GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF11 - Domain of unknown function DUF11
Pfam: PF01345 (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: CL0159
Length: 76
Sequences: 534
Seq/Len: 7.03
HH_delta: 0.693 (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
30_K64_D0.476983.277
27_S52_T0.303792.087
32_V43_V0.285141.959
34_P37_A0.267771.840
72_F75_G0.26121.794
24_P54_P0.255621.756
34_P41_D0.239971.649
24_P57_A0.230891.586
43_V70_L0.229491.577
66_L70_L0.210091.443
57_A60_V0.209931.442
32_V45_Y0.203911.401
26_L54_P0.182191.252
37_A43_V0.180081.237
30_K45_Y0.179291.232
45_Y70_L0.173151.190
32_V37_A0.170781.173
42_T71_T0.163641.124
38_N71_T0.161331.108
31_T46_T0.160211.101
28_I47_I0.158581.089
38_N41_D0.158111.086
29_T47_I0.154491.061
56_P68_A0.153851.057
39_P55_A0.152251.046
28_I62_V0.151941.044
30_K72_F0.150911.037
27_S50_T0.148371.019
24_P55_A0.148311.019
46_T69_G0.147161.011
37_A59_N0.147081.010
32_V35_S0.146881.009
43_V68_A0.146761.008
18_V71_T0.144960.996
28_I60_V0.141620.973
25_D54_P0.137760.946
54_P70_L0.137490.945
28_I61_V0.137160.942
22_A54_P0.13590.934
53_G57_A0.134570.924
47_I62_V0.134030.921
27_S57_A0.130920.899
22_A55_A0.127380.875
17_N48_T0.126080.866
27_S49_V0.125790.864
66_L72_F0.12510.859
29_T48_T0.123960.852
21_V62_V0.123270.847
25_D40_G0.122370.841
26_L40_G0.121230.833
20_V26_L0.120680.829
23_I39_P0.11970.822
33_N46_T0.119660.822
19_T46_T0.117570.808
19_T25_D0.117440.807
50_T75_G0.117430.807
35_S68_A0.117350.806
37_A40_G0.116750.802
51_N62_V0.115470.793
54_P58_T0.113460.779
26_L29_T0.113310.778
19_T22_A0.112080.770
34_P48_T0.1120.769
38_N49_V0.111990.769
17_N21_V0.111340.765
55_A74_S0.109750.754
28_I71_T0.10940.752
31_T48_T0.109090.749
32_V36_T0.108880.748
36_T43_V0.108220.743
54_P59_N0.106440.731
36_T49_V0.106170.729
33_N41_D0.105430.724
39_P56_P0.104690.719
17_N32_V0.104090.715
23_I27_S0.103110.708
50_T54_P0.102950.707
44_T63_T0.102890.707
23_I29_T0.102320.703
29_T46_T0.102010.701
41_D62_V0.101790.699
20_V33_N0.101470.697
36_T53_G0.100770.692
44_T71_T0.100450.690
17_N28_I0.09990.686
21_V54_P0.099290.682
33_N43_V0.098520.677
30_K65_T0.096690.664
22_A59_N0.094810.651
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
3qdhA0.710595.40.693
2x9zA0.697494.70.708
3iduA0.868494.60.709
2x9xA0.736894.10.716
3hr6A1940.717
2l0dA0.710592.40.733
3uxfA0.986892.30.734
2xtlA0.7237920.736
2y1vA1920.736
3kptA0.986891.20.742
If you are interested in a protein containing this domain,
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