GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ABM - Antibiotic biosynthesis monooxygenase
Pfam: PF03992 (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: CL0032
Length: 78
Sequences: 6288
Seq/Len: 80.62
HH_delta: -0.064 (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
59_S62_A2.183853.633
37_L58_E1.573152.617
14_K17_E1.482232.466
60_E64_Q1.441982.399
58_E62_A1.39422.320
38_S56_R1.335962.223
9_K50_R1.146231.907
3_T56_R1.043871.737
10_V18_F1.040551.731
11_K14_K1.028551.711
35_G62_A0.995521.656
19_L51_Y0.987771.643
36_C57_W0.959471.596
20_A24_E0.925361.540
64_Q68_K0.915081.522
19_L23_Q0.898961.496
7_K50_R0.875741.457
19_L43_R0.859521.430
43_R51_Y0.792611.319
16_E20_A0.785551.307
61_E65_A0.77211.285
61_E64_Q0.765691.274
7_K52_V0.762071.268
17_E20_A0.759951.264
70_P74_A0.756691.259
15_E43_R0.747981.244
22_F41_L0.737321.227
34_P58_E0.72441.205
40_E56_R0.715371.190
69_S72_F0.677351.127
15_E49_N0.66971.114
67_F72_F0.666271.108
5_I54_V0.666261.108
31_R36_C0.658251.095
4_V55_E0.655241.090
9_K49_N0.640681.066
9_K47_D0.626811.043
70_P73_K0.624831.040
34_P62_A0.617721.028
15_E51_Y0.617271.027
44_S50_R0.611971.018
64_Q67_F0.605571.007
63_F67_F0.604181.005
32_K71_E0.600961.000
21_A24_E0.585710.974
15_E19_L0.583820.971
17_E21_A0.578170.962
27_E31_R0.56370.938
62_A65_A0.556350.926
33_E71_E0.544950.907
33_E66_H0.538620.896
8_F53_I0.524050.872
36_C39_Y0.513130.854
26_A31_R0.51270.853
71_E74_A0.50380.838
24_E28_A0.497430.828
34_P65_A0.497020.827
16_E19_L0.495170.824
33_E69_S0.494970.823
2_I60_E0.493770.821
42_Y54_V0.485740.808
18_F22_F0.482520.803
20_A23_Q0.481310.801
2_I63_F0.478810.797
4_V63_F0.478140.795
23_Q27_E0.470270.782
28_A32_K0.467290.777
24_E27_E0.466470.776
68_K73_K0.459780.765
65_A68_K0.458920.764
26_A39_Y0.443960.739
4_V66_H0.441820.735
36_C55_E0.435880.725
3_T54_V0.42120.701
12_P15_E0.420690.700
5_I52_V0.397860.662
22_F26_A0.396910.660
35_G58_E0.387510.645
44_S47_D0.385470.641
28_A71_E0.384750.640
38_S54_V0.374310.623
36_C66_H0.368440.613
47_D50_R0.365140.607
12_P49_N0.36510.607
6_V63_F0.35520.591
39_Y66_H0.354150.589
26_A29_T0.352840.587
37_L56_R0.352250.586
6_V22_F0.350640.583
22_F53_I0.34530.574
66_H72_F0.344390.573
8_F18_F0.339350.565
55_E66_H0.332790.554
41_L51_Y0.331920.552
21_A75_F0.330950.551
29_T55_E0.330.549
53_I75_F0.327060.544
39_Y55_E0.323660.538
53_I66_H0.318760.530
33_E55_E0.318750.530
22_F25_L0.317260.528
9_K14_K0.311470.518
10_V51_Y0.3050.507
65_A69_S0.296960.494
39_Y53_I0.296350.493
8_F22_F0.294930.491
4_V53_I0.291170.484
29_T72_F0.284940.474
6_V66_H0.283820.472
18_F51_Y0.275490.458
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
4hl9A0.987299.3-0.064
4dpoA0.987299.2-0.038
3e8oA0.987299.2-0.034
2gffA0.987299.2-0.03
3gz7A0.987299.2-0.029
2omoA0.987299.2-0.027
3mcsA0.987299.2-0.023
3f44A0.987299.2-0.022
3kkfA199.2-0.021
1tuvA0.987299.2-0.017

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