GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Flavodoxin_1 - Flavodoxin
Pfam: PF00258 (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: CL0042
Length: 143
Sequences: 9611
Seq/Len: 67.21
HH_delta: 0.213 (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
29_R42_D1.453922.957
89_K120_K1.368272.782
10_T52_G1.27692.597
18_A22_R1.184122.408
90_Y119_A1.107532.252
48_L89_K1.083172.203
11_E15_E1.076652.189
31_V42_D1.032442.100
90_Y114_L1.001022.036
111_D121_R0.967571.968
29_R45_E0.963741.960
114_L119_A0.922991.877
105_A109_K0.917321.865
66_K70_E0.899851.830
18_A30_V0.884591.799
94_G107_A0.864131.757
16_A20_G0.862581.754
41_S45_E0.86221.753
52_G93_F0.859891.749
32_D35_D0.857451.744
15_E30_V0.850591.730
105_A108_K0.83871.706
29_R46_Y0.79291.612
16_A19_E0.7811.588
18_A28_V0.773871.574
20_G24_R0.76391.553
115_E121_R0.761441.548
111_D115_E0.747391.520
17_I50_I0.71281.450
53_V110_L0.692971.409
14_A52_G0.691571.406
48_L91_A0.671331.365
19_E22_R0.665291.353
17_I52_G0.656461.335
12_K16_A0.653061.328
113_R117_L0.645521.313
90_Y121_R0.644211.310
50_I91_A0.635111.292
20_G23_E0.621651.264
41_S44_S0.617261.255
17_I93_F0.614111.249
61_P109_K0.58331.186
113_R116_E0.575731.171
43_L49_L0.561531.142
55_T94_G0.560461.140
21_L26_V0.5481.114
53_V62_P0.536561.091
44_S84_D0.526811.071
70_E74_E0.518611.055
46_Y49_L0.51181.041
42_D45_E0.507541.032
68_F73_L0.497011.011
92_V110_L0.490050.997
40_P72_L0.489720.996
53_V94_G0.489430.995
19_E23_E0.482490.981
22_R28_V0.479190.974
15_E18_A0.478640.973
55_T106_A0.476750.970
49_L119_A0.465850.947
25_G28_V0.462470.940
61_P66_K0.458470.932
56_Y64_N0.457650.931
51_F114_L0.456720.929
14_A18_A0.45470.925
36_F42_D0.451570.918
92_V107_A0.451330.918
17_I20_G0.438970.893
15_E19_E0.438260.891
49_L88_K0.436880.888
90_Y111_D0.435470.886
22_R27_E0.427190.869
86_K118_G0.414240.842
82_K86_K0.410630.835
21_L28_V0.408410.831
34_D64_N0.405550.825
24_R27_E0.402440.818
51_F65_A0.40180.817
42_D46_Y0.400030.813
85_L119_A0.396780.807
31_V36_F0.39640.806
96_G100_Y0.394570.802
108_K112_E0.392550.798
61_P106_A0.388230.789
49_L90_Y0.388120.789
10_T95_L0.387870.789
71_E74_E0.38410.781
31_V35_D0.38270.778
63_D70_E0.381920.777
83_P86_K0.380350.773
9_N12_K0.372540.758
108_K111_D0.370880.754
17_I21_L0.369480.751
53_V65_A0.368190.749
112_E116_E0.367640.748
43_L46_Y0.359310.731
121_R124_P0.358450.729
68_F72_L0.358190.728
11_E32_D0.35250.717
92_V114_L0.34920.710
15_E22_R0.346120.704
12_K15_E0.343180.698
98_S102_G0.336210.684
17_I48_L0.335210.682
91_A122_V0.332710.677
61_P65_A0.331740.675
69_F113_R0.328270.668
87_G120_K0.321650.654
72_L117_L0.320610.652
56_Y62_P0.319960.651
90_Y115_E0.31930.649
66_K113_R0.318720.648
13_M95_L0.318590.648
114_L121_R0.312810.636
69_F73_L0.312220.635
10_T14_A0.30670.624
69_F72_L0.303220.617
87_G118_G0.299770.610
53_V106_A0.299610.609
112_E115_E0.297950.606
8_G11_E0.297670.605
89_K122_V0.29550.601
109_K112_E0.292990.596
73_L114_L0.290620.591
68_F71_E0.290130.590
21_L48_L0.289750.589
101_G105_A0.288030.586
47_D88_K0.287560.585
7_T56_Y0.287490.585
54_S62_P0.284120.578
40_P75_L0.282340.574
13_M16_A0.280670.571
51_F90_Y0.279590.569
61_P110_L0.277680.565
11_E30_V0.277610.565
27_E45_E0.2760.561
14_A93_F0.270690.550
63_D66_K0.270560.550
70_E113_R0.270360.550
32_D64_N0.270030.549
70_E110_L0.26970.548
62_P65_A0.268610.546
13_M93_F0.267170.543
91_A123_G0.265340.540
13_M52_G0.265180.539
89_K121_R0.263210.535
22_R25_G0.262570.534
27_E47_D0.261320.531
69_F110_L0.261180.531
36_F46_Y0.260360.529
85_L117_L0.259990.529
13_M17_I0.259830.528
75_L82_K0.259610.528
73_L76_K0.259350.527
53_V107_A0.259210.527
108_K115_E0.256290.521
14_A17_I0.252940.514
96_G101_G0.252820.514
73_L117_L0.248760.506
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
4h2dA0.96599.80.213
2bpoA0.944199.80.215
3hr4A0.923199.80.231
3f6rA0.923199.80.234
3qe2A0.930199.80.239
1tllA0.96599.80.243
1f4pA0.923199.80.248
2hnaA0.930199.80.258
1bvyF0.923199.80.26
1ykgA0.923199.80.269

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