GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fer4_13 - 4Fe-4S single cluster domain
Pfam: PF13370 (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: 58
Sequences: 20547
Seq/Len: 354.26
HH_delta: 0.027 (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
7_I53_T2.816383.723
15_I46_E1.574652.081
18_D42_E1.568852.074
41_E44_A1.568482.073
16_A47_A1.511131.997
5_K55_A1.350851.786
10_G13_V1.255991.660
15_I50_S1.227811.623
37_P40_E1.212811.603
6_C12_C1.209211.598
45_R48_A1.205461.593
41_E47_A1.199171.585
46_E49_E1.135361.501
11_L14_E1.029761.361
44_A47_A0.985521.303
48_A56_I0.95681.265
11_L50_S0.952161.259
10_G22_Y0.915611.210
46_E50_S0.874141.155
7_I11_L0.869651.149
11_L15_I0.864021.142
6_C51_C0.813891.076
18_D40_E0.786521.040
6_C9_C0.779091.030
37_P41_E0.773051.022
12_C51_C0.754110.997
38_E43_A0.748990.990
16_A41_E0.734480.971
19_V40_E0.722220.955
11_L52_P0.721780.954
23_D30_V0.698090.923
24_D27_G0.686850.908
17_P46_E0.66630.881
10_G14_E0.655730.867
9_C51_C0.646470.854
9_C12_C0.643380.850
42_E45_R0.63060.834
16_A44_A0.623610.824
41_E45_R0.611060.808
43_A46_E0.596540.788
8_G28_K0.584760.773
45_R49_E0.567860.751
53_T56_I0.564950.747
9_C16_A0.55650.736
9_C53_T0.547770.724
14_E50_S0.540970.715
22_Y29_A0.533640.705
38_E41_E0.531830.703
20_F56_I0.529790.700
42_E46_E0.525580.695
13_V22_Y0.51750.684
39_E43_A0.509170.673
3_R28_K0.508220.672
27_G37_P0.488560.646
23_D37_P0.483210.639
17_P49_E0.479120.633
17_P42_E0.472410.624
11_L53_T0.469550.621
5_K54_A0.464980.615
13_V29_A0.454050.600
7_I52_P0.452040.597
21_D30_V0.452030.597
28_K31_V0.451740.597
18_D43_A0.448340.593
25_D28_K0.447420.591
3_R43_A0.441160.583
38_E42_E0.433460.573
3_R8_G0.428130.566
5_K53_T0.425210.562
8_G29_A0.423970.560
17_P40_E0.421760.557
22_Y25_D0.419480.554
39_E42_E0.416950.551
31_V48_A0.416890.551
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
3c8yA198.70.027
1gteA0.896698.70.03
1iqzA0.982898.70.04
3i9v30.982898.70.051
1daxA0.965598.60.063
1hfeL0.896698.60.083
1xerA198.50.091
2c42A198.50.099
1dwlA0.948398.50.104
1sj1A0.982898.50.104

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