GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4115 - Domain of unknown function (DUF4115)
Pfam: PF13464 (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: 77
Sequences: 926
Seq/Len: 12.03
HH_delta: 0.787 (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
10_W45_G0.587982.973
5_A26_L0.584472.956
7_G49_A0.53372.699
12_E23_S0.496352.510
46_N49_A0.455272.302
27_K30_E0.437522.213
8_D27_K0.428732.168
6_T51_E0.400742.027
4_T31_T0.371341.878
48_G66_G0.367061.856
12_E43_R0.356221.801
42_I74_F0.323021.634
22_F32_K0.320431.620
26_L32_K0.290351.468
17_D38_E0.282451.428
2_V33_T0.275591.394
4_T53_T0.273871.385
2_V53_T0.257271.301
4_T51_E0.25651.297
48_G63_G0.249461.262
16_A21_L0.248681.258
43_R71_V0.243891.233
8_D25_T0.235521.191
36_G40_F0.231971.173
53_T58_P0.225621.141
14_T20_V0.223571.131
70_K74_F0.212321.074
63_G66_G0.209331.059
7_G28_A0.206661.045
5_A12_E0.205561.040
24_G32_K0.199021.006
34_F38_E0.195320.988
49_A73_R0.192760.975
26_L30_E0.190.961
9_S44_I0.189770.960
24_G30_E0.189180.957
44_I50_V0.183160.926
3_L50_V0.183120.926
51_E58_P0.182390.922
59_V74_F0.180510.913
9_S50_V0.179910.910
17_D36_G0.178190.901
8_D58_P0.175720.889
17_D21_L0.173180.876
5_A50_V0.172250.871
21_L36_G0.171580.868
8_D59_V0.163970.829
20_V23_S0.16230.821
39_P72_A0.16170.818
69_V74_F0.160810.813
69_V72_A0.159160.805
40_F44_I0.158330.801
33_T53_T0.156540.792
48_G51_E0.156020.789
4_T37_K0.154140.780
7_G46_N0.153810.778
41_R71_V0.152880.773
46_N66_G0.152710.772
60_D63_G0.152630.772
7_G32_K0.152550.771
20_V43_R0.152480.771
8_D18_G0.151450.766
19_K22_F0.150440.761
14_T56_G0.148470.751
40_F54_V0.146380.740
12_E20_V0.145220.734
20_V39_P0.145060.734
64_P67_Q0.145010.733
37_K55_N0.143610.726
14_T41_R0.142590.721
9_S45_G0.142180.719
27_K33_T0.140580.711
10_W43_R0.140140.709
67_Q73_R0.138920.703
59_V63_G0.138490.700
44_I70_K0.137220.694
19_K23_S0.13650.690
29_G48_G0.134850.682
35_E55_N0.13410.678
22_F28_A0.133190.674
19_K41_R0.132010.668
31_T51_E0.131890.667
16_A39_P0.131850.667
5_A72_A0.13080.661
5_A30_E0.130530.660
18_G73_R0.128960.652
2_V31_T0.128570.650
13_V24_G0.12790.647
69_V73_R0.127510.645
37_K42_I0.127480.645
61_L71_V0.127230.643
13_V21_L0.126260.639
37_K40_F0.125460.634
55_N67_Q0.124330.629
19_K53_T0.124250.628
27_K38_E0.123830.626
12_E69_V0.12370.626
1_L54_V0.123420.624
11_V26_L0.12330.624
23_S33_T0.122690.620
46_N71_V0.122030.617
10_W29_G0.12070.610
1_L66_G0.120670.610
39_P57_K0.120630.610
42_I59_V0.120330.609
43_R52_V0.120140.608
14_T30_E0.119940.607
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
3kglA0.98773.70.787
3qacA0.98770.10.792
3fz3A0.98767.80.795
3kscA0.98763.60.8
1x0cA0.97442.40.823
3u5eH0.558442.20.824
3iz5F0.558441.50.824
3zpyA0.909138.50.827
3rfzB0.7922380.827
3j3bH0.558436.30.83
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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