GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DnaJ_CXXCXGXG - DnaJ central domain
Pfam: PF00684 (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: 66
Sequences: 2886
Seq/Len: 43.73
HH_delta: 0.056 (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
3_K61_T1.97564.218
26_Q41_Q1.699113.628
20_Q46_K1.583653.381
28_T39_Q1.452833.102
16_K56_K1.26732.706
10_K57_D1.264372.700
30_R37_V1.064142.272
10_K60_K1.043992.229
27_V45_P0.984882.103
59_C62_C0.776561.658
37_V40_M0.774351.653
19_P46_K0.745131.591
28_T41_Q0.73781.575
2_P61_T0.735761.571
20_Q45_P0.720791.539
29_R42_Q0.68281.458
17_T52_K0.68181.456
15_P52_K0.625021.334
3_K10_K0.614921.313
20_Q27_V0.592131.264
19_P53_I0.583481.246
46_K61_T0.496321.060
29_R40_M0.469551.003
46_K53_I0.465080.993
13_K57_D0.443420.947
1_C59_C0.440860.941
9_A13_K0.426410.910
17_T22_N0.42520.908
31_Q40_M0.419790.896
9_A15_P0.418740.894
1_C62_C0.412040.880
60_K63_K0.410340.876
26_Q43_T0.401890.858
18_C44_C0.397260.848
3_K20_Q0.385860.824
31_Q38_F0.377440.806
43_T48_G0.376970.805
16_K53_I0.374020.799
30_R39_Q0.366750.783
3_K11_P0.366360.782
18_C21_C0.364210.778
1_C4_C0.363830.777
12_G15_P0.361040.771
30_R40_M0.356780.762
30_R38_F0.353940.756
37_V41_Q0.350940.749
16_K19_P0.348720.745
15_P57_D0.346170.739
4_C18_C0.342480.731
9_A54_I0.334330.714
24_S28_T0.329780.704
31_Q37_V0.323810.691
10_K13_K0.322690.689
15_P54_I0.31410.671
6_G64_G0.305940.653
31_Q42_Q0.30570.653
54_I58_P0.297170.634
27_V41_Q0.294710.629
7_T11_P0.293810.627
4_C44_C0.292660.625
44_C47_C0.291240.622
50_T53_I0.286760.612
11_P14_K0.286610.612
2_P5_N0.282550.603
21_C47_C0.276660.591
9_A58_P0.272420.582
28_T37_V0.271660.580
26_Q37_V0.270320.577
18_C23_G0.266460.569
24_S27_V0.266420.569
3_K60_K0.259650.554
1_C6_G0.257140.549
59_C64_G0.256040.547
6_G51_G0.25540.545
8_G64_G0.25540.545
23_G49_G0.253830.542
42_Q45_P0.247290.528
11_P57_D0.243670.520
30_R42_Q0.241930.517
58_P66_G0.237360.507
24_S42_Q0.237290.507
21_C44_C0.236890.506
29_R45_P0.235750.503
48_G65_S0.234980.502
4_C64_G0.234740.501
50_T65_S0.23230.496
29_R65_S0.23040.492
47_C59_C0.22960.490
45_P48_G0.216950.463
21_C49_G0.214410.458
44_C49_G0.21260.454
47_C62_C0.211810.452
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
1nltA0.984899.10.056
2cttA0.9242990.112
1exkA0.924298.80.161
3lczA0.596.90.522
1exkA0.80396.80.526
3pmqA196.60.543
1nltA0.848595.80.58
2cttA0.787995.60.585
2bx9A0.595.20.596
2bx9A0.621295.10.599

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