GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fer4_15 - 4Fe-4S single cluster domain
Pfam: PF13459 (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: CL0344
Length: 65
Sequences: 19491
Seq/Len: 299.86
HH_delta: 0.05 (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
9_I60_V2.63563.628
48_E51_V2.277293.135
4_D7_R1.916052.638
18_A54_A1.525892.101
7_R62_A1.448181.994
4_D64_H1.331771.833
44_P47_D1.309341.802
17_L53_E1.309031.802
12_G15_V1.10511.521
13_L16_E1.048361.443
17_L57_A1.035871.426
52_R55_A1.004651.383
12_G24_L0.978571.347
13_L57_A0.963371.326
8_C14_C0.944111.300
48_E54_A0.93161.282
18_A48_E0.875061.205
3_V63_I0.873331.202
53_E56_E0.870261.198
9_I13_L0.867551.194
8_C11_C0.85321.175
53_E57_A0.837551.153
55_A63_I0.825811.137
18_A51_V0.811331.117
18_A50_D0.808651.113
45_E50_D0.808571.113
13_L59_P0.795771.095
51_V54_A0.79281.091
20_E49_E0.735021.012
13_L17_L0.726791.001
30_A33_L0.710870.979
8_C58_C0.679130.935
3_V10_G0.649550.894
11_C18_A0.588490.810
12_G16_E0.586160.807
7_R60_V0.568650.783
19_P49_E0.5630.775
15_V24_L0.559490.770
45_E51_V0.549990.757
50_D53_E0.540040.743
46_E50_D0.538120.741
14_C58_C0.536660.739
48_E52_R0.534830.736
46_E49_E0.533240.734
45_E48_E0.530210.730
25_D31_V0.525830.724
11_C60_V0.51310.706
21_V47_D0.510470.703
27_D31_V0.510330.703
5_R10_G0.498210.686
11_C58_C0.497590.685
11_C14_C0.494610.681
28_G31_V0.487730.671
19_P22_F0.477990.658
29_K32_V0.473010.651
10_G15_V0.467170.643
19_P23_E0.462970.637
47_D50_D0.454990.626
29_K33_L0.454610.626
19_P53_E0.453820.625
49_E53_E0.448820.618
26_D30_A0.444240.612
27_D30_A0.443190.610
23_E26_D0.442690.609
23_E33_L0.440730.607
52_R56_E0.43660.601
16_E57_A0.435410.599
23_E27_D0.426590.587
9_I59_P0.42360.583
45_E49_E0.409040.563
26_D29_K0.403560.556
26_D44_P0.396630.546
6_D28_G0.396270.546
58_C62_A0.394470.543
13_L60_V0.382940.527
4_D62_A0.3820.526
17_L50_D0.377830.520
11_C24_L0.377490.520
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
1iqzA198.80.05
3c8yA0.969298.80.08
3i9v30.907798.70.108
1gteA0.830898.70.111
1daxA0.876998.60.127
1hfeL0.846298.60.138
2c42A198.50.149
3gyxB0.861598.50.152
1sj1A0.907798.50.159
1xerA0.953898.50.159

Page generated in 0.0142 seconds.