GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
zf-UBP - Zn-finger in ubiquitin-hydrolases and other protein
Pfam: PF02148 (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: 63
Sequences: 1152
Seq/Len: 18.29
HH_delta: 0.008 (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
52_C55_C0.932343.783
14_C17_C0.54942.229
4_C22_C0.545172.212
22_C29_H0.540972.195
32_K35_K0.445231.807
4_C29_H0.428791.740
34_Y37_T0.416461.690
17_C39_H0.398551.617
10_N44_S0.396351.608
15_L50_I0.381711.549
14_C39_H0.366211.486
43_V50_I0.343191.393
42_A53_Y0.308151.250
41_L57_D0.29391.193
41_L52_C0.289951.176
3_V19_Y0.289141.173
41_L50_I0.28881.172
24_R30_A0.280141.137
31_L34_Y0.274141.112
51_W60_Y0.270631.098
24_R53_Y0.26951.094
16_T40_P0.267411.085
10_N47_T0.266241.080
51_W57_D0.263341.069
30_A53_Y0.252221.023
18_G30_A0.252141.023
3_V32_K0.248341.008
25_Y28_G0.24821.007
2_S5_G0.246110.999
28_G35_K0.244170.991
46_S49_S0.241370.979
2_S7_T0.238220.967
6_S9_S0.237580.964
9_S23_G0.234870.953
44_S49_S0.233040.946
24_R56_D0.232040.942
43_V48_G0.231630.940
3_V36_E0.231190.938
44_S48_G0.229440.931
21_G45_L0.228460.927
57_D60_Y0.22840.927
12_W22_C0.226380.919
12_W42_A0.224480.911
14_C33_H0.218070.885
7_T54_A0.212270.861
12_W23_G0.205780.835
19_Y38_G0.202260.821
2_S19_Y0.200870.815
50_I59_V0.198850.807
39_H52_C0.196020.795
44_S47_T0.194950.791
6_S32_K0.193450.785
16_T55_C0.193320.784
11_L45_L0.193180.784
32_K36_E0.192130.780
26_S38_G0.191290.776
26_S44_S0.188480.765
34_Y40_P0.18810.763
11_L49_S0.185520.753
16_T48_G0.185010.751
28_G31_L0.184190.747
32_K56_D0.183920.746
50_I56_D0.183530.745
30_A42_A0.18290.742
6_S46_S0.18280.742
31_L40_P0.181690.737
9_S42_A0.18150.736
21_G30_A0.179830.730
3_V7_T0.174320.707
1_C15_L0.17380.705
35_K54_A0.171920.698
33_H39_H0.171830.697
1_C33_H0.171380.695
52_C59_V0.170260.691
18_G47_T0.170.690
1_C4_C0.169940.690
19_Y30_A0.169920.689
25_Y58_Y0.169370.687
22_C53_Y0.167470.680
7_T36_E0.167470.680
6_S36_E0.165590.672
18_G23_G0.165520.672
14_C52_C0.165250.671
12_W56_D0.16520.670
41_L48_G0.162930.661
15_L23_G0.162810.661
17_C52_C0.162550.660
38_G49_S0.16170.656
27_N32_K0.161230.654
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
3c5kA0.984199.70.008
2uzgA199.70.032
2g45A0.984199.70.039
3ihpA0.984199.70.043
2i50A199.70.053
3mhsA0.968399.60.082
2idaA199.60.091
3ihpA0.936594.90.722
2xzlA183.60.785
3lrqA0.761970.30.808

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