GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1732 - Domain of unknown function (DUF1732)
Pfam: PF08340 (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: 87
Sequences: 768
Seq/Len: 8.83
HH_delta: 0.92 (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
57_G69_V0.70063.712
53_I72_M0.433362.296
46_L79_I0.397982.109
17_L21_K0.386212.046
53_I76_I0.364011.929
13_I56_I0.344251.824
25_K29_E0.3311.754
1_A4_V0.309191.638
75_E78_K0.308861.636
30_L45_L0.304581.614
20_L49_M0.302381.602
7_L11_A0.295221.564
63_A67_N0.275131.458
28_R32_E0.263251.395
57_G70_V0.253671.344
1_A5_A0.253481.343
21_K25_K0.25341.343
43_D84_Q0.251751.334
50_N58_S0.247091.309
13_I65_I0.246561.306
9_D74_T0.243881.292
27_F49_M0.241511.280
35_G40_R0.239281.268
25_K28_R0.236421.253
24_L49_M0.234161.241
67_N71_E0.225191.193
22_S29_E0.224771.191
18_V40_R0.220681.169
9_D69_V0.219971.165
58_S66_S0.215391.141
26_Q29_E0.211551.121
27_F46_L0.208651.106
18_V75_E0.208161.103
30_L37_P0.206951.097
27_F42_L0.204921.086
45_L74_T0.202421.073
20_L76_I0.200731.064
70_V74_T0.198651.053
29_E33_S0.197451.046
32_E64_E0.195591.036
22_S26_Q0.194241.029
25_K67_N0.194111.028
34_E64_E0.190481.009
53_I69_V0.189671.005
21_K32_E0.18810.997
14_S78_K0.187780.995
12_D56_I0.187650.994
2_Q63_A0.186740.989
43_D50_N0.186450.988
63_A66_S0.184540.978
1_A9_D0.180950.959
18_V78_K0.179770.952
9_D78_K0.174840.926
24_L72_M0.172360.913
41_K77_E0.171190.907
25_K34_E0.168620.893
40_R74_T0.167410.887
65_I68_L0.167360.887
30_L42_L0.165840.879
11_A26_Q0.165110.875
73_K77_E0.163710.867
2_Q41_K0.163170.865
14_S79_I0.162730.862
29_E32_E0.162330.860
79_I83_V0.162010.858
34_E38_V0.161340.855
46_L75_E0.161090.854
24_L28_R0.160520.851
11_A70_V0.159530.845
29_E45_L0.156780.831
13_I17_L0.156660.830
14_S18_V0.156410.829
14_S75_E0.155150.822
46_L80_R0.152740.809
45_L67_N0.152520.808
1_A18_V0.151730.804
21_K64_E0.151520.803
50_N86_I0.150740.799
43_D83_V0.15010.795
27_F79_I0.148020.784
28_R71_E0.14750.782
5_A45_L0.14710.779
77_E80_R0.147090.779
33_S64_E0.147040.779
35_G64_E0.146750.778
1_A40_R0.146280.775
60_S64_E0.146270.775
2_Q6_L0.14440.765
82_Q85_N0.144030.763
63_A70_V0.14380.762
70_V76_I0.143240.759
26_Q74_T0.143190.759
4_V8_A0.143020.758
41_K71_E0.142450.755
12_D18_V0.141830.751
62_D67_N0.141410.749
12_D80_R0.140930.747
33_S71_E0.14060.745
26_Q41_K0.139910.741
58_S81_E0.139870.741
43_D82_Q0.139340.738
43_D87_E0.138130.732
7_L22_S0.137670.729
7_L61_N0.136960.726
52_E55_T0.136870.725
52_E59_K0.136870.725
55_T59_K0.136870.725
40_R62_D0.136470.723
4_V14_S0.135990.721
11_A66_S0.13540.717
21_K28_R0.135150.716
13_I60_S0.134850.714
60_S66_S0.134510.713
10_K24_L0.133930.710
69_V76_I0.133810.709
61_N68_L0.133620.708
75_E79_I0.133510.707
10_K63_A0.133160.706
7_L67_N0.131420.696
66_S80_R0.131060.694
49_M76_I0.130790.693
37_P40_R0.130180.690
33_S63_A0.130080.689
33_S38_V0.129920.688
28_R67_N0.129690.687
64_E68_L0.12950.686
6_L28_R0.128670.682
22_S49_M0.128370.680
5_A33_S0.127120.674
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
1lwuB0.551733.30.92
1r31A0.747123.80.925
4dndA0.97721.70.927
2jc9A0.597716.50.93
1oegA0.160914.80.932
3dmqA0.770114.70.932
3m9bA0.9655120.934
3q8kA0.448311.10.935
2ocyA0.942510.80.936
1gaxA0.74719.70.937
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