GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
bZIP_2 - Basic region leucine zipper
Pfam: PF07716 (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: 54
Sequences: 2012
Seq/Len: 37.26
HH_delta: 0.086 (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
39_E43_Q0.752461.843
21_Q25_Q0.735141.801
42_E46_Q0.697121.707
48_I51_L0.666061.631
32_Q36_E0.637261.561
14_E18_R0.601821.474
40_E43_Q0.595771.459
35_Q39_E0.59071.447
40_E45_R0.590341.446
5_K13_R0.560371.373
15_A19_S0.51491.261
41_N45_R0.511271.252
6_R15_A0.505871.239
7_E10_E0.499121.222
14_E17_R0.494761.212
33_E36_E0.473751.160
25_Q29_E0.467281.144
11_R17_R0.460221.127
16_A19_S0.449891.102
41_N44_L0.436821.070
18_R21_Q0.432441.059
22_R30_L0.426091.044
10_E15_A0.40030.980
34_V41_N0.397180.973
26_R31_E0.393640.964
32_Q35_Q0.391160.958
43_Q47_E0.388540.952
27_E31_E0.387870.950
9_R12_N0.382190.936
8_R18_R0.379350.929
43_Q49_A0.374720.918
42_E49_A0.37390.916
30_L34_V0.373030.914
33_E38_E0.369480.905
29_E39_E0.366850.899
15_A26_R0.366480.898
12_N15_A0.365890.896
39_E46_Q0.365830.896
15_A18_R0.36520.894
36_E49_A0.363970.891
46_Q49_A0.358390.878
11_R19_S0.355660.871
34_V37_L0.354820.869
37_L41_N0.35150.861
11_R20_R0.349140.855
47_E50_Q0.345380.846
28_E31_E0.344450.844
32_Q42_E0.342430.839
28_E32_Q0.342130.838
16_A30_L0.337660.827
6_R10_E0.337660.827
11_R15_A0.336230.824
37_L40_E0.33390.818
13_R16_A0.331870.813
39_E42_E0.327980.803
13_R19_S0.327480.802
16_A23_K0.324740.795
36_E39_E0.320950.786
13_R17_R0.319910.784
12_N16_A0.319170.782
10_E13_R0.317640.778
34_V40_E0.315260.772
31_E34_V0.308980.757
25_Q28_E0.305910.749
46_Q50_Q0.300970.737
18_R22_R0.299230.733
27_E30_L0.297840.729
35_Q45_R0.295930.725
29_E43_Q0.295220.723
13_R22_R0.293820.720
12_N20_R0.290820.712
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
1gu4A198.60.086
1hjbA198.60.087
2dgcA198.60.1
2wt7A0.96398.60.11
1jnmA0.944498.50.134
1t2kD0.944498.40.145
1ci6A0.96398.40.153
1dh3A0.944498.20.202
3a5tA197.70.312
1gd2E197.60.335

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