GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Gp49 - Phage derived protein Gp49-like (DUF891)
Pfam: PF05973 (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: CL0136
Length: 91
Sequences: 1834
Seq/Len: 20.15
HH_delta: 0.56 (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
21_L44_L0.629592.478
7_P10_E0.619742.440
33_F57_Y0.593252.335
32_L45_R0.587222.312
3_L15_L0.574712.262
80_K84_E0.496061.953
55_I67_L0.481851.897
37_K87_R0.440371.734
84_E87_R0.421591.660
30_E34_K0.411031.618
47_R50_S0.391531.541
10_E53_Y0.37661.483
35_H42_Y0.370581.459
71_F82_E0.36961.455
39_D87_R0.366281.442
21_L30_E0.350171.378
13_K48_G0.345581.360
56_L71_F0.343021.350
41_I58_F0.336781.326
36_L41_I0.330821.302
47_R52_I0.329711.298
79_P82_E0.326211.284
36_L56_L0.325711.282
14_I55_I0.315931.244
58_F69_H0.314971.240
16_A19_E0.312791.231
35_H40_G0.307791.212
8_D12_A0.303381.194
41_I87_R0.294881.161
2_F70_G0.292211.150
12_A16_A0.28621.127
14_I46_V0.285441.124
58_F68_L0.281591.108
60_D63_D0.268531.057
12_A15_L0.267181.052
42_Y57_Y0.263461.037
8_D11_R0.262241.032
71_F79_P0.259411.021
34_K47_R0.257511.014
56_L82_E0.255281.005
33_F59_F0.253370.997
22_E66_V0.250610.987
29_G32_L0.250610.987
16_A20_R0.249430.982
1_E5_S0.248450.978
52_I56_L0.248340.978
19_E23_E0.246740.971
21_L65_I0.246290.970
71_F74_K0.245810.968
61_G64_I0.244480.962
29_G33_F0.238090.937
44_L57_Y0.237860.936
3_L11_R0.236570.931
59_F65_I0.234490.923
43_E73_K0.234220.922
15_L24_H0.232730.916
34_K45_R0.231560.912
52_I72_I0.226870.893
17_Q44_L0.225460.888
81_K84_E0.22520.887
35_H39_D0.221590.872
12_A22_E0.221020.870
34_K42_Y0.215510.848
11_R15_L0.213630.841
81_K85_K0.209020.823
21_L69_H0.207990.819
46_V53_Y0.203630.802
37_K80_K0.203360.801
13_K46_V0.202720.798
1_E80_K0.200470.789
43_E52_I0.200390.789
11_R49_G0.199820.787
41_I56_L0.199790.786
8_D19_E0.199010.783
46_V55_I0.196680.774
19_E24_H0.196620.774
60_D67_L0.195480.770
1_E4_D0.193570.762
19_E22_E0.192750.759
75_T79_P0.191330.753
25_G29_G0.189820.747
36_L42_Y0.189670.747
14_I53_Y0.188910.744
56_L86_A0.187540.738
30_E33_F0.187250.737
4_D24_H0.186770.735
4_D8_D0.186570.734
17_Q32_L0.185040.728
79_P86_A0.18360.723
17_Q55_I0.17970.707
4_D15_L0.175830.692
15_L66_V0.175410.691
21_L31_P0.175170.690
1_E8_D0.175160.690
42_Y59_F0.174240.686
5_S22_E0.173450.683
1_E84_E0.172790.680
56_L69_H0.172480.679
1_E60_D0.17230.678
5_S9_K0.171710.676
32_L35_H0.170190.670
68_L71_F0.168480.663
15_L85_K0.1680.661
42_Y60_D0.167210.658
12_A62_G0.166740.656
8_D24_H0.166620.656
5_S62_G0.166160.654
20_R32_L0.163980.646
19_E84_E0.163670.644
37_K84_E0.163470.644
21_L67_L0.163270.643
58_F66_V0.161730.637
69_H79_P0.160850.633
42_Y87_R0.160570.632
72_I79_P0.159580.628
2_F6_L0.159460.628
14_I45_R0.159380.627
82_E86_A0.159380.627
39_D84_E0.158950.626
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
4fxiA0.868198.30.56
3g5oB0.791298.20.579
1wmiA0.8132980.602
2kheA0.780297.80.624
3oeiC0.747397.50.647
3bpqB0.824297.20.676
1z8mA0.8022970.684
2otrA0.9121970.686
2a6sA0.758296.30.715
3kxeA0.802284.80.801
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