GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
zf-TRAF - TRAF-type zinc finger
Pfam: PF02176 (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: CL0389
Length: 60
Sequences: 1696
Seq/Len: 28.27
HH_delta: 0.141 (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
37_R54_R1.090173.731
41_C48_C0.855282.927
7_F24_K0.566221.938
8_R23_R0.507811.738
13_P30_L0.479481.641
29_H34_C0.470341.610
36_K55_E0.44871.536
14_N30_L0.44791.533
12_C29_H0.399531.367
34_C48_C0.386561.323
12_C41_C0.377791.293
9_P22_P0.370751.269
38_P53_P0.361641.238
34_C41_C0.358961.229
39_V54_R0.356421.220
52_V57_L0.355521.217
40_P51_R0.346431.186
48_C60_H0.337411.155
41_C60_H0.307791.053
29_H48_C0.301911.033
22_P25_E0.299391.025
7_F22_P0.292931.003
29_H41_C0.292571.001
28_D33_E0.291540.998
12_C17_C0.287580.984
12_C48_C0.283850.971
24_K28_D0.283780.971
27_D31_E0.28020.959
21_I25_E0.274440.939
12_C34_C0.268690.920
43_Y49_K0.266870.913
10_V23_R0.261890.896
8_R37_R0.259770.889
23_R43_Y0.25870.885
9_P28_D0.246920.845
40_P58_E0.246050.842
17_C36_K0.245980.842
57_L60_H0.245880.841
53_P56_D0.245170.839
55_E59_E0.242840.831
38_P42_P0.241840.828
11_P14_N0.226670.776
10_V21_I0.225090.770
9_P20_M0.224170.767
13_P26_L0.22270.762
27_D39_V0.220810.756
28_D54_R0.218590.748
36_K53_P0.21550.738
30_L52_V0.214040.733
11_P20_M0.213260.730
26_L30_L0.21180.725
39_V50_E0.208990.715
20_M23_R0.206690.707
11_P28_D0.203470.696
31_E42_P0.203350.696
9_P21_I0.201660.690
42_P57_L0.197180.675
50_E53_P0.192830.660
38_P52_V0.190530.652
40_P55_E0.189660.649
18_N21_I0.188310.644
14_N20_M0.187380.641
56_D60_H0.184820.633
56_D59_E0.184660.632
19_E59_E0.18420.630
20_M35_P0.182760.625
11_P30_L0.182260.624
11_P19_E0.182080.623
24_K40_P0.181210.620
20_M59_E0.180260.617
14_N17_C0.177280.607
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
2yucA0.916798.60.141
3hcsA0.998.30.215
2yreA0.933398.20.251
2d9kA0.883397.90.307
3hcsA0.916797.50.385
2yucA0.6833970.437
2a25A0.9333970.443
2eodA0.883395.50.53
2d9kA0.583395.10.542
2yreA0.716794.40.559

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