GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Taq-exonuc - Taq polymerase exonuclease
Pfam: PF09281 (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. )
Length: 138
Sequences: 1538
Seq/Len: 11.14
HH_delta: 0.371 (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
66_R69_L0.779033.838
49_L55_D0.637283.140
56_L59_F0.468042.306
39_A44_V0.464762.290
53_T59_F0.458712.260
88_D93_L0.441652.176
46_R49_L0.384131.892
19_Y31_A0.380981.877
113_G118_E0.354231.745
55_D82_V0.353681.742
120_A124_A0.348291.716
63_R87_G0.342011.685
11_P74_A0.3381.665
98_D110_R0.334581.648
133_A137_R0.331351.632
34_A41_E0.324761.600
21_L31_A0.323091.592
131_L135_P0.321021.582
49_L82_V0.314991.552
72_D123_R0.302991.493
64_E85_E0.298991.473
93_L131_L0.296151.459
115_E119_D0.293911.448
56_L64_E0.293671.447
98_D101_N0.287381.416
40_W43_R0.287371.416
125_L129_R0.28561.407
113_G116_W0.275831.359
15_A79_R0.275661.358
104_P127_T0.275141.356
43_R47_A0.274521.352
68_A71_K0.27351.347
67_A70_A0.268661.324
92_L96_L0.266561.313
67_A90_P0.263051.296
33_L44_V0.2621.291
68_A123_R0.261221.287
20_V120_A0.259881.280
88_D135_P0.254841.256
65_V131_L0.250621.235
90_P127_T0.248531.224
22_S128_A0.247521.219
12_P71_K0.246761.216
32_E35_A0.246581.215
15_A41_E0.246291.213
26_P121_A0.242331.194
44_V47_A0.233661.151
92_L95_Y0.229651.131
71_K75_V0.229361.130
101_N110_R0.227371.120
73_L84_V0.223251.100
73_L83_V0.222261.095
90_P123_R0.219551.082
102_T110_R0.216131.065
65_V90_P0.215371.061
123_R127_T0.215191.060
108_A126_A0.213291.051
94_A103_N0.212971.049
132_R136_P0.209411.032
14_G71_K0.207171.021
43_R46_R0.206891.019
106_G110_R0.206041.015
102_T106_G0.200440.988
41_E80_E0.199010.980
72_D75_V0.198010.976
68_A90_P0.196590.969
74_A78_L0.189590.934
65_V87_G0.188720.930
114_G119_D0.184790.910
57_A132_R0.184770.910
22_S124_A0.184570.909
126_A129_R0.183660.905
113_G119_D0.183070.902
18_G32_E0.182790.901
24_P125_L0.181250.893
112_L129_R0.181130.892
55_D83_V0.180040.887
103_N114_G0.179520.884
106_G109_R0.178490.879
47_A52_P0.177230.873
107_V111_Y0.176950.872
15_A80_E0.17550.865
88_D131_L0.1740.857
18_G30_W0.172950.852
108_A112_L0.172710.851
73_L78_L0.172690.851
133_A136_P0.171730.846
12_P74_A0.170630.841
98_D137_R0.168790.832
68_A72_D0.168580.831
19_Y76_H0.167080.823
103_N106_G0.166430.820
67_A104_P0.165920.817
59_F65_V0.165880.817
11_P71_K0.16570.816
104_P126_A0.165020.813
57_A85_E0.164960.813
93_L135_P0.164820.812
20_V32_E0.164730.812
93_L96_L0.161540.796
13_E43_R0.158910.783
135_P138_L0.158310.780
18_G124_A0.156190.769
31_A48_P0.155850.768
125_L128_A0.15490.763
20_V121_A0.15440.761
55_D85_E0.152930.753
33_L134_L0.151590.747
59_F63_R0.150070.739
22_S121_A0.150040.739
20_V124_A0.149540.737
39_A47_A0.149490.736
71_K123_R0.148320.731
111_Y137_R0.14740.726
21_L29_M0.146490.722
74_A134_L0.145610.717
78_L83_V0.145060.715
116_W119_D0.143010.705
70_A104_P0.142890.704
12_P79_R0.142830.704
88_D100_S0.14160.698
59_F64_E0.14150.697
29_M121_A0.14070.693
97_L137_R0.140490.692
122_T126_A0.14030.691
25_E46_R0.140270.691
43_R83_V0.139230.686
43_R58_E0.139120.685
33_L45_A0.138820.684
22_S26_P0.138170.681
110_R134_L0.138090.680
46_R52_P0.137860.679
41_E45_A0.137850.679
126_A130_L0.137730.679
97_L138_L0.137090.675
20_V26_P0.135730.669
88_D138_L0.135590.668
66_R71_K0.134760.664
122_T129_R0.133840.659
65_V128_A0.133780.659
121_A124_A0.133340.657
107_V112_L0.133120.656
74_A100_S0.132960.655
43_R80_E0.132720.654
96_L106_G0.13190.650
67_A72_D0.131790.649
68_A91_L0.130890.645
75_V97_L0.130870.645
100_S110_R0.130670.644
104_P130_L0.130560.643
67_A94_A0.130370.642
105_E126_A0.130040.641
25_E135_P0.129990.640
90_P104_P0.12970.639
131_L136_P0.129190.636
41_E46_R0.128820.635
11_P84_V0.128320.632
57_A83_V0.128280.632
128_A132_R0.127950.630
13_E96_L0.126940.625
18_G91_L0.126640.624
97_L134_L0.126230.622
57_A129_R0.125860.620
107_V130_L0.125260.617
75_V117_P0.125190.617
16_F22_S0.124390.613
94_A111_Y0.124070.611
73_L86_P0.123680.609
120_A123_R0.123660.609
100_S113_G0.123460.608
17_L32_E0.123310.608
46_R81_G0.122720.605
94_A98_D0.12260.604
25_E125_L0.122050.601
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
3pv8A0.905899.70.371
2kfnA0.956599.60.44
4dfkA0.833399.50.462
3safA0.920399.50.463
2hbjA0.920399.40.504
2e6mA0.927599.40.518
1yt3A0.91399.30.525
1x9mA0.905899.30.525
1bgxT0.811699.30.54
3cymA0.920399.10.577

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