GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Epimerase_Csub - UDP-glucose 4-epimerase C-term subunit
Pfam: PF13950 (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. )
Length: 62
Sequences: 10926
Seq/Len: 176.23
HH_delta: 0.091 (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
4_K45_E2.223142.765
33_R39_K2.176422.706
43_S46_D1.996262.482
32_A36_L1.95862.436
5_V49_R1.849122.299
30_S34_E1.837682.285
22_P25_L1.828322.274
42_Y46_D1.753652.181
42_Y50_D1.742552.167
53_N57_K1.419831.766
3_E9_K1.377181.713
31_K35_E1.37111.705
29_I33_R1.284011.597
49_R53_N1.225051.523
42_Y47_M1.209521.504
46_D50_D1.179931.467
6_T52_W1.178971.466
3_E8_K1.174871.461
3_E10_I1.150861.431
46_D49_R1.081941.345
29_I40_P1.033961.286
5_V52_W1.012741.259
30_S33_R0.933551.161
51_A55_Q0.902481.122
52_W56_K0.899841.119
3_E12_V0.890311.107
31_K34_E0.867441.079
45_E49_R0.854241.062
53_N56_K0.838921.043
22_P27_A0.833541.037
5_V48_I0.777720.967
29_I38_W0.743030.924
51_A54_W0.741340.922
17_R23_A0.733010.912
50_D53_N0.709140.882
47_M51_A0.697450.867
5_V45_E0.679190.845
21_D25_L0.67050.834
22_P26_V0.670440.834
52_W55_Q0.664160.826
33_R40_P0.64580.803
8_K11_P0.619630.771
32_A35_E0.610760.759
16_P19_P0.603250.750
3_E6_T0.588150.731
47_M50_D0.58190.724
18_R21_D0.574240.714
15_A18_R0.56010.696
29_I32_A0.560050.696
9_K12_V0.537270.668
20_G25_L0.523810.651
25_L51_A0.51840.645
48_I51_A0.513990.639
23_A26_V0.509150.633
44_L47_M0.505780.629
40_P43_S0.49420.615
44_L48_I0.480350.597
42_Y51_A0.478840.595
44_L52_W0.457230.569
4_K9_K0.452440.563
5_V53_N0.44790.557
18_R22_P0.443460.551
6_T48_I0.439470.546
38_W51_A0.428890.533
21_D27_A0.420090.522
3_E7_G0.40640.505
17_R21_D0.405090.504
27_A38_W0.396940.494
32_A38_W0.396650.493
14_Y20_G0.388410.483
18_R27_A0.381660.475
38_W41_K0.380290.473
50_D54_W0.379360.472
34_E37_G0.374060.465
12_V15_A0.369990.460
54_W57_K0.365530.455
26_V51_A0.356530.443
3_E11_P0.341050.424
14_Y25_L0.34090.424
15_A20_G0.325890.405
20_G23_A0.324450.403
22_P51_A0.323090.402
21_D24_H0.322920.402
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
3enkA198.40.091
1udbA198.20.144
1z45A198.20.149
1ek6A198.10.169
1gy8A198.10.178
2c20A198.10.18
4egbA198.10.182
3rufA0.9839980.192
4e5yA1980.194
4b8wA1980.197

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