GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF208 - Uncharacterized BCR COG1636
Pfam: PF02677 (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: 176
Sequences: 2870
Seq/Len: 16.31
HH_delta: 0.415 (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
49_R53_K0.510612.595
26_T59_I0.469032.384
48_K52_E0.46842.381
138_F142_D0.456682.321
16_E20_E0.442072.247
45_E49_R0.433742.204
99_Y103_L0.420492.137
95_K98_Q0.41632.116
18_L109_T0.411222.090
129_R133_E0.392571.995
129_R132_K0.384261.953
28_Y99_Y0.381731.940
50_F54_L0.357591.817
13_Y131_A0.354641.802
14_P117_Y0.353451.796
18_L108_F0.331711.686
49_R52_E0.331071.683
5_I27_G0.321451.634
24_D57_P0.319721.625
98_Q102_E0.311791.585
85_C88_C0.305021.550
9_P127_G0.304441.547
48_K60_E0.274241.394
13_Y17_R0.273891.392
2_L105_F0.268631.365
45_E48_K0.26361.340
15_L56_I0.262341.333
73_K76_E0.262331.333
26_T105_F0.260021.322
16_E134_Y0.259961.321
8_A11_S0.259911.321
6_C10_C0.254251.292
115_S118_K0.247471.258
94_E98_Q0.246071.251
51_A58_L0.245811.249
99_Y102_E0.244871.245
18_L25_V0.241261.226
65_P70_R0.239751.219
112_L115_S0.239311.216
53_K132_K0.238881.214
40_Y60_E0.236211.201
9_P131_A0.235841.199
93_L110_T0.235591.197
12_T50_F0.23461.192
66_E70_R0.233371.186
46_E49_R0.22941.166
19_R55_G0.228781.163
16_E136_V0.228761.163
70_R73_K0.228331.160
5_I47_L0.225031.144
19_R54_L0.222241.130
126_I129_R0.219141.114
78_E83_K0.216381.100
68_W91_L0.212091.078
9_P124_N0.211931.077
122_L130_L0.211151.073
3_L18_L0.208151.058
5_I10_C0.207641.055
93_L97_A0.206911.052
72_V75_L0.206621.050
14_P109_T0.206471.049
122_L126_I0.206061.047
6_C111_T0.204431.039
6_C11_S0.202571.030
75_L78_E0.200641.020
16_E19_R0.199091.012
64_D67_E0.198881.011
29_F47_L0.195970.996
49_R139_L0.19570.995
127_G131_A0.195110.992
7_C10_C0.194690.990
32_P92_R0.193340.983
126_I130_L0.192830.980
67_E91_L0.189320.962
47_L51_A0.188820.960
49_R137_E0.188820.960
26_T57_P0.188510.958
83_K86_R0.187630.954
65_P69_L0.187010.950
48_K58_L0.18670.949
101_K132_K0.186380.947
11_S17_R0.186290.947
16_E54_L0.183210.931
67_E95_K0.180610.918
15_L27_G0.18010.915
28_Y59_I0.178820.909
50_F56_I0.178430.907
53_K135_G0.177930.904
28_Y95_K0.17710.900
16_E53_K0.176510.897
125_E129_R0.175140.890
47_L50_F0.174970.889
100_A105_F0.174540.887
17_R21_E0.174250.886
48_K51_A0.174020.884
86_R89_Y0.173530.882
35_H69_L0.172480.877
130_L134_Y0.172440.876
94_E97_A0.172370.876
11_S14_P0.170910.869
19_R56_I0.170090.864
90_D94_E0.169930.864
123_I126_I0.169780.863
85_C89_Y0.168740.858
124_N128_E0.168630.857
33_N64_D0.167480.851
16_E130_L0.167090.849
72_V87_V0.166460.846
40_Y62_D0.166240.845
94_E133_E0.165930.843
59_I99_Y0.163380.830
47_L58_L0.16330.830
13_Y127_G0.16320.829
131_A136_V0.162370.825
128_E140_Y0.162220.824
9_P128_E0.161780.822
19_R25_V0.161490.821
53_K56_I0.161070.819
131_A141_R0.159780.812
38_E45_E0.159260.809
51_A57_P0.158570.806
68_W94_E0.158420.805
52_E55_G0.157960.803
100_A109_T0.156410.795
27_G56_I0.153910.782
5_I12_T0.153370.780
91_L95_K0.153360.779
2_L28_Y0.153350.779
20_E134_Y0.152370.774
15_L54_L0.152310.774
45_E70_R0.151850.772
30_Y61_G0.151750.771
17_R20_E0.151720.771
28_Y61_G0.150220.763
84_R98_Q0.148620.755
17_R130_L0.147520.750
15_L19_R0.146390.744
4_H96_T0.145520.740
63_Y68_W0.145160.738
57_P102_E0.144690.735
47_L54_L0.144390.734
52_E73_K0.144140.733
59_I103_L0.144050.732
33_N63_Y0.1440.732
29_F58_L0.143940.732
65_P128_E0.143560.730
26_T99_Y0.142720.725
51_A54_L0.142450.724
22_G55_G0.142320.723
3_L14_P0.141970.722
31_N92_R0.141710.720
51_A56_I0.141160.717
88_C92_R0.140610.715
104_G121_E0.139510.709
12_T116_P0.139380.708
61_G99_Y0.138540.704
76_E79_P0.137970.701
21_E111_T0.137780.700
61_G98_Q0.137690.700
113_L118_K0.137210.697
33_N68_W0.136920.696
66_E69_L0.136870.696
3_L25_V0.136620.694
113_L116_P0.136470.694
17_R117_Y0.136380.693
38_E60_E0.136370.693
24_D102_E0.13630.693
24_D55_G0.135920.691
126_I137_E0.13560.689
91_L124_N0.135560.689
46_E50_F0.135310.688
127_G130_L0.134830.685
68_W76_E0.134710.685
3_L15_L0.13370.680
84_R88_C0.133490.678
24_D94_E0.132720.675
5_I51_A0.132630.674
106_D112_L0.132590.674
96_T136_V0.132550.674
3_L27_G0.132220.672
86_R122_L0.132140.672
48_K62_D0.13210.671
26_T103_L0.131440.668
37_Y40_Y0.131320.667
118_K121_E0.131280.667
117_Y143_F0.129880.660
21_E25_V0.129740.659
3_L111_T0.128870.655
63_Y95_K0.127950.650
15_L97_A0.127240.647
45_E53_K0.12720.646
139_L142_D0.127180.646
79_P84_R0.126710.644
8_A46_E0.12660.643
125_E132_K0.125260.637
95_K99_Y0.124560.633
34_I38_E0.124080.631
4_H7_C0.123810.629
123_I132_K0.123690.629
132_K140_Y0.123640.628
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
3p52A0.954599.90.415
3a2kA0.931899.80.423
1wy5A0.931899.80.428
3tqiA0.926199.80.444
1ni5A0.897799.80.444
3fiuA0.954599.80.451
2derA0.965999.80.455
1xngA0.943299.80.455
2e18A0.937599.80.459
2ywbA0.937599.80.459

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