GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF836 - Glutaredoxin-like domain (DUF836)
Pfam: PF05768 (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: 81
Sequences: 19048
Seq/Len: 235.16
HH_delta: -0.044 (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
10_C13_C1.959082.453
22_E73_E1.919722.403
17_K33_E1.702212.131
26_E77_R1.660912.079
72_D75_Q1.625072.034
73_E77_R1.521481.905
36_I43_F1.506811.886
6_T33_E1.501611.880
65_E79_W1.452761.819
54_H66_E1.40711.762
16_A53_L1.297431.624
27_F77_R1.285091.609
19_I73_E1.277731.600
56_D60_Q1.258681.576
36_I50_I1.184941.483
4_L17_K1.184271.483
7_K50_I1.158751.451
12_L15_E1.118841.401
26_E73_E1.091391.366
17_K21_E1.064671.333
67_L71_F1.057431.324
46_Y56_D1.056861.323
75_Q78_A1.030551.290
4_L16_A1.002021.254
55_I79_W0.997811.249
5_Y54_H0.990051.239
4_L33_E0.974791.220
19_I22_E0.971431.216
8_P35_D0.948171.187
15_E70_R0.946221.185
7_K37_D0.942861.180
35_D38_E0.927041.161
2_L20_L0.926131.159
16_A71_F0.902331.130
48_Y52_V0.900881.128
5_Y46_Y0.872741.093
6_T17_K0.857711.074
74_E78_A0.837281.048
11_H14_D0.815581.021
3_T32_E0.811311.016
60_Q64_Q0.809871.014
2_L53_L0.807871.011
20_L31_L0.806271.009
3_T56_D0.803491.006
21_E25_A0.798350.999
67_L79_W0.790530.990
71_F75_Q0.781870.979
5_Y48_Y0.776350.972
4_L12_L0.77280.967
57_G60_Q0.772270.967
12_L70_R0.754330.944
24_A28_P0.745790.934
21_E33_E0.735240.920
6_T35_D0.735020.920
75_Q79_W0.728490.912
23_V27_F0.722810.905
4_L53_L0.710950.890
52_V66_E0.708550.887
11_H15_E0.705280.883
22_E25_A0.687660.861
23_V77_R0.656870.822
23_V73_E0.652910.817
18_E22_E0.642550.804
22_E26_E0.635250.795
65_E68_K0.620290.777
70_R75_Q0.612180.766
12_L49_R0.609580.763
19_I70_R0.604280.756
2_L55_I0.59690.747
24_A31_L0.588810.737
20_L24_A0.586180.734
41_E44_E0.58610.734
30_E33_E0.585360.733
67_L70_R0.583140.730
39_D42_L0.581860.728
46_Y54_H0.579060.725
9_G50_I0.576230.721
12_L50_I0.572720.717
57_G64_Q0.564910.707
18_E21_E0.564060.706
4_L13_C0.558060.699
5_Y34_V0.554840.695
9_G37_D0.551140.690
34_V42_L0.54910.687
2_L31_L0.540990.677
43_F48_Y0.540560.677
5_Y36_I0.538250.674
4_L20_L0.53030.664
41_E45_K0.530110.664
16_A70_R0.525910.658
42_L46_Y0.522670.654
3_T34_V0.520410.651
74_E77_R0.516240.646
56_D59_R0.514790.644
14_D17_K0.514740.644
53_L76_L0.506810.634
9_G14_D0.504740.632
23_V76_L0.503760.631
10_C18_E0.497040.622
15_E19_I0.492350.616
71_F79_W0.480310.601
16_A19_I0.479790.601
71_F76_L0.476190.596
55_I80_L0.47450.594
24_A27_F0.474470.594
49_R68_K0.467710.586
8_P37_D0.462610.579
20_L76_L0.459430.575
23_V26_E0.453130.567
10_C50_I0.450680.564
42_L45_K0.449030.562
2_L29_F0.445970.558
40_P44_E0.439710.550
7_K12_L0.436110.546
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
2av4A199.4-0.044
2qgvA0.975399.3-0.022
2qsiA0.975399.3-0.021
3vfiA0.975399.3-0.006
3zzxA0.96399.3-0.001
3f8uA0.975399.30.006
3qouA0.975399.30.009
3gixA0.975399.30.01
2dj0A0.975399.30.011
2r2jA0.975399.30.012

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