GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glyco_hydro_16 - Glycosyl hydrolases family 16
Pfam: PF00722 (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: CL0004
Length: 185
Sequences: 2321
Seq/Len: 12.55
HH_delta: 0.141 (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
121_H137_D1.157826.065
52_A66_F0.808114.233
135_Y140_L0.746493.910
133_R140_L0.735983.855
140_L143_T0.679763.561
51_E124_G0.583023.054
49_R124_G0.578373.030
49_R126_E0.553622.900
15_T25_R0.527932.765
54_I66_F0.510552.674
53_R122_T0.489282.563
131_R143_T0.454352.380
14_V37_G0.420662.204
94_T141_V0.415882.178
45_F50_F0.405132.122
125_F132_I0.3872.027
133_R143_T0.369181.934
14_V39_I0.366631.921
79_E83_E0.347151.818
124_G135_Y0.332161.740
88_D91_Q0.328171.719
17_E23_V0.322031.687
126_E133_R0.307281.610
131_R145_T0.303651.591
116_P123_Y0.302821.586
23_V180_E0.294921.545
94_T134_F0.288061.509
122_T138_G0.287951.508
55_K120_F0.286071.499
92_V136_I0.284061.488
126_E135_Y0.282191.478
75_P78_G0.279931.466
80_I132_I0.278351.458
21_N180_E0.277851.455
13_N35_T0.270411.416
120_F180_E0.264821.387
55_K180_E0.263811.382
27_D35_T0.257331.348
55_K119_D0.254911.335
123_Y136_I0.252111.321
85_L167_W0.249451.307
50_F68_L0.24851.302
51_E122_T0.243351.275
161_N165_G0.241281.264
135_Y138_G0.237991.247
47_Y127_W0.234261.227
167_W170_G0.23281.219
17_E21_N0.232091.216
107_E110_V0.229621.203
38_E67_W0.225011.179
134_F144_V0.223951.173
173_A176_A0.219371.149
159_P163_A0.217241.138
93_Q167_W0.216041.132
47_Y129_P0.21371.119
49_R135_Y0.211021.105
172_W175_P0.210771.104
51_E135_Y0.208251.091
63_W67_W0.206191.080
158_T161_N0.199521.045
13_N16_V0.196071.027
128_T133_R0.195111.022
53_R182_D0.193171.012
64_P75_P0.191841.005
158_T165_G0.19141.003
63_W85_L0.190660.999
159_P165_G0.190360.997
16_V19_G0.189640.993
169_G181_V0.189530.993
66_F164_L0.188460.987
106_W109_R0.187260.981
115_D118_T0.184110.964
50_F66_F0.183790.963
102_G105_N0.183690.962
57_P64_P0.183540.961
176_A182_D0.182760.957
44_S161_N0.181940.953
106_W112_L0.179970.943
26_A162_L0.179070.938
68_L125_F0.179040.938
85_L93_Q0.178350.934
66_F82_I0.178290.934
99_N103_D0.177340.929
68_L156_F0.176440.924
166_L170_G0.17460.915
58_P117_S0.173660.910
24_L39_I0.172560.904
108_K111_P0.171530.899
21_N120_F0.168150.881
69_T77_G0.167580.878
158_T163_A0.166340.871
98_W101_D0.166210.871
160_M163_A0.163060.854
46_K155_P0.161380.845
107_E111_P0.16070.842
115_D119_D0.160630.841
113_G116_P0.159270.834
61_G65_A0.158760.832
124_G138_G0.157710.826
161_N164_L0.156960.822
99_N102_G0.156860.822
67_W165_G0.156130.818
60_P87_N0.155690.816
18_D23_V0.15540.814
109_R112_L0.154780.811
78_G97_H0.154610.810
14_V22_L0.154220.808
18_D21_N0.152720.800
96_V134_F0.152510.799
15_T23_V0.151680.795
56_A84_F0.149490.783
63_W78_G0.148380.777
65_A83_E0.147430.772
145_T148_D0.147410.772
62_V166_L0.147290.772
49_R122_T0.145610.763
160_M165_G0.145430.762
76_D99_N0.14520.761
59_G62_V0.144310.756
24_L38_E0.144240.756
