GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Taq-exonuc - Taq polymerase exonuclease
Pfam: PF09281 (v26) Consensus Sequence
Length: 138
Sequences: 4427
Seq/Len: 32.08
HH_delta: 0.203 (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
67_A70_A1.392574.188
68_A90_P1.334564.014
101_N106_G0.941572.832
103_N106_G0.926062.785
94_A102_T0.757342.278
35_A119_D0.68712.067
19_Y33_L0.665992.003
98_D111_Y0.626521.884
109_R115_E0.618761.861
21_L72_D0.599851.804
69_L72_D0.599631.803
94_A107_V0.587511.767
23_R31_A0.581171.748
108_A126_A0.571941.720
22_S32_E0.567811.708
13_E41_E0.533731.605
17_L67_A0.528871.591
39_A124_A0.528281.589
17_L77_A0.526331.583
66_R131_L0.522251.571
25_E30_W0.522161.570
32_E48_P0.518241.559
13_E63_R0.488171.468
92_L96_L0.487191.465
18_G73_L0.483751.455
57_A60_V0.478351.439
32_E79_R0.477391.436
108_A114_G0.460181.384
108_A130_L0.459341.382
14_G64_E0.456751.374
128_A132_R0.439681.322
15_A38_A0.43691.314
16_F127_T0.435671.310
38_A59_F0.435051.308
18_G123_R0.430731.295
17_L65_V0.429261.291
15_A63_R0.422211.270
65_V86_P0.420661.265
20_V123_R0.410941.236
57_A82_V0.406611.223
20_V73_L0.405751.220
122_T125_L0.405651.220
61_G85_E0.402071.209
23_R72_D0.400521.205
14_G131_L0.400181.204
25_E29_M0.396371.192
125_L129_R0.39631.192
88_D93_L0.3941.185
91_L95_Y0.380331.144
55_D58_E0.377171.134
39_A121_A0.377081.134
129_R133_T0.372511.120
114_G129_R0.369251.111
73_L123_R0.363141.092
93_L96_L0.361341.087
107_V130_L0.361131.086
94_A134_L0.343471.033
98_D134_L0.341511.027
121_A125_L0.340931.025
41_E44_V0.340621.024
74_A84_V0.336521.012
74_A87_G0.336211.011
71_K92_L0.333431.003
124_A127_T0.332080.999
16_F128_A0.330880.995
15_A40_W0.329840.992
91_L102_T0.323520.973
19_Y73_L0.322040.969
64_E88_D0.319310.960
13_E40_W0.318190.957
124_A128_A0.315270.948
68_A107_V0.315140.948
48_P52_P0.311710.938
108_A116_W0.309890.932
126_A129_R0.304340.915
16_F124_A0.303130.912
14_G66_R0.301490.907
35_A47_A0.300050.902
130_L133_T0.298930.899
19_Y77_A0.296390.891
26_P75_V0.295990.890
56_L60_V0.292950.881
26_P29_M0.292580.880
129_R132_R0.29190.878
70_A74_A0.289590.871
69_L91_L0.28540.858
70_A87_G0.282140.849
40_W63_R0.276620.832
106_G109_R0.276330.831
98_D110_R0.275850.830
67_A127_T0.269230.810
55_D60_V0.269170.810
74_A78_S0.264440.795
110_R130_L0.261040.785
42_G132_R0.256920.773
78_S84_V0.255310.768
24_P91_L0.252020.758
37_A124_A0.250210.753
114_G126_A0.249290.750
104_P126_A0.248320.747
64_E131_L0.248130.746
19_Y76_H0.246040.740
26_P76_H0.244510.735
104_P127_T0.244310.735
21_L76_H0.244210.734
97_L134_L0.244080.734
99_P110_R0.243390.732
107_V111_Y0.243010.731
105_E115_E0.240350.723
26_P30_W0.239320.720
104_P130_L0.238370.717
89_D92_L0.237360.714
41_E85_E0.235810.709
22_S33_L0.234450.705
46_R59_F0.232530.699
13_E62_Q0.231160.695
78_S83_D0.230240.692
93_L131_L0.229280.690
21_L73_L0.229090.689
116_W122_T0.22870.688
68_A104_P0.22840.687
23_R34_A0.228010.686
46_R49_D0.226110.680
54_V58_E0.226090.680
13_E64_E0.225840.679
22_S34_A0.22560.679
13_E43_R0.225590.678
14_G132_R0.224050.674
21_L33_L0.223190.671
22_S72_D0.221730.667
95_Y102_T0.221360.666
65_V85_E0.221290.666
32_E50_A0.220810.664
40_W59_F0.219830.661
127_T130_L0.218710.658
24_P72_D0.21820.656
93_L134_L0.217920.655
62_Q85_E0.217440.654
67_A73_L0.217380.654
99_P102_T0.217290.654
53_T88_D0.216020.650
89_D96_L0.21420.644
105_E126_A0.214190.644
29_M79_R0.211930.637
116_W121_A0.211520.636
95_Y99_P0.210170.632
109_R113_G0.209130.629
25_E31_A0.208930.628
17_L38_A0.208860.628
31_A79_R0.208560.627
44_V54_V0.207690.625
52_P88_D0.205010.617
94_A98_D0.204260.614
98_D102_T0.203720.613
71_K89_D0.203610.612
88_D131_L0.203470.612
70_A127_T0.20260.609
116_W126_A0.201750.607
38_A48_P0.201660.607
56_L59_F0.200370.603
111_Y130_L0.199770.601
108_A111_Y0.199330.600
102_T107_V0.198780.598
71_K75_V0.1980.596
31_A76_H0.197140.593
130_L134_L0.195690.589
23_R30_W0.194460.585
93_L97_L0.193680.583
35_A49_D0.192340.578
35_A118_E0.19090.574
72_D76_H0.189850.571
97_L100_S0.18980.571
21_L69_L0.189780.571
36_L59_F0.189530.570
23_R76_H0.189040.569
22_S31_A0.188760.568
55_D59_F0.18750.564
31_A72_D0.187320.563
48_P51_P0.187270.563
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
4dfkA0.927599.60.203
3pv8A0.956599.60.21
3safA0.985599.50.242
2kfnA0.985599.50.245
1x9mA0.891399.40.294
2hbjA0.978399.40.297
1yt3A0.978399.40.305
2e6mA0.985599.30.321
3cymA0.985599.30.343
1bgxT0.891398.90.452

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