GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
bPH_4 - Bacterial PH domain
Pfam: PF06713 (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: 74
Sequences: 1265
Seq/Len: 17.09
HH_delta: 0.833 (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
62_D65_E0.634273.150
44_D63_K0.481542.392
4_I11_I0.369371.835
65_E69_E0.348881.733
37_S57_L0.346021.719
21_I50_Y0.341681.697
28_S49_Y0.335081.664
11_I20_K0.334581.662
25_D51_G0.330211.640
32_T47_E0.325561.617
27_R51_G0.315741.568
33_K44_D0.30851.532
33_K60_P0.306111.520
31_P44_D0.301761.499
59_S62_D0.272071.351
23_I26_I0.265491.319
6_E9_Y0.262871.306
37_S43_L0.258811.285
26_I48_I0.25811.282
60_P64_E0.256371.273
44_D60_P0.240021.192
13_K20_K0.238231.183
6_E11_I0.236871.176
9_Y27_R0.233341.159
5_I23_I0.232041.152
9_Y20_K0.226751.126
49_Y53_Y0.22651.125
36_L39_P0.224691.116
10_L60_P0.217171.079
32_T45_R0.216711.076
66_F70_L0.215151.069
67_I71_Q0.213351.060
5_I65_E0.210261.044
68_A71_Q0.207241.029
58_I63_K0.206591.026
22_P25_D0.204961.018
44_D58_I0.204821.017
5_I69_E0.203441.010
10_L39_P0.201531.001
4_I13_K0.201311.000
27_R63_K0.191990.954
3_Y59_S0.190310.945
6_E20_K0.186160.925
64_E68_A0.184940.919
33_K40_A0.180790.898
10_L48_I0.17990.894
35_P57_L0.176370.876
20_K64_E0.175510.872
14_C23_I0.1740.864
32_T46_L0.172360.856
5_I66_F0.170410.846
12_I45_R0.16970.843
27_R52_K0.169330.841
46_L71_Q0.168930.839
31_P63_K0.167960.834
3_Y12_I0.165740.823
22_P70_L0.163570.812
4_I54_K0.162990.810
8_D68_A0.162760.808
2_K13_K0.161420.802
3_Y60_P0.160260.796
18_K67_I0.159350.791
26_I45_R0.159170.791
34_N43_L0.158530.787
10_L26_I0.158140.785
37_S44_D0.157390.782
12_I56_I0.155850.774
3_Y43_L0.155460.772
19_K30_R0.15540.772
42_S60_P0.15480.769
25_D46_L0.154370.767
9_Y68_A0.153760.764
48_I53_Y0.152470.757
61_K64_E0.152310.756
62_D69_E0.152310.756
31_P67_I0.151760.754
27_R53_Y0.151270.751
9_Y64_E0.149440.742
4_I31_P0.146590.728
42_S59_S0.14580.724
34_N39_P0.145770.724
16_F59_S0.145230.721
14_C65_E0.144760.719
5_I31_P0.143740.714
49_Y52_K0.143250.711
24_E71_Q0.142420.707
9_Y18_K0.142380.707
25_D44_D0.142180.706
63_K66_F0.141570.703
11_I40_A0.141180.701
11_I18_K0.141090.701
25_D63_K0.140940.700
30_R47_E0.140880.700
35_P49_Y0.14070.699
29_I48_I0.140520.698
61_K65_E0.140240.697
3_Y51_G0.139420.692
21_I64_E0.138230.687
36_L55_S0.1370.680
3_Y71_Q0.136360.677
12_I21_I0.135680.674
47_E62_D0.134930.670
26_I53_Y0.134150.666
31_P55_S0.133250.662
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
1btkA0.9865300.833
1x05A123.60.841
2q8rE0.864923.20.841
2i5fA122.90.842
2gclA0.918922.30.842
1pg6A0.878419.70.846
2lulA0.986518.20.849
1icwA0.878417.30.85
1eigA0.878416.40.851
1g2sA0.905416.40.851
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 0.0128 seconds.