GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ACP_syn_III - 3-Oxoacyl-acyl-carrier-protein (ACP) synthase III
Pfam: PF08545 (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: CL0046
Length: 80
Sequences: 13274
Seq/Len: 165.93
HH_delta: 0.039 (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
28_N62_S2.370673.287
18_A22_A2.328483.228
19_A23_S1.756042.435
17_A29_A1.744862.419
32_V58_A1.663632.306
19_A25_R1.653812.293
21_I63_R1.539982.135
28_N60_V1.52912.120
15_D19_A1.393291.932
26_A29_A1.376191.908
20_L25_R1.316521.825
20_L26_A1.291141.790
14_L61_L1.252511.736
5_Q12_Y1.213791.683
42_D46_R1.156391.603
17_A31_V1.144731.587
34_G56_A1.136171.575
21_I61_L1.082131.500
16_V19_A1.081641.500
19_A22_A1.072441.487
27_K63_R1.052431.459
30_L60_V1.035431.436
13_A31_V1.016511.409
5_Q8_A1.01071.401
42_D48_T1.01041.401
16_V20_L0.93931.302
17_A61_L0.922041.278
35_D52_F0.918861.274
43_R49_A0.900281.248
36_R39_R0.83591.159
21_I24_G0.830321.151
10_F59_V0.825781.145
31_V61_L0.816131.131
14_L31_V0.794141.101
30_L58_A0.748131.037
12_Y16_V0.717640.995
15_D25_R0.704190.976
37_L52_F0.68330.947
20_L23_S0.673950.934
36_R54_D0.666890.925
3_I16_V0.649990.901
41_V50_F0.627320.870
8_A11_L0.618090.857
4_N54_D0.595690.826
47_Q50_F0.576490.799
28_N31_V0.569360.789
9_G13_A0.536250.743
3_I13_A0.525070.728
40_I52_F0.5190.720
12_Y15_D0.509110.706
38_S54_D0.502390.697
20_L29_A0.474650.658
2_D9_G0.470280.652
27_K62_S0.458540.636
44_T49_A0.450840.625
14_L59_V0.447980.621
6_A9_G0.44690.620
8_A12_Y0.439060.609
33_G57_A0.433530.601
24_G63_R0.431230.598
10_F31_V0.420950.584
22_A63_R0.417770.579
15_D18_A0.40620.563
17_A21_I0.403990.560
7_C56_A0.388610.539
35_D53_G0.386530.536
35_D50_F0.386390.536
10_F57_A0.3850.534
3_I11_L0.376070.521
24_G27_K0.373540.518
26_A63_R0.36720.509
18_A61_L0.366210.508
4_N40_I0.364910.506
22_A25_R0.36370.504
43_R50_F0.363450.504
37_L56_A0.362530.503
46_R49_A0.362520.503
4_N9_G0.362420.502
18_A63_R0.35630.494
39_R51_I0.347950.482
48_T51_I0.340860.473
21_I60_V0.336850.467
35_D38_S0.334240.463
31_V59_V0.333180.462
33_G59_V0.331890.460
41_V44_T0.330680.458
5_Q9_G0.327910.455
37_L40_I0.326920.453
8_A33_G0.325610.451
35_D56_A0.324620.450
34_G58_A0.321880.446
5_Q36_R0.319720.443
41_V65_E0.31350.435
4_N39_R0.311140.431
28_N64_D0.30930.429
38_S51_I0.306260.425
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
3ledA199.40.039
3gwaA199.40.062
3h78A199.30.069
3il6A0.97599.30.075
3il3A0.97599.30.079
3vs8A199.30.091
4ewpA0.97599.30.094
4efiA0.97599.30.095
4dfeA0.97599.30.096
3s3lA0.987599.30.098

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