GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Polyketide_cyc2 - Polyketide cyclase dehydrase and lipid transport
Pfam: PF10604 (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: CL0209
Length: 139
Sequences: 8250
Seq/Len: 59.35
HH_delta: 0.153 (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
67_D71_R1.545313.185
9_E94_V1.43312.954
94_V99_R1.418182.923
7_S99_R1.395292.876
9_E99_R1.376252.837
92_E101_T1.368072.820
13_P16_A1.348232.779
92_E99_R1.290392.660
14_P93_P1.289332.658
91_F98_T1.274432.627
12_A17_V1.266612.611
26_N29_R1.234332.544
21_L91_F1.1922.457
5_E103_T1.184142.441
7_S101_T1.145562.361
8_I135_K1.094982.257
65_E72_R1.000892.063
5_E101_T0.975832.012
72_R90_R0.946621.951
72_R88_R0.907491.871
3_K103_T0.906371.868
15_E70_P0.850771.754
23_D26_N0.826681.704
3_K105_E0.819971.690
64_T76_R0.800171.649
90_R103_T0.796281.641
6_V124_K0.782681.613
67_D70_P0.768481.584
65_E74_T0.765361.578
6_V128_R0.7591.565
62_E76_R0.749741.545
14_P91_F0.730131.505
12_A16_A0.728851.502
74_T88_R0.7231.490
18_W66_Y0.714681.473
14_P98_T0.713111.470
62_E78_V0.700631.444
29_R137_A0.692611.428
10_V100_V0.685011.412
20_L26_N0.683641.409
90_R101_T0.669091.379
67_D72_R0.667651.376
15_E19_D0.664661.370
9_E97_G0.663151.367
128_R132_E0.653641.347
88_R103_T0.652211.344
18_W70_P0.648011.336
21_L89_W0.646691.333
14_P71_R0.631491.302
10_V17_V0.622761.284
76_R86_T0.621641.281
10_V135_K0.617041.272
74_T86_T0.598521.234
100_V131_L0.593641.224
75_W87_G0.58751.211
93_P96_D0.574621.184
87_G102_W0.565011.165
16_A19_D0.536791.106
19_D23_D0.535391.104
19_D68_P0.530211.093
8_I132_E0.521231.074
133_N137_A0.51931.070
133_N136_R0.51911.070
14_P70_P0.50281.036
94_V97_G0.490071.010
64_T74_T0.47150.972
11_P97_G0.469730.968
88_R105_E0.469610.968
85_G104_V0.464410.957
17_V91_F0.461760.952
22_S66_Y0.452090.932
20_L137_A0.445660.919
124_K128_R0.439750.906
48_E60_R0.437910.903
8_I131_L0.437420.902
30_W130_A0.425710.878
120_R124_K0.419970.866
50_T58_T0.414790.855
26_N137_A0.399020.823
86_T105_E0.39860.822
132_E136_R0.397950.820
15_E68_P0.39320.811
89_W102_W0.392750.810
17_V98_T0.388550.801
13_P98_T0.384910.793
43_G46_G0.378690.781
18_W22_S0.378630.780
61_E75_W0.373580.770
64_T86_T0.372920.769
127_V130_A0.372170.767
32_P133_N0.371810.766
117_P121_P0.367980.759
84_N107_E0.36740.757
87_G104_V0.365490.753
75_W89_W0.365440.753
93_P97_G0.364810.752
73_I89_W0.354110.730
102_W127_V0.349940.721
30_W134_L0.338140.697
18_W68_P0.337740.696
129_E133_N0.333780.688
13_P17_V0.33340.687
15_E93_P0.331960.684
40_L48_E0.331550.683
18_W71_R0.330840.682
22_S68_P0.328810.678
104_V127_V0.327590.675
76_R84_N0.325320.671
18_W91_F0.324650.669
9_E98_T0.323660.667
66_Y73_I0.323490.667
132_E135_K0.323020.666
40_L50_T0.322740.665
28_P37_V0.322440.665
89_W100_V0.318980.658
125_R129_E0.317440.654
25_E28_P0.317060.654
11_P135_K0.316950.653
93_P98_T0.316440.652
122_A126_I0.316180.652
121_P125_R0.314860.649
75_W102_W0.312390.644
38_E50_T0.311460.642
61_E77_F0.311450.642
77_F85_G0.308880.637
100_V134_L0.308760.636
61_E102_W0.305910.631
20_L29_R0.303390.625
18_W73_I0.299240.617
83_T107_E0.29730.613
14_P17_V0.297140.613
12_A20_L0.295850.610
45_P60_R0.293890.606
14_P97_G0.293410.605
87_G127_V0.292680.603
6_V127_V0.290890.600
9_E96_D0.290120.598
53_V56_R0.287290.592
117_P120_R0.285360.588
65_E88_R0.283390.584
49_R61_E0.281240.580
113_W116_G0.280010.577
41_S46_G0.272390.561
75_W85_G0.27170.560
122_A125_R0.266430.549
114_L117_P0.265870.548
9_E95_G0.264280.545
125_R128_R0.258610.533
71_R92_E0.258260.532
85_G130_A0.25760.531
112_G118_L0.253930.523
63_I66_Y0.252280.520
35_K52_R0.251080.518
121_P124_K0.249510.514
27_W33_G0.249270.514
27_W30_W0.248490.512
41_S48_E0.248460.512
77_F104_V0.245340.506
19_D22_S0.244850.505
84_N105_E0.241910.499
129_E132_E0.240520.496
7_S92_E0.239750.494
50_T60_R0.239550.494
34_V37_V0.239080.493
68_P71_R0.238870.492
41_S44_G0.238740.492
32_P130_A0.236940.488
81_G85_G0.236770.488
22_S73_I0.232280.479
6_V125_R0.232240.479
61_E85_G0.231790.478
20_L134_L0.231420.477
16_A20_L0.230970.476
66_Y70_P0.230150.474
108_P116_G0.22970.473
77_F83_T0.228010.470
27_W53_V0.2270.468
27_W89_W0.225750.465
27_W31_W0.224810.463
59_V87_G0.224210.462
32_P129_E0.223680.461
59_V77_F0.223390.460
31_W106_F0.223370.460
24_P28_P0.222810.459
104_V107_E0.221840.457
19_D26_N0.220350.454
49_R87_G0.21990.453
91_F100_V0.219690.453
27_W102_W0.218650.451
104_V123_V0.218430.450
121_P126_I0.218220.450
61_E64_T0.218030.449
129_E136_R0.217990.449
10_V131_L0.217340.448
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
2d4rA0.992899.70.153
3ggnA0.978499.60.166
3tfzA0.992899.60.174
3ijtA0.978499.60.174
3f08A0.956899.60.175
2le1A0.985699.60.176
3tl1A199.60.177
2m47A0.971299.60.185
3tvqA199.60.188
1t17A0.971299.60.208

Page generated in 0.0184 seconds.