GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PIG-L - GlcNAc-PI de-N-acetylase
Pfam: PF02585 (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. )
Length: 128
Sequences: 2480
Seq/Len: 19.38
HH_delta: 0.073 (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
60_A63_E0.90833.218
33_L120_V0.842412.985
75_F91_D0.80112.838
29_V99_F0.795892.820
3_I124_V0.71712.541
2_V18_I0.711842.522
29_V71_I0.652582.312
20_K24_A0.649022.299
21_L26_H0.591412.095
11_E61_A0.590662.093
29_V69_N0.54791.941
35_D55_R0.537381.904
119_A122_R0.530441.879
31_V95_L0.51611.829
71_I98_E0.490761.739
5_A107_P0.479821.700
106_T124_V0.478141.694
118_R122_R0.450331.595
88_L123_A0.446761.583
56_A59_R0.436341.546
14_C105_F0.428191.517
32_T58_A0.426311.510
21_L105_F0.417811.480
89_V126_E0.410541.455
73_L91_D0.408221.446
93_E97_R0.407051.442
1_L96_I0.405271.436
2_V10_E0.405161.435
27_R68_E0.404711.434
8_D114_H0.404611.434
17_T21_L0.403171.428
56_A60_A0.393681.395
27_R69_N0.389021.378
55_R74_D0.368571.306
3_I31_V0.360021.276
55_R59_R0.355471.259
18_I65_L0.354921.257
4_A107_P0.348021.233
71_I95_L0.347711.232
19_A65_L0.338271.198
1_L31_V0.33381.183
18_I22_A0.332841.179
37_E51_G0.327591.161
10_E58_A0.327331.160
94_D98_E0.326651.157
95_L99_F0.324731.151
54_R77_D0.319531.132
62_A70_V0.316941.123
22_A28_V0.31611.120
13_G16_G0.306951.088
2_V105_F0.29791.055
31_V92_L0.296881.052
52_E56_A0.294161.042
71_I99_F0.293751.041
30_V62_A0.292861.038
108_D111_D0.29041.029
11_E58_A0.288731.023
40_H50_L0.286441.015
59_R70_V0.280610.994
3_I33_L0.276640.980
104_V124_V0.274490.973
92_L123_A0.266090.943
80_L116_D0.265530.941
19_A23_E0.262620.930
96_I104_V0.261930.928
89_V93_E0.261230.926
77_D116_D0.259360.919
87_E91_D0.25820.915
15_G19_A0.256920.910
106_T121_A0.256250.908
7_P10_E0.25450.902
4_A10_E0.253140.897
87_E90_R0.252990.896
91_D94_D0.252450.894
49_E52_E0.250730.888
60_A64_I0.24960.884
69_N99_F0.248360.880
9_D117_H0.248340.880
33_L92_L0.246560.874
89_V127_A0.244620.867
27_R102_D0.244210.865
10_E30_V0.243750.864
95_L98_E0.242150.858
76_P79_Q0.241580.856
18_I28_V0.241160.854
59_R63_E0.240490.852
109_P121_A0.233840.828
1_L99_F0.232240.823
6_H9_D0.228530.810
59_R72_F0.225860.800
19_A22_A0.22560.799
97_R100_R0.22550.799
55_R72_F0.225460.799
107_P111_D0.222140.787
35_D74_D0.221690.785
8_D117_H0.219550.778
86_E90_R0.219540.778
114_H117_H0.216820.768
7_P36_G0.215470.763
57_E77_D0.215450.763
39_G77_D0.21540.763
111_D118_R0.213370.756
22_A68_E0.212970.755
91_D95_L0.212220.752
33_L73_L0.211050.748
61_A65_L0.210080.744
85_W119_A0.209380.742
38_A79_Q0.207780.736
36_G54_R0.206520.732
90_R94_D0.205110.727
26_H105_F0.204090.723
1_L95_L0.203920.722
1_L101_P0.200140.709
32_T70_V0.199550.707
8_D54_R0.198770.704
38_A76_P0.197760.701
108_D118_R0.196250.695
13_G108_D0.19620.695
32_T72_F0.19580.694
58_A72_F0.195610.693
62_A67_V0.194860.690
25_G28_V0.193830.687
57_E114_H0.193740.686
12_L58_A0.193330.685
85_W122_R0.191520.679
85_W89_V0.190750.676
85_W126_E0.18990.673
4_A13_G0.187760.665
17_T105_F0.186940.662
16_G19_A0.18540.657
36_G39_G0.185130.656
54_R57_E0.18470.654
5_A13_G0.183870.651
119_A123_A0.183830.651
121_A125_R0.183810.651
4_A30_V0.183770.651
11_E15_G0.183350.650
3_I120_V0.183020.648
111_D121_A0.182240.646
89_V98_E0.181960.645
85_W88_L0.181540.643
82_G85_W0.181030.641
3_I92_L0.180730.640
16_G116_D0.177020.627
15_G65_L0.176160.624
10_E32_T0.176140.624
36_G77_D0.175830.623
16_G20_K0.174420.618
33_L88_L0.174380.618
96_I101_P0.173780.616
18_I62_A0.173710.615
1_L29_V0.173470.615
93_E127_A0.171510.608
6_H117_H0.171180.606
30_V67_V0.168650.598
26_H102_D0.168080.595
34_T80_L0.1680.595
52_E55_R0.167170.592
112_G118_R0.167030.592
20_K23_E0.165740.587
37_E76_P0.16560.587
92_L95_L0.165390.586
11_E65_L0.164820.584
103_V106_T0.164640.583
118_R121_A0.162710.576
120_V124_V0.162690.576
41_P82_G0.162490.576
87_E98_E0.162130.574
75_F88_L0.161490.572
30_V65_L0.161420.572
41_P49_E0.160040.567
4_A32_T0.160020.567
15_G22_A0.15920.564
93_E126_E0.158550.562
88_L91_D0.158480.561
13_G111_D0.158390.561
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
2ixdA0.92191000.073
1uanA0.92191000.081
1q74A11000.095
3dfiA0.99221000.102
3dffA0.99221000.103
3ih5A0.789190.70.854
1efvA0.765689.80.857
1o97D0.773487.40.863
3ot5A0.812577.50.877
2x6qA0.773476.10.878

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