GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
2_5_RNA_ligase2 - 2-5 RNA ligase superfamily
Pfam: PF13563 (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: CL0247
Length: 153
Sequences: 2110
Seq/Len: 13.79
HH_delta: 0.237 (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
57_F141_V0.540853.519
58_E140_T0.48983.187
31_A92_R0.481563.133
65_G75_F0.475893.096
58_E138_S0.426542.775
65_G77_N0.334672.177
60_R138_S0.324872.114
59_L84_L0.311072.024
61_L78_V0.304491.981
103_D106_R0.288231.875
54_F90_A0.271111.764
30_L144_L0.263951.717
9_I76_L0.26251.708
88_H92_R0.26121.699
25_P149_S0.254931.659
73_V113_T0.252221.641
47_L91_L0.247841.612
8_E11_A0.242681.579
67_F75_F0.239911.561
51_A144_L0.239821.560
18_D115_A0.233581.520
61_L112_I0.227411.480
32_F116_R0.225511.467
32_F149_S0.223231.452
30_L88_H0.209071.360
125_E128_E0.207921.353
61_L76_L0.203951.327
37_D40_L0.200561.305
116_R149_S0.198861.294
10_E13_R0.197831.287
29_T113_T0.194821.267
60_R79_E0.193571.259
29_T111_H0.189911.236
49_R94_A0.186311.212
125_E129_K0.186231.212
41_D44_V0.185811.209
11_A15_Q0.183861.196
21_Y116_R0.183141.192
100_F103_D0.182491.187
31_A102_Q0.18231.186
11_A48_A0.181151.179
82_P86_A0.180931.177
124_A128_E0.180171.172
28_I59_L0.17921.166
45_E49_R0.177721.156
94_A97_P0.176091.146
33_P95_L0.174961.138
50_L54_F0.173061.126
43_L95_L0.172781.124
44_V48_A0.172511.122
53_G90_A0.171951.119
67_F73_V0.171351.115
116_R147_V0.170881.112
30_L108_F0.17051.109
92_R102_Q0.169981.106
86_A90_A0.169741.104
20_R23_R0.169671.104
21_Y26_P0.169621.104
94_A98_F0.167711.091
32_F75_F0.164521.070
9_I12_L0.162651.058
63_G78_V0.158491.031
31_A100_F0.158111.029
110_P116_R0.157151.022
33_P100_F0.155691.013
88_H110_P0.154231.003
91_L94_A0.154221.003
139_F147_V0.153791.001
134_F140_T0.153360.998
46_A95_L0.152270.991
67_F111_H0.151880.988
49_R52_A0.151620.986
85_E89_R0.15060.980
61_L139_F0.149470.972
58_E86_A0.147670.961
68_P71_G0.147440.959
18_D21_Y0.146950.956
95_L98_F0.145290.945
13_R18_D0.143220.932
34_F110_P0.14080.916
47_L146_L0.140160.912
25_P147_V0.13890.904
25_P34_F0.138030.898
25_P33_P0.137840.897
78_V112_I0.137220.893
32_F35_D0.136670.889
31_A43_L0.136530.888
71_G117_R0.136430.888
13_R26_P0.135870.884
9_I114_I0.1340.872
92_R114_I0.133930.871
13_R23_R0.133580.869
30_L91_L0.133490.868
51_A122_Q0.132750.864
90_A94_A0.132470.862
37_D90_A0.132430.862
27_H111_H0.13180.857
81_S84_L0.130840.851
34_F108_F0.129550.843
36_I43_L0.129340.841
24_W116_R0.129040.840
47_L144_L0.128640.837
73_V149_S0.127810.832
134_F137_I0.127720.831
19_K22_P0.127590.830
42_E53_G0.127280.828
59_L141_V0.127180.827
90_A142_D0.12650.823
54_F79_E0.125630.817
127_I130_L0.125360.816
40_L46_A0.125310.815
84_L108_F0.125150.814
39_S55_P0.124890.813
32_F73_V0.124660.811
20_R74_I0.123860.806
36_I40_L0.122670.798
50_L94_A0.122330.796
27_H67_F0.121310.789
91_L144_L0.121230.789
72_R117_R0.121030.787
12_L17_G0.120930.787
103_D108_F0.120770.786
68_P74_I0.120730.785
24_W149_S0.120720.785
38_D83_E0.120430.784
73_V108_F0.120380.783
57_F81_S0.120090.781
66_S71_G0.120.781
76_L114_I0.120.781
22_P25_P0.119690.779
48_A140_T0.119680.779
16_K72_R0.119650.778
142_D150_D0.119240.776
73_V116_R0.119120.775
31_A108_F0.118890.773
42_E45_E0.118290.770
24_W115_A0.118150.769
51_A54_F0.118010.768
68_P84_L0.117730.766
20_R26_P0.117530.765
28_I108_F0.117280.763
25_P36_I0.116910.761
8_E135_P0.116330.757
44_V53_G0.116260.756
34_F116_R0.116180.756
126_A143_E0.116090.755
12_L134_F0.116010.755
15_Q18_D0.116010.755
59_L139_F0.11550.751
96_R100_F0.115270.750
53_G82_P0.115040.748
67_F113_T0.114690.746
53_G58_E0.114350.744
124_A129_K0.113570.739
38_D56_P0.113290.737
9_I112_I0.113070.736
16_K71_G0.112070.729
56_P140_T0.111970.728
45_E52_A0.111850.728
75_F149_S0.111820.727
35_D149_S0.111790.727
129_K133_E0.111450.725
86_A89_R0.110990.722
82_P122_Q0.110660.720
62_D79_E0.110650.720
33_P73_V0.110080.716
24_W34_F0.109840.715
57_F84_L0.109670.714
104_S107_P0.109440.712
34_F100_F0.109390.712
42_E46_A0.109340.711
49_R53_G0.109280.711
62_D78_V0.108860.708
43_L51_A0.108750.708
34_F149_S0.108530.706
65_G73_V0.108440.706
31_A34_F0.108390.705
78_V110_P0.108390.705
139_F145_A0.108270.704
68_P76_L0.108120.703
9_I145_A0.108040.703
53_G120_P0.107910.702
28_I112_I0.107480.699
91_L95_L0.107430.699
19_K24_W0.107250.698
18_D116_R0.10720.697
83_E87_L0.107070.697
31_A95_L0.106590.693
10_E23_R0.106550.693
54_F82_P0.106510.693
21_Y25_P0.105690.688
41_D47_L0.105650.687
46_A52_A0.105540.687
100_F123_A0.104980.683
144_L149_S0.104870.682
41_D107_P0.104760.682
110_P115_A0.104360.679
10_E17_G0.104240.678
64_F139_F0.104190.678
64_F76_L0.103870.676
80_P85_E0.103670.674
117_R149_S0.103150.671
46_A94_A0.102760.669
80_P84_L0.102720.668
32_F108_F0.102430.666
50_L144_L0.102390.666
30_L51_A0.102130.664
74_I88_H0.102110.664
39_S48_A0.101940.663
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
1iuhA0.947799.80.237
1vgjA0.980499.80.238
2d4gA0.967399.80.264
1jh6A0.954299.80.277
2vfkA0.980499.70.312
4h7wA0.980499.40.45
2fsqA0.941297.20.752
1iuhA0.5294820.853
3pm9A0.686347.80.883
3j25A0.601335.20.891

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