GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
zf-AD - Zinc-finger associated domain (zf-AD)
Pfam: PF07776 (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: CL0361
Length: 75
Sequences: 1538
Seq/Len: 20.51
HH_delta: 0.069 (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
2_C5_C0.581122.629
61_F65_C0.569032.574
54_K57_Q0.560632.536
6_L68_S0.454452.056
54_K64_K0.447672.025
33_T65_C0.404731.831
28_M59_Y0.371381.680
32_C59_Y0.354911.606
28_M56_Q0.352431.594
4_L68_S0.34481.560
62_R65_C0.334141.512
4_L33_T0.32821.485
31_E62_R0.326581.477
63_R67_E0.321531.455
4_L29_I0.31721.435
33_T58_F0.315221.426
34_G62_R0.313411.418
30_E36_Q0.298121.349
67_E71_K0.296221.340
35_I69_Q0.283281.282
4_L58_F0.279071.263
59_Y63_R0.271441.228
4_L61_F0.263721.193
24_S27_E0.25681.162
62_R66_R0.254861.153
18_D21_E0.254541.152
32_C62_R0.243691.102
3_R44_P0.242711.098
55_L61_F0.239271.082
67_E70_E0.23771.075
42_D45_Q0.237311.074
6_L43_L0.231681.048
31_E59_Y0.226931.027
38_S70_E0.224961.018
29_I37_I0.224441.015
49_S57_Q0.219830.995
41_D45_Q0.216620.980
50_S54_K0.215280.974
58_F66_R0.2130.964
56_Q60_R0.208850.945
16_I19_S0.208510.943
34_G66_R0.206840.936
13_L46_Q0.205940.932
6_L72_L0.201530.912
6_L69_Q0.199960.905
52_W56_Q0.199630.903
33_T62_R0.199490.903
33_T69_Q0.197330.893
40_D43_L0.195610.885
31_E63_R0.189550.858
44_P72_L0.189420.857
19_S22_E0.188430.852
37_I41_D0.188240.852
17_F41_D0.187930.850
13_L16_I0.18780.850
44_P69_Q0.186470.844
55_L58_F0.185880.841
48_C51_C0.183290.829
39_P67_E0.182720.827
11_E19_S0.180010.814
30_E33_T0.179910.814
35_I55_L0.179550.812
15_S18_D0.17930.811
50_S60_R0.178890.809
18_D30_E0.178090.806
36_Q66_R0.174590.790
10_N30_E0.173570.785
39_P42_D0.173170.783
19_S25_L0.169710.768
8_E64_K0.169380.766
25_L28_M0.16810.761
49_S63_R0.167660.759
20_S28_M0.166570.754
8_E12_N0.165030.747
26_A37_I0.164170.743
10_N13_L0.162560.735
15_S45_Q0.162050.733
36_Q52_W0.160360.725
39_P60_R0.160330.725
33_T38_S0.160130.724
4_L47_I0.158230.716
9_S13_L0.158130.715
25_L52_W0.15790.714
14_V29_I0.156040.706
15_S21_E0.155350.703
11_E49_S0.155040.701
50_S53_E0.1550.701
15_S54_K0.154530.699
32_C58_F0.153860.696
28_M58_F0.153470.694
39_P45_Q0.152970.692
63_R66_R0.151950.687
42_D71_K0.15030.680
24_S60_R0.149580.677
65_C72_L0.148880.674
58_F61_F0.148160.670
15_S46_Q0.147170.666
32_C65_C0.147130.666
47_I59_Y0.147120.666
47_I52_W0.14620.661
27_E49_S0.145050.656
66_R69_Q0.144390.653
12_N25_L0.144150.652
23_S70_E0.143890.651
42_D70_E0.143770.650
28_M32_C0.143640.650
52_W69_Q0.14350.649
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
1pzwA199.30.069
3eyyA0.7242.60.791
1dvpA0.5640.70.793
2fe3A0.6834.80.8
2xigA0.666734.70.8
2o03A0.626733.60.801
3mwmA0.6832.90.802
1jocA0.52290.808
4etsA0.7226.80.811
3mpxA0.5624.70.814

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