GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
OmdA - Bacteriocin-protection YdeI or OmpD-Associated
Pfam: PF13376 (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: CL0021
Length: 63
Sequences: 772
Seq/Len: 12.25
HH_delta: 0.811 (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_K25_E0.656512.681
42_A51_R0.652012.663
11_E15_E0.603572.465
9_D48_R0.462061.887
49_A53_A0.446861.825
10_L55_L0.425511.738
17_N60_A0.418471.709
44_T47_T0.418391.709
42_A47_T0.397461.623
15_E21_K0.384441.570
23_F26_S0.358471.464
23_F27_L0.356481.456
10_L52_I0.352841.441
52_I56_I0.347111.417
46_E50_K0.343091.401
10_L14_L0.338111.381
27_L59_L0.308361.259
50_K54_K0.306171.250
6_V36_I0.282491.154
12_A49_A0.281881.151
38_W55_L0.281141.148
45_E49_A0.272451.113
8_E12_A0.269561.101
34_E37_R0.269221.099
43_K47_T0.269191.099
54_K58_M0.269121.099
33_R37_R0.268131.095
23_F31_Y0.261071.066
53_A57_E0.25811.054
28_T31_Y0.253931.037
19_E60_A0.246571.007
30_S33_R0.243240.993
36_I52_I0.240230.981
13_A16_A0.239390.978
13_A49_A0.238880.975
4_V33_R0.235830.963
6_V11_E0.234440.957
22_E26_S0.226020.923
23_F62_G0.221870.906
47_T51_R0.221760.906
20_A60_A0.221630.905
37_R41_S0.221150.903
41_S51_R0.215120.878
7_P48_R0.214880.877
19_E22_E0.213610.872
12_A19_E0.212510.868
50_K53_A0.209330.855
14_L59_L0.20720.846
35_Y40_N0.206160.842
14_L21_K0.201190.822
20_A59_L0.200460.819
35_Y55_L0.198650.811
39_I55_L0.197960.808
51_R54_K0.195350.798
31_Y35_Y0.194950.796
6_V21_K0.18870.771
10_L39_I0.187140.764
3_E28_T0.18530.757
6_V24_F0.184780.755
9_D45_E0.184270.752
9_D52_I0.184260.752
58_M63_K0.183940.751
12_A15_E0.183920.751
34_E41_S0.181830.743
22_E25_E0.181280.740
24_F35_Y0.179370.732
27_L37_R0.173640.709
6_V14_L0.171570.701
37_R55_L0.171460.700
53_A60_A0.169960.694
7_P10_L0.169460.692
28_T37_R0.169380.692
14_L17_N0.167610.684
30_S42_A0.16760.684
13_A17_N0.167450.684
27_L62_G0.166520.680
29_P32_R0.164460.672
49_A60_A0.164460.672
25_E32_R0.164380.671
31_Y34_E0.161310.659
14_L35_Y0.160590.656
40_N48_R0.158380.647
29_P54_K0.157970.645
11_E21_K0.157860.645
8_E45_E0.157840.645
45_E48_R0.157550.643
33_R38_W0.157030.641
12_A57_E0.156820.640
29_P33_R0.155670.636
35_Y38_W0.155090.633
24_F27_L0.155050.633
24_F54_K0.154790.632
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
4ghkA0.968354.60.811
3al0B137.50.829
3ph1A0.857134.50.832
3ip4B132.50.834
4h7nA0.952429.20.838
4kreA0.904828.40.838
2hz7A127.60.839
4f3tA0.904827.50.84
2wmeA0.952427.20.84
4e3xA0.952426.70.841
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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