GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PolyA_pol - Poly A polymerase head domain
Pfam: PF01743 (v26) Consensus Sequence
Clan: CL0260
Length: 126
Sequences: 2153
Seq/Len: 17.09
HH_delta: 0.007 (11Mar13)
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
118_E122_N0.838143.281
119_D126_R0.742652.907
91_L102_A0.688532.695
35_L54_V0.587352.299
98_I120_L0.583822.285
115_G118_E0.575192.252
104_N107_T0.563772.207
104_N109_K0.558392.186
1_A22_I0.542952.125
3_L7_A0.517772.027
73_G79_F0.480121.879
11_L103_Y0.476371.865
117_L121_K0.472961.851
101_L117_L0.467181.829
98_I125_I0.465691.823
86_T89_E0.465531.822
68_T89_E0.453641.776
23_V66_F0.447611.752
87_I102_A0.446391.747
112_D116_G0.445261.743
51_T64_A0.443341.735
92_L114_F0.430641.686
101_L113_P0.42771.674
22_I61_I0.419251.641
88_E113_P0.41271.616
13_L120_L0.396681.553
2_Y66_F0.396211.551
30_E33_K0.393121.539
27_D30_E0.389841.526
77_N81_V0.365021.429
74_D77_N0.342341.340
17_P20_I0.341641.337
97_T126_R0.335391.313
3_L20_I0.335211.312
118_E121_K0.334751.310
101_L110_L0.3341.307
25_D66_F0.333891.307
55_V60_S0.308381.207
120_L123_K0.30671.201
71_Y78_P0.304511.192
29_E33_K0.298421.168
32_A44_V0.297721.165
80_V83_F0.294751.154
32_A47_K0.293731.150
32_A52_V0.29271.146
87_I91_L0.287741.126
28_P65_T0.286621.122
76_H83_F0.284671.114
24_V31_L0.284441.113
12_L120_L0.283591.110
72_I80_V0.279441.094
121_K124_I0.277261.085
12_L117_L0.275441.078
46_G49_F0.267721.048
104_N111_I0.267471.047
6_G19_D0.267061.045
23_V90_D0.263851.033
75_G78_P0.263591.032
102_A113_P0.255431.000
2_Y87_I0.254020.994
45_V53_R0.253290.992
23_V91_L0.252970.990
53_R60_S0.248590.973
49_F53_R0.245160.960
35_L39_L0.244280.956
4_V102_A0.244220.956
72_I79_F0.244110.956
52_V64_A0.242810.950
38_A52_V0.240940.943
115_G122_N0.236530.926
6_G10_D0.236380.925
5_G9_R0.234760.919
10_D15_R0.232980.912
24_V35_L0.229350.898
71_Y79_F0.227320.890
91_L113_P0.227120.889
30_E34_L0.22420.878
57_G60_S0.223830.876
67_R93_R0.223480.875
72_I76_H0.222390.871
113_P116_G0.220850.865
46_G62_D0.218820.857
69_E78_P0.217510.851
24_V62_D0.215150.842
31_L52_V0.214470.840
22_I63_I0.212470.832
6_G21_D0.210050.822
72_I78_P0.209050.818
66_F87_I0.208110.815
67_R90_D0.204230.799
91_L114_F0.20360.797
11_L20_I0.202810.794
103_Y110_L0.199930.783
26_G30_E0.198390.777
68_T82_K0.19480.763
102_A114_F0.193770.759
66_F90_D0.193720.758
90_D94_R0.193590.758
1_A25_D0.193350.757
107_T115_G0.192080.752
2_Y111_I0.190750.747
90_D102_A0.188320.737
100_A114_F0.187730.735
33_K36_A0.187230.733
69_E76_H0.186720.731
71_Y75_G0.185820.727
77_N82_K0.185730.727
27_D31_L0.185430.726
55_V58_G0.184180.721
69_E75_G0.184030.720
77_N80_V0.183590.719
11_L17_P0.182750.715
25_D87_I0.182610.715
24_V66_F0.181690.711
26_G66_F0.181130.709
7_A17_P0.180270.706
117_L124_I0.17980.704
106_N109_K0.179570.703
115_G119_D0.178290.698
6_G9_R0.178030.697
26_G31_L0.17790.696
49_F64_A0.177250.694
26_G34_L0.176580.691
34_L115_G0.174450.683
78_P83_F0.173490.679
21_D99_N0.172530.675
118_E124_I0.172480.675
89_E92_L0.17170.672
31_L54_V0.17070.668
7_A11_L0.170660.668
106_N121_K0.169930.665
76_H79_F0.169860.665
101_L114_F0.169570.664
73_G76_H0.168730.661
104_N108_G0.16830.659
88_E92_L0.168230.659
95_D99_N0.167920.657
74_D78_P0.167420.655
79_F82_K0.166010.650
56_F60_S0.165010.646
56_F59_G0.164920.646
53_R62_D0.164490.644
33_K106_N0.164050.642
19_D94_R0.164040.642
70_F75_G0.163740.641
54_V63_I0.163340.639
26_G96_F0.163010.638
8_V76_H0.162720.637
3_L125_I0.160510.628
37_K55_V0.16040.628
64_A93_R0.159570.625
87_I114_F0.159460.624
6_G99_N0.159280.624
26_G65_T0.158820.622
101_L120_L0.158240.619
24_V65_T0.157960.618
17_P103_Y0.15750.617
49_F67_R0.156160.611
13_L98_I0.156080.611
5_G10_D0.155090.607
33_K37_K0.154060.603
15_R74_D0.154020.603
38_A56_F0.152930.599
53_R64_A0.152790.598
71_Y80_V0.152420.597
28_P83_F0.152150.596
23_V64_A0.152030.595
15_R78_P0.151210.592
2_Y91_L0.150530.589
28_P52_V0.150220.588
3_L22_I0.149210.584
82_K123_K0.148440.581
20_I103_Y0.148390.581
47_K64_A0.147950.579
51_T78_P0.147660.578
75_G79_F0.14660.574
47_K52_V0.145820.571
10_D19_D0.145720.570
69_E93_R0.145090.568
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
3h38A0.98411000.007
1miwA0.96031000.041
1vfgA0.98411000.043
1ou5A0.97621000.048
3aqlA0.96031000.084
2la3A0.817593.60.868
4e8jA0.920679.80.896
2fclA0.833326.70.926
3c98A0.37315.80.933
1dn1A0.37313.50.935

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