GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3804 - Protein of unknown function (DUF3804)
Pfam: PF12707 (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. )
Clan: CL0051
Length: 128
Sequences: 2559
Seq/Len: 19.99
HH_delta: 0.278 (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
19_M22_F0.702672.963
106_V109_V0.672542.836
42_D45_G0.668962.821
74_D105_K0.536112.261
42_D46_F0.532782.247
9_L103_F0.512762.162
28_T113_S0.510162.151
100_T116_Q0.501312.114
20_K24_I0.458621.934
82_L97_S0.446361.882
29_P43_A0.442271.865
102_I114_W0.427611.803
27_A115_M0.422251.781
22_F25_D0.394811.665
78_C103_F0.391161.649
104_K113_S0.38351.617
28_T111_K0.380281.604
16_R22_F0.378921.598
12_E22_F0.378451.596
101_S115_M0.376811.589
44_K48_G0.371261.566
27_A31_F0.368781.555
68_L76_A0.368411.554
4_Q7_E0.365651.542
6_I68_L0.359551.516
47_E51_D0.354331.494
10_I103_F0.351761.483
106_V111_K0.348341.469
72_S77_M0.345541.457
28_T106_V0.33061.394
16_R26_N0.314491.326
31_F46_F0.303421.279
77_M102_I0.297471.254
8_S12_E0.291331.228
4_Q8_S0.291041.227
6_I9_L0.290431.225
100_T114_W0.286581.208
24_I43_A0.286511.208
13_F17_E0.286061.206
76_A110_W0.285851.205
70_F76_A0.285161.202
80_F99_Y0.27941.178
7_E11_E0.277931.172
45_G48_G0.275731.163
17_E23_L0.272361.149
101_S112_I0.271.139
10_I80_F0.265741.121
79_A100_T0.265061.118
25_D111_K0.262061.105
70_F73_D0.25971.095
99_Y103_F0.251751.062
97_S115_M0.248481.048
21_S47_E0.23961.010
46_F50_M0.236220.996
10_I78_C0.234330.988
13_F26_N0.233170.983
75_W102_I0.22680.956
12_E26_N0.225470.951
45_G49_M0.225450.951
24_I44_K0.224260.946
13_F23_L0.2220.936
10_I101_S0.212480.896
44_K47_E0.211520.892
6_I110_W0.209210.882
43_A47_E0.20920.882
75_W104_K0.209110.882
103_F112_I0.208380.879
24_I47_E0.206720.872
33_F115_M0.203940.860
43_A46_F0.203460.858
72_S75_W0.202020.852
74_D104_K0.201190.848
5_E105_K0.200670.846
17_E35_R0.200010.843
21_S51_D0.198620.838
99_Y115_M0.198340.836
34_I79_A0.197480.833
13_F27_A0.186860.788
9_L112_I0.186270.785
99_Y102_I0.184980.780
28_T104_K0.184030.776
20_K51_D0.183250.773
11_E14_A0.183040.772
76_A105_K0.182740.771
14_A99_Y0.182150.768
48_G51_D0.182040.768
102_I113_S0.181540.766
9_L26_N0.181180.764
31_F116_Q0.17910.755
26_N112_I0.178680.753
27_A82_L0.178440.752
27_A101_S0.175550.740
13_F103_F0.175510.740
41_I46_F0.175310.739
32_L114_W0.174880.737
15_N19_M0.173910.733
80_F115_M0.173860.733
41_I45_G0.171720.724
88_Y91_T0.17140.723
53_G56_V0.171270.722
14_A115_M0.170620.719
6_I76_A0.170350.718
21_S25_D0.169580.715
86_F95_D0.168840.712
14_A82_L0.167930.708
61_E81_T0.167250.705
21_S24_I0.16710.705
14_A101_S0.166250.701
86_F97_S0.165670.699
21_S43_A0.165660.699
12_E25_D0.163130.688
75_W113_S0.162680.686
30_D69_E0.162010.683
46_F49_M0.16190.683
9_L12_E0.160920.679
34_I114_W0.16090.678
68_L78_C0.160120.675
25_D109_V0.160010.675
91_T94_D0.159680.673
32_L36_P0.159310.672
13_F80_F0.15930.672
12_E109_V0.158870.670
6_I103_F0.158620.669
18_Q22_F0.158430.668
83_G96_L0.158040.666
13_F35_R0.157420.664
13_F97_S0.156930.662
81_T98_T0.156780.661
73_D107_D0.156350.659
83_G94_D0.155650.656
5_E9_L0.155540.656
10_I33_F0.155440.655
105_K110_W0.155130.654
27_A112_I0.154760.653
57_Q60_S0.154630.652
22_F26_N0.154570.652
37_S93_N0.154270.651
86_F96_L0.153640.648
9_L29_P0.152630.644
5_E8_S0.150720.636
10_I14_A0.150150.633
82_L101_S0.149870.632
33_F97_S0.149530.631
58_E61_E0.149520.631
59_S82_L0.149420.630
43_A69_E0.149160.629
8_S87_S0.148780.627
24_I46_F0.148480.626
14_A27_A0.148170.625
80_F84_E0.148070.624
35_R115_M0.147830.623
8_S67_R0.146410.617
80_F98_T0.146190.616
12_E16_R0.145350.613
16_R19_M0.144760.610
56_V91_T0.144570.610
78_C112_I0.144310.609
46_F115_M0.144210.608
13_F33_F0.143760.606
74_D108_G0.143750.606
56_V59_S0.143730.606
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
3hzpA199.70.278
3fsdA0.929799.60.346
2r4iA0.929799.60.353
3kspA0.945399.60.354
3bb9A0.882899.50.371
3soyA0.984499.50.382
3f7sA0.953199.50.384
3h51A0.992299.50.385
2f86B0.960999.50.397
3robA0.945399.40.404

Page generated in 0.0331 seconds.