GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PTS_EIIA_2 - Phosphoenolpyruvate-dependent sugar phosphotransferase system EIIA 2
Pfam: PF00359 (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: CL0340
Length: 144
Sequences: 4189
Seq/Len: 29.09
HH_delta: 0.027 (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
94_K129_L1.356623.360
5_K135_E1.068882.647
22_K41_I0.908842.251
133_D136_E0.883432.188
16_D19_E0.880152.180
26_D30_E0.842072.086
35_N70_K0.831792.060
24_L98_L0.826192.046
44_L98_L0.812062.011
126_E130_K0.805681.996
25_A41_I0.803771.991
13_E80_K0.789221.955
11_N78_R0.787831.951
82_P94_K0.759251.881
14_A20_V0.738491.829
73_G100_A0.730471.809
14_A23_Q0.727991.803
9_F27_K0.716761.775
29_I34_V0.693911.719
24_L77_V0.68711.702
79_L96_I0.684391.695
11_N80_K0.683381.693
40_F100_A0.676921.677
42_E46_E0.660741.637
79_L82_P0.639921.585
72_P102_P0.629321.559
132_K136_E0.628721.557
33_Y71_K0.628211.556
48_E53_T0.614261.521
20_V96_I0.611171.514
7_L31_Q0.606171.501
12_V77_V0.602751.493
21_I44_L0.593061.469
135_E139_E0.591841.466
9_F23_Q0.575411.425
6_E31_Q0.563631.396
69_V100_A0.563491.396
15_K19_E0.551391.366
27_K30_E0.544491.349
33_Y73_G0.541411.341
48_E55_I0.541341.341
46_E49_E0.539221.336
18_E49_E0.533721.322
125_I129_L0.519641.287
5_K138_I0.51451.274
25_A44_L0.505981.253
93_V96_I0.497171.231
67_E103_K0.489951.214
79_L94_K0.488061.209
18_E45_L0.485381.202
84_K92_P0.479591.188
131_A140_I0.476291.180
58_G94_K0.474611.176
25_A98_L0.473731.173
77_V98_L0.472871.171
108_H112_L0.463741.149
10_L78_R0.462061.144
4_D7_L0.453371.123
18_E22_K0.449861.114
78_R95_V0.446971.107
47_R53_T0.445091.102
8_I137_F0.441571.094
131_A137_F0.441361.093
84_K90_G0.440831.092
57_N125_I0.439241.088
29_I36_D0.438171.085
76_I137_F0.437331.083
76_I95_V0.436111.080
8_I134_P0.43451.076
134_P138_I0.422761.047
14_A79_L0.422421.046
28_L100_A0.415691.030
131_A136_E0.412771.022
22_K45_L0.412171.021
46_E50_I0.410731.017
5_K134_P0.40991.015
27_K75_S0.407881.010
26_D37_K0.407031.008
43_D46_E0.394840.978
74_I111_L0.392280.972
21_I41_I0.388560.962
28_L75_S0.387850.961
85_W96_I0.386380.957
127_E130_K0.385820.956
138_I142_K0.384920.953
43_D64_A0.384220.952
72_P101_I0.381730.945
41_I45_L0.381130.944
17_W85_W0.377790.936
115_L119_L0.377120.934
26_D29_I0.375680.930
28_L73_G0.364550.903
101_I105_D0.359370.890
34_V40_F0.356530.883
116_S120_E0.355180.880
27_K31_Q0.352640.873
12_V23_Q0.351860.871
19_E22_K0.350820.869
32_G70_K0.346970.859
85_W93_V0.343330.850
2_L111_L0.341580.846
40_F44_L0.341070.845
136_E139_E0.34070.844
29_I37_K0.338130.837
37_K68_N0.336260.833
113_S117_R0.335050.830
22_K26_D0.334640.829
17_W48_E0.334310.828
113_S116_S0.333770.827
23_Q27_K0.33230.823
24_L75_S0.330880.820
13_E81_Q0.329730.817
118_L124_F0.328470.814
114_E117_R0.327870.812
121_D124_F0.323790.802
20_V79_L0.322090.798
79_L83_I0.318680.789
66_S69_V0.31780.787
58_G129_L0.317650.787
43_D68_N0.31630.783
17_W86_D0.312390.774
128_L137_F0.310150.768
29_I41_I0.309990.768
7_L33_Y0.307650.762
127_E140_I0.307320.761
82_P92_P0.306640.759
54_Y85_W0.304090.753
20_V83_I0.303530.752
116_S119_L0.302710.750
124_F140_I0.301580.747
53_T62_P0.300840.745
26_D41_I0.295410.732
56_G59_I0.289840.718
109_L113_S0.289180.716
78_R137_F0.28730.712
43_D66_S0.283640.703
139_E142_K0.28180.698
47_R62_P0.27960.693
17_W21_I0.277760.688
103_K106_E0.276230.684
48_E62_P0.27590.683
47_R51_G0.272660.675
21_I45_L0.271990.674
55_I101_I0.27050.670
126_E129_L0.268350.665
74_I97_F0.267340.662
23_Q26_D0.26730.662
59_I119_L0.267130.662
95_V129_L0.265240.657
23_Q77_V0.264240.654
123_E127_E0.262090.649
10_L137_F0.261330.647
14_A77_V0.257070.637
55_I116_S0.256010.634
127_E136_E0.254790.631
9_F12_V0.254510.630
45_L49_E0.253180.627
35_N68_N0.251010.622
97_F115_L0.247840.614
54_Y91_K0.247590.613
28_L34_V0.247190.612
54_Y92_P0.246680.611
28_L40_F0.245080.607
19_E23_Q0.244130.605
127_E131_A0.243080.602
74_I115_L0.2430.602
110_K117_R0.242310.600
61_L112_L0.242170.600
22_K42_E0.24090.597
15_K23_Q0.23950.593
75_S98_L0.238760.591
108_H116_S0.238260.590
14_A19_E0.237490.588
8_I138_I0.234520.581
15_K81_Q0.233180.578
27_K77_V0.232880.577
99_L108_H0.232370.576
24_L27_K0.229790.569
101_I111_L0.22880.567
47_R52_S0.227490.563
20_V77_V0.225460.558
10_L134_P0.224710.557
48_E52_S0.22410.555
4_D31_Q0.223650.554
54_Y61_L0.223470.553
57_N91_K0.221130.548
134_P137_F0.221050.548
13_E23_Q0.21890.542
4_D138_I0.218050.540
40_F98_L0.21710.538
74_I99_L0.216140.535
60_A93_V0.215760.534
9_F134_P0.215380.533
55_I109_L0.214950.532
25_A40_F0.214080.530
131_A134_P0.211580.524
4_D71_K0.20960.519
78_R132_K0.209150.518
86_D90_G0.208810.517
30_E42_E0.208530.516
60_A63_H0.207510.514
6_E134_P0.20750.514
54_Y84_K0.206330.511
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
2a0jA0.993199.90.027
3urrA0.986199.90.03
1a6jA0.993199.90.03
3oxpA0.979299.90.031
1a3aA0.972299.90.037
2oq3A0.972299.90.039
3lf6A0.979299.90.041
2oqtA0.965399.90.047
3bjvA0.965399.90.049
3t43A0.881999.90.097

Page generated in 0.0511 seconds.