GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1703 - Protein of unknown function (DUF1703)
Pfam: PF08011 (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: CL0236
Length: 105
Sequences: 584
Seq/Len: 5.56
HH_delta: 0.816 (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
70_E74_E0.645895.070
73_K90_K0.434223.409
5_F8_G0.283542.226
10_L93_I0.244491.919
49_I72_I0.221031.735
36_V49_I0.215691.693
35_L52_L0.209671.646
68_A92_G0.206231.619
48_Y91_I0.205231.611
69_L92_G0.201681.583
7_H24_S0.196721.544
37_L50_I0.193131.516
38_E84_K0.190161.493
26_R80_E0.184251.446
78_A90_K0.180271.415
70_E73_K0.18011.414
10_L52_L0.17831.400
67_E70_E0.166411.306
23_K83_E0.166021.303
9_F12_G0.162581.276
61_L94_V0.159981.256
72_I77_Y0.157871.239
66_E70_E0.154231.211
28_S33_I0.152751.199
46_Y89_I0.148791.168
8_G12_G0.146241.148
12_G24_S0.145781.144
65_A92_G0.145091.139
76_K79_E0.141081.107
30_K49_I0.139911.098
77_Y92_G0.139671.096
91_I100_R0.137221.077
9_F17_S0.135371.063
48_Y89_I0.135031.060
25_E33_I0.134481.056
32_R75_K0.133311.046
24_S27_E0.132911.043
4_K8_G0.132721.042
22_V37_L0.129191.014
13_Y24_S0.12831.007
31_G77_Y0.127381.000
62_E97_G0.127230.999
94_V103_V0.126940.996
47_I86_K0.125850.988
69_L90_K0.125830.988
66_E82_K0.124350.976
4_K7_H0.123070.966
11_L18_S0.122550.962
89_I93_I0.121410.953
29_G65_A0.120310.944
33_I100_R0.118180.928
12_G25_E0.116950.918
4_K33_I0.116620.915
2_D5_F0.115440.906
45_K87_K0.115380.906
30_K99_E0.115070.903
23_K38_E0.114860.902
46_Y86_K0.114420.898
26_R83_E0.11350.891
6_Y61_L0.113230.889
46_Y84_K0.112770.885
83_E87_K0.111750.877
64_S94_V0.109340.858
4_K9_F0.109310.858
24_S29_G0.109080.856
38_E86_K0.107970.848
45_K76_K0.107340.843
12_G29_G0.107240.842
15_S101_N0.106490.836
7_H25_E0.106480.836
30_K98_K0.105670.829
19_G100_R0.10560.829
11_L17_S0.10550.828
76_K84_K0.105440.828
21_E38_E0.105130.825
14_L82_K0.104930.824
50_I67_E0.104760.822
69_L86_K0.103690.814
6_Y92_G0.102940.808
64_S93_I0.101950.800
64_S67_E0.101630.798
94_V100_R0.101570.797
96_S102_I0.101320.795
23_K28_S0.101260.795
93_I102_I0.100870.792
9_F45_K0.100680.790
11_L22_V0.100220.787
69_L74_E0.100010.785
7_H26_R0.09990.784
66_E96_S0.099740.783
2_D35_L0.099140.778
48_Y68_A0.098540.774
15_S63_K0.098390.772
35_L50_I0.098360.772
2_D8_G0.098250.771
78_A82_K0.098080.770
21_E75_K0.097140.763
38_E49_I0.097010.762
6_Y77_Y0.096920.761
13_Y22_V0.096840.760
30_K85_G0.096340.756
9_F101_N0.095230.748
96_S103_V0.094850.745
14_L87_K0.094670.743
32_R102_I0.094430.741
66_E99_E0.094020.738
52_L63_K0.093780.736
96_S99_E0.093660.735
9_F100_R0.093440.733
33_I97_G0.093270.732
74_E77_Y0.092920.729
79_E82_K0.092920.729
47_I81_L0.092520.726
93_I97_G0.092380.725
33_I101_N0.092240.724
82_K87_K0.091940.722
68_A77_Y0.091420.718
69_L77_Y0.091270.716
3_E6_Y0.091110.715
23_K87_K0.090420.710
68_A71_Q0.08940.702
22_V35_L0.089230.700
2_D24_S0.089050.699
36_V69_L0.088790.697
61_L65_A0.088510.695
6_Y12_G0.088470.694
68_A72_I0.088340.693
72_I98_K0.0880.691
33_I91_I0.087820.689
29_G47_I0.087670.688
82_K88_I0.087560.687
83_E86_K0.087520.687
9_F28_S0.087440.686
24_S94_V0.086880.682
20_Y32_R0.086820.682
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
2vldA0.895294.90.816
3h1tA0.838187.40.851
2w00A0.895283.50.859
2wcwA0.828636.10.897
1ob8A0.857132.60.899
1hh1A0.81928.70.902
2eo0A0.828628.50.902
4ic1A0.857122.20.906
1gefA0.714314.50.914
1y88A0.895213.50.914
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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