GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
bPH_5 - Bacterial PH domain
Pfam: PF10882 (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: 100
Sequences: 578
Seq/Len: 5.78
HH_delta: 0.854 (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
88_D91_E0.389243.490
3_Y86_P0.290682.606
29_V97_K0.226572.031
86_P92_F0.219261.966
22_P25_E0.217961.954
7_D23_L0.197581.772
9_G20_T0.195561.753
73_I92_F0.175351.572
10_L23_L0.168151.508
5_V23_L0.1591.426
62_V83_V0.154331.384
49_Y85_S0.15371.378
3_Y92_F0.152041.363
73_I93_I0.150341.348
27_E78_K0.146251.311
11_I73_I0.141771.271
14_W17_G0.141711.271
77_T82_Y0.138891.245
40_R43_G0.138721.244
9_G23_L0.138641.243
31_L93_I0.137791.235
68_R85_S0.13651.224
10_L20_T0.1361.219
32_V74_L0.134251.204
74_L83_V0.1311.175
31_L84_I0.129441.161
73_I89_P0.128781.155
6_D11_I0.126621.135
39_I87_E0.12581.128
21_I82_Y0.125411.124
46_G49_Y0.122661.100
85_S92_F0.122311.097
42_F46_G0.12141.089
10_L22_P0.120091.077
12_I21_I0.119011.067
16_F43_G0.117831.056
67_T92_F0.115981.040
34_D72_V0.11491.030
5_V10_L0.113081.014
9_G22_P0.112791.011
49_Y65_Y0.112391.008
28_S34_D0.112321.007
72_V85_S0.112321.007
75_I80_K0.111060.996
6_D9_G0.109540.982
66_A85_S0.108890.976
91_E95_A0.108780.975
56_N62_V0.107140.961
12_I94_E0.106790.958
20_T90_E0.10640.954
8_D23_L0.105840.949
34_D64_L0.105130.943
29_V84_I0.104910.941
54_F84_I0.104450.937
11_I18_K0.104050.933
56_N73_I0.103930.932
28_S76_K0.10220.916
43_G66_A0.101980.914
78_K95_A0.101580.911
76_K81_T0.101110.907
41_T45_G0.100890.905
21_I88_D0.099150.889
58_G79_D0.09880.886
64_L72_V0.09860.884
42_F72_V0.098110.880
10_L76_K0.09810.880
5_V92_F0.098090.880
69_N85_S0.097790.877
31_L97_K0.097490.874
87_E91_E0.097420.873
20_T27_E0.096830.868
12_I15_P0.096720.867
66_A86_P0.09650.865
25_E78_K0.095580.857
53_R56_N0.095560.857
30_E90_E0.095510.856
83_V86_P0.09510.853
12_I67_T0.09420.845
91_E94_E0.093490.838
44_S53_R0.092930.833
14_W80_K0.092910.833
93_I97_K0.092720.831
19_I22_P0.092680.831
70_K88_D0.092680.831
12_I24_A0.092330.828
11_I20_T0.092080.826
71_N89_P0.091490.820
67_T86_P0.090760.814
6_D18_K0.090610.812
73_I78_K0.090390.810
26_I72_V0.089510.803
66_A69_N0.087420.784
30_E76_K0.087230.782
92_F96_L0.087060.781
26_I31_L0.086670.777
92_F95_A0.086520.776
24_A55_R0.086440.775
26_I29_V0.085890.770
34_D83_V0.085730.769
45_G64_L0.085710.769
14_W69_N0.085570.767
35_L72_V0.085560.767
4_E18_K0.085350.765
74_L81_T0.085310.765
14_W47_F0.085120.763
45_G60_G0.085120.763
5_V33_D0.084740.760
43_G65_Y0.084720.760
41_T92_F0.084680.759
53_R80_K0.084660.759
47_F62_V0.084620.759
41_T61_K0.08440.757
10_L96_L0.084310.756
29_V92_F0.084290.756
25_E58_G0.08420.755
28_S90_E0.084060.754
42_F53_R0.08390.752
41_T47_F0.083880.752
12_I25_E0.083630.750
17_G66_A0.083440.748
56_N61_K0.083420.748
6_D82_Y0.083290.747
23_L29_V0.082980.744
24_A61_K0.082940.744
14_W42_F0.082930.744
70_K94_E0.082690.741
14_W49_Y0.082220.737
93_I96_L0.081840.734
45_G59_Y0.081780.733
94_E97_K0.081560.731
78_K90_E0.081460.730
21_I77_T0.081250.729
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
2d9zA0.6942.50.854
2coaA0.69370.859
1xr0B0.6926.60.869
2kuqA0.6919.90.876
2kupA0.6915.10.882
1p5tA0.6914.80.882
1ib8A0.3714.30.883
2dlwA0.6914.10.883
1j0wA0.6912.10.887
3g3tA0.34120.887
If you are interested in a protein containing this domain,
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