GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fer4_21 - 4Fe-4S dicluster domain
Pfam: PF14697 (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: 59
Sequences: 20751
Seq/Len: 351.71
HH_delta: -0.077 (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
20_D42_I1.716982.240
41_C47_C1.514281.975
17_A46_L1.454461.897
8_C14_C1.452571.895
44_C47_C1.404061.832
17_A50_V1.302891.700
45_G48_V1.299351.695
37_N40_K1.245171.624
18_C47_C1.214541.584
18_C41_C1.20451.571
12_G15_V1.153561.505
7_K56_A1.145731.495
11_C14_C1.092721.425
8_C11_C1.055631.377
20_D40_K1.012971.321
9_I13_K0.962811.256
13_K50_V0.961341.254
46_L49_K0.945181.233
8_C51_C0.933841.218
41_C44_C0.93081.214
28_V34_V0.91891.199
10_G34_V0.90441.180
13_K16_R0.891.161
46_L50_V0.876651.144
13_K17_A0.840131.096
19_P46_L0.834111.088
18_C44_C0.833691.088
12_G16_R0.80881.055
38_P44_C0.798961.042
9_I52_P0.786161.026
48_V57_I0.771061.006
13_K52_P0.749340.978
35_P38_P0.729960.952
27_E30_E0.719320.938
43_G46_L0.706490.922
48_V55_D0.696960.909
11_C51_C0.68440.893
14_C51_C0.681690.889
9_I12_G0.68050.888
51_C56_A0.666180.869
29_D32_K0.665340.868
24_D27_E0.66150.863
25_A28_V0.654490.854
38_P43_G0.618190.806
39_D42_I0.59780.780
39_D43_G0.550010.718
24_D28_V0.547320.714
45_G49_K0.536750.700
28_V32_K0.526160.686
40_K43_G0.519780.678
12_G28_V0.501520.654
9_I55_D0.500470.653
40_K44_C0.488370.637
30_E33_K0.487560.636
28_V31_G0.472350.616
16_R50_V0.468050.611
42_I49_K0.454320.593
7_K55_D0.450240.587
42_I46_L0.449890.587
5_E10_G0.444040.579
20_D25_A0.440560.575
17_A49_K0.432240.564
24_D37_N0.430270.561
36_V57_I0.425520.555
17_A57_I0.424790.554
16_R19_P0.419220.547
42_I45_G0.416070.543
50_V55_D0.412840.539
20_D43_G0.409620.534
27_E33_K0.405850.529
5_E26_I0.401320.524
41_C45_G0.398740.520
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
2c42A0.983198.8-0.077
1hfeL0.932298.8-0.051
3c8yA0.983198.7-0.036
3gyxB0.966198.7-0.027
1gteA0.915398.7-0.02
1jnrB0.966198.6-0.004
1xerA0.983198.60.008
3i9v90.983198.60.014
2ivfB0.949298.60.017
7fd1A0.915398.60.021

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