G0.191850.673
45_G80_L0.190310.667
5_V167_I0.190110.667
3_V169_I0.189460.664
9_L28_S0.188320.660
164_R167_I0.187740.658
19_D22_G0.186870.655
15_S169_I0.185530.651
27_Q31_H0.184930.649
75_I107_D0.183650.644
74_I108_I0.183040.642
12_T49_Y0.182580.640
116_Y175_F0.182410.640
78_G148_L0.182020.638
159_G164_R0.181570.637
117_L124_E0.181250.636
22_G125_F0.181220.636
121_E125_F0.18060.633
120_D137_L0.180270.632
2_E139_R0.179670.630
142_F148_L0.179230.629
158_S161_G0.178210.625
52_Q98_K0.177690.623
84_K87_I0.177420.622
12_T93_Q0.176740.620
117_L125_F0.176340.618
133_T145_L0.176120.618
53_A97_P0.174760.613
148_L152_F0.173010.607
108_I122_V0.17220.604
117_L135_P0.17220.604
10_D28_S0.172170.604
13_N106_Y0.172120.604
102_V126_A0.169610.595
7_E159_G0.169440.594
138_Y142_F0.168920.592
100_F104_D0.168840.592
22_G72_E0.167680.588
6_T9_L0.166310.583
120_D128_E0.1650.579
26_F100_F0.164720.578
77_Y176_H0.164030.575
90_N93_Q0.163540.574
21_D57_F0.163070.572
17_Y107_D0.162950.571
76_I100_F0.162590.570
121_E128_E0.162550.570
6_T119_W0.162350.569
80_L100_F0.162290.569
117_L173_D0.162180.569
10_D79_E0.162120.569
15_S32_I0.161690.567
27_Q165_E0.161610.567
76_I105_I0.161580.567
83_A101_Y0.161260.566
108_I111_Q0.161110.565
122_V176_H0.160790.564
145_L148_L0.160780.564
126_A131_L0.158820.557
12_T80_L0.158480.556
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
2hvqA0.940999.90.277
1s68A0.935599.90.292
1xdnA0.989299.90.292
1x9nA0.876399.90.328
3gdeA0.844199.90.335
3w1bA0.87199.90.335
2cfmA0.854899.90.339
2hivA0.854899.90.341
3l2pA0.87199.90.363
1vs0A0.838799.80.376

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