GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
bPH_2 - Bacterial PH domain
Pfam: PF03703 (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: CL0266
Length: 80
Sequences: 1928
Seq/Len: 24.1
HH_delta: 0.755 (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_G73_A0.665642.971
72_D75_E0.494192.206
16_R24_T0.446341.992
3_N22_K0.420181.876
33_Q56_A0.418321.867
43_Q48_L0.40831.823
39_Q70_I0.373791.669
43_Q67_F0.356271.590
68_L73_A0.336081.500
6_Y19_L0.334161.492
37_I49_G0.323191.443
9_T12_R0.319111.424
14_I24_T0.313091.398
7_T14_I0.312971.397
39_Q49_G0.30371.356
33_Q57_G0.303121.353
38_K52_K0.300871.343
50_T66_P0.297161.326
54_D57_G0.296111.322
13_L53_I0.287081.281
34_S54_D0.282991.263
40_N43_Q0.277981.241
48_L73_A0.275591.230
74_E78_D0.269711.204
71_E75_E0.264191.179
25_T34_S0.259961.160
32_I53_I0.25911.157
69_S72_D0.255281.140
47_G70_I0.255071.139
12_R26_I0.251911.124
29_L32_I0.241931.080
31_R56_A0.241131.076
5_G16_R0.241021.076
4_T15_I0.238621.065
42_L45_L0.237091.058
43_Q50_T0.236521.056
70_I74_E0.232461.038
48_L69_S0.230171.027
33_Q48_L0.230021.027
49_G70_I0.229281.023
10_D71_E0.22721.014
39_Q44_R0.224721.003
38_K64_E0.222430.993
27_I55_T0.219540.980
2_R45_L0.21880.977
3_N16_R0.217540.971
7_T11_D0.21480.959
47_G69_S0.212080.947
51_I78_D0.209870.937
34_S55_T0.209770.936
75_E78_D0.208510.931
8_I29_L0.205430.917
42_L46_F0.201210.898
17_S25_T0.20030.894
8_I75_E0.199920.892
9_T14_I0.198290.885
15_I63_I0.197430.881
52_K64_E0.197420.881
38_K50_T0.194420.868
49_G71_E0.192210.858
3_N19_L0.187910.839
53_I58_G0.186320.832
31_R76_I0.186160.831
37_I77_Y0.185170.827
18_G44_R0.184330.823
25_T63_I0.183410.819
68_L72_D0.181690.811
52_K59_S0.180610.806
36_S52_K0.179760.802
27_I54_D0.179130.800
51_I73_A0.178620.797
11_D71_E0.17850.797
23_R38_K0.177740.793
13_L63_I0.174670.780
4_T66_P0.174260.778
28_P44_R0.173730.776
4_T35_V0.171720.767
40_N50_T0.170420.761
21_S66_P0.169010.754
33_Q54_D0.166650.744
31_R55_T0.164870.736
33_Q55_T0.164490.734
16_R43_Q0.164150.733
29_L63_I0.162940.727
6_Y25_T0.161510.721
74_E77_Y0.160870.718
29_L35_V0.160360.716
41_P45_L0.160190.715
20_F69_S0.158040.705
28_P56_A0.156740.700
3_N30_D0.156380.698
5_G14_I0.156190.697
37_I52_K0.155510.694
64_E72_D0.155370.694
4_T17_S0.155050.692
8_I13_L0.15460.690
43_Q49_G0.154080.688
69_S73_A0.153620.686
10_D48_L0.152740.682
15_I25_T0.152420.680
22_K77_Y0.152320.680
26_I41_P0.150860.673
17_S23_R0.150590.672
33_Q58_G0.150550.672
14_I53_I0.150370.671
7_T26_I0.149410.667
50_T69_S0.149080.665
25_T51_I0.148950.665
11_D75_E0.148270.662
12_R31_R0.14790.660
65_I68_L0.14670.655
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
3hsaA0.9580.90.755
3b77A0.937577.90.762
2cayA0.97561.60.787
2hthB0.97553.90.797
4ekuA0.937518.90.838
2yf0A0.914.10.847
2gclA0.987513.60.848
1o57A0.975130.849
2ebfX0.975130.849
4f7gA0.8512.20.851
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0227 seconds.