GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fer2_2 - 2Fe-2S binding domain
Pfam: PF01799 (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: CL0486
Length: 75
Sequences: 2997
Seq/Len: 39.96
HH_delta: -0.081 (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
21_H75_Q2.203144.278
49_E74_R1.994723.874
12_H38_Y1.440962.798
48_T51_E1.36452.650
52_I74_R1.335172.593
38_Y42_R1.205292.341
37_A73_V1.169742.272
21_H71_E1.160612.254
16_Q20_E1.153832.241
44_N51_E1.075922.089
20_E75_Q1.009821.961
53_R70_V0.908151.764
14_I34_I0.899351.746
2_V34_I0.761791.479
67_R71_E0.748031.453
39_A43_R0.723161.404
32_G59_N0.693561.347
44_N47_P0.693561.347
14_I38_Y0.693271.346
40_L55_A0.673581.308
56_L73_V0.664581.291
23_A72_A0.648611.260
18_F30_T0.645541.254
7_S10_E0.607461.180
23_A30_T0.59961.164
36_A58_G0.596581.158
14_I37_A0.572111.111
33_M56_L0.546021.060
18_F37_A0.533921.037
14_I41_L0.530471.030
50_E54_E0.52411.018
49_E71_E0.522121.014
11_L15_Q0.52091.012
43_R55_A0.513710.998
5_L38_Y0.513040.996
41_L47_P0.494710.961
5_L35_M0.488530.949
12_H15_Q0.4790.930
19_V22_G0.473980.920
18_F34_I0.47190.916
49_E70_V0.466160.905
50_E53_R0.465830.905
22_G68_P0.455020.884
70_V74_R0.452490.879
37_A56_L0.450110.874
17_A75_Q0.448290.871
40_L44_N0.444660.863
22_G65_G0.436640.848
24_V30_T0.427180.830
18_F24_V0.42110.818
40_L52_I0.416680.809
49_E53_R0.415750.807
8_D11_L0.415580.807
68_P71_E0.414320.805
22_G64_T0.412070.800
51_E55_A0.408750.794
26_C29_C0.399550.776
40_L47_P0.388950.755
47_P55_A0.388270.754
18_F33_M0.388260.754
35_M55_A0.381340.741
52_I73_V0.375950.730
64_T67_R0.374670.728
26_C63_C0.371260.721
12_H16_Q0.371110.721
6_A10_E0.370940.720
37_A41_L0.370090.719
29_C63_C0.368760.716
18_F23_A0.366530.712
71_E75_Q0.364770.708
33_M69_I0.364460.708
24_V68_P0.361150.701
17_A20_E0.359160.697
39_A42_R0.356260.692
40_L73_V0.355260.690
22_G60_L0.345890.672
9_G13_P0.344960.670
5_L34_I0.342610.665
6_A11_L0.341490.663
21_H72_A0.341210.663
41_L45_P0.335180.651
23_A68_P0.33270.646
24_V65_G0.331470.644
5_L12_H0.329060.639
19_V24_V0.327830.637
31_P36_A0.325310.632
47_P51_E0.315080.612
36_A55_A0.308660.599
26_C61_C0.305670.594
40_L45_P0.300260.583
29_C61_C0.296230.575
16_Q19_V0.295750.574
7_S11_L0.292420.568
30_T33_M0.290360.564
25_Q66_Y0.289970.563
33_M65_G0.287090.558
36_A54_E0.286040.555
58_G66_Y0.285570.555
19_V67_R0.282160.548
33_M58_G0.281360.546
24_V28_F0.280010.544
33_M64_T0.279890.544
64_T68_P0.279310.542
14_I73_V0.277680.539
22_G36_A0.277430.539
15_Q34_I0.267440.519
36_A59_N0.266660.518
11_L16_Q0.262920.511
16_Q75_Q0.261540.508
18_F72_A0.261190.507
33_M57_S0.260350.506
41_L44_N0.259910.505
59_N69_I0.259340.504
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
3uncA1100-0.081
3zyvA1100-0.079
3nvwA1100-0.067
3hrdD1100-0.058
2w3sA0.9467100-0.022
1ffvA1100-0.008
1n62A1100-0.003
1vlbA11000.016
1dgjA11000.017
1rm6C199.90.106

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