GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Gly_transf_sug - Glycosyltransferase sugar-binding region containing DXD motif
Pfam: PF04488 (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: 103
Sequences: 1177
Seq/Len: 11.43
HH_delta: 0.498 (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
37_I52_N0.662783.592
7_S10_S0.437282.370
18_Y80_I0.34811.886
9_E13_R0.343251.860
69_L73_V0.341421.850
72_L76_K0.315071.707
66_S70_R0.301381.633
47_F50_L0.29471.597
15_N92_L0.292321.584
23_W69_L0.29061.575
48_L52_N0.27331.481
21_I77_Y0.2661.441
6_C9_E0.264561.434
11_W82_L0.262931.425
10_S88_C0.257771.397
11_W88_C0.256881.392
44_T47_F0.247721.342
81_Y85_D0.241721.310
28_D51_Y0.241691.310
15_N88_C0.237851.289
18_Y94_D0.23311.263
91_P94_D0.224311.216
38_E42_E0.215911.170
21_I27_S0.211981.149
63_A67_D0.209041.133
84_L87_I0.203381.102
92_L96_W0.202881.099
80_I92_L0.202041.095
25_D65_K0.200571.087
10_S66_S0.197751.072
68_L75_Y0.197091.068
10_S14_H0.196731.066
15_N91_P0.196661.066
5_Q9_E0.19621.063
8_I20_Y0.195921.062
37_I41_F0.195191.058
86_V96_W0.192251.042
63_A85_D0.190291.031
6_C13_R0.189611.027
28_D69_L0.187611.017
47_F72_L0.18681.012
28_D72_L0.185251.004
23_W73_V0.184511.000
51_Y65_K0.184370.999
50_L68_L0.18330.993
49_E68_L0.183210.993
64_H67_D0.182680.990
88_C92_L0.181770.985
24_T27_S0.178680.968
9_E12_A0.178270.966
91_P95_P0.170710.925
38_E49_E0.170590.924
37_I74_L0.170390.923
25_D69_L0.170270.923
17_D91_P0.168890.915
11_W50_L0.167950.910
45_P59_Y0.166520.902
3_R85_D0.16520.895
59_Y68_L0.163290.885
20_Y71_Y0.162840.882
42_E52_N0.162430.880
20_Y89_L0.162120.879
63_A66_S0.160650.871
12_A20_Y0.160570.870
3_R7_S0.15860.859
5_Q8_I0.158560.859
25_D51_Y0.158160.857
7_S27_S0.156220.847
43_K76_K0.155330.842
74_L78_G0.155320.842
16_P90_R0.154520.837
22_L64_H0.153780.833
18_Y74_L0.151070.819
82_L86_V0.150960.818
81_Y89_L0.150660.816
49_E62_Y0.147450.799
46_W72_L0.147290.798
38_E52_N0.147110.797
5_Q13_R0.146680.795
63_A71_Y0.145110.786
25_D66_S0.144680.784
13_R16_P0.144640.784
38_E58_R0.142740.773
4_F84_L0.142050.770
12_A19_E0.140860.763
50_L94_D0.140560.762
45_P91_P0.140440.761
59_Y96_W0.139810.758
17_D77_Y0.139660.757
68_L71_Y0.138670.751
21_I69_L0.138090.748
44_T76_K0.137860.747
23_W77_Y0.137660.746
45_P48_L0.136940.742
71_Y74_L0.136930.742
27_S86_V0.136690.741
65_K80_I0.134850.731
11_W89_L0.133980.726
68_L72_L0.13350.723
50_L59_Y0.133280.722
12_A87_I0.132610.719
27_S69_L0.131880.715
15_N18_Y0.131810.714
19_E94_D0.131710.714
23_W64_H0.130950.710
21_I75_Y0.129930.704
10_S87_I0.129730.703
46_W80_I0.129590.702
16_P91_P0.129070.699
68_L85_D0.129060.699
82_L88_C0.128550.697
28_D73_V0.128280.695
21_I73_V0.127660.692
46_W60_P0.126920.688
39_F59_Y0.126510.686
65_K72_L0.12540.680
62_Y75_Y0.124960.677
65_K82_L0.124360.674
4_F15_N0.124110.673
82_L96_W0.123970.672
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
2vk9A0.970999.10.498
2bvlA0.9806990.511
4dmvA0.980698.90.533
3jszA0.951594.90.785
1ll2A0.951581.90.837
3u2uA0.951565.70.856
3tztA0.9417630.858
1g9rA0.951553.90.866
4akrB0.854413.40.9
2wmiA0.88358.40.908

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