GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glyco_tranf_2_4 - Glycosyl transferase family 2
Pfam: PF13704 (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: CL0110
Length: 97
Sequences: 30923
Seq/Len: 318.79
HH_delta: 0.056 (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
3_E80_A4.34983.493
4_A32_G3.224292.589
34_R38_R2.696282.165
64_A68_R2.66422.140
26_D29_S2.43921.959
8_P36_I2.386371.917
8_P12_A2.324211.867
9_E83_F2.307071.853
34_R47_R2.299051.846
78_L84_L2.244191.802
4_A36_I2.222331.785
32_G35_E2.159231.734
8_P40_L2.145131.723
2_N30_T2.11661.700
3_E6_Y2.060311.655
12_A40_L2.042881.641
21_H44_G2.013811.617
26_D47_R1.971461.583
60_A64_A1.967811.580
64_A67_E1.953541.569
21_H72_A1.943531.561
61_W64_A1.908051.532
76_L84_L1.737021.395
59_R62_R1.721811.383
59_R63_N1.693191.360
8_P39_A1.693081.360
24_I37_L1.620641.302
36_I39_A1.574721.265
61_W65_L1.572771.263
13_H83_F1.518061.219
11_L22_I1.501681.206
48_W52_Y1.446111.161
26_D34_R1.421151.141
48_W64_A1.415861.137
2_N29_S1.40881.131
11_L24_I1.405831.129
36_I40_L1.392451.118
35_E38_R1.369771.100
14_H78_L1.350521.085
10_W13_H1.329521.068
63_N67_E1.322841.062
13_H84_L1.320511.061
10_W78_L1.319581.060
62_R79_D1.31171.053
34_R45_I1.276721.025
38_R47_R1.232940.990
11_L40_L1.219990.980
32_G36_I1.196160.961
62_R66_I1.176930.945
12_A15_L1.13750.914
3_E79_D1.129750.907
63_N66_I1.128250.906
35_E39_A1.125550.904
16_A86_P1.117570.898
21_H71_D1.11610.896
25_Y65_L1.101380.885
48_W51_P1.086170.872
12_A16_A1.073560.862
49_V52_Y1.067220.857
78_L82_E1.060720.852
21_H70_F1.051610.845
62_R65_L1.023070.822
14_H22_I1.011850.813
61_W66_I1.011670.812
50_D53_R0.999660.803
9_E12_A0.985480.791
37_L45_I0.970470.779
4_A8_P0.965780.776
10_W84_L0.952280.765
62_R77_F0.940840.756
15_L42_G0.937740.753
10_W80_A0.929320.746
1_R51_P0.909730.731
11_L15_L0.886250.712
7_L80_A0.880250.707
10_W14_H0.87840.705
60_A63_N0.87710.704
48_W60_A0.869530.698
44_G47_R0.867850.697
9_E13_H0.865990.695
10_W81_D0.854090.686
14_H84_L0.839390.674
1_R27_D0.838870.674
4_A7_L0.833470.669
23_Y44_G0.828490.665
18_G87_P0.827190.664
7_L37_L0.815650.655
66_I70_F0.806270.648
65_L68_R0.805470.647
15_L40_L0.803850.646
45_I49_V0.789310.634
25_Y64_A0.781890.628
1_R30_T0.780440.627
27_D79_D0.777280.624
43_V49_V0.768980.618
70_F75_V0.763340.613
33_T37_L0.76270.613
43_V47_R0.762260.612
44_G49_V0.749260.602
6_Y9_E0.738960.593
47_R51_P0.737760.592
48_W53_R0.736970.592
25_Y48_W0.732610.588
10_W82_E0.728240.585
62_R67_E0.720420.579
74_W82_E0.72030.578
49_V53_R0.714040.573
23_Y70_F0.707740.568
77_F84_L0.69330.557
5_D36_I0.685330.550
59_R64_A0.673540.541
27_D48_W0.668660.537
47_R50_D0.667110.536
46_I64_A0.666670.535
6_Y82_E0.661210.531
15_L43_V0.658670.529
76_L82_E0.653190.525
66_I77_F0.652540.524
1_R28_G0.648020.520
70_F73_D0.64770.520
3_E7_L0.63120.507
6_Y83_F0.629560.506
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
3l7iA0.938199.30.056
2d7iA0.938199.20.107
2ffuA0.938199.20.111
1qg8A0.938199.20.112
3bcvA0.927899.20.125
1xhbA0.938199.20.133
2z86A0.927899.20.135
4fixA0.969199.10.165
3ckjA0.9381990.191
2z86A0.9485990.197

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