GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AraC_binding_2 - AraC-binding-like domain
Pfam: PF14525 (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: 172
Sequences: 1451
Seq/Len: 8.44
HH_delta: 0.694 (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
38_R100_R0.392933.761
40_S100_R0.252422.416
140_R144_R0.241132.308
138_L163_L0.240642.303
62_L102_L0.238682.284
63_S100_R0.233642.236
71_G89_Q0.218822.094
69_E74_E0.216982.077
67_R74_E0.211562.025
69_E92_R0.210032.010
54_D108_R0.200691.921
58_L84_L0.19891.904
3_D7_R0.190631.824
77_L81_D0.184311.764
61_P77_L0.174931.674
67_R94_E0.174791.673
86_D89_Q0.171261.639
126_D132_G0.16581.587
65_S96_S0.164281.572
67_R76_E0.164031.570
136_A140_R0.158771.520
58_L135_L0.157241.505
66_A95_F0.153021.465
66_A101_Q0.149971.435
61_P66_A0.148871.425
158_L165_D0.147471.411
162_H165_D0.147031.407
22_F170_L0.146821.405
70_Q73_R0.146781.405
81_D124_R0.145821.396
78_A81_D0.144881.387
9_F12_H0.143431.373
57_L103_S0.140161.341
158_L162_H0.140161.341
65_S78_A0.138981.330
82_V125_I0.137981.321
162_H169_A0.137831.319
42_G98_G0.137421.315
41_Y44_Q0.135951.301
61_P81_D0.133941.282
49_S52_P0.132091.264
12_H41_Y0.131171.255
34_L104_L0.129571.240
155_D158_L0.12891.234
59_V85_L0.126091.207
70_Q75_V0.124591.192
28_H35_R0.122121.169
86_D108_R0.121831.166
95_F101_Q0.121821.166
41_Y99_C0.120591.154
9_F37_S0.117881.128
137_R141_S0.117161.121
56_Y86_D0.115591.106
145_E148_G0.115511.106
10_G59_V0.114771.098
81_D127_A0.114531.096
6_S14_L0.11411.092
127_A132_G0.113431.086
37_S103_S0.112981.081
149_L168_A0.112961.081
83_V93_L0.112151.073
57_L101_Q0.110161.054
59_V93_L0.109721.050
14_L57_L0.108421.038
47_V51_A0.108211.036
60_L82_V0.108121.035
17_A43_A0.107581.030
55_H105_R0.107551.029
62_L100_R0.106711.021
39_I57_L0.10671.021
101_Q106_I0.106611.020
5_V9_F0.106261.017
47_V50_D0.105361.008
133_R168_A0.105251.007
35_R105_R0.105051.005
133_R139_L0.103950.995
82_V127_A0.103490.990
127_A130_G0.102860.984
106_I111_L0.101850.975
5_V10_G0.101110.968
156_S160_A0.100940.966
123_P170_L0.100650.963
17_A79_P0.100610.963
13_D109_A0.099720.954
13_D47_V0.099340.951
39_I59_V0.099140.949
15_R23_H0.09910.948
60_L134_L0.098810.946
59_V91_Y0.098640.944
25_R40_S0.098430.942
15_R60_L0.098420.942
57_L105_R0.09830.941
161_Q165_D0.098030.938
40_S133_R0.097860.937
6_S104_L0.097750.936
113_R116_G0.097430.932
5_V12_H0.097360.932
125_I132_G0.09730.931
146_L157_P0.097040.929
13_D48_R0.096980.928
57_L91_Y0.096820.927
63_S79_P0.095950.918
10_G13_D0.095890.918
10_G14_L0.095840.917
88_G108_R0.09540.913
65_S76_E0.095080.910
115_L139_L0.094210.902
17_A142_L0.093910.899
59_V101_Q0.093650.896
42_G82_V0.093320.893
33_G73_R0.093230.892
62_L98_G0.093040.890
9_F85_L0.092720.887
159_A162_H0.092690.887
36_L102_L0.092350.884
75_V90_P0.092060.881
3_D6_S0.091780.878
150_D154_A0.091360.874
27_S147_A0.091260.873
21_R138_L0.090880.870
9_F39_I0.09050.866
129_S132_G0.090260.864
107_P122_A0.090050.862
4_A13_D0.089940.861
58_L95_F0.089910.861
59_V103_S0.089450.856
48_R92_R0.089440.856
