GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4065 - Protein of unknown function (DUF4065)
Pfam: PF13274 (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: 108
Sequences: 700
Seq/Len: 6.48
HH_delta: 0.882 (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
30_Y95_S0.550643.278
5_L37_V0.471362.806
25_F34_P0.463322.758
72_S75_E0.457822.726
9_D25_F0.412642.457
8_A79_I0.375412.235
9_D21_F0.3732.221
3_K99_H0.351372.092
12_Y16_Y0.3291.959
92_W95_S0.32561.938
35_S39_D0.320891.910
21_F25_F0.311621.855
11_Y86_Y0.288651.719
71_L76_K0.287891.714
33_V99_H0.277571.653
8_A20_L0.274911.637
10_G14_K0.266221.585
26_E35_S0.258351.538
7_F98_S0.249461.485
89_K97_L0.245591.462
4_L86_Y0.233851.392
95_S99_H0.226841.351
103_S106_K0.224021.334
4_L91_A0.220611.313
9_D19_P0.216681.290
28_W35_S0.215661.284
4_L87_G0.214871.279
3_K98_S0.213381.270
45_G49_I0.209521.247
79_I83_I0.207341.234
12_Y78_I0.203681.213
91_A95_S0.202921.208
23_D36_D0.19891.184
16_Y78_I0.186441.110
32_P98_S0.180511.075
86_Y97_L0.180251.073
103_S107_N0.179291.067
7_F106_K0.174071.036
8_A83_I0.173911.035
89_K93_E0.173551.033
11_Y15_K0.172861.029
33_V38_Y0.171381.020
76_K80_D0.170441.015
78_I82_V0.17021.013
30_Y92_W0.169471.009
39_D42_K0.169071.007
13_L19_P0.167360.996
28_W33_V0.164580.980
80_D84_N0.162230.966
80_D83_I0.162180.966
71_L79_I0.158930.946
66_F71_L0.158810.945
44_N49_I0.15810.941
28_W38_Y0.157870.940
12_Y20_L0.155720.927
83_I104_P0.154930.922
99_H105_W0.151680.903
7_F10_G0.14970.891
9_D24_D0.14850.884
13_L25_F0.148260.883
11_Y14_K0.147180.876
7_F97_L0.146660.873
9_D13_L0.14570.867
5_L22_G0.14380.856
2_Q38_Y0.140190.835
71_L75_E0.139140.828
9_D22_G0.1390.828
38_Y42_K0.138210.823
7_F103_S0.138150.822
10_G104_P0.135950.809
35_S78_I0.135840.809
77_E84_N0.135340.806
100_K103_S0.133090.792
6_Y104_P0.132680.790
6_Y14_K0.130940.780
46_E49_I0.130540.777
27_A104_P0.130410.776
68_L73_E0.128280.764
90_S93_E0.12810.763
100_K106_K0.127380.758
27_A105_W0.126780.755
27_A38_Y0.12660.754
17_G107_N0.126120.751
29_K95_S0.12570.748
7_F82_V0.125050.744
88_D100_K0.124420.741
10_G25_F0.123830.737
18_K69_E0.123260.734
77_E81_E0.123030.732
7_F37_V0.120910.720
47_I88_D0.120410.717
2_Q45_G0.119550.712
6_Y27_A0.119070.709
12_Y75_E0.117510.700
83_I86_Y0.117480.699
88_D97_L0.117340.699
15_K81_E0.116040.691
27_A99_H0.115970.690
18_K51_E0.114930.684
29_K85_K0.113920.678
10_G41_L0.113740.677
33_V95_S0.11320.674
23_D35_S0.113120.673
4_L94_L0.11250.670
29_K41_L0.112470.670
75_E78_I0.111880.666
27_A86_Y0.111440.663
4_L8_A0.111250.662
33_V105_W0.109470.652
73_E100_K0.109070.649
67_D70_E0.109050.649
82_V104_P0.108210.644
69_E77_E0.107020.637
5_L25_F0.106860.636
79_I100_K0.106720.635
2_Q7_F0.106620.635
42_K46_E0.106610.635
32_P38_Y0.105410.628
32_P105_W0.105280.627
6_Y32_P0.104560.623
44_N47_I0.10430.621
9_D14_K0.104220.620
15_K77_E0.10420.620
17_G77_E0.104040.619
22_G25_F0.104030.619
21_F41_L0.10270.611
81_E84_N0.102690.611
49_I52_F0.102650.611
23_D106_K0.102370.609
25_F36_D0.10160.605
24_D36_D0.101240.603
25_F95_S0.101210.603
3_K28_W0.101170.602
87_G94_L0.101090.602
77_E100_K0.100720.600
28_W99_H0.100380.598
85_K93_E0.099830.594
40_D96_E0.099680.593
83_I87_G0.099460.592
82_V87_G0.098730.588
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
1s4kA0.851929.20.882
1p6rA0.388917.40.893
2g9wA0.398117.10.893
1ecaA0.333311.40.901
3oljA0.8426110.902
1sd4A0.398110.80.902
1okrA0.398190.905
3mkbA0.34268.40.906
3kdwA0.9638.30.906
2zetC0.58.10.907
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0372 seconds.