GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PTS_EIIA_1 - phosphoenolpyruvate-dependent sugar phosphotransferase system EIIA 1
Pfam: PF00358 (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: CL0105
Length: 132
Sequences: 2154
Seq/Len: 16.32
HH_delta: -0.072 (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
27_K31_D1.322093.511
51_T63_R1.193543.169
46_V64_S0.994792.642
10_S39_D0.961642.554
91_K94_D0.946942.515
74_I103_I0.923122.451
47_D97_K0.910172.417
109_K113_A0.892262.369
89_L101_P0.875332.324
87_E104_E0.856572.275
41_K101_P0.843582.240
65_D95_K0.838992.228
80_K115_Y0.824652.190
89_L104_E0.811782.156
19_V34_A0.787022.090
41_K104_E0.739751.964
84_E113_A0.709351.884
85_G109_K0.706891.877
49_T95_K0.697861.853
97_K100_Q0.693211.841
36_I116_D0.691481.836
42_V72_I0.690671.834
57_K88_T0.667411.772
6_Y98_A0.662591.759
20_P116_D0.65451.738
40_G107_L0.63691.691
74_I105_F0.628851.670
47_D98_A0.617511.640
12_K36_I0.612811.627
17_E27_K0.591471.571
9_V42_V0.585151.554
108_E111_K0.580541.542
94_D100_Q0.543031.442
117_P120_P0.534661.420
49_T63_R0.529361.406
84_E109_K0.528651.404
108_E112_E0.519521.380
9_V119_T0.514881.367
48_G62_I0.510481.356
20_P118_T0.510291.355
14_I118_T0.507821.348
43_Y101_P0.500411.329
107_L111_K0.499921.328
107_L117_P0.489291.299
22_P26_Q0.486821.293
13_V33_V0.480641.276
36_I117_P0.469981.248
10_S38_S0.462191.227
50_V60_I0.461741.226
50_V90_V0.451371.199
46_V62_I0.439721.168
31_D126_S0.437631.162
60_I103_I0.42791.136
44_A62_I0.423931.126
61_G124_T0.422741.123
34_A118_T0.417021.107
53_I92_E0.413381.098
47_D65_D0.409511.087
109_K112_E0.408491.085
88_T103_I0.407981.083
81_L109_K0.40771.083
44_A47_D0.404661.075
105_F110_I0.388971.033
46_V70_I0.386751.027
15_P18_E0.386591.027
53_I88_T0.368340.978
69_E125_N0.364560.968
63_R69_E0.364260.967
23_V28_M0.35970.955
74_I119_T0.35840.952
81_L85_G0.357990.951
21_D24_F0.347430.923
36_I111_K0.346210.919
101_P104_E0.344830.916
33_V123_V0.341220.906
76_I120_P0.339210.901
33_V121_V0.339110.900
5_I46_V0.338550.899
62_I72_I0.334470.888
123_V126_S0.332950.884
42_V105_F0.33290.884
50_V62_I0.33280.884
14_I19_V0.329530.875
57_K87_E0.328120.871
7_A35_I0.32260.857
14_I34_A0.320810.852
81_L84_E0.319380.848
16_L27_K0.317320.843
85_G113_A0.31170.828
90_V94_D0.311570.827
81_L110_I0.310520.825
106_D109_K0.308260.819
52_M92_E0.307860.818
16_L19_V0.30470.809
7_A10_S0.300620.798
111_K117_P0.289820.770
110_I115_Y0.286910.762
58_H73_H0.285170.757
77_D80_K0.282680.751
9_V35_I0.281260.747
14_I18_E0.277430.737
85_G115_Y0.275030.730
21_D59_A0.274220.728
29_L124_T0.269340.715
64_S68_V0.267060.709
51_T61_G0.265850.706
53_I60_I0.257360.683
60_I102_L0.256710.682
98_A101_P0.256210.680
23_V29_L0.255830.679
35_I121_V0.25540.678
21_D25_S0.254930.677
34_A120_P0.252430.670
16_L32_G0.251870.669
41_K89_L0.251530.668
5_I123_V0.249220.662
52_M61_G0.247460.657
52_M60_I0.246430.654
50_V96_V0.243710.647
125_N128_E0.240030.637
53_I57_K0.238850.634
70_I123_V0.236980.629
24_F30_G0.236490.628
90_V100_Q0.236210.627
19_V118_T0.235730.626
109_K114_G0.235130.624
8_P121_V0.23480.623
49_T93_G0.232270.617
39_D107_L0.232250.617
62_I102_L0.231670.615
61_G69_E0.22880.608
69_E124_T0.228750.607
20_P76_I0.227370.604
55_P82_N0.222710.591
53_I103_I0.222680.591
14_I36_I0.219750.584
60_I72_I0.219650.583
72_I102_L0.218530.580
89_L103_I0.215740.573
57_K60_I0.215180.571
72_I121_V0.214670.570
21_D71_L0.214350.569
110_I117_P0.212260.564
46_V98_A0.210870.560
55_P92_E0.210480.559
72_I120_P0.20990.557
5_I121_V0.209540.556
20_P25_S0.209350.556
81_L115_Y0.208880.555
68_V123_V0.207820.552
12_K38_S0.207550.551
9_V37_P0.207160.550
88_T92_E0.206910.549
24_F59_A0.202640.538
28_M55_P0.201920.536
116_D119_T0.200280.532
36_I118_T0.199850.531
21_D30_G0.199420.530
9_V105_F0.197620.525
40_G108_E0.197530.525
7_A33_V0.196690.522
60_I90_V0.196480.522
44_A79_V0.195810.520
24_F58_H0.19350.514
23_V59_A0.193480.514
107_L110_I0.191120.508
40_G104_E0.191070.507
53_I90_V0.189950.504
42_V119_T0.189490.503
16_L122_V0.189340.503
40_G105_F0.18910.502
84_E112_E0.188980.502
46_V121_V0.187680.498
40_G101_P0.186010.494
57_K89_L0.185010.491
49_T92_E0.182720.485
56_T80_K0.181540.482
33_V68_V0.181030.481
78_T86_F0.180910.480
59_A71_L0.180690.480
29_L52_M0.179980.478
53_I58_H0.179860.478
21_D58_H0.17920.476
10_S43_Y0.178260.473
24_F71_L0.177870.472
58_H78_T0.177260.471
73_H79_V0.176820.470
23_V54_F0.176620.469
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
3ourB1100-0.072
1ax3A1100-0.013
1f3zA1100-0.009
2gprA0.9924100-0.006
2gu1A0.931897.50.8
3sluA0.901597.40.803
3tufB0.931897.40.805
2hsiA0.916797.30.806
1qwyA0.871297.30.808
1z6hA0.537997.20.811

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