GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DNA_pol3_beta - DNA polymerase III beta subunit N-terminal domain
Pfam: PF00712 (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: CL0060
Length: 120
Sequences: 3354
Seq/Len: 27.95
HH_delta: -0.023 (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
32_N69_L1.065663.889
3_F90_I0.86193.145
41_K56_T0.819772.991
36_E67_S0.77512.828
70_V97_L0.61892.258
4_T87_E0.59992.189
4_T89_T0.584532.133
2_K91_E0.582612.126
21_I72_A0.579992.116
38_K65_E0.57822.110
73_K77_D0.550562.009
43_T56_T0.516121.883
47_T117_P0.503121.836
6_N9_E0.484891.769
41_K58_P0.479121.748
2_K89_T0.466431.702
13_A44_L0.453581.655
13_A55_T0.444251.621
97_L108_L0.44121.610
34_L67_S0.428861.565
35_I44_L0.424261.548
29_I69_L0.423341.545
89_T100_K0.421941.540
10_L88_I0.41441.512
98_T105_R0.410041.496
7_K11_L0.40431.475
22_P25_S0.396671.447
100_K105_R0.390121.424
97_L110_T0.383661.400
38_K41_K0.381821.393
36_E43_T0.375131.369
16_K55_T0.37191.357
20_V46_A0.368631.345
37_A61_I0.36841.344
35_I42_L0.363121.325
47_T52_S0.363061.325
27_I49_L0.361511.319
18_S76_F0.358531.308
91_E100_K0.351221.282
69_L111_L0.342741.251
6_N87_E0.339951.241
78_I106_F0.335491.224
40_N58_P0.334771.222
29_I114_E0.334341.220
43_T54_R0.321841.174
77_D80_K0.313261.143
13_A57_I0.312681.141
39_D65_E0.306561.119
14_L33_I0.305771.116
13_A17_V0.291361.063
68_I92_V0.29131.063
33_I44_L0.290541.060
38_K43_T0.289181.055
32_N111_L0.286391.045
68_I110_T0.284651.039
45_T119_L0.281571.027
20_V53_I0.281281.026
42_L57_I0.272120.993
14_L75_L0.271410.990
37_A66_G0.27090.989
29_I115_D0.268840.981
35_I75_L0.267740.977
25_S31_S0.266710.973
26_T30_L0.263460.961
30_L117_P0.261240.953
86_E102_G0.257940.941
82_L101_S0.255980.934
78_I108_L0.249410.910
17_V20_V0.245090.894
22_P27_I0.244660.893
47_T116_F0.242980.887
45_T54_R0.240060.876
37_A59_A0.239860.875
8_E84_D0.238970.872
74_K108_L0.238640.871
17_V53_I0.237870.868
14_L76_F0.236250.862
35_I70_V0.234720.857
35_I68_I0.233830.853
28_P31_S0.232810.850
20_V32_N0.232060.847
40_N62_E0.230010.839
17_V44_L0.228340.833
9_E58_P0.227470.830
34_L45_T0.22680.828
24_K29_I0.226430.826
39_D42_L0.224920.821
91_E98_T0.222460.812
96_K107_K0.221820.809
34_L116_F0.221460.808
41_K60_E0.214770.784
84_D101_S0.214280.782
34_L69_L0.212720.776
90_I99_I0.212420.775
5_I10_L0.208930.762
33_I75_L0.208560.761
98_T107_K0.208420.761
30_L49_L0.20740.757
97_L109_P0.205960.752
46_A72_A0.205610.750
74_K106_F0.204840.747
67_S115_D0.203220.742
71_P109_P0.201620.736
11_L76_F0.201230.734
29_I111_L0.199930.730
79_V83_P0.199140.727
21_I33_I0.198850.726
90_I97_L0.197430.720
37_A64_E0.197240.720
19_K81_K0.192240.702
2_K64_E0.191960.700
47_T50_E0.190660.696
11_L79_V0.189810.693
14_L79_V0.189410.691
67_S114_E0.189040.690
109_P112_D0.188990.690
40_N60_E0.187150.683
93_E96_K0.184780.674
20_V51_I0.183710.670
48_D77_D0.180910.660
21_I26_T0.178920.653
94_E102_G0.178860.653
21_I25_S0.178510.651
48_D80_K0.176840.645
54_R119_L0.176580.644
96_K109_P0.173590.633
72_A75_L0.173140.632
33_I86_E0.172970.631
10_L14_L0.17270.630
75_L79_V0.17220.628
26_T29_I0.171730.627
66_G79_V0.171310.625
49_L72_A0.170540.622
4_T84_D0.17030.621
4_T60_E0.169560.619
18_S21_I0.168780.616
20_V25_S0.168720.616
4_T18_S0.168440.615
52_S109_P0.168250.614
2_K62_E0.166940.609
70_V110_T0.166660.608
83_P102_G0.166220.607
27_I114_E0.166020.606
6_N48_D0.164750.601
33_I46_A0.162950.595
9_E12_K0.162940.595
92_V97_L0.162850.594
58_P89_T0.162730.594
70_V75_L0.162450.593
48_D109_P0.161940.591
72_A79_V0.161820.590
31_S118_E0.161720.590
45_T52_S0.161210.588
82_L102_G0.160550.586
21_I100_K0.159770.583
42_L59_A0.159370.582
28_P116_F0.15930.581
14_L104_S0.159280.581
15_S76_F0.159190.581
8_E12_K0.158460.578
62_E118_E0.158030.577
76_F79_V0.157090.573
12_K16_K0.15580.569
36_E65_E0.155310.567
46_A116_F0.154650.564
11_L15_S0.154450.564
32_N116_F0.154390.563
27_I50_E0.153740.561
92_V110_T0.152910.558
41_K89_T0.152880.558
37_A65_E0.152260.556
96_K105_R0.151880.554
96_K108_L0.151680.553
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
3p16A0.983399.9-0.023
3t0pA0.983399.9-0.018
4k3lA199.9-0.017
3d1gA0.991799.9-0.007
2avtA0.983399.90.007
1vpkA0.991799.90.014
4k3lA0.991799.70.192
3t0pA0.991799.70.192
3d1gA0.991799.70.204
2avtA0.991799.70.209

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