GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Dabb - Stress responsive AB Barrel Domain
Pfam: PF07876 (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: CL0032
Length: 97
Sequences: 4512
Seq/Len: 46.52
HH_delta: 0.117 (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
63_S66_D1.945413.818
36_V62_E1.565383.073
64_E68_D1.181652.319
13_A17_E1.136982.232
37_S60_T1.005271.973
34_G66_D0.992771.949
10_K88_E0.902241.771
62_E66_D0.852521.673
15_E42_R0.840141.649
68_D72_T0.820081.610
35_I61_F0.805531.581
17_E20_E0.799491.569
19_E23_E0.785171.541
8_K54_D0.780361.532
10_K13_A0.777871.527
65_E68_D0.760291.492
12_D15_E0.755841.484
9_L18_I0.731891.437
13_A86_I0.714331.402
78_A81_E0.703051.380
8_K88_E0.681441.338
15_E48_D0.675531.326
24_A82_F0.670831.317
33_P62_E0.654011.284
42_R55_H0.649991.276
73_H76_H0.610341.198
74_P78_A0.604631.187
78_A82_F0.596491.171
6_L56_A0.590481.159
74_P77_Q0.577571.134
68_D71_Q0.545851.071
65_E69_A0.541151.062
32_I73_H0.541081.062
19_E42_R0.536281.053
4_I58_V0.533151.046
19_E55_H0.53061.041
16_E20_E0.529851.040
4_I56_A0.529671.040
32_I75_A0.526261.033
32_I70_Y0.520081.021
6_L54_D0.517321.015
15_E19_E0.512381.006
8_K46_P0.51161.004
39_E60_T0.507750.997
70_Y76_H0.506710.995
26_R38_F0.493750.969
33_P66_D0.488130.958
67_L71_Q0.483010.948
26_R30_D0.478780.940
43_N46_P0.473910.930
34_G69_A0.473140.929
30_D35_I0.46920.921
77_Q80_V0.469130.921
77_Q81_E0.467890.918
43_N54_D0.466010.915
72_T77_Q0.464560.912
31_K75_A0.453210.890
35_I38_F0.448140.880
69_A72_T0.444980.873
20_E24_A0.444160.872
41_G58_V0.442830.869
17_E86_I0.43410.852
71_Q76_H0.430480.845
76_H80_V0.430170.844
27_A30_D0.429790.844
75_A78_A0.428930.842
33_P69_A0.428390.841
66_D69_A0.423120.831
24_A27_A0.422170.829
16_E19_E0.414570.814
17_E21_V0.413150.811
28_L31_K0.40480.795
20_E23_E0.404620.794
40_V55_H0.396470.778
82_F85_P0.394290.774
23_E27_A0.393820.773
35_I59_S0.390040.766
7_F57_L0.386860.759
59_S70_Y0.382440.751
24_A28_L0.381950.750
15_E55_H0.380980.748
81_E84_K0.378070.742
8_K48_D0.361120.709
22_L26_R0.359820.706
32_I66_D0.359820.706
9_L55_H0.356160.699
21_V82_F0.351270.689
11_P48_D0.348070.683
80_V83_L0.345530.678
29_K71_Q0.344520.676
17_E82_F0.343880.675
25_L79_F0.339690.667
38_F70_Y0.339020.665
22_L40_V0.338250.664
29_K38_F0.330570.649
18_I22_L0.325510.639
79_F83_L0.324520.637
38_F59_S0.321920.632
83_L87_L0.321580.631
41_G44_F0.31950.627
41_G56_A0.310190.609
37_S58_V0.306410.601
42_R46_P0.304630.598
46_P54_D0.302840.594
36_V60_T0.299960.589
21_V24_A0.299110.587
5_V57_L0.295140.579
22_L83_L0.293320.576
23_E26_R0.292130.573
69_A73_H0.292040.573
35_I70_Y0.285130.560
28_L75_A0.27870.547
27_A31_K0.27740.544
41_G60_T0.271180.532
76_H83_L0.269120.528
29_K35_I0.268960.528
29_K76_H0.263080.516
29_K59_S0.260180.511
80_V84_K0.259890.510
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
1q4rA199.40.117
1tr0A199.40.121
3bb5A199.40.127
3bguA0.979499.40.136
2qycA0.979499.40.143
3bn7A0.989799.40.155
3fmbA0.969199.30.163
1rjjA0.969199.30.166
3bdeA0.969199.30.172
3f44A0.938199.30.204

Page generated in 0.0255 seconds.