GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DnaJ - DnaJ domain
Pfam: PF00226 (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: CL0392
Length: 64
Sequences: 12669
Seq/Len: 197.95
HH_delta: -0.137 (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
25_S44_F2.721652.901
41_E45_A2.708592.887
13_S16_E2.670542.846
26_K32_K2.399882.558
14_D57_P2.073742.210
28_Y43_K1.752981.868
2_P53_I1.749061.864
1_N4_E1.696291.808
44_F48_N1.666871.777
12_A17_I1.661091.770
51_Y55_S1.652571.761
43_K46_R1.596891.702
24_L27_Q1.586971.691
48_N52_E1.562921.666
8_L12_A1.417691.511
20_A24_L1.37391.464
59_R62_R1.371251.462
20_A23_R1.295661.381
33_N40_A1.255491.338
56_D59_R1.202111.281
24_L47_I1.19891.278
28_Y47_I1.165421.242
58_E62_R1.154211.230
24_L28_Y1.141051.216
12_A16_E1.12351.197
21_Y48_N1.057061.127
42_E45_A1.049231.118
8_L17_I1.019171.086
23_R26_K0.992071.057
8_L20_A0.98781.053
2_P49_E0.982981.048
18_K51_Y0.978261.043
45_A48_N0.966721.030
28_Y33_N0.957081.020
5_I46_R0.954941.018
57_P61_R0.909060.969
2_P63_Y0.870140.927
18_K22_R0.867330.924
14_D55_S0.839870.895
52_E59_R0.836560.892
22_R26_K0.836470.892
2_P50_A0.823930.878
42_E46_R0.810290.864
58_E61_R0.803440.856
5_I50_A0.79420.847
1_N10_P0.776730.828
3_Y8_L0.775540.827
33_N37_E0.767930.819
2_P5_I0.752550.802
18_K55_S0.737050.786
7_G20_A0.733780.782
7_G24_L0.711880.759
25_S48_N0.701110.747
28_Y40_A0.68530.730
15_E19_K0.677780.722
16_E19_K0.672370.717
21_Y51_Y0.671580.716
36_D40_A0.67120.715
3_Y54_L0.639010.681
21_Y25_S0.638330.680
9_P12_A0.636690.679
34_S37_E0.635550.677
33_N36_D0.629950.671
49_E52_E0.59560.635
17_I54_L0.588730.628
15_E22_R0.579040.617
37_E41_E0.57640.614
56_D60_R0.571420.609
45_A49_E0.553160.590
6_L50_A0.550210.586
55_S63_Y0.540990.577
17_I55_S0.517520.552
60_R63_Y0.512340.546
19_K23_R0.505750.539
53_I59_R0.495760.528
23_R27_Q0.493880.526
53_I63_Y0.493050.526
6_L20_A0.48660.519
5_I47_I0.485620.518
16_E20_A0.481940.514
49_E53_I0.476250.508
52_E55_S0.465780.496
14_D18_K0.454620.485
22_R29_H0.450980.481
1_N62_R0.442840.472
12_A20_A0.436930.466
17_I51_Y0.431790.460
9_P16_E0.428830.457
8_L16_E0.427420.456
37_E42_E0.418640.446
5_I43_K0.410030.437
57_P60_R0.392850.419
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
3lz8A0.968899.6-0.137
3apoA0.984499.5-0.111
3apqA0.984499.5-0.083
2lgwA199.5-0.079
2m6yA0.937599.5-0.079
2l6lA199.5-0.079
2dmxA199.5-0.072
2ctqA0.984499.5-0.071
2ej7A199.5-0.069
2yuaA0.984499.5-0.068

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