GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AraC_N - AraC-type transcriptional regulator N-terminus
Pfam: PF06719 (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: CL0029
Length: 155
Sequences: 2908
Seq/Len: 18.76
HH_delta: 0.451 (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
35_R44_E0.500982.501
46_D49_Q0.482732.410
31_Q73_L0.482422.408
21_V59_V0.479432.393
138_I141_E0.466192.327
117_A142_I0.464182.317
33_S44_E0.460892.301
35_R42_V0.436912.181
19_P59_V0.403672.015
24_P55_V0.400281.998
23_E78_E0.398971.992
33_S46_D0.398571.990
116_D119_L0.376261.878
134_L141_E0.369611.845
34_K72_Y0.360541.800
31_Q47_A0.348621.740
30_L75_L0.345191.723
39_G57_L0.328631.640
137_L140_R0.328121.638
120_R138_I0.315381.574
25_S76_S0.311161.553
41_Q103_Q0.297911.487
130_D144_Y0.293721.466
137_L144_Y0.288611.441
28_I118_L0.285671.426
37_H42_V0.279231.394
137_L141_E0.268421.340
141_E145_R0.266981.333
120_R141_E0.266891.332
21_V25_S0.266341.330
18_M58_P0.252811.262
30_L73_L0.25251.260
27_C76_S0.251851.257
28_I50_Y0.250821.252
25_S59_V0.246121.229
34_K45_Y0.246081.228
134_L138_I0.244931.223
29_V72_Y0.241221.204
19_P25_S0.240851.202
140_R144_Y0.240761.202
31_Q71_P0.24071.202
86_E90_E0.239371.195
133_I137_L0.232691.162
45_Y51_L0.232221.159
116_D123_R0.231071.153
54_S57_L0.228571.141
124_L138_I0.226241.129
114_L142_I0.226121.129
27_C74_A0.225611.126
25_S78_E0.225571.126
34_K51_L0.222361.110
61_S74_A0.220871.103
61_S72_Y0.218761.092
113_E127_D0.218571.091
27_C51_L0.215161.074
52_V55_V0.214661.072
50_Y118_L0.21031.050
79_L84_L0.207061.034
27_C36_V0.206711.032
86_E140_R0.205191.024
72_Y76_S0.200621.001
49_Q109_P0.198890.993
90_E140_R0.194760.972
74_A78_E0.192630.962
134_L144_Y0.192490.961
114_L146_L0.190730.952
120_R124_L0.190080.949
83_L139_L0.188650.942
85_A89_L0.187340.935
91_L94_Q0.185030.924
29_V74_A0.184570.921
141_E144_Y0.184170.919
29_V32_G0.183010.914
119_L123_R0.182610.912
36_V51_L0.182470.911
41_Q124_L0.181140.904
36_V74_A0.181010.904
118_L142_I0.180570.901
61_S76_S0.179130.894
25_S74_A0.178050.889
131_I135_A0.174620.872
22_Y80_D0.174030.869
49_Q107_V0.173130.864
116_D120_R0.170780.853
36_V108_A0.170090.849
112_E116_D0.170060.849
46_D128_P0.16990.848
138_I142_I0.169010.844
25_S53_S0.168920.843
113_E145_R0.167720.837
36_V72_Y0.166950.833
136_P140_R0.164440.821
31_Q70_E0.164110.819
29_V34_K0.163220.815
68_P89_L0.160690.802
43_F46_D0.159150.794
60_E76_S0.158810.793
104_G118_L0.158660.792
38_L43_F0.157970.789
128_P131_I0.157540.786
34_K61_S0.157540.786
86_E136_P0.15690.783
110_A114_L0.156790.783
79_L83_L0.156020.779
20_C23_E0.155990.779
83_L143_L0.155830.778
124_L144_Y0.15520.775
22_Y56_D0.154970.774
121_L139_L0.154850.773
117_A145_R0.154680.772
23_E38_L0.154430.771
86_E89_L0.154270.770
77_L121_L0.153960.769
120_R123_R0.153870.768
29_V33_S0.153790.768
26_I143_L0.153530.766
124_L128_P0.153520.766
73_L122_L0.15320.765
55_V81_P0.152850.763
87_L120_R0.152790.763
20_C56_D0.152590.762
36_V63_V0.152550.762
24_P52_V0.152080.759
79_L146_L0.150990.754
117_A120_R0.150170.750
121_L135_A0.149890.748
19_P76_S0.149860.748
49_Q110_A0.149790.748
34_K74_A0.14940.746
39_G53_S0.148550.742
51_L107_V0.147690.737
81_P85_A0.147630.737
86_E129_E0.146860.733
26_I50_Y0.146640.732
20_C52_V0.146190.730
21_V24_P0.145080.724
63_V72_Y0.143990.719
44_E112_E0.14340.716
89_L93_P0.143030.714
25_S28_I0.142780.713
26_I118_L0.142660.712
68_P136_P0.142530.711
89_L108_A0.142170.710
113_E118_L0.142130.709
33_S67_S0.141970.709
20_C25_S0.141870.708
86_E115_L0.141540.707
84_L113_E0.141280.705
103_Q109_P0.141210.705
28_I115_L0.140960.704
92_P133_I0.140890.703
38_L57_L0.140450.701
41_Q68_P0.139110.694
88_V125_L0.138860.693
26_I131_I0.138670.692
18_M60_E0.138620.692
95_P101_A0.137480.686
26_I79_L0.136830.683
25_S55_V0.136640.682
24_P27_C0.1360.679
25_S79_L0.135290.675
69_E103_Q0.13410.669
21_V61_S0.133840.668
20_C76_S0.133220.665
117_A124_L0.132370.661
127_D131_I0.132210.660
51_L62_E0.132210.660
19_P22_Y0.132210.660
35_R62_E0.131150.655
29_V45_Y0.131010.654
115_L119_L0.130630.652
141_E146_L0.130180.650
33_S102_S0.130060.649
58_P87_L0.129930.649
110_A115_L0.129350.646
112_E117_A0.129070.644
89_L92_P0.128870.643
47_A113_E0.128770.643
90_E132_P0.12830.640
20_C58_P0.128270.640
17_P60_E0.128170.640
122_L126_D0.128010.639
136_P147_L0.127540.637
87_L91_L0.126870.633
23_E56_D0.126760.633
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
2arcA0.948499.20.451
3gbgA0.9871990.497
4i4aA0.625898.90.507
1vj2A0.522698.50.577
3cewA0.645298.50.579
1o4tA0.503298.50.585
2b8mA0.593598.50.589
1yhfA0.503298.50.589
2f4pA0.619498.40.593
2bnmA0.490398.40.6

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