GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glutaredoxin - Glutaredoxin
Pfam: PF00462 (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: 60
Sequences: 31128
Seq/Len: 518.8
HH_delta: -0.073 (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
2_V29_V2.860883.097
2_V27_E2.157432.335
5_T12_C2.136192.312
5_T28_E2.128912.304
11_Y14_K2.087732.260
9_C12_C2.015332.181
3_V16_K1.82941.980
15_A53_V1.771651.918
4_Y54_F1.637911.773
18_F22_K1.622191.756
2_V54_F1.431491.549
16_K28_E1.410941.527
55_I58_K1.274321.379
5_T16_K1.253151.356
17_E21_E1.226611.328
16_K20_D1.182371.280
7_P30_D1.146981.242
3_V19_L1.142121.236
19_L26_Y1.130041.223
11_Y49_T1.1271.220
20_D26_Y1.082251.171
54_F57_G1.07731.166
40_E43_E1.075181.164
47_V52_Q1.073941.162
30_D33_E1.070071.158
3_V15_A1.060721.148
40_E44_L1.038591.124
41_L44_L1.004561.087
27_E30_D0.991351.073
11_Y50_V0.990891.073
6_K50_V0.985481.067
15_A18_F0.951761.030
31_V42_K0.911820.987
32_D35_E0.876770.949
4_Y31_V0.874880.947
15_A19_L0.872130.944
10_P14_K0.824040.892
13_K17_E0.818310.886
39_E42_K0.81230.879
29_V33_E0.802260.868
18_F21_E0.801410.867
42_K48_R0.767790.831
44_L54_F0.764710.828
38_R42_K0.764520.828
3_V53_V0.756040.818
4_Y29_V0.748420.810
41_L45_S0.738480.799
37_A40_E0.734250.795
8_G13_K0.71760.777
39_E43_E0.713890.773
54_F58_K0.71360.772
31_V50_V0.7080.766
45_S54_F0.695660.753
30_D34_D0.679020.735
17_E20_D0.66650.721
14_K17_E0.665280.720
10_P13_K0.663450.718
3_V11_Y0.65870.713
37_A42_K0.636170.689
45_S52_Q0.629490.681
35_E38_R0.619810.671
8_G32_D0.614860.666
6_K32_D0.604110.654
49_T52_Q0.583010.631
6_K9_C0.576520.624
37_A48_R0.575830.623
34_D37_A0.572710.620
3_V28_E0.567190.614
19_L53_V0.565410.612
12_C16_K0.560450.607
6_K49_T0.514720.557
5_T30_D0.492740.533
36_E40_E0.490690.531
6_K33_E0.487190.527
31_V35_E0.477520.517
4_Y44_L0.47710.516
14_K18_F0.475950.515
41_L52_Q0.474110.513
9_C13_K0.472530.511
33_E37_A0.471190.510
24_I27_E0.470290.509
32_D36_E0.468960.508
12_C50_V0.468560.507
27_E31_V0.460380.498
29_V34_D0.460040.498
3_V50_V0.458980.497
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
3uiwA198.6-0.073
3qmxA198.5-0.052
2lqoA198.5-0.039
2ht9A198.5-0.03
2cq9A198.5-0.018
3kp9A198.4-0.014
2hzeA198.4-0.013
4f2iA0.983398.4-0.012
3rhbA198.4-0.012
3zitA198.4-0.009

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