GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4343 - Domain of unknown function (DUF4343)
Pfam: PF14243 (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: 130
Sequences: 14831
Seq/Len: 114.08
HH_delta: 0.31 (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
83_Q87_A1.958913.074
22_S25_D1.823412.861
2_R23_G1.799342.823
74_D77_V1.732422.718
102_T106_G1.588892.493
19_V43_V1.522.385
75_P79_A1.374632.157
78_V82_I1.358162.131
100_G110_V1.349032.117
80_F83_Q1.241431.948
79_A83_Q1.232291.934
5_F43_V1.22221.918
77_V80_F1.214691.906
101_V107_W1.169191.835
97_L112_A1.135711.782
23_G27_I1.13151.775
80_F84_A1.09951.725
5_F19_V1.078681.692
77_V101_V1.041671.634
44_V108_A1.041581.634
79_A82_I1.032761.620
84_A107_W1.001391.571
82_I86_A0.988761.551
5_F18_R0.972881.526
4_V40_V0.965631.515
49_E53_F0.949991.491
102_T108_A0.925531.452
59_V86_A0.904481.419
21_R25_D0.890731.398
52_C81_A0.875281.373
48_S101_V0.867761.362
80_F106_G0.867571.361
9_P37_P0.867051.360
21_R45_E0.837451.314
6_I40_V0.821731.289
73_P77_V0.818591.284
30_G36_T0.804871.263
49_E98_D0.796441.250
75_P78_V0.791891.243
76_D80_F0.787021.235
54_I85_L0.777091.219
2_R26_L0.769861.208
50_W81_A0.756091.186
96_V117_S0.742081.164
50_W101_V0.739691.161
42_E108_A0.72371.136
95_Y115_G0.721381.132
64_P68_D0.709661.113
83_Q86_A0.673161.056
10_D35_D0.664911.043
2_R22_S0.663121.040
7_K41_S0.636280.998
84_A87_A0.627820.985
101_V105_G0.6260.982
80_F107_W0.625380.981
76_D79_A0.622190.976
51_R54_I0.621420.975
51_R55_V0.62130.975
61_T82_I0.619420.972
74_D105_G0.618270.970
76_D105_G0.607860.954
6_I38_V0.607830.954
110_V113_N0.605760.950
42_E102_T0.59890.940
55_V95_Y0.589790.925
9_P39_L0.58560.919
45_E102_T0.585520.919
10_D37_P0.581710.913
6_I29_F0.573390.900
54_I97_L0.573050.899
85_L99_V0.57040.895
98_D117_S0.562790.883
92_P95_Y0.557320.874
14_S96_V0.552530.867
94_A115_G0.552490.867
96_V115_G0.551080.865
52_C99_V0.549850.863
44_V102_T0.548460.861
25_D28_G0.54380.853
52_C85_L0.542020.850
77_V105_G0.536050.841
14_S18_R0.534330.838
51_R96_V0.533480.837
64_P67_G0.531960.835
49_E54_I0.531840.834
3_P21_R0.530160.832
3_P19_V0.529760.831
98_D115_G0.527720.828
24_E27_I0.523370.821
4_V20_F0.520160.816
6_I20_F0.517080.811
51_R115_G0.517080.811
99_V107_W0.514840.808
84_A88_A0.507650.797
20_F29_F0.501070.786
49_E55_V0.497410.780
63_S69_W0.494050.775
88_A97_L0.486060.763
81_A99_V0.485480.762
63_S70_D0.483780.759
54_I59_V0.474360.744
88_A109_L0.473390.743
51_R98_D0.469690.737
97_L109_L0.468680.735
49_E117_S0.464950.730
101_V106_G0.464190.728
99_V109_L0.460790.723
7_K12_D0.459070.720
43_V100_G0.458990.720
96_V113_N0.458550.719
84_A99_V0.457480.718
53_F98_D0.456650.717
7_K98_D0.449380.705
53_F96_V0.446910.701
41_S98_D0.443540.696
9_P38_V0.438310.688
80_F87_A0.434110.681
64_P69_W0.429930.675
47_E100_G0.428890.673
10_D36_T0.428470.672
48_S51_R0.424110.665
111_E115_G0.423730.665
45_E100_G0.423060.664
13_K115_G0.422020.662
63_S67_G0.421880.662
49_E96_V0.420250.659
13_K65_Y0.416510.654
11_D16_T0.41540.652
50_W99_V0.413770.649
81_A85_L0.413740.649
56_D59_V0.413690.649
92_P112_A0.413410.649
45_E104_D0.413140.648
16_T32_L0.41250.647
7_K11_D0.411890.646
53_F117_S0.407610.640
74_D101_V0.407290.639
30_G34_P0.399960.628
65_Y96_V0.399580.627
44_V100_G0.392720.616
29_F38_V0.390320.612
81_A107_W0.388440.609
79_A86_A0.388380.609
51_R94_A0.388310.609
12_D117_S0.380750.597
57_G91_L0.372830.585
58_E86_A0.371270.583
30_G33_D0.370050.581
31_S34_P0.369890.580
33_D36_T0.369190.579
56_D93_P0.365910.574
96_V116_W0.36580.574
42_E106_G0.364470.572
49_E111_E0.358290.562
59_V62_G0.358220.562
113_N117_S0.356120.559
48_S72_E0.355730.558
24_E28_G0.354030.555
52_C82_I0.35380.555
3_P43_V0.352110.552
98_D113_N0.349390.548
12_D96_V0.349140.548
3_P20_F0.34820.546
4_V26_L0.34780.546
44_V47_E0.347580.545
88_A112_A0.346370.543
49_E100_G0.343650.539
13_K110_V0.3430.538
85_L97_L0.342840.538
14_S53_F0.339020.532
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
1i7nA0.976999.60.31
1pk8A0.976999.60.318
4eg0A0.976999.60.319
3k3pA0.969299.60.324
2p0aA0.976999.60.327
3e5nA0.969299.60.328
1iowA0.969299.60.329
3r5xA0.961599.60.336
2i87A0.969299.60.339
3tqtA0.969299.60.341

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