GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fer4_10 - 4Fe-4S dicluster domain
Pfam: PF13237 (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: 52
Sequences: 21604
Seq/Len: 415.46
HH_delta: -0.057 (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_A42_I2.15762.666
5_D8_K1.998962.470
41_C44_C1.595731.971
37_D40_R1.499981.853
18_V46_A1.471861.818
45_G48_V1.409691.742
41_C47_C1.393471.722
18_V50_V1.381751.707
25_I29_D1.341281.657
9_C15_C1.283651.586
46_A49_E1.182971.461
10_I14_R1.148111.418
44_C47_C1.121931.386
19_C44_C1.090621.347
12_C15_C1.079241.333
21_A40_R1.03511.279
13_G16_V1.033681.277
9_C12_C0.999631.235
19_C47_C0.974781.204
46_A50_V0.970831.199
27_I31_E0.970761.199
14_R18_V0.952081.176
43_G46_A0.944991.167
25_I28_D0.939291.160
14_R50_V0.927281.146
14_R17_K0.91671.133
39_E42_I0.893411.104
9_C51_C0.882391.090
12_C51_C0.858781.061
20_P46_A0.837931.035
19_C41_C0.818041.011
11_G34_V0.751920.929
45_G49_E0.739380.913
15_C51_C0.684070.845
10_I13_G0.681630.842
38_P43_G0.664710.821
13_G29_D0.659960.815
10_I52_P0.639280.790
30_G33_K0.634640.784
14_R52_P0.600530.742
6_E11_G0.582320.719
26_A29_D0.56650.700
18_V49_E0.564690.698
42_I46_A0.555570.686
13_G17_K0.550420.680
35_E38_P0.523170.646
28_D31_E0.522030.645
29_D34_V0.5120.633
21_A43_G0.509130.629
36_I39_E0.505820.625
20_P49_E0.504790.624
29_D32_K0.470060.581
32_K35_E0.459340.567
16_V27_I0.453760.561
16_V34_V0.452740.559
27_I30_G0.448970.555
26_A40_R0.442940.547
20_P42_I0.441710.546
39_E43_G0.435970.539
15_C47_C0.413230.511
21_A25_I0.403010.498
21_A49_E0.400420.495
16_V21_A0.397860.492
20_P40_R0.357630.442
17_K50_V0.352430.435
7_D10_I0.351450.434
25_I30_G0.347770.430
18_V42_I0.347590.429
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
2c42A198.4-0.057
1gteA0.980898.3-0.017
1hfeL0.961598.3-0.013
3c8yA198.3-0.009
3gyxB198.20.017
2ivfB0.980898.20.03
1jnrB0.980898.20.035
3i9v3198.10.04
7fd1A0.923198.10.049
1q16B0.980898.10.055

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