GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF488 - Protein of unknown function DUF488
Pfam: PF04343 (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: 122
Sequences: 1158
Seq/Len: 9.49
HH_delta: 0.877 (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
5_F104_L0.609893.010
105_C113_C0.487282.405
3_E12_N0.472622.332
32_N35_D0.45982.269
73_F77_R0.419512.070
103_L122_L0.419262.069
5_F36_L0.4112.028
109_D112_R0.386651.908
73_F120_E0.384221.896
62_W75_R0.380831.879
81_E121_Y0.372271.837
113_C116_R0.368881.820
3_E102_A0.352911.741
71_E74_E0.349961.727
12_N102_A0.349091.723
57_R114_H0.349071.723
77_R117_I0.324461.601
105_C115_R0.31941.576
40_L92_R0.309251.526
107_E113_C0.301691.489
32_N36_L0.300251.482
68_D71_E0.289061.426
65_E68_D0.274141.353
71_E75_R0.271011.337
1_S11_K0.270041.333
64_H68_D0.269381.329
59_L62_W0.267161.318
88_E91_E0.25851.276
57_R61_K0.25631.265
54_G114_H0.255271.260
30_G33_K0.248711.227
106_A114_H0.243591.202
91_E95_E0.241731.193
56_S79_E0.241041.189
14_I40_L0.238561.177
114_H117_I0.23751.172
40_L50_L0.235071.160
25_R56_S0.233971.155
90_L94_A0.233731.153
89_G92_R0.230531.138
90_L121_Y0.225911.115
3_E13_G0.223671.104
12_N15_R0.223021.101
105_C116_R0.22261.098
69_W117_I0.22121.092
7_D110_P0.220531.088
3_E15_R0.217481.073
89_G93_L0.215771.065
62_W68_D0.215121.062
92_R96_L0.213821.055
50_L89_G0.213661.054
59_L71_E0.213661.054
55_P72_F0.213351.053
97_A101_V0.209021.031
107_E115_R0.208051.027
110_P116_R0.20220.998
95_E98_R0.202050.997
117_I121_Y0.197060.972
22_L56_S0.19650.970
19_D114_H0.196170.968
2_I115_R0.19540.964
110_P113_C0.195040.962
105_C110_P0.194780.961
55_P79_E0.193560.955
74_E78_A0.19250.950
63_Y113_C0.189620.936
5_F31_F0.188430.930
23_W56_S0.187520.925
3_E11_K0.187140.923
50_L53_L0.184620.911
69_W112_R0.176820.873
19_D106_A0.175950.868
50_L54_G0.173750.857
14_I39_F0.173040.854
80_L121_Y0.172650.852
16_V96_L0.171520.846
3_E7_D0.171380.846
77_R120_E0.170030.839
73_F82_S0.169920.838
63_Y105_C0.169190.835
68_D73_F0.1680.829
95_E99_E0.167610.827
53_L90_L0.164230.810
55_P59_L0.162790.803
70_D73_F0.161510.797
9_L102_A0.160520.792
9_L91_E0.160230.791
78_A81_E0.159330.786
78_A82_S0.159160.785
19_D108_K0.158680.783
22_L114_H0.158390.782
57_R77_R0.157950.779
25_R49_W0.157810.779
87_Q91_E0.154970.765
69_W72_F0.154960.765
30_G72_F0.154840.764
92_R95_E0.153750.759
52_E122_L0.15230.752
65_E112_R0.152190.751
89_G97_A0.151980.750
14_I53_L0.151250.746
13_G102_A0.15120.746
50_L93_L0.150520.743
30_G60_R0.150180.741
23_W59_L0.150080.741
35_D38_S0.14960.738
59_L72_F0.149270.737
24_P49_W0.148310.732
58_E61_K0.14830.732
4_R49_W0.148190.731
24_P33_K0.147080.726
63_Y112_R0.146810.724
69_W119_A0.146590.723
14_I50_L0.145670.719
14_I96_L0.145240.717
59_L75_R0.144650.714
7_D15_R0.14430.712
3_E9_L0.144250.712
31_F36_L0.143960.710
5_F17_L0.143950.710
105_C114_H0.143610.709
97_A100_G0.143590.709
76_Y94_A0.143460.708
15_R101_V0.142610.704
52_E89_G0.142290.702
69_W73_F0.140250.692
22_L55_P0.139430.688
74_E112_R0.138870.685
14_I107_E0.138770.685
80_L117_I0.138690.684
14_I114_H0.138260.682
50_L96_L0.137610.679
6_Y49_W0.137490.678
65_E107_E0.137380.678
55_P63_Y0.13540.668
52_E92_R0.135390.668
56_S72_F0.135180.667
82_S88_E0.134570.664
61_K108_K0.134190.662
62_W71_E0.133930.661
73_F117_I0.132640.655
59_L63_Y0.132190.652
23_W49_W0.131950.651
9_L40_L0.131690.650
14_I77_R0.131650.650
62_W66_D0.131420.649
116_R119_A0.131070.647
32_N38_S0.130860.646
22_L33_K0.128780.635
60_R72_F0.128290.633
2_I113_C0.127920.631
72_F117_I0.127150.627
13_G16_V0.127140.627
93_L101_V0.127090.627
79_E118_L0.125930.621
93_L97_A0.125590.620
22_L63_Y0.124710.615
77_R81_E0.124020.612
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
1fpzA0.778789.60.877
3nmeA0.795186.30.883
1ywfA0.91885.80.884
2f46A0.745985.40.885
3rz2A0.729585.30.885
3s4oA0.737783.50.887
3rgoA0.745982.40.889
3f81A0.795179.30.892
2m3vA0.672177.90.893
1oheA0.704977.40.894
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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