GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
bZIP_1 - bZIP transcription factor
Pfam: PF00170 (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: CL0018
Length: 64
Sequences: 2310
Seq/Len: 36.09
HH_delta: 0.066 (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
48_E53_K1.073122.634
55_E60_K0.740471.818
22_Q26_Q0.684651.680
35_V38_L0.61021.498
40_S44_E0.604691.484
15_E19_R0.602551.479
41_E46_K0.602541.479
43_E47_K0.597551.467
7_E11_E0.59581.462
12_R20_S0.577031.416
6_R10_R0.567131.392
56_I59_L0.563331.383
49_L52_L0.550251.351
10_R14_R0.543891.335
17_A20_S0.516781.268
36_E40_S0.508791.249
54_K57_Q0.506311.243
34_K37_E0.502591.234
26_Q30_E0.490511.204
33_E37_E0.483661.187
10_R25_K0.474851.166
42_N45_L0.470961.156
19_R23_R0.466181.144
11_E15_E0.434251.066
12_R17_A0.42891.053
51_Q54_K0.423441.039
15_E18_R0.418631.028
9_R13_N0.409881.006
13_N17_A0.409361.005
49_L56_I0.403560.991
50_E54_K0.400110.982
27_Y32_E0.398990.979
17_A23_R0.394760.969
12_R18_R0.389440.956
44_E48_E0.37860.929
38_L42_N0.376450.924
49_L53_K0.376040.923
13_N16_A0.373270.916
13_N20_S0.370290.909
31_L35_V0.367920.903
8_R11_E0.364460.895
12_R15_E0.363230.892
9_R27_Y0.363110.891
14_R20_S0.361960.888
28_I32_E0.3610.886
55_E58_S0.356350.875
33_E43_E0.356150.874
14_R17_A0.355680.873
36_E39_E0.348810.856
51_Q55_E0.347560.853
47_K50_E0.346760.851
8_R22_Q0.346710.851
10_R27_Y0.342680.841
54_K60_K0.338670.831
41_E45_L0.337790.829
52_L56_I0.33710.827
36_E46_K0.335710.824
25_K29_E0.331610.814
34_K39_E0.330.810
8_R12_R0.326490.801
16_A20_S0.325710.799
43_E57_Q0.325660.799
42_N46_K0.324260.796
41_E44_E0.319380.784
44_E47_K0.317260.779
29_E32_E0.316190.776
29_E47_K0.315040.773
50_E53_K0.30840.757
23_R31_L0.30680.753
54_K58_S0.30410.746
5_K13_N0.302740.743
16_A21_R0.302660.743
12_R21_R0.296430.728
6_R14_R0.29140.715
11_E16_A0.289280.710
37_E40_S0.289080.710
56_I60_K0.288690.709
11_E14_R0.288190.707
17_A29_E0.287150.705
43_E50_E0.281930.692
17_A25_K0.276840.680
55_E59_L0.276330.678
14_R31_L0.275620.677
8_R14_R0.273840.672
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
2wt7A0.953198.90.066
1jnmA0.937598.90.068
1t2kD0.937598.90.07
1ci6A0.953198.70.138
2dgcA0.921998.60.176
1dh3A0.859498.50.186
1hjbA198.50.2
1gu4A198.50.201
3a5tA198.30.257
1gd2E198.30.259

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