GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Thioredoxin - Thioredoxin
Pfam: PF00085 (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: CL0172
Length: 103
Sequences: 21554
Seq/Len: 209.26
HH_delta: -0.116 (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
29_C32_C2.070142.455
41_K93_A1.878462.228
57_C64_C1.868382.216
45_E97_I1.863162.210
97_I101_E1.840362.183
76_I86_R1.70972.028
92_N95_S1.64491.951
25_Y54_K1.553121.842
20_V51_K1.546781.835
18_K51_K1.504521.784
19_P79_K1.48621.763
36_K54_K1.451181.721
85_K99_F1.4031.664
57_C72_V1.3741.630
83_E86_R1.348521.599
93_A97_I1.316121.561
46_Y97_I1.300871.543
38_I93_A1.297621.539
35_F75_I1.28671.526
20_V53_A1.271991.509
19_P77_F1.220441.448
10_E66_K1.201611.425
67_Y78_F1.186761.408
76_I83_E1.166691.384
11_K15_E1.125391.335
46_Y101_E1.096421.300
38_I41_K1.096281.300
23_Y36_K1.081791.283
23_Y75_I1.050231.246
23_Y35_F1.037111.230
21_V75_I1.027021.218
69_V74_T1.02441.215
10_E14_N1.014721.204
78_F83_E0.99171.176
56_D59_E0.988141.172
95_S98_E0.986051.170
45_E93_A0.985571.169
21_V39_L0.980471.163
22_V78_F0.960511.139
87_Y91_R0.940461.115
31_P34_A0.939571.114
77_F99_F0.938751.113
23_Y54_K0.924521.097
34_A90_P0.92251.094
74_T86_R0.903381.071
21_V77_F0.898271.065
87_Y99_F0.893471.060
79_K82_K0.88691.052
24_F67_Y0.877771.041
36_K40_E0.871441.034
91_R95_S0.870361.032
63_L67_Y0.869741.032
27_P56_D0.864781.026
12_F51_K0.849851.008
43_A47_K0.846941.005
25_Y36_K0.845951.003
23_Y31_P0.844191.001
26_A72_V0.828960.983
42_L45_E0.828350.982
94_E98_E0.824310.978
95_S99_F0.804310.954
10_E13_I0.789560.936
82_K85_K0.777620.922
42_L46_Y0.772760.917
30_P33_K0.769720.913
40_E44_K0.76910.912
24_F76_I0.768260.911
67_Y76_I0.766760.909
62_E66_K0.761650.903
12_F53_A0.75770.899
62_E65_K0.755990.897
40_E54_K0.747380.886
87_Y90_P0.746230.885
24_F69_V0.737790.875
22_V53_A0.719790.854
91_R96_L0.716690.850
26_A58_D0.704570.836
79_K84_V0.697780.828
75_I78_F0.686630.814
30_P34_A0.682440.809
41_K45_E0.672850.798
42_L93_A0.656150.778
35_F38_I0.654960.777
91_R99_F0.63510.753
90_P95_S0.635010.753
79_K83_E0.628620.746
28_W33_K0.625420.742
25_Y56_D0.625350.742
24_F57_C0.623430.739
11_K14_N0.622670.739
27_P58_D0.614170.728
42_L97_I0.605130.718
41_K44_K0.600730.713
19_P80_N0.600160.712
35_F91_R0.594860.706
12_F20_V0.593660.704
34_A38_I0.592590.703
37_P41_K0.591870.702
75_I96_L0.586860.696
37_P40_E0.578440.686
12_F17_D0.572930.680
94_E97_I0.572820.679
35_F90_P0.572630.679
98_E101_E0.570590.677
61_K65_K0.564160.669
79_K85_K0.563460.668
31_P90_P0.563040.668
60_N63_L0.559690.664
18_K49_N0.558630.663
17_D80_N0.550570.653
28_W72_V0.548280.650
21_V52_F0.546430.648
19_P23_Y0.541510.642
31_P71_S0.527550.626
23_Y39_L0.527380.626
55_V63_L0.524530.622
28_W58_D0.511430.607
24_F55_V0.5090.604
33_K36_K0.505920.600
43_A52_F0.504630.599
39_L52_F0.503650.597
23_Y32_C0.501770.595
18_K80_N0.496670.589
25_Y33_K0.496390.589
63_L66_K0.492190.584
24_F63_L0.483610.574
9_F13_I0.480830.570
70_K88_N0.47650.565
15_E18_K0.475980.565
29_C37_P0.475390.564
77_F100_I0.473540.562
10_E15_E0.462250.548
12_F15_E0.4610.547
35_F96_L0.451260.535
19_P50_V0.445050.528
31_P72_V0.437630.519
35_F39_L0.432780.513
37_P42_L0.429950.510
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
3vfiA199.8-0.116
3f8uA0.990399.7-0.063
3apoA0.990399.7-0.059
2b5eA0.990399.7-0.057
3qouA199.7-0.057
2r2jA0.990399.7-0.051
4ekzA0.990399.7-0.051
2qgvA0.990399.7-0.046
2qsiA199.7-0.046
2av4A199.7-0.038

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