GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GalKase_gal_bdg - Galactokinase galactose-binding signature
Pfam: PF10509 (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: 52
Sequences: 1207
Seq/Len: 23.21
HH_delta: -0.062 (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
17_S44_R1.446434.090
5_E11_E0.803652.272
3_E7_F0.798162.257
10_E50_S0.749012.118
13_E51_P0.71572.024
23_N38_P0.698591.975
23_N27_E0.647141.830
29_T32_N0.626421.771
15_V48_A0.619831.752
4_F50_S0.574241.624
3_E6_E0.557191.575
28_H31_Y0.547921.549
29_T35_F0.507511.435
22_V41_I0.456721.291
27_E38_P0.452031.278
5_E9_G0.442021.250
30_D36_V0.388761.099
2_E6_E0.383551.084
22_V38_P0.377231.067
21_R30_D0.374911.060
29_T34_G0.374271.058
23_N30_D0.373011.055
16_A39_A0.352470.997
2_E5_E0.342070.967
23_N31_Y0.341530.966
25_I38_P0.337880.955
16_A47_V0.337480.954
17_S46_Y0.33270.941
32_N35_F0.328380.928
25_I31_Y0.327690.926
2_E10_E0.324690.918
10_E13_E0.305370.863
12_P48_A0.298160.843
4_F8_F0.296640.839
21_R31_Y0.294580.833
3_E9_G0.292920.828
31_Y38_P0.292750.828
3_E10_E0.290450.821
20_G29_T0.287790.814
2_E7_F0.278760.788
22_V39_A0.276990.783
30_D34_G0.27680.783
6_E51_P0.262920.743
10_E51_P0.261410.739
17_S43_L0.260370.736
5_E12_P0.258810.732
5_E10_E0.25730.727
5_E13_E0.257070.727
18_A47_V0.25690.726
2_E15_V0.255490.722
3_E15_V0.253950.718
2_E11_E0.252940.715
15_V46_Y0.248180.702
41_I45_T0.246450.697
43_L52_R0.244990.693
5_E14_V0.242350.685
25_I30_D0.241140.682
23_N29_T0.240590.680
42_D47_V0.240210.679
6_E9_G0.230320.651
22_V25_I0.228470.646
18_A32_N0.223780.633
7_F13_E0.223660.632
16_A49_V0.221380.626
21_R38_P0.217980.616
2_E13_E0.216110.611
26_G34_G0.21310.602
16_A42_D0.21120.597
43_L47_V0.210070.594
30_D38_P0.20960.593
22_V31_Y0.207080.585
23_N28_H0.204070.577
7_F14_V0.202570.573
3_E11_E0.202250.572
43_L50_S0.200540.567
39_A43_L0.200480.567
23_N26_G0.200260.566
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
3v2uC199.7-0.062
2a2cA199.40.186
1wuuA199.30.212
1pieA199.30.236
3k17A0.865499.10.283
1kvkA0.846299.10.293
3k85A0.807799.10.299
2pg9A0.807798.90.345
2cz9A0.769298.70.399
4hacA0.961598.70.416

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