GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4379 - Domain of unknown function (DUF4379)
Pfam: PF14311 (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. )
Length: 55
Sequences: 350
Seq/Len: 6.36
HH_delta: 0.754 (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
8_D37_E0.497432.897
6_E45_R0.443682.584
7_W12_N0.343061.998
15_D18_E0.319191.859
27_V42_V0.314381.831
8_D28_W0.31051.808
8_D12_N0.277491.616
45_R51_G0.272631.588
52_C55_C0.250991.462
7_W19_V0.247411.441
29_W45_R0.228371.330
8_D11_K0.225251.312
16_P36_H0.221591.290
26_K39_K0.209861.222
6_E29_W0.201921.176
22_G51_G0.201661.174
14_L25_K0.201391.173
8_D30_K0.192131.119
12_N28_W0.189151.102
28_W37_E0.179011.042
11_K28_W0.17391.013
28_W39_K0.172241.003
44_D48_R0.168790.983
6_E32_P0.168070.979
4_A16_P0.166920.972
26_K53_P0.164520.958
11_K37_E0.16280.948
3_L6_E0.161040.938
22_G44_D0.156680.912
32_P37_E0.154820.902
33_K54_Y0.152910.890
29_W40_A0.152110.886
40_A45_R0.151750.884
5_K49_G0.150880.879
28_W32_P0.149830.873
41_S44_D0.149690.872
6_E38_W0.149630.871
4_A15_D0.14710.857
25_K28_W0.146050.851
3_L29_W0.14560.848
44_D50_K0.145030.845
40_A44_D0.142210.828
20_T48_R0.138420.806
4_A21_P0.136580.795
26_K38_W0.134070.781
30_K46_T0.132650.773
16_P25_K0.132150.770
6_E40_A0.131640.767
7_W27_V0.131150.764
24_N40_A0.129850.756
46_T51_G0.129580.755
32_P54_Y0.128920.751
23_S40_A0.127980.745
4_A12_N0.127160.741
7_W39_K0.127030.740
22_G46_T0.125820.733
30_K35_G0.125610.732
22_G43_N0.125460.731
26_K44_D0.12310.717
22_G50_K0.122370.713
23_S46_T0.12120.706
24_N43_N0.119360.695
38_W51_G0.119140.694
19_V23_S0.119040.693
11_K15_D0.118930.693
11_K21_P0.117490.684
11_K39_K0.116110.676
21_P41_S0.114980.670
5_K13_K0.113360.660
18_E24_N0.112590.656
32_P35_G0.112410.655
4_A18_E0.111360.649
5_K22_G0.111160.647
5_K14_L0.110470.643
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
3a43A0.945591.50.754
4aybP0.527391.30.756
2kdxA0.854587.90.772
2lcqA0.854586.40.777
3pwfA0.709184.20.783
2gmgA0.927382.50.787
1lkoA0.890982.40.787
1yuzA0.872778.70.795
6rxnA0.563674.10.802
1twfL0.781869.40.809
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0242 seconds.