GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fer4_14 - 4Fe-4S single cluster domain
Pfam: PF13394 (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: 119
Sequences: 12237
Seq/Len: 102.83
HH_delta: 0.255 (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
35_E73_Y2.009693.134
39_D77_R1.532832.390
73_Y77_R1.419882.214
93_T96_K1.368252.134
10_L90_T1.332832.078
30_S33_E1.309212.042
9_N88_N1.298972.026
31_I69_E1.207611.883
73_Y76_E1.165571.818
68_I72_E1.146551.788
53_F83_I1.131511.765
35_E39_D1.090731.701
31_I35_E1.056341.647
42_K77_R1.027451.602
105_E108_S1.01721.586
29_M33_E0.977731.525
53_F70_L0.945371.474
35_E69_E0.942381.470
33_E36_E0.933761.456
51_V74_L0.925131.443
39_D73_Y0.922971.439
67_L85_I0.922161.438
53_F71_I0.918411.432
50_T84_R0.910071.419
75_K83_I0.89641.398
34_L70_L0.882951.377
40_E44_K0.880841.374
36_E40_E0.849571.325
56_G59_L0.835731.303
72_E76_E0.831271.296
39_D43_E0.829681.294
69_E73_Y0.827311.290
31_I73_Y0.826921.290
10_L88_N0.807931.260
12_C15_C0.79581.241
75_K103_L0.792291.236
36_E39_D0.780951.218
52_V84_R0.772171.204
39_D42_K0.766031.195
59_L85_I0.744841.162
66_D69_E0.738061.151
74_L83_I0.736511.149
29_M37_I0.728251.136
8_C12_C0.719351.122
41_L46_F0.707741.104
16_Y54_T0.707481.103
40_E43_E0.706031.101
104_E108_S0.703321.097
49_S81_I0.690471.077
8_C15_C0.689291.075
31_I66_D0.676921.056
69_E72_E0.67371.051
11_R19_S0.665361.038
35_E77_R0.642091.001
38_I74_L0.637990.995
50_T82_K0.636690.993
57_E87_T0.631880.985
32_E36_E0.605520.944
7_G28_E0.598910.934
54_T86_E0.596290.930
17_N86_E0.593030.925
103_L106_C0.580910.906
72_E103_L0.566190.883
74_L78_G0.560860.875
9_N91_L0.555670.867
71_I83_I0.55550.866
78_G81_I0.554070.864
17_N54_T0.552820.862
52_V86_E0.551160.859
34_L37_I0.537620.838
72_E75_K0.530670.828
92_P95_E0.525840.820
66_D70_L0.521280.813
10_L89_G0.518390.808
49_S82_K0.518020.808
90_T93_T0.51380.801
32_E35_E0.510680.796
34_L38_I0.501710.782
16_Y19_S0.49760.776
16_Y86_E0.493730.770
103_L108_S0.492430.768
75_K104_E0.485220.757
96_K105_E0.483840.755
68_I96_K0.472520.737
42_K78_G0.449470.701
88_N91_L0.447510.698
29_M34_L0.431970.674
14_Y54_T0.431480.673
25_K28_E0.420260.655
17_N51_V0.418030.652
53_F74_L0.417650.651
65_E69_E0.417430.651
18_K23_P0.414160.646
57_E89_G0.40770.636
89_G92_P0.407460.635
24_K28_E0.401990.627
17_N52_V0.400490.625
14_Y17_N0.400010.624
6_S25_K0.393120.613
41_L45_G0.39230.612
5_T67_L0.385260.601
37_I40_E0.382090.596
30_S34_L0.375820.586
51_V83_I0.374520.584
6_S17_N0.368320.574
38_I51_V0.364940.569
35_E76_E0.362650.566
87_T90_T0.352630.550
37_I41_L0.350790.547
43_E46_F0.347250.542
42_K81_I0.343830.536
52_V55_G0.343530.536
39_D78_G0.342460.534
5_T53_F0.342120.534
72_E106_C0.338240.527
22_S25_K0.336590.525
11_R18_K0.334180.521
74_L81_I0.333730.520
17_N84_R0.331740.517
9_N57_E0.331320.517
42_K45_G0.328830.513
68_I71_I0.328360.512
25_K44_K0.322980.504
27_E33_E0.320380.500
68_I105_E0.318710.497
16_Y55_G0.318170.496
23_P26_G0.317970.496
49_S53_F0.315940.493
16_Y52_V0.315110.491
45_G78_G0.313960.490
59_L91_L0.312970.488
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
4k36A0.941299.60.255
1tv8A0.91699.50.287
3c8fA0.924499.50.298
2a5hA0.91699.40.341
2yx0A0.924499.20.39
2z2uA0.882499.20.398
3iixA0.899299.20.406
3rfaA0.882499.20.407
1r30A0.9076990.455
3t7vA0.91698.90.471

Page generated in 0.0212 seconds.