GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FDX-ACB - Ferredoxin-fold anticodon binding domain
Pfam: PF03147 (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. )
Length: 94
Sequences: 2000
Seq/Len: 21.28
HH_delta: -0.06 (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
16_E45_R1.345943.759
15_P53_K1.271133.550
36_E63_Q1.103343.081
62_Y78_H1.043592.914
11_S57_T0.951642.658
67_R73_E0.911992.547
35_L60_L0.818282.285
26_V89_L0.766782.141
19_P22_D0.761062.125
41_F57_T0.738422.062
21_A25_E0.738162.061
7_E59_R0.653921.826
24_E28_R0.64111.790
20_F58_Y0.630791.762
16_E52_G0.617181.724
27_I81_I0.584171.631
84_A88_K0.557681.557
43_V54_K0.538681.504
40_L56_L0.537971.502
79_D83_K0.537191.500
82_I93_L0.507991.419
53_K92_E0.503181.405
64_S67_R0.495151.383
75_N79_D0.493071.377
20_F56_L0.485911.357
46_G49_L0.475091.327
5_S61_T0.469231.310
29_S88_K0.468691.309
83_K86_E0.463851.295
83_K87_K0.455241.271
50_P53_K0.438671.225
86_E92_E0.434421.213
11_S41_F0.432061.207
8_R75_N0.425031.187
85_L91_A0.423511.183
42_D57_T0.410831.147
55_S94_R0.400691.119
12_F85_L0.394811.103
36_E61_T0.394511.102
62_Y77_I0.391851.094
1_S63_Q0.383931.072
10_I78_H0.37921.059
11_S94_R0.3791.058
23_I56_L0.377171.053
10_I60_L0.367021.025
14_V23_I0.365941.022
8_R71_D0.361661.010
37_S61_T0.35720.998
13_V50_P0.356710.996
30_A84_A0.348910.974
8_R78_H0.345550.965
71_D75_N0.343750.960
11_S55_S0.342070.955
24_E38_V0.338390.945
62_Y74_V0.333990.933
36_E65_P0.330310.922
64_S73_E0.330110.922
79_D82_I0.329570.920
47_E51_E0.323960.905
20_F24_E0.319290.892
40_L58_Y0.317470.887
2_K71_D0.30780.860
43_V56_L0.30710.858
34_L67_R0.302440.845
32_G35_L0.301610.842
26_V30_A0.29870.834
27_I58_Y0.296780.829
46_G50_P0.293520.820
7_E12_F0.287550.803
4_P68_T0.284380.794
47_E50_P0.278420.778
60_L81_I0.276540.772
14_V91_A0.270690.756
79_D86_E0.266150.743
58_Y89_L0.263710.736
44_Y50_P0.261910.731
8_R74_V0.261670.731
68_T71_D0.260960.729
72_E75_N0.260020.726
26_V88_K0.259980.726
13_V49_L0.258370.722
39_E59_R0.257820.720
26_V29_S0.25670.717
49_L53_K0.256680.717
34_L77_I0.252420.705
21_A24_E0.251370.702
14_V18_V0.250050.698
33_P80_K0.248950.695
12_F91_A0.248220.693
11_S91_A0.246510.688
41_F59_R0.245990.687
22_D89_L0.243550.680
46_G52_G0.24230.677
22_D25_E0.240340.671
14_V54_K0.240240.671
6_V71_D0.23330.652
30_A80_K0.230510.644
28_R38_V0.227910.636
23_I89_L0.227630.636
27_I38_V0.225440.630
7_E61_T0.220570.616
34_L69_L0.219840.614
50_P92_E0.219170.612
26_V84_A0.219110.612
85_L89_L0.218150.609
15_P90_G0.218030.609
11_S40_L0.218010.609
3_F64_S0.215320.601
23_I58_Y0.215050.601
24_E58_Y0.213080.595
29_S76_E0.209750.586
24_E37_S0.207530.580
81_I85_L0.20750.579
16_E54_K0.206050.575
82_I86_E0.205730.575
18_V91_A0.205440.574
65_P72_E0.204840.572
2_K8_R0.204640.571
31_G81_I0.202110.564
72_E76_E0.201920.564
2_K5_S0.200620.560
49_L52_G0.200320.559
3_F68_T0.19690.550
68_T77_I0.195890.547
22_D88_K0.194890.544
5_S63_Q0.194520.543
44_Y48_K0.194490.543
31_G62_Y0.192810.538
31_G35_L0.192350.537
4_P74_V0.191070.534
8_R57_T0.190120.531
29_S84_A0.190020.531
65_P79_D0.189610.530
29_S33_P0.187950.525
79_D87_K0.18780.524
25_E28_R0.186690.521
44_Y49_L0.185210.517
42_D55_S0.183740.513
23_I68_T0.179530.501
4_P63_Q0.177590.496
48_K51_E0.176860.494
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
3pcoB199.9-0.06
1b7yB0.989499.9-0.039
3cmqA0.978799.9-0.014
2rhqB0.978799.9-0.013
2odrD0.946899.50.362
2du7A0.936299.50.363
2odrA0.946899.50.363
2odrB0.946899.50.363
2odrC0.968199.50.371
1q8kA0.893657.30.867

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