GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4388 - Domain of unknown function (DUF4388)
Pfam: PF14332 (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: 103
Sequences: 635
Seq/Len: 6.17
HH_delta: 0.847 (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
23_G72_F0.366083.323
16_L38_F0.305252.771
36_I43_I0.269062.442
45_H82_T0.256492.328
55_G58_A0.254752.312
34_G48_S0.189041.716
96_R100_E0.173631.576
12_L68_G0.167151.517
34_G58_A0.163471.484
17_E88_E0.160491.457
72_F75_D0.159141.444
15_L70_F0.156291.419
45_H55_G0.156131.417
34_G55_G0.14681.332
11_D19_S0.143381.301
63_L94_A0.138541.257
92_L99_D0.136421.238
69_T75_D0.135841.233
12_L70_F0.135571.231
7_F15_L0.135271.228
25_L72_F0.134131.217
59_L90_L0.13321.209
14_Q92_L0.131691.195
65_W93_E0.127161.154
46_A55_G0.126961.152
29_S32_G0.125471.139
21_K72_F0.124951.134
6_D101_W0.124871.133
60_F93_E0.1231.116
10_P22_T0.122711.114
6_D27_V0.12131.101
14_Q53_L0.120641.095
9_L62_L0.120531.094
59_L94_A0.120021.089
22_T41_G0.118291.074
14_Q21_K0.117891.070
19_S70_F0.117371.065
45_H79_E0.116961.062
12_L72_F0.116911.061
31_G37_Y0.116221.055
35_R98_L0.115411.048
52_R85_L0.115041.044
7_F70_F0.113431.030
34_G45_H0.113211.028
34_G62_L0.112251.019
55_G85_L0.112051.017
12_L87_T0.110631.004
40_D64_S0.10980.997
94_A97_R0.109640.995
34_G82_T0.109290.992
53_L61_E0.10770.978
62_L89_E0.107180.973
79_E82_T0.107050.972
23_G38_F0.106360.965
55_G87_T0.102670.932
19_S23_G0.102320.929
48_S58_A0.10220.928
17_E87_T0.10190.925
59_L67_E0.101370.920
29_S38_F0.100650.914
47_S52_R0.100620.913
89_E93_E0.100110.909
31_G73_E0.09980.906
71_E86_S0.098630.895
13_L38_F0.09660.877
31_G67_E0.096290.874
34_G65_W0.095820.870
29_S65_W0.095790.869
92_L95_L0.094910.861
92_L100_E0.09480.860
13_L17_E0.094750.860
46_A77_P0.09440.857
10_P94_A0.093840.852
53_L71_E0.093480.848
13_L59_L0.093040.844
60_F64_S0.092950.844
37_Y45_H0.092890.843
12_L15_L0.092440.839
34_G46_A0.092440.839
46_A58_A0.092420.839
10_P35_R0.091850.834
43_I70_F0.091690.832
48_S81_R0.091320.829
20_R93_E0.091070.827
47_S71_E0.090810.824
19_S22_T0.090710.823
36_I86_S0.090410.821
47_S53_L0.090160.818
63_L91_L0.090160.818
11_D35_R0.089950.816
22_T60_F0.08970.814
34_G49_G0.089660.814
33_E56_E0.089570.813
33_E77_P0.089530.813
17_E42_R0.089360.811
37_Y95_L0.089270.810
16_L21_K0.089240.810
30_G33_E0.089210.810
73_E93_E0.08840.802
63_L66_K0.08820.801
43_I77_P0.088170.800
75_D86_S0.088020.799
8_S24_V0.087940.798
12_L28_Q0.087810.797
24_V87_T0.087150.791
66_K71_E0.086790.788
33_E67_E0.086570.786
48_S52_R0.086530.785
27_V33_E0.086470.785
55_G82_T0.086380.784
66_K80_P0.0860.781
39_R56_E0.085970.780
6_D78_P0.085650.777
13_L87_T0.085380.775
30_G65_W0.085330.775
47_S56_E0.085280.774
86_S89_E0.085120.773
76_P91_L0.084930.771
13_L55_G0.084850.770
14_Q94_A0.084740.769
9_L36_I0.084390.766
47_S66_K0.084180.764
43_I76_P0.084060.763
31_G80_P0.08390.762
75_D97_R0.08360.759
13_L60_F0.083520.758
61_E101_W0.08350.758
17_E65_W0.08340.757
22_T76_P0.083210.755
27_V74_P0.082930.753
57_E64_S0.082770.751
61_E64_S0.082550.749
27_V54_Q0.082410.748
36_I91_L0.081770.742
9_L35_R0.081490.740
37_Y73_E0.081190.737
58_A61_E0.081170.737
34_G63_L0.081140.736
21_K70_F0.081030.735
49_G61_E0.080980.735
23_G87_T0.080670.732
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
1zjcA0.941764.50.847
2ayiA0.941760.30.851
3gr5A0.873822.30.882
4g08A0.873818.70.886
2l48A0.601914.50.891
4glxA0.970914.20.892
1nkqA0.708710.20.898
4dpzX0.84479.90.898
3jslA0.951590.901
3racA0.611790.901
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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