GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PBP - Phosphatidylethanolamine-binding protein
Pfam: PF01161 (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. )
Length: 146
Sequences: 1916
Seq/Len: 13.12
HH_delta: 0.145 (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
112_P133_H1.032154.548
29_A36_Y0.850533.747
15_C94_C0.831673.664
38_L108_L0.725983.199
63_N116_P0.688383.033
40_M106_F0.647462.853
83_S91_L0.61052.690
44_D103_R0.507742.237
105_V141_A0.477192.102
42_D102_H0.452541.994
3_K143_N0.437891.929
7_K71_E0.436461.923
126_L130_F0.368761.625
37_T126_L0.353921.559
4_L142_G0.34811.534
41_V55_P0.347041.529
124_F129_A0.338961.493
19_N92_G0.338351.491
93_P145_F0.331971.463
42_D58_H0.327361.442
92_G96_P0.315791.391
90_Y93_P0.307941.357
62_T121_A0.295631.303
40_M90_Y0.294891.299
108_L138_A0.293841.295
129_A132_G0.292671.290
111_Q130_F0.291421.284
96_P104_Y0.280751.237
45_A96_P0.279061.230
57_L88_A0.278241.226
103_R141_A0.278081.225
79_G126_L0.275481.214
62_T79_G0.265441.170
22_P106_F0.259031.141
101_P145_F0.252191.111
62_T126_L0.251551.108
7_K18_N0.25081.105
58_H104_Y0.249321.099
4_L93_P0.247511.091
112_P134_G0.246281.085
44_D58_H0.24471.078
34_K110_A0.242091.067
95_P102_H0.241551.064
8_F23_P0.241051.062
57_L123_K0.240751.061
63_N115_L0.240151.058
107_L137_P0.235211.036
63_N114_P0.233631.029
100_G145_F0.228441.007
44_D102_H0.228351.006
35_S63_N0.225040.992
58_H95_P0.224020.987
8_F71_E0.223690.986
58_H102_H0.218810.964
38_L64_I0.218720.964
125_D128_E0.21850.963
47_S54_G0.217690.959
26_W136_G0.214870.947
125_D129_A0.213610.941
45_A56_F0.212970.938
36_Y108_L0.211520.932
59_W90_Y0.209980.925
41_V107_L0.209630.924
113_S133_H0.208710.920
35_S113_S0.208160.917
109_Y134_G0.207380.914
33_T110_A0.206890.912
35_S111_Q0.20620.909
37_T130_F0.205530.906
41_V57_L0.20550.905
54_G124_F0.20230.891
58_H96_P0.202280.891
30_P110_A0.196720.867
118_S121_A0.195250.860
21_S24_L0.19510.860
26_W36_Y0.194920.859
42_D45_A0.194430.857
60_L79_G0.193030.850
43_P105_V0.192070.846
54_G57_L0.191250.843
7_K20_V0.191190.842
20_V26_W0.191160.842
128_E131_K0.190550.840
111_Q134_G0.188960.833
29_A33_T0.188910.832
39_I60_L0.188830.832
88_A120_G0.188820.832
8_F106_F0.188770.832
78_Q89_P0.185920.819
95_P104_Y0.185140.816
130_F134_G0.185040.815
37_T111_Q0.185020.815
55_P84_G0.184250.812
134_G137_P0.183980.811
43_P103_R0.183770.810
19_N91_L0.182850.806
57_L60_L0.182060.802
3_K145_F0.181490.800
121_A124_F0.178850.788
112_P115_L0.178260.785
120_G134_G0.178060.785
24_L140_L0.176410.777
60_L126_L0.173560.765
53_F127_R0.173460.764
60_L88_A0.173370.764
110_A136_G0.172830.761
24_L28_N0.171540.756
85_Q89_P0.170660.752
47_S55_P0.170120.750
56_F128_E0.168910.744
131_K137_P0.168580.743
88_A119_D0.167340.737
16_P144_Y0.167290.737
42_D104_Y0.16710.736
24_L142_G0.16680.735
46_P103_R0.166730.735
80_I88_A0.166590.734
33_T36_Y0.164730.726
43_P95_P0.164580.725
22_P26_W0.164560.725
30_P61_V0.164350.724
6_V16_P0.163940.722
83_S90_Y0.163890.722
30_P33_T0.163660.721
41_V105_V0.163050.718
46_P53_F0.162430.716
45_A53_F0.161990.714
20_V71_E0.161870.713
28_N31_T0.161360.711
21_S96_P0.161020.709
3_K6_V0.159610.703
117_L121_A0.159230.702
40_M70_P0.159060.701
82_S92_G0.158440.698
35_S114_P0.15650.690
123_K127_R0.156450.689
39_I126_L0.156320.689
55_P127_R0.155650.686
79_G123_K0.15460.681
18_N143_N0.153930.678
56_F92_G0.153870.678
112_P135_L0.153460.676
141_A145_F0.152050.670
26_W62_T0.151530.668
81_N85_Q0.151030.665
21_S59_W0.150460.663
59_W65_P0.150450.663
121_A125_D0.149940.661
121_A129_A0.149750.660
135_L140_L0.148840.656
99_S145_F0.14780.651
65_P84_G0.147720.651
17_G100_G0.147110.648
110_A135_L0.146830.647
29_A32_G0.14610.644
64_I108_L0.146040.643
60_L122_T0.14540.641
127_R130_F0.14520.640
34_K114_P0.144720.638
56_F96_P0.143560.633
35_S110_A0.143190.631
90_Y100_G0.143080.630
104_Y142_G0.140260.618
63_N111_Q0.139920.616
91_L101_P0.138410.610
137_P140_L0.137850.607
80_I85_Q0.137610.606
26_W110_A0.137520.606
62_T118_S0.137110.604
39_I130_F0.13710.604
59_W106_F0.137060.604
37_T79_G0.13640.601
20_V27_Q0.135130.595
43_P46_P0.134890.594
116_P119_D0.134180.591
81_N106_F0.134080.591
26_W29_A0.13290.586
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
3n08A0.93151000.145
1fuxA0.95211000.154
1fjjA0.93841000.176
2evvA0.92471000.207
2jyzA0.92471000.214
2iqyA0.90411000.22
2gzqA0.93841000.24
1wpxB0.97951000.243
1wkoA0.89041000.245
3axyA0.890499.90.259

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