50_F125_F0.14380.753
154_Y160_M0.14340.751
69_T163_A0.143130.750
53_R120_F0.14220.745
19_G22_L0.141360.740
28_K34_Y0.140930.738
150_P153_P0.140010.733
55_K118_T0.139910.733
168_P171_D0.138360.725
128_T131_R0.137730.721
21_N53_R0.137540.720
107_E112_L0.13710.718
17_E180_E0.136180.713
82_I125_F0.135810.711
134_F141_V0.135120.708
45_F68_L0.135090.708
109_R113_G0.135040.707
45_F75_P0.135040.707
106_W113_G0.134910.707
70_G142_R0.134240.703
93_Q109_R0.133550.700
146_N154_Y0.133530.699
89_P183_W0.133520.699
65_A163_A0.133410.699
164_L167_W0.133330.698
80_I96_V0.132980.697
50_F158_T0.132760.695
64_P161_N0.132510.694
67_W83_E0.132180.692
58_P89_P0.131040.686
96_V108_K0.130830.685
125_F134_F0.130270.682
48_G127_W0.129240.677
68_L80_I0.128350.672
95_N107_E0.128340.672
38_E165_G0.128110.671
11_P37_G0.127950.670
22_L49_R0.127550.668
12_D18_D0.127470.668
101_D153_P0.127290.667
147_S150_P0.126820.664
106_W110_V0.126740.664
87_N90_T0.126510.663
126_E140_L0.125780.659
38_E85_L0.125630.658
40_Q122_T0.125620.658
67_W81_D0.124870.654
98_W149_V0.124060.650
84_F87_N0.123140.645
86_G116_P0.122520.642
24_L45_F0.122350.641
17_E25_R0.122240.640
96_V144_V0.121950.639
68_L82_I0.121670.637
37_G40_Q0.121210.635
65_A81_D0.121110.634
65_A69_T0.121090.634
63_W75_P0.120030.629
82_I143_T0.119870.628
106_W111_P0.11940.625
13_N25_R0.11930.625
90_T115_D0.119210.624
86_G142_R0.118850.623
148_D156_F0.118770.622
113_G119_D0.118570.621
62_V162_L0.118550.621
94_T142_R0.118330.620
126_E131_R0.118310.620
95_N141_V0.118130.619
12_D17_E0.118010.618
170_G173_A0.117320.615
22_L75_P0.116850.612
165_G172_W0.116850.612
67_W163_A0.116750.612
36_S163_A0.116510.610
175_P181_V0.116450.610
83_E95_N0.116040.608
86_G123_Y0.115990.608
87_N168_P0.115930.607
49_R183_W0.115780.606
80_I156_F0.115620.606
63_W169_G0.115530.605
51_E64_P0.114870.602
40_Q161_N0.114670.601
90_T112_L0.11460.600
12_D149_V0.114370.599
33_P113_G0.11410.598
69_T75_P0.114060.597
149_V154_Y0.1140.597
80_I125_F0.113720.596
92_V141_V0.113270.593
69_T161_N0.113080.592
56_A64_P0.113020.592
86_G89_P0.112890.591
26_A166_L0.112780.591
154_Y165_G0.112550.590
121_H136_I0.112360.589
171_D175_P0.112240.588
65_A79_E0.112110.587
69_T76_D0.112090.587
42_K45_F0.111990.587
101_D104_S0.111590.585
47_Y80_I0.111390.583
131_R139_K0.111230.583
149_V153_P0.110920.581
112_L115_D0.110810.580
40_Q44_S0.110590.579
38_E134_F0.110450.579
64_P169_G0.110050.576
38_E78_G0.109960.576
130_D146_N0.109340.573
64_P67_W0.108870.570
85_L168_P0.108790.570
101_D105_N0.108790.570
67_W82_I0.108550.569
24_L92_V0.108530.569
101_D139_K0.108480.568
85_L116_P0.108450.568
132_I154_Y0.107720.564
108_K142_R0.10760.564
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
3o5sA0.95141000.141
3ilnA0.98921000.152
3i4iA0.94591000.156
2hykA11000.181
2ayhA0.94591000.183
2uwaA0.95141000.187
1umzA0.95141000.191
3juuA0.96761000.204
4awdA0.98381000.207
3rq0A0.93511000.221

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