GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PTS-HPr - PTS HPr component phosphorylation site
Pfam: PF00381 (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: 84
Sequences: 2166
Seq/Len: 25.79
HH_delta: -0.02 (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
5_E60_E1.249173.055
65_A74_L1.000172.446
31_S69_D0.984532.408
29_F76_A0.916412.241
4_R78_A0.875262.141
30_D68_E0.846552.070
3_E62_E0.834282.040
6_V78_A0.799071.954
71_E75_E0.79161.936
25_I28_K0.789141.930
22_L77_I0.74241.816
3_E64_E0.740941.812
34_T41_T0.729951.785
78_A82_E0.718091.756
37_K59_D0.712511.743
7_T60_E0.708981.734
79_E83_S0.708981.734
25_I76_A0.697481.706
30_D69_D0.695381.701
5_E62_E0.662381.620
2_I71_E0.64211.570
29_F73_A0.636641.557
36_R62_E0.630531.542
36_R64_E0.625131.529
36_R41_T0.599581.466
22_L44_A0.586551.434
41_T64_E0.585761.433
75_E79_E0.555271.358
32_D66_E0.499041.220
2_I74_L0.494111.208
11_P57_K0.491521.202
69_D72_E0.491371.202
42_V53_L0.485671.188
72_E76_A0.474251.160
31_S65_A0.459761.124
72_E75_E0.45141.104
2_I70_E0.444351.087
55_A61_I0.439461.075
8_I55_A0.438691.073
36_R39_G0.432851.059
4_R75_E0.410831.005
9_K82_E0.410491.004
33_I73_A0.409611.002
56_K59_D0.40580.992
42_V48_L0.400080.978
34_T64_E0.399830.978
48_L52_S0.391720.958
15_H18_P0.391250.957
10_N80_F0.383720.938
22_L35_I0.383630.938
14_L22_L0.382950.937
21_E24_Q0.379920.929
21_E80_F0.377690.924
26_A77_I0.368690.902
32_D45_K0.356080.871
67_G73_A0.354130.866
75_E78_A0.344290.842
26_A33_I0.342480.838
26_A73_A0.337470.825
13_G17_R0.332030.812
48_L51_M0.324460.793
31_S73_A0.315050.770
31_S67_G0.312730.765
23_V47_I0.312580.764
25_I80_F0.310070.758
10_N81_L0.307490.752
23_V50_L0.306930.751
76_A79_E0.302780.740
12_N18_P0.302160.739
31_S45_K0.300570.735
42_V52_S0.295030.722
37_K55_A0.294410.720
21_E25_I0.292130.714
40_K50_L0.289070.707
43_D48_L0.284850.697
26_A45_K0.284640.696
46_S49_G0.280770.687
43_D49_G0.279480.683
20_A51_M0.278870.682
33_I65_A0.278250.680
31_S70_E0.277430.678
42_V49_G0.275210.673
63_I77_I0.275010.673
32_D43_D0.270.660
63_I74_L0.268650.657
52_S55_A0.266030.651
43_D46_S0.26180.640
47_I55_A0.260760.638
61_I81_L0.257360.629
35_I50_L0.256140.626
22_L63_I0.255920.626
2_I66_E0.252130.617
24_Q27_S0.249890.611
4_R74_L0.248190.607
8_I61_I0.247030.604
67_G70_E0.241660.591
33_I44_A0.240520.588
19_A49_G0.238730.584
74_L78_A0.232880.570
44_A63_I0.232760.569
29_F45_K0.232370.568
13_G19_A0.2310.565
9_K57_K0.227050.555
19_A26_A0.226910.555
33_I58_G0.226560.554
20_A24_Q0.225310.551
10_N57_K0.223670.547
22_L50_L0.223620.547
52_S80_F0.223370.546
14_L19_A0.222370.544
6_V81_L0.222210.543
20_A52_S0.218340.534
63_I81_L0.213970.523
29_F69_D0.213670.523
4_R63_I0.213240.521
2_I35_I0.211680.518
65_A70_E0.208130.509
16_A20_A0.207660.508
15_H80_F0.207450.507
27_S48_L0.207270.507
27_S47_I0.206470.505
18_P21_E0.205980.504
60_E82_E0.20570.503
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
3le1A199.9-0.02
3ihsA0.976299.9-0.012
1kklH199.9-0.004
1sphA199.9-0.002
1ptfA199.9-0.002
1y51A199.9-0.001
3ccdA199.90
1ka5A199.90.001
1pchA0.988199.90.023
2jpiA0.916771.30.844

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