GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cass2 - Integron-associated effector binding protein
Pfam: PF14526 (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: CL0319
Length: 150
Sequences: 2476
Seq/Len: 16.51
HH_delta: 0.09 (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
7_S86_E0.644983.344
97_V108_A0.590233.060
4_E91_K0.506282.625
7_S89_A0.48712.526
9_T84_I0.48482.514
14_R65_D0.450542.336
96_T145_E0.429282.226
3_V94_V0.409892.125
109_W146_I0.390312.024
52_G66_Y0.386882.006
56_D65_D0.383341.988
94_V147_Y0.37961.968
91_K123_Y0.367921.908
9_T86_E0.365871.897
95_F112_I0.36541.895
3_V147_Y0.348581.807
93_A115_W0.343641.782
67_E85_I0.341071.768
131_F147_Y0.329161.707
93_A116_F0.328791.705
4_E89_A0.316161.639
8_F87_I0.315691.637
116_F121_N0.313051.623
55_H67_E0.312981.623
103_E107_E0.309661.606
10_V69_G0.309121.603
98_K143_E0.29731.542
12_G67_E0.293761.523
133_V145_E0.293171.520
123_Y150_I0.290921.508
118_E121_N0.287541.491
95_F108_A0.275131.427
15_V34_E0.275081.426
11_I82_F0.274231.422
108_A146_I0.264581.372
128_G149_P0.262981.364
101_Y144_V0.256481.330
31_L68_V0.255481.325
114_E118_E0.251891.306
99_G144_V0.250921.301
92_Y131_F0.24871.290
2_I93_A0.247151.281
54_Y66_Y0.247091.281
12_G85_I0.244871.270
3_V145_E0.243841.264
90_G126_A0.243391.262
16_R63_D0.240421.247
113_W125_R0.23771.232
107_E110_Q0.234911.218
52_G68_V0.234411.215
14_R67_E0.232231.204
16_R65_D0.230451.195
137_D140_E0.229681.191
10_V85_I0.226191.173
7_S88_P0.22411.162
117_E121_N0.221781.150
34_E81_G0.221531.149
1_E94_V0.220721.144
96_T143_E0.218441.133
14_R83_V0.2151.115
133_V147_Y0.214511.112
115_W118_E0.214341.111
5_L8_F0.213041.105
97_V103_E0.211861.099
2_I91_K0.211551.097
109_W130_D0.210851.093
30_E33_Q0.209671.087
94_V145_E0.207081.074
38_E82_F0.206261.069
31_L35_F0.204811.062
13_I31_L0.203041.053
110_Q114_E0.200611.040
9_T75_D0.197061.022
112_I148_I0.196551.019
5_L92_Y0.196511.019
19_N64_Y0.195921.016
60_Y63_D0.19541.013
116_F123_Y0.193271.002
49_P133_V0.191410.992
11_I72_V0.18930.982
32_W68_V0.189280.981
13_I82_F0.188020.975
29_G132_E0.186930.969
49_P71_P0.183380.951
100_P103_E0.1820.944
111_K115_W0.18180.943
137_D142_Y0.181220.940
13_I34_E0.179750.932
51_Y69_G0.178150.924
17_T28_I0.176890.917
125_R130_D0.17370.901
101_Y134_Y0.173260.898
88_P91_K0.171880.891
109_W148_I0.170020.882
91_K150_I0.16990.881
48_G71_P0.169530.879
2_I150_I0.167610.869
109_W132_E0.165830.860
88_P129_P0.165280.857
79_P82_F0.164370.852
135_P145_E0.164360.852
6_P89_A0.163120.846
17_T58_E0.16250.843
136_E142_Y0.160510.832
112_I146_I0.160460.832
92_Y147_Y0.159630.828
13_I35_F0.158810.823
53_V69_G0.15810.820
18_P63_D0.157840.818
88_P128_G0.156850.813
17_T57_Y0.155950.809
2_I123_Y0.155620.807
32_W52_G0.155620.807
115_W121_N0.154840.803
97_V109_W0.152240.789
34_E38_E0.151980.788
78_V81_G0.15150.786
29_G33_Q0.150590.781
41_L44_I0.148890.772
113_W117_E0.148240.769
17_T65_D0.148220.769
5_L131_F0.146960.762
12_G83_V0.146760.761
101_Y142_Y0.146670.760
37_K41_L0.146090.757
64_Y113_W0.145870.756
30_E55_H0.145610.755
32_W66_Y0.144850.751
55_H65_D0.144720.750
36_F70_V0.144030.747
35_F39_G0.14390.746
117_E125_R0.143720.745
13_I81_G0.142920.741
59_S63_D0.142160.737
132_E146_I0.141490.734
38_E42_P0.1410.731
97_V144_V0.137910.715
97_V102_P0.137670.714
13_I37_K0.137270.712
54_Y64_Y0.13680.709
52_G105_I0.136750.709
51_Y71_P0.136590.708
58_E65_D0.136550.708
32_W95_F0.133580.693
33_Q37_K0.133250.691
87_I92_Y0.132420.687
10_V20_Y0.132160.685
11_I57_Y0.132140.685
75_D105_I0.131850.684
111_K116_F0.131720.683
54_Y109_W0.13120.680
91_K121_N0.130560.677
54_Y67_E0.129760.673
129_P149_P0.128490.666
97_V105_I0.128230.665
99_G105_I0.127670.662
35_F51_Y0.127060.659
35_F68_V0.1270.659
8_F69_G0.126520.656
95_F148_I0.125760.652
33_Q36_F0.125730.652
50_I54_Y0.125570.651
52_G132_E0.125350.650
98_K141_N0.125110.649
39_G70_V0.124170.644
54_Y130_D0.123930.643
32_W112_I0.123520.640
66_Y132_E0.123470.640
126_A150_I0.123250.639
35_F66_Y0.122690.636
97_V100_P0.122490.635
113_W148_I0.122170.633
30_E75_D0.121970.632
54_Y132_E0.121880.632
134_Y139_S0.121840.632
126_A149_P0.121210.628
35_F90_G0.120440.624
18_P89_A0.120230.623
101_Y138_P0.120060.623
107_E111_K0.119450.619
116_F125_R0.118460.614
17_T66_Y0.116910.606
5_L147_Y0.116690.605
35_F70_V0.116230.603
57_Y62_G0.116010.602
37_K45_K0.115720.600
32_W134_Y0.11570.600
87_I116_F0.115380.598
32_W64_Y0.11520.597
10_V67_E0.114910.596
14_R18_P0.114620.594
50_I71_P0.114290.593
16_R30_E0.113690.589
45_K98_K0.113690.589
19_N105_I0.113540.589
75_D84_I0.113210.587
35_F92_Y0.112440.583
75_D79_P0.112440.583
93_A112_I0.112430.583
9_T74_E0.112410.583
97_V142_Y0.11240.583
17_T64_Y0.112360.583
111_K114_E0.11190.580
95_F116_F0.111390.578
39_G68_V0.111330.577
35_F38_E0.11120.577
112_I130_D0.110920.575
135_P138_P0.109970.570
32_W51_Y0.109690.569
50_I56_D0.109060.565
58_E71_P0.108740.564
18_P61_E0.108180.561
125_R150_I0.108180.561
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
3gk6A0.946799.90.09
1d5yA0.9699.80.127
3e0hA0.946799.80.132
3lurA0.966799.80.139
1jyhA0.946799.80.194
3b49A0.953399.60.276
1r8eA0.933399.60.278
3e0hA0.4696.20.758
3b49A0.446795.50.771
1r8eA0.453394.20.789

Page generated in 0.0494 seconds.