GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1049 - Protein of unknown function (DUF1049)
Pfam: PF06305 (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: 68
Sequences: 847
Seq/Len: 12.46
HH_delta: 0.792 (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
50_I53_L0.575912.984
57_L60_L0.550862.854
56_E61_E0.531222.752
2_Q12_L0.405642.101
49_R54_R0.398742.066
32_A35_G0.347031.798
18_L23_L0.34171.770
46_L50_I0.314091.627
49_R53_L0.283151.467
4_T19_P0.257481.334
24_I27_A0.249381.292
9_V23_L0.242411.256
48_R51_R0.241981.254
2_Q13_F0.233941.212
11_F14_G0.230151.192
20_L24_I0.22421.161
20_L23_L0.222191.151
53_L57_L0.214071.109
2_Q32_A0.21151.096
40_L44_L0.207241.074
23_L27_A0.206571.070
36_W47_R0.204921.062
56_E60_L0.201151.042
48_R52_R0.198421.028
9_V28_F0.198181.027
54_R58_K0.195831.015
33_L57_L0.192120.995
7_V47_R0.190440.987
29_L32_A0.186630.967
7_V20_L0.185960.963
56_E59_K0.184790.957
9_V24_I0.184760.957
39_S42_S0.183650.951
29_L35_G0.182520.946
28_F39_S0.178140.923
52_R61_E0.17760.920
51_R55_K0.1740.901
21_G45_R0.171110.886
15_Q30_L0.170480.883
4_T21_G0.166590.863
20_L45_R0.165310.856
49_R52_R0.164840.854
45_R52_R0.16270.843
10_N15_Q0.162160.840
8_T17_P0.161650.837
35_G39_S0.160470.831
36_W39_S0.16030.830
37_L61_E0.160130.830
6_P49_R0.158610.822
25_L44_L0.158540.821
39_S51_R0.158290.820
49_R61_E0.157840.818
42_S46_L0.157260.815
35_G38_L0.156150.809
24_I33_L0.153490.795
37_L49_R0.15260.791
14_G17_P0.152370.789
58_K61_E0.151570.785
43_R46_L0.151160.783
4_T25_L0.151160.783
30_L52_R0.150160.778
2_Q14_G0.14910.772
5_Q11_F0.14890.771
27_A42_S0.148150.768
7_V54_R0.148070.767
17_P23_L0.147720.765
7_V18_L0.147430.764
28_F43_R0.14730.763
32_A38_L0.14560.754
26_I54_R0.145550.754
4_T13_F0.14460.749
26_I61_E0.143160.742
38_L41_P0.142720.739
10_N13_F0.141090.731
37_L59_K0.140620.728
43_R47_R0.139310.722
13_F39_S0.138270.716
7_V52_R0.138260.716
19_P22_L0.137430.712
4_T40_L0.137260.711
36_W43_R0.136930.709
10_N14_G0.134530.697
46_L52_R0.132890.688
16_F51_R0.13280.688
7_V34_L0.131640.682
35_G50_I0.131240.680
36_W40_L0.130860.678
15_Q41_P0.130210.675
45_R59_K0.129210.669
43_R51_R0.128090.664
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
1scfA0.970661.40.792
3errA155.20.799
2hi2A0.7547.40.808
2j5uA0.676547.40.808
3sokA0.7544.80.81
1rtm10.352941.80.814
3pjsK138.60.817
1oqwA0.7536.50.819
3rvyA130.10.827
3ra3B0.397129.50.827
If you are interested in a protein containing this domain,
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