GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1730 - Domain of unknown function (DUF1730)
Pfam: PF08331 (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: 78
Sequences: 972
Seq/Len: 12.46
HH_delta: 0.871 (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
3_D6_K0.549182.889
60_A72_Y0.524022.757
41_R44_W0.434082.284
19_F55_K0.356561.876
54_K58_Q0.34691.825
39_I43_A0.325691.714
61_E64_R0.311941.641
38_R44_W0.301581.587
46_R50_K0.289131.521
54_K61_E0.287691.514
53_K75_F0.286741.509
51_V55_K0.283021.489
31_P38_R0.272541.434
46_R54_K0.265551.397
16_V63_I0.265041.394
64_R69_D0.25831.359
60_A64_R0.251361.322
17_L56_L0.248961.310
61_E65_E0.242341.275
10_G71_E0.242321.275
31_P34_P0.240791.267
8_L11_A0.234871.236
32_P69_D0.23161.219
32_P35_G0.229331.207
7_L75_F0.228211.201
58_Q61_E0.224291.180
67_G71_E0.220351.159
4_P75_F0.218931.152
33_G36_R0.209971.105
38_R55_K0.209841.104
8_L75_F0.209151.100
29_P32_P0.207231.090
64_R71_E0.194461.023
42_Y75_F0.192271.012
23_P40_A0.190311.001
57_E61_E0.187870.988
41_R76_V0.187820.988
15_I63_I0.184570.971
57_E74_I0.183090.963
68_P71_E0.179770.946
64_R67_G0.178970.942
3_D52_L0.178370.938
45_G59_L0.178220.938
62_W66_L0.177720.935
8_L72_Y0.175030.921
36_R44_W0.172190.906
39_I57_E0.171650.903
67_G70_F0.171550.903
60_A74_I0.169820.893
62_W65_E0.167970.884
17_L52_L0.167610.882
21_Y40_A0.166450.876
11_A19_F0.166350.875
58_Q66_L0.165990.873
15_I62_W0.164280.864
7_L53_K0.164210.864
1_R7_L0.163660.861
44_W60_A0.159760.841
30_P33_G0.158450.834
22_Y63_I0.157880.831
1_R51_V0.157120.827
12_R35_G0.154490.813
6_K14_V0.15440.812
30_P58_Q0.154370.812
45_G55_K0.153130.806
42_Y49_H0.152040.800
36_R66_L0.151670.798
9_P71_E0.151360.796
73_R78_T0.150150.790
6_K65_E0.149790.788
30_P67_G0.149320.786
30_P36_R0.149010.784
9_P73_R0.148140.779
18_A22_Y0.146650.772
61_E66_L0.145730.767
36_R65_E0.144860.762
54_K62_W0.144670.761
5_R68_P0.143940.757
58_Q62_W0.142840.752
37_G78_T0.141780.746
23_P53_K0.141630.745
4_P53_K0.141620.745
23_P52_L0.141420.744
16_V41_R0.140740.740
38_R41_R0.140080.737
7_L14_V0.139270.733
17_L76_V0.13910.732
22_Y75_F0.138880.731
50_K53_K0.13840.728
1_R59_L0.137110.721
65_E69_D0.13710.721
21_Y56_L0.136910.720
58_Q65_E0.13540.712
30_P38_R0.13530.712
63_I70_F0.134450.707
34_P69_D0.133380.702
29_P65_E0.133320.701
23_P75_F0.132820.699
18_A52_L0.132730.698
44_W51_V0.131490.692
9_P37_G0.131390.691
7_L23_P0.13110.690
32_P37_G0.130760.688
39_I42_Y0.130440.686
57_E60_A0.129860.683
2_I34_P0.129470.681
36_R78_T0.128930.678
13_S76_V0.128590.677
20_P51_V0.128320.675
33_G45_G0.128120.674
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
3ff1A0.9231510.871
3s44A0.897445.70.875
3qkiA0.935920.60.894
2q8nA0.923119.90.895
2vl7A0.884619.70.895
4em6D0.935914.20.901
3ljkA0.935913.60.902
3rxzA0.9231110.906
1jmsA0.769210.50.907
1sjjA0.935910.40.907
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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