GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fer4_7 - 4Fe-4S dicluster domain
Pfam: PF12838 (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: 23531
Seq/Len: 452.52
HH_delta: -0.045 (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
3_I50_T3.008493.801
14_T39_T1.728652.184
11_A43_A1.530381.934
38_C41_C1.335611.688
11_A47_V1.250661.580
42_G45_V1.229261.553
34_D37_K1.228731.553
6_G9_V1.17431.484
43_A46_E1.132951.432
6_G19_L1.102951.394
41_C44_C1.077241.361
43_A47_V1.077071.361
38_C44_C1.062031.342
4_G31_M1.053791.332
2_C8_C1.030061.302
19_L22_E1.008151.274
7_A47_V1.003641.268
7_A10_E0.967471.222
16_A37_K0.927831.172
19_L31_M0.905461.144
3_I7_A0.904581.143
32_V35_P0.88471.118
12_C44_C0.846821.070
42_G46_E0.843891.066
7_A49_P0.83831.059
7_A11_A0.818911.035
4_G19_L0.812031.026
9_V19_L0.795371.005
5_C8_C0.767830.970
6_G10_E0.752180.950
18_R21_E0.746720.944
36_D39_T0.72230.913
13_P43_A0.707340.894
12_C15_G0.686590.868
12_C41_C0.679930.859
45_V51_G0.669120.845
14_T17_I0.668760.845
40_G43_A0.641350.810
12_C38_C0.636430.804
2_C48_C0.631310.798
5_C48_C0.630550.797
18_R34_D0.62280.787
48_C52_A0.595040.752
14_T37_K0.588190.743
7_A50_T0.582630.736
35_P40_G0.571620.722
3_I49_P0.561210.709
33_I36_D0.540010.682
29_P33_I0.518880.656
8_C48_C0.511670.647
36_D40_G0.50780.642
14_T40_G0.500180.632
18_R32_V0.496480.627
2_C5_C0.485970.614
3_I6_G0.483530.611
39_T43_A0.481360.608
39_T42_G0.480650.607
15_G21_E0.471520.596
37_K40_G0.471150.595
15_G18_R0.457350.578
22_E29_P0.442720.559
13_P37_K0.42920.542
18_R33_I0.427960.541
4_G29_P0.421990.533
17_I21_E0.418370.529
38_C42_G0.417130.527
29_P32_V0.408490.516
22_E30_K0.402780.509
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
2c42A198.4-0.045
3i9v9198.4-0.031
1hfeL0.884698.4-0.02
3c8yA198.3-0.006
3gyxB0.923198.30.017
1jnrB0.923198.20.033
3i9v30.980898.20.036
1xerA198.20.04
2ivfB0.903898.20.043
1gteA0.884698.20.044

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