98_G130_G0.089260.854
61_P79_P0.089220.854
25_R32_G0.089190.854
135_L155_D0.088730.849
58_L106_I0.087770.840
5_V11_P0.087510.838
41_Y66_A0.087270.835
133_R136_A0.087120.834
163_L169_A0.087070.833
69_E129_S0.086940.832
48_R107_P0.08630.826
84_L135_L0.086170.825
115_L118_P0.086110.824
75_V122_A0.08610.824
165_D169_A0.085940.823
71_G116_G0.085790.821
71_G92_R0.085740.821
72_G78_A0.085740.821
26_I64_G0.085090.814
34_L102_L0.085060.814
137_R142_L0.084940.813
12_H91_Y0.084930.813
6_S10_G0.084910.813
67_R92_R0.084910.813
33_G159_A0.08470.811
34_L82_V0.08470.811
57_L61_P0.08460.810
70_Q107_P0.084520.809
41_Y101_Q0.084430.808
5_V37_S0.08430.807
6_S95_F0.084150.805
73_R89_Q0.08410.805
47_V60_L0.083970.804
118_P121_F0.083970.804
28_H37_S0.083920.803
64_G100_R0.08380.802
114_R169_A0.083750.802
138_L159_A0.083690.801
48_R90_P0.083640.801
10_G105_R0.083610.800
163_L166_L0.083610.800
31_L155_D0.083010.794
63_S67_R0.0830.794
65_S69_E0.082980.794
10_G57_L0.082940.794
70_Q86_D0.082810.793
84_L164_E0.082730.792
130_G134_L0.082460.789
23_H78_A0.082120.786
57_L85_L0.081930.784
96_S119_L0.081780.783
33_G164_E0.08150.780
98_G102_L0.081450.780
33_G139_L0.081360.779
77_L83_V0.081230.777
12_H85_L0.08110.776
32_G142_L0.081090.776
66_A77_L0.081070.776
5_V39_I0.080970.775
36_L59_V0.080830.774
39_I101_Q0.08060.771
150_D155_D0.080530.771
67_R137_R0.080480.770
5_V16_P0.080370.769
4_A8_A0.080360.769
69_E72_G0.080310.769
32_G160_A0.080250.768
3_D8_A0.080230.768
54_D105_R0.079930.765
104_L159_A0.079890.765
63_S155_D0.079880.765
158_L168_A0.079850.764
60_L102_L0.079560.761
70_Q124_R0.079540.761
121_F124_R0.079080.757
115_L140_R0.0790.756
5_V14_L0.078870.755
45_R134_L0.078870.755
82_V139_L0.078760.754
83_V124_R0.078750.754
10_G88_G0.078610.752
8_A82_V0.078440.751
132_G136_A0.078430.751
148_G160_A0.07840.750
73_R121_F0.078180.748
41_Y45_R0.078040.747
80_G107_P0.077850.745
5_V26_I0.077730.744
36_L115_L0.07770.744
90_P120_R0.077620.743
20_D24_A0.077610.743
112_E118_P0.077580.743
5_V47_V0.077480.742
110_L168_A0.077480.742
69_E94_E0.077440.741
4_A28_H0.07740.741
29_R53_D0.077290.740
65_S89_Q0.077260.739
70_Q164_E0.077160.738
49_S55_H0.076890.736
86_D122_A0.076840.735
55_H108_R0.076480.732
86_D93_L0.076120.729
42_G93_L0.076050.728
86_D107_P0.075810.726
116_G170_L0.075750.725
137_R140_R0.075730.725
78_A115_L0.075690.724
95_F105_R0.075640.724
41_Y61_P0.075610.724
70_Q85_L0.075230.720
47_V99_C0.075110.719
136_A167_L0.075030.718
50_D97_A0.074980.718
46_R91_Y0.074940.717
163_L168_A0.07490.717
31_L76_E0.074810.716
96_S131_V0.074740.715
7_R10_G0.074720.715
39_I99_C0.074270.711
25_R45_R0.074090.709
70_Q123_P0.074060.709
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
2arcA0.889597.80.694
3gbgA0.825697.20.735
1vj2A0.639596.70.757
4i4aA0.703596.40.766
1yhfA0.622196.30.768
3cewA0.709396.20.769
2b8mA0.662896.10.773
4e2gA0.662895.90.776
3fjsA0.56495.80.779
3h8uA0.668695.70.781
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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