GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
oligo_HPY - Oligopeptidedipeptide transporter C-terminal region
Pfam: PF08352 (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: 64
Sequences: 6473
Seq/Len: 101.14
HH_delta: -0.025 (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
4_G9_I1.994533.688
5_P8_D1.910613.533
51_C57_C1.526232.822
19_R59_Y1.512542.797
57_C64_C1.215812.248
23_A35_Q1.211382.240
9_I18_T1.165092.154
49_N54_A1.141892.111
54_A60_A1.057811.956
1_V52_P1.037951.919
38_P58_P1.029991.904
20_A37_I1.023171.892
7_E11_D0.972851.799
19_R23_A0.919121.699
51_C64_C0.910691.684
47_S52_P0.863141.596
8_D12_N0.804751.488
1_V15_H0.759631.405
20_A53_F0.748751.384
10_F22_L0.736481.362
4_G8_D0.680551.258
4_G13_P0.676571.251
13_P22_L0.674831.248
37_I53_F0.661411.223
27_S30_P0.615121.137
50_G54_A0.595281.101
6_T10_F0.593641.098
4_G10_F0.56921.052
44_L47_S0.558351.032
41_P52_P0.553541.023
53_F56_R0.533830.987
16_P57_C0.530140.980
51_C56_R0.522030.965
25_V28_I0.486040.899
14_R19_R0.485350.897
28_I32_K0.481170.890
43_S46_E0.479580.887
42_P48_D0.474560.877
48_D54_A0.469390.868
10_F13_P0.467650.865
20_A23_A0.45370.839
19_R58_P0.444910.823
53_F57_C0.444360.822
48_D55_P0.436270.807
34_L37_I0.434260.803
20_A39_G0.425020.786
17_Y21_L0.419010.775
60_A64_C0.402950.745
39_G42_P0.39590.732
6_T9_I0.393990.728
35_Q58_P0.391260.723
27_S32_K0.390720.722
36_S41_P0.38950.720
59_Y62_E0.38020.703
46_E49_N0.373170.690
23_A58_P0.366010.677
44_L48_D0.364530.674
34_L41_P0.357860.662
52_P55_P0.355340.657
8_D11_D0.351150.649
25_V41_P0.350250.648
41_P44_L0.347930.643
25_V40_E0.347620.643
11_D14_R0.343670.635
20_A24_A0.338110.625
30_P35_Q0.333150.616
33_R38_P0.327750.606
12_N19_R0.327220.605
39_G56_R0.319620.591
40_E43_S0.3130.579
10_F25_V0.310440.574
15_H19_R0.302860.560
57_C60_A0.298040.551
34_L38_P0.295780.547
40_E44_L0.290250.537
16_P59_Y0.284750.527
58_P61_T0.281910.521
30_P33_R0.280030.518
18_T21_L0.273210.505
32_K35_Q0.272780.504
16_P51_C0.272350.504
41_P55_P0.263650.487
41_P47_S0.263190.487
24_A41_P0.26060.482
42_P54_A0.258280.478
47_S55_P0.258150.477
23_A34_L0.256640.475
29_D32_K0.253130.468
37_I40_E0.252320.467
40_E47_S0.251730.465
6_T24_A0.249610.462
2_E18_T0.246240.455
22_L25_V0.24590.455
2_E15_H0.243520.450
23_A59_Y0.243010.449
42_P46_E0.242430.448
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
4fwiB199.5-0.025
3pihA0.390688.70.717
3tuiC0.921987.60.722
2oljA0.406249.30.792
1b0uA0.484446.40.796
2onkA0.546929.30.816
4huqB0.828124.90.822
2ff7A0.406223.10.825
4hluD0.734419.40.83
2vf7A0.406216.20.836

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