GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
fn3 - Fibronectin type III domain
Pfam: PF00041 (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: CL0159
Length: 85
Sequences: 13215
Seq/Len: 155.47
HH_delta: -0.127 (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
60_I71_F2.321073.448
36_E72_R2.119463.148
34_R76_V1.849352.747
76_V81_E1.84172.736
32_G76_V1.727362.566
37_Y60_I1.627532.417
34_R81_E1.626442.416
38_R70_E1.521962.261
37_Y71_F1.504392.235
34_R74_R1.500632.229
17_T59_T1.444592.146
74_R81_E1.441432.141
75_A82_G1.347182.001
17_T57_S1.248641.855
12_S15_S1.239441.841
77_N80_G1.186871.763
5_N21_K1.178161.750
36_E74_R1.114471.655
18_V71_F0.987031.466
7_S19_S0.981861.458
39_S67_T0.960881.427
16_V71_F0.926361.376
22_P33_Y0.907361.348
35_V73_V0.902611.341
39_S64_Q0.859481.277
13_P65_P0.856961.273
9_S19_S0.839151.246
63_L69_Y0.830841.234
46_W49_V0.79711.184
40_V70_E0.768311.141
64_Q67_T0.74841.112
18_V35_V0.748121.111
9_S17_T0.748061.111
14_T65_P0.730611.085
6_L18_V0.725661.078
33_Y75_A0.719061.068
15_S59_T0.676551.005
29_P77_N0.667220.991
10_N17_T0.651390.968
19_S57_S0.649340.965
60_I63_L0.644470.957
35_V58_Y0.636450.945
64_Q69_Y0.62130.923
8_V11_I0.61680.916
6_L73_V0.590280.877
8_V18_V0.590280.877
27_N77_N0.588050.873
30_I33_Y0.587280.872
31_T77_N0.586510.871
11_I16_V0.584020.867
31_T78_S0.557190.828
38_R72_R0.535390.795
20_W35_V0.524810.780
27_N30_I0.523320.777
36_E48_E0.52180.775
7_S21_K0.512170.761
23_P33_Y0.511110.759
32_G50_T0.5070.753
2_A83_P0.498340.740
23_P30_I0.497350.739
74_R82_G0.483830.719
30_I75_A0.483450.718
20_W73_V0.478840.711
23_P27_N0.475560.706
47_Q51_V0.47520.706
38_R46_W0.472130.701
11_I17_T0.464660.690
46_W50_T0.46230.687
4_E21_K0.460490.684
22_P56_T0.45970.683
39_S42_S0.455940.677
23_P29_P0.452730.672
8_V16_V0.450560.669
13_P66_G0.447890.665
41_N44_S0.439720.653
36_E81_E0.422810.628
39_S70_E0.422350.627
16_V60_I0.422080.627
40_V68_T0.418530.622
50_T53_G0.411370.611
38_R44_S0.409780.609
18_V60_I0.409370.608
38_R42_S0.399770.594
49_V58_Y0.394330.586
37_Y49_V0.391050.581
38_R41_N0.390420.580
30_I77_N0.390410.580
46_W51_V0.380230.565
53_G56_T0.37410.556
47_Q50_T0.373920.555
58_Y61_T0.373840.555
15_S61_T0.372550.553
11_I14_T0.371070.551
16_V63_L0.366180.544
51_V58_Y0.359020.533
6_L20_W0.357520.531
10_N15_S0.350110.520
63_L67_T0.343020.510
43_T46_W0.341580.507
28_G77_N0.340060.505
30_I79_D0.337490.501
6_L35_V0.334640.497
3_P82_G0.33440.497
14_T66_G0.329330.489
33_Y73_V0.327010.486
4_E23_P0.325520.484
12_S17_T0.324590.482
31_T76_V0.323530.481
3_P73_V0.321460.477
21_K56_T0.318570.473
3_P75_A0.318280.473
20_W58_Y0.318130.473
52_P55_E0.317150.471
54_N57_S0.315540.469
46_W55_E0.30910.459
40_V44_S0.307070.456
30_I80_G0.300670.447
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
3utoA0.976598.8-0.127
2e7hA198.8-0.112
2djsA0.988298.8-0.106
1wfnA198.7-0.097
1v5jA0.964798.7-0.096
2ed7A198.7-0.093
1x5fA198.7-0.09
3n1fC198.7-0.087
3fl7A0.976598.7-0.085
1x5lA0.988298.7-0.084

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