GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Polysacc_deac_1 - Polysaccharide deacetylase
Pfam: PF01522 (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: CL0158
Length: 123
Sequences: 7639
Seq/Len: 62.11
HH_delta: -0.016 (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
28_K56_A2.164753.344
40_G65_W1.524732.356
52_E56_A1.479352.286
86_R120_Y1.374622.124
74_S77_E1.353222.091
80_R84_R1.307672.020
75_P110_N1.261711.949
65_W84_R1.247051.927
79_R117_E1.23791.913
90_E96_P1.232071.904
83_E118_A1.13491.753
26_L30_Y1.129181.745
62_N85_S1.125181.738
63_H67_H1.085461.677
38_V50_L1.041031.608
37_F101_R1.033091.596
54_A95_R1.021861.579
69_N104_F1.010241.561
66_S81_E0.996771.540
98_K121_K0.988541.527
78_L111_T0.978751.512
47_P92_I0.943211.457
69_N106_S0.921021.423
62_N86_R0.917131.417
83_E87_E0.911681.409
27_L34_A0.903871.396
87_E91_E0.903231.395
79_R118_A0.889831.375
79_R83_E0.887691.371
37_F61_G0.877221.355
21_D52_E0.867241.340
36_F58_H0.849081.312
34_A58_H0.846671.308
75_P79_R0.819241.266
65_W88_I0.812021.255
73_L77_E0.810591.252
51_R55_A0.79461.228
38_V53_L0.790161.221
9_A35_T0.789811.220
86_R96_P0.783751.211
44_E88_I0.779541.204
35_T61_G0.778831.203
86_R90_E0.776961.200
37_F99_G0.762711.178
107_Y112_L0.754641.166
25_P52_E0.748541.156
59_E99_G0.735521.136
114_A117_E0.732971.132
108_D111_T0.721741.115
25_P29_K0.721521.115
75_P113_Q0.720351.113
115_L120_Y0.713021.102
71_S106_S0.701061.083
84_R87_E0.697911.078
43_V50_L0.692171.069
79_R114_A0.688651.064
100_F115_L0.688021.063
82_I115_L0.687081.062
48_D51_R0.683081.055
88_I91_E0.682581.055
62_N120_Y0.668971.034
88_I92_I0.665551.028
113_Q117_E0.658821.018
52_E55_A0.65691.015
68_P81_E0.649151.003
51_R92_I0.644710.996
114_A118_A0.641650.991
20_Y24_L0.641120.991
78_L114_A0.640890.990
64_G100_F0.640670.990
24_L58_H0.639040.987
20_Y49_Q0.636750.984
26_L29_K0.634950.981
40_G85_S0.62790.970
22_R25_P0.619220.957
36_F53_L0.617060.953
67_H103_P0.615690.951
39_I64_G0.61350.948
35_T59_E0.60880.941
54_A60_I0.603490.932
112_L116_R0.600340.928
24_L53_L0.599980.927
14_D63_H0.599550.926
21_D49_Q0.597850.924
64_G68_P0.596420.921
26_L32_I0.593790.917
12_F27_L0.592850.916
107_Y111_T0.59060.912
24_L28_K0.590.912
24_L56_A0.58620.906
101_R105_G0.586110.906
11_T101_R0.582140.899
33_P58_H0.579690.896
78_L110_N0.577430.892
86_R97_P0.561940.868
89_L97_P0.561150.867
21_D25_P0.561070.867
51_R54_A0.556810.860
90_E97_P0.552710.854
39_I42_W0.548180.847
83_E86_R0.539070.833
75_P117_E0.536770.829
22_R26_L0.533020.824
28_K58_H0.532180.822
77_E80_R0.530550.820
38_V60_I0.523820.809
80_R83_E0.516070.797
54_A93_T0.513310.793
61_G99_G0.51170.791
75_P114_A0.507890.785
68_P73_L0.485770.751
76_E80_R0.482670.746
41_S65_W0.481540.744
19_N22_R0.480690.743
111_T114_A0.478830.740
17_R49_Q0.472790.730
87_E90_E0.467620.722
109_D113_Q0.465070.719
102_Y107_Y0.460580.712
77_E81_E0.459240.710
92_I95_R0.454660.702
62_N82_I0.451560.698
14_D67_H0.441620.682
69_N72_T0.436610.675
24_L52_E0.433550.670
47_P51_R0.426680.659
70_L100_F0.426140.658
43_V47_P0.425380.657
102_Y105_G0.418370.646
110_N113_Q0.416570.644
19_N36_F0.416190.643
44_E47_P0.416090.643
39_I85_S0.414450.640
89_L93_T0.414340.640
50_L53_L0.409250.632
40_G88_I0.408360.631
9_A59_E0.406870.629
49_Q52_E0.405410.626
64_G70_L0.404440.625
10_L27_L0.399830.618
81_E84_R0.398770.616
16_Y42_W0.397880.615
13_D63_H0.395130.610
47_P88_I0.394370.609
41_S66_S0.39430.609
53_L60_I0.393730.608
84_R88_I0.392840.607
70_L78_L0.391880.605
53_L58_H0.389920.602
10_L32_I0.38310.592
39_I63_H0.380830.588
25_P56_A0.380140.587
65_W85_S0.378020.584
82_I100_F0.376560.582
19_N23_L0.375250.580
14_D39_I0.37490.579
73_L81_E0.363580.562
61_G101_R0.36230.560
50_L93_T0.361760.559
90_E93_T0.361730.559
102_Y115_L0.353070.545
12_F34_A0.349370.540
18_D21_D0.34830.538
60_I93_T0.346440.535
17_R21_D0.344910.533
70_L111_T0.342370.529
15_G104_F0.340550.526
109_D112_L0.339980.525
62_N100_F0.339240.524
10_L34_A0.33620.519
12_F23_L0.33560.518
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
2y8uA199.9-0.016
2iw0A199.9-0.013
2cc0A0.991999.9-0.01
2j13A199.9-0
1ny1A199.90.003
2vyoA199.90.008
2w3zA199.90.03
2c1iA0.975699.90.034
4f9dA199.90.055
2c71A0.983799.90.062

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