GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FecR - FecR protein
Pfam: PF04773 (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. )
Length: 98
Sequences: 3720
Seq/Len: 37.96
HH_delta: 0.841 (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
56_G59_R1.559093.657
24_G48_E1.347823.162
52_D76_R1.298933.047
76_R94_E1.211462.842
41_R64_R1.200172.815
71_G98_Q1.162162.726
30_S43_R1.029422.415
50_L76_R1.02912.414
12_E22_R0.934232.192
7_A26_N0.863622.026
12_E20_R0.86152.021
21_V29_V0.831541.951
62_E71_G0.811341.903
20_R52_D0.754011.769
28_R46_S0.751111.762
62_E69_T0.745491.749
64_R69_T0.726481.704
43_R64_R0.721961.694
73_R98_Q0.704221.652
4_R28_R0.689121.617
70_I90_V0.663241.556
90_V97_V0.645841.515
14_A20_R0.617841.449
73_R96_S0.601151.410
52_D94_E0.593611.392
8_G25_P0.589861.384
3_I31_V0.566871.330
68_A88_T0.566241.328
30_S45_L0.551111.293
6_G9_S0.549641.289
28_R45_L0.538711.264
32_D35_S0.537761.261
22_R52_D0.534091.253
92_V97_V0.513011.203
48_E80_R0.511091.199
19_S53_V0.509271.195
53_V61_F0.500551.174
32_D43_R0.490341.150
82_D85_D0.481111.129
76_R93_L0.479981.126
72_V75_T0.46871.099
75_T97_V0.468661.099
41_R62_E0.462861.086
26_N46_S0.45541.068
14_A18_G0.452951.063
55_P72_V0.440271.033
3_I13_I0.421380.988
65_T88_T0.413970.971
50_L93_L0.409790.961
17_D40_T0.40410.948
72_V95_G0.402330.944
40_T43_R0.400540.940
66_P83_A0.39720.932
39_P62_E0.390670.916
19_S54_S0.388650.912
10_R22_R0.385450.904
51_F77_F0.384550.902
53_V72_V0.37650.883
3_I11_A0.376180.882
29_V42_L0.366930.861
41_R69_T0.364930.856
7_A25_P0.357730.839
92_V95_G0.356210.836
68_A90_V0.346830.814
72_V77_F0.342410.803
6_G25_P0.34080.799
61_F77_F0.336870.790
21_V49_I0.336820.790
67_T88_T0.333460.782
77_F97_V0.33320.782
15_L21_V0.332340.780
46_S83_A0.330470.775
5_T27_S0.32860.771
73_R95_G0.326090.765
53_V75_T0.32590.764
48_E82_D0.325250.763
54_S72_V0.324070.760
66_P88_T0.322640.757
83_A86_G0.321160.753
18_G54_S0.315570.740
80_R91_A0.315520.740
55_P94_E0.314740.738
56_G60_P0.311950.732
51_F63_V0.305780.717
19_S40_T0.304380.714
51_F61_F0.293370.688
5_T11_A0.290660.682
60_P71_G0.289050.678
15_L19_S0.288180.676
63_V77_F0.285360.669
74_G94_E0.276080.648
42_L51_F0.274180.643
10_R24_G0.2680.629
40_T61_F0.265680.623
55_P95_G0.261450.613
5_T10_R0.255190.599
63_V72_V0.253440.595
6_G11_A0.253160.594
19_S51_F0.252210.592
5_T25_P0.249930.586
9_S91_A0.247690.581
21_V51_F0.247540.581
72_V92_V0.247240.580
27_S82_D0.246550.578
74_G97_V0.246250.578
84_E89_R0.244040.572
70_I97_V0.243810.572
55_P73_R0.243710.572
32_D41_R0.243060.570
23_L49_I0.23390.549
83_A87_S0.233110.547
5_T26_N0.23290.546
55_P75_T0.232460.545
65_T68_A0.229980.539
75_T94_E0.227560.534
38_E57_K0.22690.532
65_T70_I0.225310.529
63_V74_G0.222410.522
15_L40_T0.221230.519
45_L49_I0.219410.515
5_T9_S0.217510.510
29_V49_I0.217070.509
37_S59_R0.216140.507
19_S61_F0.215450.505
24_G82_D0.215110.505
38_E59_R0.213420.501
90_V93_L0.209050.490
16_S31_V0.206790.485
45_L95_G0.206460.484
8_G48_E0.204890.481
32_D36_G0.204790.480
60_P73_R0.204090.479
47_G95_G0.201620.473
22_R50_L0.201350.472
7_A85_D0.200140.469
88_T91_A0.198760.466
14_A38_E0.198280.465
51_F72_V0.196130.460
55_P74_G0.194320.456
75_T92_V0.193610.454
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
1eybA0.959238.30.841
4aq2A0.938826.20.853
3qc5X0.357125.10.854
2phlA0.979615.30.867
3u5cE0.908214.70.868
3iz6D0.908214.60.869
3kbgA0.908213.60.87
1ywkA0.908213.60.87
3s7iA0.979613.30.871
3j20E0.938813.10.871
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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