GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4145 - Domain of unknown function (DUF4145)
Pfam: PF13643 (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. )
Clan: CL0291
Length: 87
Sequences: 664
Seq/Len: 7.63
HH_delta: 0.778 (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
19_R64_G0.808955.366
58_H61_R0.547453.631
16_V68_A0.319432.119
13_A17_M0.297051.970
75_T78_D0.293341.946
14_A18_A0.247681.643
26_V30_G0.242481.608
22_L37_L0.241161.600
6_C17_M0.231881.538
50_P53_I0.226811.504
22_L57_L0.222871.478
2_E10_D0.222311.475
10_D17_M0.220741.464
38_N61_R0.211331.402
17_M20_R0.199561.324
6_C13_A0.196471.303
65_N69_H0.196361.303
43_K47_K0.194451.290
30_G40_K0.189751.259
7_Y14_A0.189311.256
38_N68_A0.18891.253
38_N42_N0.18771.245
19_R69_H0.181351.203
23_E40_K0.180541.198
3_A18_A0.179771.192
7_Y11_P0.17331.150
3_A83_L0.172731.146
6_C9_S0.171561.138
51_P55_D0.171341.137
12_R20_R0.169931.127
27_K40_K0.167781.113
25_I28_E0.163781.086
60_I64_G0.163051.082
38_N58_H0.160511.065
18_A79_A0.159861.060
76_E81_D0.1561.035
21_A25_I0.153631.019
16_V67_A0.151881.007
19_R37_L0.150881.001
37_L64_G0.147880.981
23_E70_E0.147660.979
44_L48_G0.144550.959
12_R17_M0.142960.948
61_R65_N0.140990.935
79_A83_L0.139630.926
18_A60_I0.137590.913
2_E17_M0.135640.900
15_A22_L0.132330.878
30_G46_K0.132110.876
11_P76_E0.132010.876
37_L57_L0.131760.874
22_L26_V0.131060.869
12_R23_E0.130180.864
20_R68_A0.12980.861
3_A17_M0.129280.858
5_R52_D0.128190.850
15_A74_I0.127180.844
20_R24_F0.126760.841
5_R9_S0.126210.837
14_A80_E0.125120.830
26_V40_K0.125070.830
13_A16_V0.125040.829
41_I61_R0.124050.823
60_I72_K0.123570.820
47_K59_A0.122790.814
5_R33_K0.121840.808
51_P59_A0.121610.807
6_C14_A0.121030.803
66_D78_D0.121010.803
16_V20_R0.120950.802
4_E23_E0.120430.799
21_A39_E0.120210.797
15_A79_A0.119720.794
4_E29_L0.119290.791
42_N58_H0.118980.789
13_A20_R0.11890.789
18_A25_I0.118470.786
3_A13_A0.118410.785
73_E82_A0.117610.780
26_V29_L0.116450.772
14_A28_E0.115530.766
14_A54_R0.11490.762
9_S84_E0.114670.761
41_I54_R0.114370.759
50_P55_D0.11360.754
31_I40_K0.1130.750
39_E42_N0.112970.749
34_G51_P0.112750.748
22_L83_L0.112520.746
23_E26_V0.112440.746
36_N51_P0.111650.741
53_I80_E0.111150.737
54_R58_H0.110770.735
42_N54_R0.110680.734
6_C10_D0.110420.732
11_P14_A0.110420.732
11_P79_A0.110130.731
30_G48_G0.109980.730
27_K30_G0.10940.726
35_K50_P0.108810.722
45_R54_R0.108310.718
18_A82_A0.107890.716
36_N55_D0.107460.713
41_I57_L0.10740.712
45_R55_D0.107320.712
33_K52_D0.107230.711
7_Y80_E0.105960.703
26_V46_K0.104850.695
25_I40_K0.104430.693
47_K52_D0.104230.691
19_R60_I0.103460.686
32_K57_L0.103020.683
35_K39_E0.10210.677
8_N50_P0.100730.668
58_H62_K0.100550.667
64_G82_A0.099880.663
8_N11_P0.099480.660
36_N61_R0.099190.658
66_D70_E0.098930.656
15_A66_D0.09840.653
14_A49_L0.098060.650
40_K67_A0.097990.650
81_D84_E0.097680.648
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
2hsbA187.30.778
1o3uA186.50.781
1ufbA180.40.796
1wolA0.977790.798
2jpuA0.965577.30.801
1jogA0.95462.80.82
3o10A161.80.821
1wtyA0.8966590.824
1ylmA1470.835
1wwpA0.908450.838
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