GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Sialidase - Sialidase N-terminal domain
Pfam: PF02973 (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: 190
Sequences: 3125
Seq/Len: 16.45
HH_delta: 0.297 (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
106_N124_N0.993264.844
40_R107_T0.733513.577
175_R181_E0.729523.557
120_K127_L0.686323.347
102_N106_N0.666823.252
38_V109_A0.640413.123
42_K166_T0.578012.819
178_S181_E0.576992.814
173_Y177_L0.497132.424
42_K105_F0.472782.306
127_L130_T0.432242.108
38_V107_T0.427762.086
38_V171_K0.422442.060
34_E113_D0.409641.998
109_A182_L0.405191.976
39_I170_L0.396351.933
41_F108_V0.375691.832
43_S106_N0.344011.678
40_R168_D0.343761.676
43_S163_F0.343571.675
40_R169_N0.342221.669
38_V177_L0.33651.641
113_D116_N0.324521.583
40_R105_F0.318961.555
152_G162_P0.312621.524
44_D164_N0.303621.481
163_F167_I0.301631.471
39_I52_L0.299971.463
149_Q152_G0.288661.408
111_V176_A0.286731.398
39_I108_V0.286581.398
101_N106_N0.284791.389
177_L182_L0.281891.375
76_F110_F0.281851.374
41_F52_L0.27771.354
120_K130_T0.274961.341
179_D182_L0.261871.277
51_S54_S0.251991.229
122_Y127_L0.24581.199
118_G130_T0.242841.184
55_I144_G0.236241.152
178_S182_L0.233111.137
68_Y75_G0.231931.131
101_N104_T0.230541.124
171_K177_L0.225621.100
43_S101_N0.220141.074
111_V122_Y0.219331.070
39_I67_L0.21481.047
104_T124_N0.214681.047
110_F119_Y0.214111.044
36_T109_A0.212651.037
177_L181_E0.210771.028
150_I170_L0.203450.992
74_L108_V0.201880.984
53_F170_L0.199450.973
70_S75_G0.197940.965
43_S102_N0.196920.960
38_V173_Y0.196340.957
155_R160_A0.196310.957
105_F168_D0.196270.957
34_E112_A0.195470.953
63_E66_S0.1910.931
102_N124_N0.19080.930
111_V120_K0.190280.928
36_T122_Y0.187040.912
67_L76_F0.186480.909
35_G112_A0.186070.907
53_F65_F0.185210.903
38_V169_N0.184340.899
76_F119_Y0.182290.889
36_T111_V0.181130.883
41_F106_N0.18070.881
150_I167_I0.17960.876
112_A117_K0.176720.862
40_R109_A0.176460.861
36_T182_L0.17210.839
67_L110_F0.17150.836
36_T176_A0.170040.829
42_K104_T0.169440.826
112_A119_Y0.169420.826
109_A125_G0.169310.826
123_V128_V0.169150.825
55_I65_F0.168450.821
142_I172_I0.168140.820
37_I53_F0.166540.812
51_S154_N0.165080.805
37_I172_I0.165070.805
105_F166_T0.164760.803
111_V182_L0.162750.794
122_Y173_Y0.162460.792
98_G126_E0.161780.789
34_E117_K0.161340.787
107_T169_N0.159880.780
41_F74_L0.159570.778
58_S78_L0.158890.775
49_I70_S0.158190.771
107_T125_G0.157880.770
68_Y174_N0.157350.767
67_L121_L0.156490.763
54_S66_S0.155980.761
59_T143_P0.15370.750
106_N123_V0.153580.749
36_T173_Y0.153290.748
107_T182_L0.153210.747
46_N102_N0.153010.746
80_D138_F0.152960.746
109_A173_Y0.152630.744
44_D103_V0.151570.739
113_D117_K0.151160.737
124_N152_G0.149860.731
79_R119_Y0.149760.730
41_F100_K0.149360.728
54_S149_Q0.149320.728
111_V118_G0.148890.726
37_I170_L0.148770.725
32_L35_G0.148760.725
127_L179_D0.148730.725
72_N180_E0.14790.721
69_V74_L0.14770.720
50_Q53_F0.146910.716
108_V123_V0.146630.715
110_F121_L0.145550.710
76_F107_T0.145290.709
80_D83_G0.144750.706
121_L129_S0.144730.706
53_F148_V0.144220.703
109_A122_Y0.143450.700
134_K167_I0.142640.696
39_I150_I0.142090.693
147_S156_A0.141370.689
72_N103_V0.140560.685
134_K156_A0.139590.681
54_S154_N0.139340.679
54_S146_N0.138840.677
134_K138_F0.138090.673
118_G132_S0.138070.673
122_Y125_G0.137360.670
152_G166_T0.136250.664
58_S145_L0.136150.664
55_I147_S0.136030.663
56_S155_R0.135990.663
55_I148_V0.135760.662
109_A177_L0.135680.662
100_K106_N0.135590.661
108_V166_T0.135530.661
50_Q79_R0.1330.649
54_S148_V0.132710.647
47_S71_N0.132550.646
50_Q58_S0.132110.644
100_K123_V0.131840.643
51_S66_S0.131610.642
149_Q154_N0.13130.640
33_E128_V0.131170.640
127_L131_L0.130740.638
49_I57_N0.130440.636
41_F163_F0.130060.634
119_Y133_S0.129840.633
39_I167_I0.12930.631
63_E153_T0.129260.630
121_L131_L0.128930.629
42_K103_V0.12790.624
131_L179_D0.126950.619
78_L85_Q0.126870.619
43_S69_V0.126650.618
111_V179_D0.126130.615
49_I161_Y0.126130.615
66_S69_V0.125390.611
175_R178_S0.125290.611
57_N121_L0.124640.608
83_G135_S0.124550.607
52_L163_F0.124480.607
63_E68_Y0.124420.607
64_Y77_E0.124410.607
156_A160_A0.124050.605
70_S104_T0.123920.604
65_F68_Y0.123380.602
52_L69_V0.123340.601
54_S152_G0.121960.595
55_I146_N0.121460.592
166_T173_Y0.121340.592
45_S128_V0.120550.588
66_S155_R0.120530.588
36_T125_G0.120170.586
49_I54_S0.119980.585
176_A182_L0.119820.584
145_L149_Q0.119650.583
160_A180_E0.119290.582
40_R166_T0.119140.581
52_L74_L0.119020.580
119_Y131_L0.118420.577
82_K159_N0.118380.577
77_E172_I0.118040.576
56_S128_V0.117760.574
84_N159_N0.117750.574
131_L153_T0.117470.573
54_S162_P0.117280.572
128_V156_A0.117180.571
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
2sliA0.989599.80.297
2v73A0.957999.80.323
2jkbA0.994799.80.324
3pvnA0.894799.80.341
3flpA0.915899.80.345
4avsA0.889599.80.348
3kqrA0.889599.80.348
4dqaA0.873799.80.364
1a8dA0.931699.60.458
2nyyA0.936899.50.485

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