GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF393 - Protein of unknown function DUF393
Pfam: PF04134 (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: 114
Sequences: 1043
Seq/Len: 9.15
HH_delta: 0.829 (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
66_G102_R0.536693.569
16_F20_R0.392612.611
99_R103_W0.362452.410
1_V26_L0.287381.911
45_I50_A0.27491.828
46_S49_D0.27461.826
56_L69_A0.269381.791
67_S97_A0.257871.715
14_V28_F0.256711.707
103_W111_W0.253721.687
100_L104_I0.25311.683
103_W107_N0.24671.640
26_L73_L0.241991.609
1_V73_L0.238451.586
2_F63_V0.235721.567
33_S36_D0.232521.546
13_E74_L0.232171.544
73_L77_L0.230891.535
70_V74_L0.229991.529
72_R75_R0.217341.445
4_D108_R0.207851.382
78_P82_R0.205711.368
87_L90_L0.205221.365
46_S50_A0.203111.351
6_D109_Y0.202721.348
71_L97_A0.197781.315
7_C10_C0.197171.311
67_S98_D0.196011.303
64_Y72_R0.187851.249
109_Y112_F0.187181.245
2_F31_I0.18671.241
25_R76_R0.185191.231
9_L13_E0.183741.222
101_Y105_A0.183241.218
96_L99_R0.181711.208
37_Q50_A0.179781.195
64_Y69_A0.179711.195
100_L103_W0.17681.176
8_P12_R0.172021.144
5_G14_V0.165931.103
68_D72_R0.162661.082
4_D7_C0.158581.055
104_I107_N0.156431.040
26_L55_H0.15371.022
4_D9_L0.148910.990
28_F53_R0.148910.990
8_P14_V0.147240.979
1_V54_L0.146470.974
21_D77_L0.145440.967
15_R18_R0.1450.964
53_R65_R0.144050.958
13_E30_D0.143590.955
58_D72_R0.143220.952
105_A109_Y0.142720.949
103_W106_R0.142410.947
17_L26_L0.141130.938
75_R85_A0.140980.937
82_R86_W0.140710.936
22_R48_E0.140460.934
9_L112_F0.139620.928
20_R81_W0.138960.924
85_A88_L0.138470.921
30_D55_H0.138310.920
32_Q107_N0.137270.913
52_S66_G0.137060.911
54_L67_S0.136110.905
41_A58_D0.135570.901
79_G83_W0.135320.900
61_E75_R0.13440.894
47_P50_A0.133810.890
54_L68_D0.133560.888
55_H72_R0.132690.882
41_A96_L0.132560.881
28_F31_I0.13220.879
26_L43_Y0.13120.872
9_L104_I0.130970.871
97_A112_F0.130140.865
67_S70_V0.129260.860
4_D10_C0.128920.857
18_R33_S0.12710.845
9_L31_I0.127080.845
3_Y52_S0.126490.841
68_D89_R0.126080.838
8_P11_R0.12510.832
3_Y8_P0.124950.831
21_D24_G0.12480.830
68_D98_D0.124640.829
54_L105_A0.12430.827
21_D67_S0.124030.825
2_F8_P0.123450.821
50_A53_R0.123260.820
68_D92_G0.123040.818
43_Y59_D0.121930.811
3_Y82_R0.121690.809
53_R66_G0.121550.808
90_L97_A0.120580.802
61_E93_I0.120150.799
5_G28_F0.120140.799
3_Y97_A0.119490.795
5_G67_S0.1190.791
61_E86_W0.118650.789
34_E96_L0.118160.786
30_D36_D0.118010.785
29_V35_P0.117890.784
55_H63_V0.117820.783
17_L48_E0.117180.779
42_S79_G0.116950.778
54_L65_R0.116940.778
68_D71_L0.116360.774
27_R72_R0.115340.767
77_L111_W0.114270.760
82_R85_A0.113170.753
99_R102_R0.113060.752
34_E41_A0.112890.751
2_F56_L0.112030.745
1_V23_G0.111980.745
5_G10_C0.111820.744
21_D36_D0.111770.743
17_L21_D0.111370.741
79_G82_R0.111330.740
1_V78_P0.111170.739
75_R84_L0.11070.736
8_P53_R0.11060.735
53_R73_L0.110420.734
3_Y11_R0.110350.734
24_G29_V0.110160.733
30_D40_L0.109550.728
44_G84_L0.109420.728
43_Y58_D0.109250.726
71_L85_A0.109230.726
3_Y50_A0.109170.726
60_G99_R0.1090.725
34_E37_Q0.108660.723
35_P42_S0.108580.722
13_E17_L0.108520.722
29_V33_S0.108410.721
46_S92_G0.108380.721
10_C108_R0.108170.719
100_L110_R0.107680.716
27_R58_D0.107230.713
31_I53_R0.107080.712
21_D25_R0.106990.711
8_P31_I0.106780.710
79_G104_I0.106680.709
47_P51_D0.106540.708
64_Y76_R0.106490.708
88_L92_G0.106360.707
65_R98_D0.10620.706
29_V41_A0.105780.703
93_I97_A0.105640.702
82_R87_L0.105460.701
14_V70_V0.1050.698
8_P30_D0.104540.695
18_R88_L0.104520.695
16_F52_S0.104460.695
41_A45_I0.104420.694
59_D90_L0.1040.692
20_R86_W0.10350.688
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
1nm3A0.596591.10.829
1abaA0.61489.70.834
3mszA0.684289.30.835
1fovA0.666788.40.838
2klxA0.701887.40.84
3qmxA0.69386.60.842
1kngA0.728184.30.847
3ctgA0.719384.10.847
2hzeA0.754483.90.847
3fk8A0.684283.20.849
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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