GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
zf-C3HC4_3 - Zinc finger C3HC4 type (RING finger)
Pfam: PF13920 (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: CL0229
Length: 50
Sequences: 15588
Seq/Len: 311.76
HH_delta: -0.195 (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_F30_A1.844652.525
40_C43_C1.700092.328
5_C8_C1.573512.154
27_E31_E1.5482.119
26_C29_C1.385581.897
6_P42_I1.323721.812
3_E11_N1.295931.774
17_L23_L1.246511.707
8_C29_C1.239911.698
12_P15_V1.195621.637
17_L25_F1.07131.467
4_E11_N1.044191.430
34_L47_I0.897941.229
4_E9_F0.88061.206
15_V18_L0.856981.173
15_V26_C0.815221.116
8_C26_C0.781791.070
29_C40_C0.780671.069
18_L22_H0.769531.054
3_E12_P0.757181.037
16_V27_E0.739541.012
8_C20_C0.737731.010
6_P9_F0.737271.009
33_L44_R0.716470.981
33_L39_K0.702490.962
32_R36_R0.692820.949
39_K44_R0.69010.945
25_F41_P0.675770.925
33_L38_K0.669390.916
32_R35_K0.663430.908
34_L38_K0.660970.905
25_F42_I0.645320.883
28_E31_E0.632770.866
7_I10_E0.628470.860
22_H42_I0.624490.855
20_C43_C0.607280.831
15_V23_L0.594270.814
17_L21_G0.588520.806
9_F42_I0.564110.772
7_I44_R0.561060.768
9_F44_R0.55720.763
20_C40_C0.535040.733
25_F33_L0.506430.693
39_K46_P0.501170.686
14_D27_E0.499910.684
16_V21_G0.496570.680
33_L37_K0.495750.679
6_P25_F0.49160.673
3_E23_L0.490730.672
19_P45_Q0.48670.666
38_K46_P0.485360.664
13_R23_L0.452150.619
15_V27_E0.451130.618
18_L30_A0.448450.614
30_A33_L0.44630.611
31_E35_K0.446130.611
12_P23_L0.445570.610
15_V31_E0.443320.607
9_F33_L0.439830.602
28_E32_R0.43540.596
12_P26_C0.431280.590
8_C22_H0.424090.581
11_N23_L0.42140.577
30_A41_P0.416930.571
7_I41_P0.413420.566
26_C33_L0.40510.555
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
4aycA0.9898.3-0.195
2y1nA0.9898.3-0.185
2cklB0.9898.2-0.167
1z6uA0.9898.2-0.166
3fl2A0.9898.2-0.164
3lrqA0.9898.2-0.161
2cklA0.9898.2-0.157
3l11A0.9898.1-0.154
2csyA0.9898.1-0.152
2d8tA0.9898.1-0.152

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