GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF188 - Uncharacterized BCR YaiIYqxD family COG1671
Pfam: PF02639 (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: CL0280
Length: 130
Sequences: 657
Seq/Len: 5.05
HH_delta: 0.903 (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
44_Y48_H0.489653.725
64_S68_A0.363042.762
66_L71_A0.360762.745
66_L73_V0.351962.678
44_Y47_N0.295932.252
3_I15_F0.282512.149
11_I128_L0.278592.120
12_P30_E0.252281.919
58_Q76_P0.247971.887
75_N81_Y0.234031.781
49_A55_V0.233491.776
8_R125_D0.224691.710
72_Y127_L0.22281.695
113_T116_D0.213271.623
103_G106_T0.213131.622
43_F65_L0.211421.609
16_V41_A0.209731.596
112_F117_R0.206521.571
1_E117_R0.205741.565
1_E121_A0.203051.545
94_H98_K0.197291.501
49_A71_A0.19631.494
14_I30_E0.192741.466
32_I44_Y0.190841.452
68_A87_D0.188231.432
64_S90_L0.188051.431
67_L85_N0.187231.425
106_T109_P0.185021.408
10_G28_Y0.183261.394
118_Q122_N0.179351.365
55_V66_L0.179071.362
32_I48_H0.177331.349
114_K117_R0.175231.333
61_G90_L0.168931.285
6_A13_V0.167641.275
40_A43_F0.167321.273
46_V69_K0.161871.232
115_K119_R0.161821.231
58_Q75_N0.161561.229
2_I13_V0.15951.214
21_H31_M0.159161.211
21_H99_L0.156591.191
2_I15_F0.155711.185
5_V128_L0.153561.168
49_A66_L0.15281.163
67_L94_H0.151261.151
67_L95_L0.15051.145
119_R126_R0.148851.133
16_V45_I0.148761.132
99_L104_K0.147131.119
97_A101_R0.147011.119
35_D38_F0.146491.115
7_K27_P0.146111.112
72_Y80_E0.14591.110
47_N65_L0.141881.079
74_L124_L0.141341.075
18_N45_I0.141161.074
20_S31_M0.13951.061
102_A106_T0.138961.057
80_E123_A0.138211.052
56_I69_K0.137561.047
73_V81_Y0.136271.037
126_R129_Q0.135341.030
3_I29_V0.134771.025
16_V48_H0.132571.009
18_N97_A0.132071.005
1_E112_F0.131381.000
64_S87_D0.12950.985
123_A127_L0.128980.981
14_I48_H0.1280.974
92_M116_D0.127580.971
23_L31_M0.126770.965
41_A45_I0.125770.957
3_I24_P0.125250.953
4_R121_A0.124870.950
114_K119_R0.122520.932
101_R105_R0.122460.932
30_E35_D0.122430.931
39_D43_F0.121070.921
95_L118_Q0.119030.906
58_Q81_Y0.11690.889
15_F23_L0.116770.888
98_K102_A0.115730.881
51_P70_G0.115610.880
85_N88_E0.115560.879
87_D94_H0.114850.874
18_N34_V0.114790.873
86_I102_A0.111940.852
61_G94_H0.111840.851
65_L87_D0.111830.851
116_D119_R0.111690.850
77_R103_G0.111680.850
1_E118_Q0.111460.848
5_V121_A0.111420.848
75_N89_L0.111160.846
43_F47_N0.111110.845
6_A71_A0.110960.844
1_E5_V0.110810.843
72_Y130_R0.110790.843
18_N40_A0.110030.837
1_E9_Y0.109640.834
38_F46_V0.10910.830
67_L86_I0.10790.821
60_I96_M0.107550.818
93_R100_R0.107330.817
110_K127_L0.106940.814
14_I122_N0.106480.810
17_A74_L0.105790.805
9_Y125_D0.10570.804
27_P50_K0.105140.800
67_L83_K0.10490.798
108_G111_K0.104720.797
2_I56_I0.104550.795
74_L123_A0.103880.790
16_V44_Y0.103780.790
55_V71_A0.103550.788
16_V99_L0.10310.784
51_P74_L0.103080.784
80_E127_L0.10290.783
91_A98_K0.102580.780
77_R128_L0.102080.777
5_V118_Q0.101290.771
95_L99_L0.101280.771
5_V89_L0.101070.769
34_V100_R0.100830.767
81_Y85_N0.100350.764
85_N89_L0.099250.755
27_P110_K0.099140.754
118_Q121_A0.098820.752
49_A130_R0.098440.749
87_D91_A0.098420.749
91_A94_H0.09840.749
33_V128_L0.098310.748
75_N79_K0.097960.745
119_R123_A0.097960.745
37_G40_A0.097920.745
87_D95_L0.097670.743
54_I89_L0.097410.741
88_E92_M0.097380.741
46_V66_L0.097150.739
60_I89_L0.096250.732
46_V52_G0.095090.723
30_E51_P0.095010.723
2_I38_F0.094950.722
34_V44_Y0.094520.719
12_P28_Y0.094280.717
67_L72_Y0.094050.716
20_S99_L0.093570.712
15_F31_M0.093430.711
65_L101_R0.093280.710
46_V55_V0.092880.707
45_I57_T0.092570.704
25_R92_M0.09240.703
17_A60_I0.090980.692
121_A125_D0.090690.690
19_Y23_L0.090640.690
54_I80_E0.090450.688
125_D129_Q0.090330.687
46_V56_I0.090320.687
1_E98_K0.090310.687
17_A76_P0.089940.684
6_A124_L0.089720.683
57_T73_V0.089690.682
92_M95_L0.089680.682
51_P72_Y0.089630.682
73_V90_L0.089410.680
6_A66_L0.089410.680
11_I69_K0.08920.679
60_I101_R0.089040.677
60_I90_L0.088990.677
80_E126_R0.088430.673
17_A37_G0.088070.670
60_I77_R0.087780.668
32_I46_V0.087750.668
43_F113_T0.087680.667
49_A70_G0.087640.667
3_I130_R0.087120.663
2_I69_K0.086990.662
91_A95_L0.086940.661
1_E85_N0.086120.655
1_E11_I0.086120.655
77_R96_M0.086040.655
16_V49_A0.086030.655
123_A126_R0.085530.651
63_A81_Y0.085380.650
68_A130_R0.08530.649
18_N21_H0.084670.644
113_T126_R0.084520.643
41_A93_R0.084460.643
54_I128_L0.084440.642
10_G115_K0.084310.641
27_P71_A0.084210.641
65_L91_A0.084180.640
88_E91_A0.084170.640
54_I127_L0.084030.639
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
1o4wA0.638591.10.903
3i8oA0.607790.50.905
1bgxT0.823190.10.905
2vpqA0.946286.60.911
3hblA0.946284.30.914
3n6rA0.946280.90.917
2hwjA0.969280.70.917
2izoA0.953880.30.917
2dzdA0.9462780.919
3u9tA0.946277.90.919
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