GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF723 - Protein of unknown function (DUF723)
Pfam: PF05265 (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: 60
Sequences: 299
Seq/Len: 4.98
HH_delta: 0.745 (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
26_G29_T0.588684.237
3_M11_R0.326962.353
35_C38_H0.29122.096
22_V31_V0.267711.927
4_T7_S0.265391.910
49_F55_G0.239911.727
41_F45_T0.224791.618
5_F9_A0.220711.588
16_F55_G0.219291.578
19_Y35_C0.211291.521
42_T45_T0.190521.371
38_H55_G0.189561.364
8_A12_F0.18871.358
12_F21_L0.187271.348
35_C55_G0.179451.291
19_Y49_F0.17581.265
25_S29_T0.172261.240
56_C59_C0.167911.208
16_F33_I0.155221.117
17_P20_S0.152711.099
16_F35_C0.149241.074
12_F17_P0.14751.062
5_F23_E0.146961.058
15_K55_G0.14051.011
16_F39_G0.136080.979
8_A31_V0.135560.976
19_Y33_I0.133620.962
10_S14_E0.13180.949
27_V54_H0.129820.934
50_I54_H0.129510.932
37_K50_I0.129260.930
11_R50_I0.12890.928
20_S37_K0.128430.924
33_I49_F0.128050.922
22_V50_I0.127640.919
6_E13_E0.125110.900
14_E18_H0.120850.870
19_Y41_F0.120830.870
10_S18_H0.119780.862
34_R53_K0.119380.859
9_A14_E0.119170.858
10_S13_E0.116080.835
14_E60_G0.115980.835
12_F33_I0.114630.825
21_L31_V0.11360.818
48_S52_S0.112120.807
5_F8_A0.11170.804
35_C49_F0.109350.787
16_F49_F0.108930.784
7_S30_P0.108520.781
13_E44_S0.108120.778
8_A49_F0.107560.774
4_T10_S0.107520.774
8_A21_L0.106910.769
42_T46_F0.106690.768
12_F22_V0.10540.759
27_V44_S0.105050.756
20_S34_R0.104080.749
8_A38_H0.103460.745
19_Y31_V0.103050.742
8_A35_C0.102750.739
18_H32_T0.102470.737
31_V57_P0.101970.734
14_E42_T0.100120.721
29_T48_S0.099890.719
10_S58_E0.099750.718
21_L32_T0.099670.717
8_A33_I0.099270.714
32_T40_N0.098780.711
8_A19_Y0.098560.709
7_S11_R0.098540.709
28_A58_E0.098160.706
21_L33_I0.097850.704
23_E29_T0.097280.700
3_M7_S0.096860.697
30_P47_N0.095930.690
34_R57_P0.095550.688
28_A44_S0.094520.680
39_G42_T0.093890.676
12_F49_F0.09320.671
8_A46_F0.092910.669
4_T30_P0.092880.668
34_R38_H0.091970.662
40_N47_N0.091890.661
34_R41_F0.091580.659
13_E19_Y0.091180.656
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
2k2dA0.866791.30.745
1h7bA0.883389.20.756
3a43A186.90.765
1lkoA0.916785.10.771
4aybP0.483382.40.778
1gh9A0.4581.50.78
3pwfA0.816780.10.783
2lcqA0.8577.60.788
2kdxA0.916775.40.791
1twfL0.8573.60.794
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