GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fer2 - 2Fe-2S iron-sulfur cluster binding domain
Pfam: PF00111 (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: 78
Sequences: 5754
Seq/Len: 73.77
HH_delta: 0.02 (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_E25_R1.618743.431
45_V72_A1.613843.420
20_L33_Y1.463563.102
13_P16_E1.294322.743
12_V22_A1.259052.668
46_R68_G1.07742.283
24_E36_G1.067052.261
23_L31_I0.918771.947
12_V77_V0.897551.902
24_E33_Y0.890121.886
60_E63_E0.807281.711
16_E22_A0.803221.702
17_T21_D0.802691.701
61_D65_A0.724351.535
31_I72_A0.716321.518
59_L63_E0.646221.370
56_E64_L0.611411.296
20_L24_E0.588891.248
19_L72_A0.58181.233
33_Y36_G0.565541.199
19_L75_T0.549451.164
3_I23_L0.534351.132
22_A26_A0.533561.131
44_R71_L0.530961.125
34_S42_T0.51351.088
4_N7_G0.509391.080
61_D64_L0.507011.074
52_V75_T0.492751.044
37_G42_T0.489691.038
10_V22_A0.475191.007
21_D36_G0.47351.003
26_A29_I0.471330.999
54_S76_R0.457450.969
17_T76_R0.457160.969
21_D24_E0.451380.957
56_E60_E0.448640.951
39_G57_T0.44680.947
44_R68_G0.44340.940
3_I6_K0.442710.938
47_V52_V0.440720.934
40_C43_C0.436570.925
35_C40_C0.419770.890
16_E21_D0.417180.884
46_R66_E0.409940.869
5_G8_V0.408180.865
6_K9_T0.401760.851
41_G44_R0.401710.851
23_L29_I0.39930.846
10_V26_A0.398050.844
31_I41_G0.394590.836
44_R58_F0.394490.836
59_L64_L0.39030.827
23_L72_A0.388670.824
13_P22_A0.372030.788
34_S39_G0.370670.786
62_E66_E0.367550.779
11_E14_P0.366920.778
39_G45_V0.36570.775
58_F62_E0.359350.762
47_V51_E0.355450.753
35_C43_C0.354150.751
34_S37_G0.346130.734
10_V23_L0.345940.733
15_G76_R0.345790.733
3_I10_V0.342190.725
37_G44_R0.342010.725
33_Y39_G0.340820.722
21_D37_G0.33910.719
58_F63_E0.337750.716
39_G74_Q0.328760.697
53_Q56_E0.325370.690
17_T22_A0.323340.685
58_F64_L0.321140.681
62_E65_A0.32080.680
60_E64_L0.320620.679
42_T74_Q0.320150.678
62_E68_G0.308880.655
39_G42_T0.307970.653
52_V67_G0.30770.652
56_E61_D0.30620.649
12_V16_E0.304270.645
58_F71_L0.303720.644
54_S75_T0.300790.637
41_G63_E0.29990.636
23_L34_S0.292640.620
12_V19_L0.292090.619
47_V75_T0.289080.613
4_N48_L0.288870.612
44_R57_T0.282840.599
63_E67_G0.281190.596
13_P25_R0.279030.591
56_E66_E0.277520.588
21_D30_G0.275310.583
63_E66_E0.273340.579
55_N58_F0.272590.578
32_P42_T0.272370.577
35_C73_C0.272140.577
3_I8_V0.266710.565
52_V77_V0.265420.562
17_T20_L0.264810.561
24_E30_G0.264760.561
20_L23_L0.262690.557
8_V29_I0.261980.555
53_Q74_Q0.260510.552
34_S38_G0.2580.547
9_T14_P0.25690.544
53_Q75_T0.24940.529
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
2piaA0.948799.60.02
3zyyX0.961599.60.024
1krhA0.961599.60.041
1b9rA0.961599.50.09
1jq4A0.961599.50.092
1uwmA0.961599.50.097
1doiA0.961599.50.098
2bt6A0.961599.50.101
3huiA0.961599.50.103
2y5cA0.961599.50.105

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