GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2392 - Protein of unknown function (DUF2392)
Pfam: PF10288 (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: 2807
Seq/Len: 26.23
HH_delta: 0.244 (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
90_E97_V1.14693.487
2_A100_V0.812432.470
43_K47_A0.731042.223
73_S76_M0.725862.207
42_L45_E0.683072.077
5_T104_A0.634511.929
95_S99_T0.587741.787
50_N55_L0.577361.755
48_F52_L0.570031.733
80_E92_N0.565191.718
13_R17_L0.562371.710
79_N82_T0.558931.699
49_Y53_C0.554181.685
5_T100_V0.536181.630
84_D88_N0.527811.605
78_I82_T0.515761.568
14_G17_L0.501061.523
2_A97_V0.479271.457
5_T20_Q0.467641.422
76_M79_N0.459171.396
19_W22_S0.455031.384
99_T102_R0.45141.372
88_N91_E0.444771.352
7_S74_K0.442061.344
75_N78_I0.434861.322
50_N57_S0.434821.322
44_K48_F0.434581.321
2_A104_A0.430991.310
38_L41_L0.430611.309
88_N92_N0.42831.302
47_A59_L0.416381.266
62_S79_N0.412271.254
5_T9_V0.412111.253
24_G33_K0.400841.219
10_A93_Y0.380881.158
2_A86_I0.372651.133
96_T100_V0.369991.125
10_A89_L0.367391.117
78_I81_L0.364341.108
44_K90_E0.359961.094
9_V103_T0.357231.086
95_S98_S0.357221.086
46_I50_N0.355361.080
2_A101_V0.353441.075
18_P103_T0.339041.031
47_A51_R0.329241.001
42_L97_V0.323780.984
3_I87_D0.321440.977
23_D40_D0.320720.975
10_A96_T0.318160.967
42_L90_E0.315510.959
4_K79_N0.314460.956
10_A100_V0.313910.954
84_D91_E0.312510.950
89_L96_T0.309410.941
8_N17_L0.304830.927
85_F88_N0.30390.924
6_L86_I0.296570.902
7_S81_L0.28180.857
102_R105_D0.28150.856
90_E96_T0.27780.845
17_L20_Q0.277330.843
21_V39_R0.275770.838
80_E84_D0.273080.830
90_E95_S0.271680.826
4_K8_N0.270130.821
5_T101_V0.26850.816
41_L49_Y0.266630.811
10_A85_F0.260920.793
45_E48_F0.26090.793
6_L96_T0.260110.791
73_S78_I0.259540.789
45_E49_Y0.258750.787
13_R99_T0.25860.786
44_K105_D0.255580.777
97_V101_V0.254870.775
81_L85_F0.254450.774
2_A96_T0.250770.762
8_N43_K0.250150.761
38_L46_I0.249120.757
42_L98_S0.248990.757
18_P21_V0.24880.756
58_V61_P0.246570.750
5_T103_T0.245980.748
40_D105_D0.245980.748
93_Y96_T0.245230.746
7_S79_N0.243590.741
30_W54_G0.243140.739
82_T87_D0.24260.738
15_F18_P0.240.730
44_K47_A0.239610.729
56_E105_D0.2350.715
93_Y99_T0.234580.713
8_N103_T0.234360.713
76_M82_T0.231160.703
86_I96_T0.228860.696
10_A92_N0.22810.694
60_V87_D0.227550.692
14_G18_P0.227530.692
13_R103_T0.225880.687
30_W34_I0.225610.686
86_I90_E0.223670.680
52_L84_D0.222840.678
85_F89_L0.218980.666
50_N59_L0.217510.661
8_N96_T0.216420.658
10_A86_I0.215250.654
80_E93_Y0.214980.654
74_K84_D0.212710.647
2_A95_S0.212220.645
4_K7_S0.209520.637
53_C56_E0.206820.629
30_W33_K0.204750.623
86_I100_V0.204220.621
49_Y58_V0.203920.620
43_K83_E0.202940.617
48_F98_S0.201840.614
31_D61_P0.201470.613
96_T99_T0.201410.612
16_S61_P0.201120.612
11_K78_I0.200750.610
5_T18_P0.197960.602
41_L45_E0.195910.596
75_N80_E0.195170.593
8_N79_N0.194210.590
86_I97_V0.193870.589
8_N13_R0.193850.589
79_N83_E0.193370.588
52_L59_L0.19320.587
50_N58_V0.191850.583
24_G45_E0.189080.575
40_D101_V0.187490.570
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
3vrhA0.906599.60.244
1ni5A0.906599.60.255
3a2kA0.906599.60.261
1wy5A0.869299.50.322
2derA0.859897.50.679
3tqiA0.925297.40.682
2dplA0.962697.40.685
2hmaA0.859897.30.691
3k32A0.78597.30.692
2ywbA0.906597.10.706

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