GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3250 - Protein of unknown function (DUF3250)
Pfam: PF11618 (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: 107
Sequences: 4045
Seq/Len: 37.8
HH_delta: 0.256 (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
16_P27_F1.112174.297
56_L61_E1.056324.082
66_G85_A0.726182.806
17_V55_A0.622922.407
62_T65_A0.612982.368
84_S97_T0.610432.359
84_S99_E0.598472.312
53_H62_T0.574472.220
82_H99_E0.536922.075
55_A60_F0.533962.063
86_T97_T0.508051.963
47_S67_Q0.481981.862
49_T65_A0.445611.722
13_Q29_S0.418291.616
47_S69_S0.417831.614
52_L87_L0.397571.536
50_L100_Y0.395111.527
51_E65_A0.384131.484
53_H60_F0.37651.455
14_T17_V0.361511.397
50_L98_L0.361131.395
64_A87_L0.349341.350
15_T29_S0.342751.324
19_R55_A0.299731.158
13_Q31_Y0.295771.143
85_A100_Y0.292941.132
74_L77_N0.291611.127
51_E62_T0.288191.114
15_T18_V0.272761.054
32_K76_S0.272251.052
84_S87_L0.256890.993
67_Q71_R0.256850.992
45_T71_R0.254250.982
12_T31_Y0.249440.964
21_L61_E0.249420.964
20_G63_L0.248550.960
76_S81_I0.248290.959
21_L63_L0.244730.946
72_P83_G0.24310.939
73_L81_I0.235350.909
49_T67_Q0.234350.906
29_S32_K0.233950.904
45_T65_A0.232370.898
78_G103_R0.230230.890
62_T90_V0.226920.877
73_L102_I0.224550.868
99_E103_R0.224530.868
66_G98_L0.22430.867
18_V22_N0.222190.859
65_A91_S0.220240.851
16_P26_D0.220160.851
68_I102_I0.218920.846
96_G101_W0.215590.833
24_F32_K0.214580.829
18_V25_Y0.214020.827
45_T76_S0.20980.811
89_G95_F0.209630.810
54_Q61_E0.208260.805
12_T51_E0.204710.791
57_G95_F0.204510.790
30_Q101_W0.203380.786
21_L54_Q0.198580.767
14_T59_D0.198350.766
69_S72_P0.197260.762
47_S82_H0.195460.755
96_G102_I0.195340.755
13_Q32_K0.194510.752
49_T66_G0.194190.750
55_A59_D0.193430.747
52_L64_A0.193070.746
82_H101_W0.193010.746
16_P25_Y0.192450.744
48_L70_L0.192430.744
77_N90_V0.190270.735
60_F94_D0.188460.728
74_L78_G0.187460.724
83_G103_R0.185530.717
69_S76_S0.184150.712
25_Y54_Q0.183950.711
17_V54_Q0.183210.708
52_L62_T0.181740.702
30_Q70_L0.180650.698
54_Q63_L0.18030.697
20_G23_P0.17880.691
18_V27_F0.178430.689
64_A102_I0.178050.688
23_P54_Q0.177920.687
68_I81_I0.17780.687
68_I85_A0.177730.687
18_V52_L0.177050.684
14_T55_A0.176530.682
53_H96_G0.175610.679
58_S83_G0.175220.677
86_T95_F0.173710.671
33_V70_L0.173640.671
29_S63_L0.171560.663
18_V54_Q0.170460.659
12_T15_T0.170260.658
72_P78_G0.169790.656
18_V23_P0.167750.648
69_S81_I0.167610.648
47_S88_V0.166580.644
49_T69_S0.165530.640
67_Q75_E0.165450.639
63_L95_F0.163970.634
31_Y65_A0.163710.633
47_S83_G0.163290.631
53_H103_R0.16290.629
88_V94_D0.162340.627
22_N76_S0.160720.621
66_G84_S0.160330.619
53_H77_N0.159380.616
54_Q59_D0.159330.616
33_V58_S0.158630.613
46_G58_S0.157990.610
13_Q27_F0.157290.608
34_T48_L0.156590.605
32_K36_D0.155990.603
46_G74_L0.155930.602
81_I87_L0.154930.599
32_K35_M0.154880.598
12_T19_R0.153310.592
67_Q96_G0.152250.588
11_E31_Y0.151930.587
26_D30_Q0.151640.586
11_E30_Q0.151080.584
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
2dmhA0.934699.40.256
1wfjA0.897299.30.262
2fk9A0.859899.30.275
3bxjA0.906599.30.284
1djxA0.878599.30.286
3m7fB0.925299.30.293
3l9bA0.925299.20.302
3b7yA0.915999.20.307
2r83A0.934699.20.311
3ohmB0.859899.20.313

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