GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ACP_syn_III_C - 3-Oxoacyl-acyl-carrier-protein (ACP) synthase III C terminal
Pfam: PF08541 (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: 90
Sequences: 9117
Seq/Len: 101.3
HH_delta: -0.069 (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_A35_P1.779752.726
7_S10_D1.644632.519
58_A62_E1.635662.506
6_L68_P1.397622.141
34_P37_R1.380652.115
61_L66_I1.362122.087
6_L11_I1.342612.057
57_L69_G1.278251.958
12_D66_I1.213931.860
48_T55_I1.133551.736
28_A38_F1.1191.714
1_L8_P1.08261.658
13_H60_A1.052251.612
1_L4_A1.04721.604
52_S56_N1.04411.599
60_A64_G1.016471.557
8_P14_F1.014841.555
21_K25_D0.971521.488
55_I59_D0.961971.474
11_I14_F0.920391.410
12_D70_D0.919091.408
41_N60_A0.915091.402
26_S30_R0.885261.356
60_A63_E0.846891.297
67_K70_D0.84211.290
6_L71_R0.81741.252
11_I68_P0.810651.242
40_D43_A0.780121.195
25_D35_P0.779381.194
23_I27_I0.774461.186
44_E59_D0.773411.185
13_H40_D0.771061.181
24_L38_F0.736441.128
75_V79_A0.732941.123
22_K26_S0.729711.118
21_K40_D0.710651.089
16_P24_L0.698121.069
11_I70_D0.679341.041
59_D62_E0.67881.040
59_D63_E0.676791.037
1_L6_L0.668751.024
6_L10_D0.668331.024
12_D71_R0.653581.001
21_K43_A0.645840.989
13_H70_D0.644010.987
41_N59_D0.641450.983
39_P56_N0.622230.953
47_N52_S0.621480.952
17_H47_N0.601530.921
45_Y55_I0.598560.917
75_V80_G0.595680.913
17_H52_S0.594270.910
16_P72_V0.589670.903
75_V81_F0.582970.893
58_A61_L0.582790.893
12_D37_R0.566490.868
41_N45_Y0.561460.860
16_P27_I0.554050.849
12_D67_K0.552210.846
43_A48_T0.546380.837
9_D37_R0.537170.823
13_H66_I0.532890.816
39_P60_A0.528180.809
41_N63_E0.527410.808
43_A47_N0.52620.806
49_G77_F0.519060.795
24_L27_I0.518720.795
24_L28_A0.511560.784
2_E7_S0.511210.783
4_A11_I0.50490.773
8_P31_L0.498740.764
16_P39_P0.49820.763
41_N56_N0.496920.761
56_N59_D0.495030.758
1_L11_I0.492640.755
57_L71_R0.491260.753
49_G78_G0.490360.751
29_K32_G0.48580.744
25_D29_K0.480520.736
41_N64_G0.478370.733
18_Q47_N0.476310.730
13_H64_G0.474420.727
9_D32_G0.471460.722
44_E47_N0.469540.719
27_I30_R0.468460.718
20_S23_I0.45580.698
13_H65_R0.455610.698
55_I58_A0.454080.696
54_P71_R0.450280.690
62_E65_R0.444930.682
2_E5_G0.442910.678
27_I31_L0.442610.678
53_I71_R0.437990.671
8_P32_G0.432970.663
40_D60_A0.432650.663
76_G79_A0.431770.661
15_I56_N0.430750.660
44_E48_T0.427680.655
14_F70_D0.420250.644
8_P11_I0.415210.636
20_S49_G0.41420.635
49_G52_S0.41150.630
19_A23_I0.409510.627
16_P23_I0.405580.621
47_N50_S0.40550.621
56_N60_A0.396330.607
33_I38_F0.395710.606
53_I74_L0.391840.600
28_A31_L0.391770.600
23_I75_V0.391760.600
52_S81_F0.388040.594
40_D44_E0.386020.591
18_Q39_P0.382360.586
54_P79_A0.377520.578
17_H78_G0.374840.574
27_I75_V0.373890.573
51_A81_F0.373560.572
12_D68_P0.373340.572
28_A33_I0.373280.572
60_A66_I0.372530.571
20_S77_F0.371750.569
51_A56_N0.368840.565
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
3gwaA199.8-0.069
3il3A199.8-0.06
3s21A199.8-0.056
4efiA199.8-0.055
4dfeA199.8-0.052
4ewpA199.8-0.046
4jaqD0.988999.8-0.035
3h78A0.977899.8-0.028
3s3lA0.988999.8-0.003
3ledA0.977899.80.007

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