GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PolyA_pol - Poly A polymerase head domain
Pfam: PF01743 (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: CL0260
Length: 126
Sequences: 2673
Seq/Len: 21.21
HH_delta: 0.019 (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
119_D126_R0.913383.233
118_E122_N0.869513.077
91_L102_A0.733472.596
11_L103_Y0.692712.452
115_G118_E0.677242.397
1_A22_I0.66572.356
35_L54_V0.651322.305
117_L121_K0.647382.291
104_D109_K0.63122.234
104_D107_T0.590992.092
3_L7_A0.588072.081
98_I120_L0.574152.032
86_T89_E0.551661.952
51_T64_A0.537091.901
98_I125_I0.526091.862
68_G89_E0.521681.846
13_L120_L0.51661.828
22_I61_I0.515121.823
27_D30_E0.513241.816
101_L117_L0.506031.791
101_L113_P0.494821.751
112_D116_G0.485151.717
77_N81_V0.474521.679
92_K114_F0.46681.652
23_V66_F0.457761.620
87_I102_A0.438621.552
2_Y66_F0.432241.530
88_E113_P0.43051.524
101_L110_L0.427931.515
3_L20_I0.415951.472
30_E33_K0.406221.438
97_T126_R0.401261.420
72_I80_V0.397271.406
80_V83_F0.388491.375
118_E121_K0.380791.348
25_N66_F0.355791.259
74_D77_N0.346441.226
12_L117_L0.343991.217
17_P20_I0.338051.196
55_V60_S0.335981.189
2_Y87_I0.330431.169
120_L123_K0.312141.105
68_G82_E0.307931.090
78_P81_V0.305581.081
87_I91_L0.299971.062
71_Y78_P0.299641.060
32_A52_V0.298731.057
29_E33_K0.296751.050
24_T31_F0.296261.049
71_Y75_G0.292481.035
53_R60_S0.291841.033
32_A44_V0.291081.030
4_V102_A0.290321.027
32_A47_K0.288841.022
35_L39_L0.284871.008
46_G49_F0.279350.989
91_L113_P0.278240.985
121_K124_I0.277360.982
12_L120_L0.276910.980
69_E78_P0.273360.967
23_V90_D0.272960.966
22_I63_I0.268550.950
49_F53_R0.264460.936
5_G9_R0.262070.928
31_F52_V0.258770.916
6_G19_D0.258260.914
24_T35_L0.257280.911
67_R93_R0.255430.904
38_K52_V0.25270.894
6_G10_D0.25270.894
103_Y110_L0.252250.893
53_R62_D0.251760.891
77_N80_V0.249840.884
30_E34_L0.248940.881
91_L114_F0.247070.874
40_G54_V0.244210.864
67_R90_D0.243440.862
72_I78_P0.241640.855
28_P65_S0.240750.852
37_K55_V0.239960.849
6_G9_R0.239650.848
90_D102_A0.23840.844
102_A113_P0.237250.840
26_A30_E0.236190.836
52_V64_A0.235220.832
88_E92_K0.235160.832
76_R83_F0.232280.822
6_G21_D0.230790.817
33_K37_K0.23060.816
104_D111_I0.230130.814
3_L125_I0.229260.811
75_G78_P0.226840.803
69_E93_R0.226320.801
27_D31_F0.225570.798
113_P116_G0.225030.796
77_N82_E0.224190.793
11_L20_I0.223910.792
2_Y111_I0.223720.792
10_D15_R0.222850.789
90_D94_R0.222770.788
64_A93_R0.222480.787
115_G122_N0.222410.787
45_V53_R0.22070.781
66_F87_I0.219150.776
78_P83_F0.217970.771
7_A11_L0.217550.770
43_F60_S0.215140.761
1_A25_N0.214990.761
54_V63_I0.211920.750
95_D99_N0.210810.746
102_A114_F0.209640.742
101_L114_F0.209560.742
101_L120_L0.208950.740
25_N87_I0.207590.735
118_E124_I0.206750.732
46_G62_D0.206580.731
89_E92_K0.206080.729
72_I76_R0.205910.729
49_F64_A0.204860.725
2_Y104_D0.2030.718
74_D81_V0.202050.715
69_E76_R0.199890.707
47_K52_V0.199280.705
29_E32_A0.198570.703
110_L113_P0.19770.700
12_L101_L0.196790.696
23_V91_L0.196590.696
20_I103_Y0.194910.690
35_L63_I0.191270.677
70_F80_V0.190770.675
44_V81_V0.188730.668
33_K36_A0.187880.665
3_L22_I0.184950.655
23_V64_A0.18480.654
26_A66_F0.184060.651
1_A19_D0.182490.646
34_L37_K0.182190.645
7_A17_P0.182140.645
100_A114_F0.181250.641
26_A34_L0.180840.640
32_A109_K0.179120.634
78_P82_E0.177910.630
11_L17_P0.177670.629
8_V116_G0.17590.623
11_L107_T0.175260.620
56_F59_G0.17510.620
14_G122_N0.174530.618
104_D108_G0.173270.613
10_D19_D0.17310.613
28_P83_F0.172740.611
12_L98_I0.171780.608
53_R64_A0.171520.607
34_L115_G0.171110.606
66_F90_D0.170480.603
117_L124_I0.169640.600
51_T65_S0.168870.598
26_A65_S0.168840.598
109_K118_E0.168750.597
30_E37_K0.166480.589
45_V51_T0.166090.588
20_I74_D0.165580.586
24_T65_S0.162320.574
107_T115_G0.161970.573
64_A75_G0.16180.573
52_V65_S0.161760.572
115_G119_D0.161690.572
18_K103_Y0.160860.569
97_T119_D0.16080.569
4_V96_F0.16070.569
44_V52_V0.160260.567
72_I77_N0.159880.566
15_R18_K0.158680.562
69_E75_G0.158370.560
98_I101_L0.157590.558
110_L117_L0.157290.557
106_E109_K0.157070.556
7_A108_G0.156840.555
34_L58_G0.155630.551
5_G10_D0.155550.551
100_A116_G0.155460.550
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
3h38A0.98411000.019
1miwA0.96031000.053
1vfgA0.98411000.055
1ou5A0.97621000.056
3aqlA0.96031000.093
2la3A0.857195.50.854
4e8jA0.801680.30.896
1q79A0.888930.80.924
2hhpA0.920626.60.926
1knyA0.888915.10.933

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