GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2255 - Uncharacterized protein conserved in bacteria (DUF2255)
Pfam: PF10012 (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: 116
Sequences: 2949
Seq/Len: 25.42
HH_delta: 0.282 (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
15_A27_P1.008473.613
16_P54_A0.870863.120
13_H27_P0.629272.255
12_L63_I0.552711.980
17_F58_Q0.535721.920
61_G74_F0.532681.909
32_V65_A0.522031.870
13_H66_G0.499771.791
9_A32_V0.496881.780
30_I41_V0.475061.702
6_I65_A0.473341.696
9_A65_A0.460831.651
13_H64_R0.432761.551
33_V86_I0.422171.513
7_D34_R0.41971.504
43_S51_W0.418251.499
43_S52_Y0.413771.483
39_L63_I0.404471.449
35_V85_A0.399731.432
82_L85_A0.386111.383
4_D8_A0.381191.366
17_F21_G0.369991.326
85_A89_A0.365441.309
46_G49_S0.359121.287
12_L32_V0.354021.268
27_P64_R0.353181.265
35_V89_A0.352241.262
28_T54_A0.348851.250
60_A73_T0.325871.168
31_W94_Y0.318541.141
16_P61_G0.315861.132
23_T62_R0.315571.131
33_V93_K0.310331.112
80_P84_D0.30831.105
19_E57_A0.30731.101
14_I61_G0.299661.074
42_R49_S0.298541.070
34_R38_D0.298471.069
55_A61_G0.295891.060
33_V40_Y0.291121.043
12_L30_I0.289581.038
80_P83_N0.287191.029
62_R71_D0.286721.027
53_R56_L0.284091.018
52_Y56_L0.283381.015
50_R54_A0.279291.001
32_V63_I0.277980.996
86_I90_Y0.27340.980
41_V72_V0.270190.968
6_I34_R0.269780.967
83_N87_D0.269440.965
43_S49_S0.268960.964
55_A74_F0.268040.960
88_A92_A0.267720.959
33_V89_A0.262870.942
34_R37_D0.259510.930
81_A84_D0.25930.929
64_R69_E0.257980.924
5_R9_A0.256980.921
40_Y86_I0.250920.899
35_V38_D0.250190.896
29_W64_R0.248880.892
90_Y94_Y0.248810.892
42_R87_D0.245650.880
17_F23_T0.241870.867
77_V82_L0.240170.861
89_A93_K0.239190.857
34_R39_L0.237120.850
75_E82_L0.232870.834
23_T27_P0.232160.832
16_P55_A0.229890.824
87_D90_Y0.229490.822
47_R56_L0.228040.817
46_G51_W0.22660.812
20_D23_T0.222650.798
57_A60_A0.220970.792
5_R67_G0.214840.770
84_D88_A0.214320.768
16_P28_T0.213090.764
36_D85_A0.206830.741
19_E50_R0.204930.734
49_S64_R0.204680.733
27_P62_R0.204270.732
59_G73_T0.202690.726
31_W49_S0.202680.726
55_A76_P0.202420.725
87_D91_R0.202120.724
78_T84_D0.202110.724
12_L41_V0.201310.721
11_E66_G0.201280.721
18_R54_A0.200990.720
14_I51_W0.197770.709
87_D95_G0.197450.707
11_E64_R0.197330.707
4_D81_A0.196180.703
16_P21_G0.195650.701
48_N52_Y0.194550.697
17_F20_D0.194430.697
50_R71_D0.194280.696
28_T51_W0.193860.695
90_Y93_K0.193350.693
24_L50_R0.192770.691
13_H65_A0.192430.689
30_I51_W0.192140.688
41_V51_W0.192130.688
52_Y76_P0.192090.688
40_Y85_A0.191970.688
59_G75_E0.190510.683
14_I55_A0.189430.679
11_E31_W0.18550.665
56_L59_G0.185340.664
82_L86_I0.18510.663
48_N53_R0.185090.663
8_A92_A0.1850.663
50_R53_R0.184980.663
15_A62_R0.184010.659
33_V67_G0.183460.657
63_I70_K0.182680.655
91_R96_G0.181860.652
24_L54_A0.181840.652
36_D92_A0.181750.651
24_L28_T0.181410.650
65_A70_K0.181250.649
9_A68_V0.180910.648
4_D7_D0.179640.644
15_A23_T0.179160.642
6_I39_L0.178090.638
47_R52_Y0.176790.633
56_L76_P0.174230.624
16_P51_W0.173550.622
47_R78_T0.169970.609
79_D83_N0.169250.606
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
2fg9A0.956999.60.282
3f7eA0.956999.60.289
2iabA0.939799.60.29
2htiA0.948399.60.303
1rfeA0.956999.60.308
2asfA0.922499.60.309
2furA0.956999.60.31
3db0A0.913899.60.314
3u35A0.922499.60.32
3swjA0.956999.60.321

Page generated in 0.0153 seconds.