GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Thioredoxin_7 - Thioredoxin-like
Pfam: PF13899 (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: 82
Sequences: 17321
Seq/Len: 211.23
HH_delta: -0.001 (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_C1.790862.471
18_K54_V1.701342.347
20_V54_V1.586772.189
25_G57_K1.512732.087
36_E57_K1.413271.950
35_L77_F1.367731.887
60_V67_A1.31631.816
20_V56_V1.276491.761
23_D36_E1.150721.588
21_L39_V1.110811.533
68_Q71_R1.040261.435
60_V74_Y1.037541.431
26_A74_Y1.037221.431
46_Q50_N1.015781.401
31_P34_K1.010281.394
23_D57_K0.984521.358
59_D62_D0.971461.340
19_P79_F0.953211.315
23_D35_L0.935041.290
21_L77_F0.93211.286
23_D31_P0.882031.217
27_D59_D0.849761.172
43_P47_E0.846211.168
43_P75_P0.841381.161
24_F78_F0.838811.157
48_A52_N0.818511.129
22_V80_L0.781571.078
25_G36_E0.777211.072
64_D67_A0.766541.058
19_P53_F0.765621.056
24_F60_V0.759691.048
34_K38_E0.759651.048
27_D66_N0.758791.047
25_G59_D0.755881.043
43_P46_Q0.752661.038
46_Q75_P0.736721.016
21_L79_F0.732221.010
69_F80_L0.723820.999
49_L55_L0.716310.988
63_E66_N0.696630.961
18_K52_N0.672110.927
45_V48_A0.666180.919
23_D77_F0.652150.900
45_V49_L0.644890.890
44_E47_E0.644040.889
63_E67_A0.63970.883
35_L39_V0.637530.880
30_P34_K0.622420.859
37_R43_P0.620670.856
34_K37_R0.6180.853
31_P74_Y0.615570.849
21_L55_L0.614660.848
71_R76_T0.608230.839
14_K18_K0.603450.833
19_P52_N0.580230.801
24_F58_V0.572670.790
28_W72_Q0.572030.789
48_A51_K0.570.786
46_Q49_L0.567820.783
24_F69_F0.564560.779
16_E19_P0.55750.769
14_K17_G0.556630.768
44_E48_A0.555160.766
33_K36_E0.554310.765
30_P33_K0.550340.759
19_P23_D0.548630.757
49_L52_N0.541340.747
39_V55_L0.534070.737
31_P73_G0.53270.735
70_D80_L0.526220.726
27_D61_D0.524410.724
27_D62_D0.522170.720
51_K55_L0.516240.712
49_L53_F0.512520.707
28_W74_Y0.511710.706
29_C37_R0.500530.691
35_L38_E0.492810.680
70_D78_F0.492730.680
22_V56_V0.48930.675
16_E54_V0.483220.667
75_P79_F0.482260.665
23_D32_C0.459750.634
26_A61_D0.458630.633
28_W61_D0.458370.632
25_G33_K0.454390.627
39_V45_V0.446530.616
72_Q76_T0.445420.615
15_K20_V0.43960.607
24_F76_T0.438030.604
50_N55_L0.433980.599
28_W33_K0.433010.597
58_V66_N0.432070.596
38_E45_V0.429970.593
61_D66_N0.428210.591
52_N55_L0.428040.591
75_P80_L0.418330.577
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
3ph9A199.4-0.001
3iraA199.30.007
3f9uA199.30.045
2ju5A0.987899.10.101
1senA0.951299.10.102
2lstA0.987899.10.105
2av4A0.93999.10.11
2dlxA199.10.116
3fk8A0.963499.10.135
4fybB199.10.141

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