GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2384 - Protein of unknown function (DUF2384)
Pfam: PF09722 (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: 54
Sequences: 700
Seq/Len: 12.96
HH_delta: 0.709 (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
4_A14_A0.646563.036
29_T32_E0.584112.742
19_R31_L0.339721.595
18_L34_L0.329941.549
37_E41_E0.316921.488
48_D51_E0.306891.441
4_A40_A0.303761.426
24_A46_Y0.301261.414
37_E40_A0.289871.361
30_P39_G0.288581.355
4_A7_V0.279321.311
42_R45_D0.275131.292
16_R20_T0.26621.250
25_L29_T0.263681.238
38_A42_R0.257551.209
28_R32_E0.254631.196
3_Q44_L0.252711.187
49_R52_Y0.24351.143
11_E16_R0.243271.142
22_N27_G0.240591.130
10_D13_K0.235361.105
7_V50_I0.228831.074
38_A41_E0.225141.057
12_D16_R0.223131.048
18_L30_P0.223041.047
23_P27_G0.219771.032
17_W24_A0.21270.999
19_R29_T0.208630.980
18_L36_T0.208530.979
3_Q48_D0.203230.954
19_R28_R0.19960.937
28_R41_E0.197920.929
34_L37_E0.1960.920
21_P29_T0.195250.917
48_D52_Y0.192770.905
3_Q47_L0.19210.902
33_L36_T0.190760.896
50_I53_G0.185940.873
3_Q51_E0.18530.870
22_N44_L0.182640.858
34_L40_A0.181910.854
33_L39_G0.181040.850
5_E11_E0.180150.846
36_T39_G0.179630.843
25_L30_P0.178940.840
14_A17_W0.17860.839
3_Q6_E0.177650.834
3_Q42_R0.177090.831
20_T33_L0.175770.825
5_E26_G0.175730.825
7_V47_L0.174190.818
12_D15_R0.172780.811
33_L37_E0.172650.811
12_D29_T0.172260.809
8_F50_I0.169960.798
2_K6_E0.167190.785
41_E44_L0.166950.784
26_G42_R0.165940.779
8_F47_L0.164180.771
28_R40_A0.163440.767
4_A37_E0.163260.767
14_A47_L0.162280.762
13_K23_P0.160650.754
13_K42_R0.160170.752
32_E35_R0.160160.752
11_E28_R0.157530.740
8_F33_L0.157280.738
7_V46_Y0.15320.719
33_L42_R0.150250.705
12_D32_E0.149730.703
8_F17_W0.149580.702
6_E25_L0.149270.701
17_W35_R0.149040.700
22_N46_Y0.146770.689
37_E50_I0.145390.683
13_K36_T0.144440.678
10_D19_R0.143930.676
13_K30_P0.143220.672
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
2kfsA0.944488.40.709
3m97X0.925939.50.797
1cxcA0.9815350.802
3bl4A0.388931.50.806
1oqyA129.30.81
1i8oA0.907426.70.813
2vz8A0.888925.10.815
1vydA0.925920.50.822
3kd8A0.870419.90.824
2bh4X0.96319.20.825
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