GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Biotin_lipoyl_2 - Biotin-lipoyl like
Pfam: PF13533 (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: CL0105
Length: 50
Sequences: 17671
Seq/Len: 353.42
HH_delta: -0.034 (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
15_S32_V3.004643.033
17_Y32_V2.855482.883
25_K28_D2.452772.476
17_Y29_V2.29712.319
35_S39_Q2.157142.178
42_L46_E2.118582.139
19_K22_Q1.811891.829
29_V32_V1.747771.764
18_V28_D1.714091.730
43_Q46_E1.632041.648
16_V31_L1.612651.628
13_V31_L1.571521.587
39_Q43_Q1.483351.498
41_Q44_Q1.357981.371
7_A31_L1.317971.331
14_E34_D1.247011.259
18_V22_Q1.239991.252
11_G33_L1.233111.245
22_Q28_D1.212321.224
8_P12_R1.211761.223
41_Q45_A1.175461.187
24_V30_L1.161611.173
14_E32_V1.153151.164
39_Q42_L1.088291.099
8_P37_D1.068511.079
37_D41_Q0.952940.962
7_A10_S0.893770.902
7_A33_L0.85430.862
3_V7_A0.825790.834
9_V38_L0.795230.803
40_A43_Q0.772430.780
43_Q47_A0.764370.772
36_P39_Q0.759880.767
32_V35_S0.732990.740
13_V16_V0.73270.740
42_L45_A0.723830.731
20_E38_L0.71930.726
44_Q47_A0.710250.717
35_S38_L0.70830.715
14_E17_Y0.661710.668
12_R36_P0.638780.645
6_Q12_R0.638770.645
29_V41_Q0.636140.642
16_V20_E0.628790.635
12_R34_D0.593230.599
36_P40_A0.588510.594
23_Q26_K0.577170.583
37_D40_A0.553390.559
26_K29_V0.547410.553
6_Q21_G0.546210.551
21_G38_L0.540290.545
12_R16_V0.538820.544
3_V8_P0.53160.537
8_P33_L0.531330.536
6_Q10_S0.528360.533
14_E35_S0.521950.527
9_V37_D0.515750.521
40_A44_Q0.511130.516
8_P34_D0.492820.498
17_Y20_E0.491570.496
38_L42_L0.486290.491
8_P47_A0.480230.485
24_V28_D0.46590.470
9_V35_S0.453420.458
4_T7_A0.451670.456
40_A47_A0.447150.451
4_T8_P0.444270.449
6_Q9_V0.440390.445
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
4l8jA198.4-0.034
1vf7A198.4-0.027
2f1mA198.3-0.026
3fppA198.3-0.025
4dk0A198.3-0.018
3lnnA198.20.037
3ne5B1980.068
2k32A0.9897.80.124
3hblA197.40.225
3n6rA197.40.226

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