GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Exonuc_VII_S - Exonuclease VII small subunit
Pfam: PF02609 (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: 53
Sequences: 1401
Seq/Len: 26.43
HH_delta: -0.062 (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
7_R31_E1.881475.050
30_E49_K1.121063.009
4_A38_K1.001752.689
14_K28_L0.831542.232
41_E45_E0.62321.673
14_K24_E0.581681.561
40_Q44_E0.580551.558
24_E27_K0.549451.475
30_E34_E0.547451.469
23_D42_R0.496861.334
10_E14_K0.495271.329
4_A39_C0.487711.309
20_L28_L0.481741.293
26_L46_A0.478661.285
21_S25_S0.476891.280
48_Q52_E0.45261.215
1_F5_M0.443571.191
12_V16_E0.422821.135
47_E51_E0.418861.124
29_Y33_M0.418031.122
2_E21_S0.40261.081
38_K42_R0.399861.073
3_E6_E0.399141.071
27_K30_E0.392081.052
1_F29_Y0.383081.028
44_E48_Q0.381311.023
12_V36_I0.376251.010
6_E10_E0.371620.997
7_R10_E0.363470.976
37_K41_E0.360160.967
1_F26_L0.353050.948
11_I28_L0.352520.946
32_G36_I0.350630.941
10_E13_E0.348170.935
34_E38_K0.335360.900
2_E5_M0.33230.892
22_L25_S0.323660.869
8_L12_V0.321420.863
38_K41_E0.319630.858
3_E14_K0.317650.853
25_S28_L0.315060.846
50_I53_L0.306650.823
13_E17_S0.299530.804
23_D50_I0.298170.800
4_A42_R0.297540.799
48_Q51_E0.295490.793
1_F25_S0.294190.790
31_E35_L0.28070.753
1_F46_A0.266190.714
42_R45_E0.261370.702
11_I19_E0.255070.685
8_L35_L0.254920.684
29_Y36_I0.254910.684
40_Q50_I0.253960.682
30_E36_I0.249960.671
34_E37_K0.249030.668
4_A35_L0.247880.665
15_L25_S0.246650.662
10_E41_E0.246190.661
31_E34_E0.242180.650
4_A31_E0.241680.649
28_L39_C0.236740.635
21_S24_E0.234420.629
2_E22_L0.230340.618
3_E10_E0.230160.618
28_L32_G0.229750.617
16_E50_I0.22890.614
33_M36_I0.224140.602
2_E39_C0.22220.596
6_E9_E0.220260.591
9_E39_C0.216990.582
14_K17_S0.215070.577
20_L33_M0.212930.572
17_S24_E0.212910.571
44_E47_E0.212540.570
28_L31_E0.210770.566
12_V18_G0.21010.564
13_E34_E0.208650.560
8_L36_I0.207620.557
11_I15_L0.207520.557
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
1vp7A199.4-0.062
3vkgA133.20.783
3u0cA118.90.806
4fz4A0.396218.60.807
3tulA0.867918.50.807
4jkvA0.981118.20.808
3iv1A0.792517.70.809
3ub0A0.905717.40.809
2b5uA117.30.81
1orjA0.9811140.816

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