GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PqqD - Coenzyme PQQ synthesis protein D (PqqD)
Pfam: PF05402 (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: 68
Sequences: 1057
Seq/Len: 15.54
HH_delta: 0.091 (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
31_T34_E0.533742.161
25_L38_A0.51532.086
46_D49_E0.50222.033
22_I35_I0.497342.013
19_A57_F0.471021.907
45_V50_A0.445411.803
36_V54_V0.43781.772
21_F25_L0.437551.771
36_V51_E0.433131.753
7_D10_S0.407051.648
37_D47_P0.397481.609
7_D11_G0.392671.590
32_V55_E0.38721.567
25_L42_E0.364851.477
30_R38_A0.352491.427
40_A45_V0.317021.283
27_D30_R0.310631.257
38_A41_E0.307451.245
60_Q63_E0.307351.244
21_F42_E0.298461.208
55_E59_E0.297791.205
24_E42_E0.29591.198
22_I54_V0.295411.196
51_E55_E0.286981.162
21_F24_E0.285271.155
37_D41_E0.28291.145
40_A50_A0.280381.135
32_V58_L0.27321.106
49_E53_D0.263581.067
50_A53_D0.260511.055
15_L23_W0.249141.009
61_L66_L0.247811.003
60_Q64_K0.24630.997
25_L30_R0.244370.989
6_L9_E0.238330.965
33_E37_D0.237930.963
15_L19_A0.237930.963
30_R34_E0.237550.962
23_W66_L0.236920.959
44_D49_E0.235740.954
33_E51_E0.235680.954
59_E63_E0.233140.944
34_E37_D0.229690.930
13_F66_L0.224260.908
36_V47_P0.221630.897
16_N50_A0.220110.891
6_L11_G0.218150.883
17_E21_F0.217340.880
57_F61_L0.215060.871
19_A66_L0.207820.841
33_E59_E0.206910.838
57_F64_K0.206740.837
14_T56_E0.200920.813
17_E20_A0.200230.811
47_P51_E0.197710.800
57_F66_L0.197510.800
48_E51_E0.196260.794
34_E41_E0.194240.786
43_Y53_D0.193260.782
7_D57_F0.189990.769
28_G31_T0.189350.767
58_L62_R0.188480.763
59_E62_R0.188440.763
18_T22_I0.188250.762
8_P11_G0.184910.749
24_E58_L0.184360.746
26_L35_I0.182320.738
20_A24_E0.181720.736
7_D61_L0.181110.733
18_T39_L0.178660.723
8_P57_F0.178160.721
33_E55_E0.177940.720
27_D35_I0.177680.719
37_D60_Q0.174910.708
16_N19_A0.173760.703
30_R35_I0.172750.699
23_W26_L0.171660.695
40_A48_E0.171520.694
11_G39_L0.169790.687
10_S67_I0.169550.686
5_L12_E0.168230.681
10_S19_A0.167090.676
19_A61_L0.165920.672
34_E59_E0.165690.671
16_N53_D0.165660.671
40_A47_P0.162150.656
58_L67_I0.16090.651
18_T43_Y0.160440.649
8_P23_W0.159430.645
14_T57_F0.158380.641
25_L35_I0.157910.639
22_I39_L0.157420.637
41_E45_V0.156720.634
5_L50_A0.156240.632
13_F39_L0.155790.631
20_A23_W0.155020.628
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
3g2bA0.985399.30.091
3deeA0.985388.30.71
3h5nA0.882484.70.725
2k4bA0.941283.10.731
1okrA0.838281.60.735
1sd4A0.838280.10.738
1tbxA0.808873.60.752
1p6rA0.823572.10.755
2xvcA0.8235690.76
2g9wA0.823568.40.761

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