GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PEP-utilisers_N - PEP-utilising enzyme N-terminal
Pfam: PF05524 (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: 123
Sequences: 1746
Seq/Len: 14.2
HH_delta: 0.037 (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
41_E87_E0.763773.774
39_R97_E0.722283.569
40_L86_V0.649333.208
37_I91_R0.610323.016
48_R78_E0.534582.641
90_I96_A0.489892.421
101_Q105_E0.478352.364
37_I87_E0.46962.320
36_E96_A0.457012.258
89_L93_G0.449522.221
38_E42_Q0.42112.081
32_D35_A0.418962.070
111_F114_M0.416912.060
108_I112_E0.397271.963
55_A71_E0.392981.942
34_E91_R0.392521.939
89_L102_E0.387571.915
85_E103_V0.38451.900
52_E74_L0.37181.837
86_V100_V0.333371.647
51_L74_L0.331681.639
117_P120_R0.31861.574
40_L44_L0.316141.562
36_E39_R0.295721.461
107_Y111_F0.293211.449
88_E92_E0.288041.423
35_A38_E0.285811.412
45_E49_E0.276811.368
87_E91_R0.275541.361
109_E112_E0.270861.338
25_I98_Y0.264531.307
38_E41_E0.260861.289
57_R61_K0.255831.264
115_D120_R0.251791.244
49_E52_E0.247451.223
84_D87_E0.245961.215
72_A76_M0.240511.188
59_E64_E0.239761.185
114_M119_L0.238851.180
27_E98_Y0.2381.176
47_A77_L0.232531.149
89_L106_E0.231561.144
82_L104_I0.226511.119
44_L83_I0.218211.078
48_R74_L0.21691.072
58_A70_F0.214811.061
117_P121_E0.213681.056
8_P104_I0.212861.052
47_A54_L0.208431.030
30_I95_N0.205691.016
85_E88_E0.205351.015
30_I33_I0.204631.011
63_G67_A0.203531.006
52_E56_E0.200530.991
75_M118_Y0.199360.985
73_H79_D0.198460.981
105_E109_E0.192660.952
112_E123_A0.191390.946
42_Q45_E0.188760.933
40_L90_I0.188450.931
71_E118_Y0.187710.927
28_R95_N0.187450.926
108_I114_M0.186990.924
88_E91_R0.186890.923
56_E59_E0.185790.918
55_A67_A0.18350.907
113_A119_L0.183250.905
34_E37_I0.182610.902
69_I73_H0.180120.890
26_P97_E0.178920.884
6_V73_H0.178560.882
68_A71_E0.177520.877
39_R63_G0.176860.874
98_Y102_E0.176760.873
30_I94_K0.175450.867
83_I87_E0.174550.862
40_L83_I0.174530.862
42_Q49_E0.173750.858
118_Y122_R0.172360.852
118_Y121_E0.171130.846
81_E84_D0.170750.844
54_L70_F0.170390.842
59_E66_E0.169630.838
109_E113_A0.16850.833
70_F77_L0.167510.828
83_I86_V0.167430.827
47_A50_E0.167360.827
76_M114_M0.166820.824
41_E83_I0.164290.812
55_A59_E0.163240.807
109_E120_R0.163040.806
82_L100_V0.163030.806
60_S67_A0.162540.803
35_A49_E0.162240.802
18_L21_P0.161820.800
96_A99_A0.161730.799
84_D88_E0.161340.797
49_E60_S0.160540.793
73_H116_D0.1560.771
34_E38_E0.15590.770
49_E53_Q0.154630.764
100_V111_F0.15410.761
4_I7_S0.149890.741
75_M79_D0.148860.736
98_Y101_Q0.148610.734
44_L79_D0.148510.734
82_L123_A0.148450.733
52_E78_E0.148420.733
37_I41_E0.146090.722
58_A63_G0.145840.721
68_A72_A0.145440.719
30_I93_G0.145350.718
82_L86_V0.144490.714
89_L103_V0.144280.713
73_H80_P0.14250.704
100_V118_Y0.142180.703
47_A76_M0.142050.702
94_K98_Y0.141540.699
42_Q46_K0.141440.699
85_E106_E0.141360.698
82_L103_V0.14120.698
49_E56_E0.140590.695
16_F76_M0.140530.694
7_S82_L0.140220.693
36_E90_I0.14020.693
58_A62_L0.140160.693
91_R94_K0.139550.690
55_A73_H0.139140.687
13_G58_A0.139090.687
94_K102_E0.138920.686
41_E44_L0.138870.686
75_M104_I0.138680.685
45_E48_R0.138480.684
110_Q113_A0.138450.684
1_L45_E0.138170.683
108_I119_L0.138160.683
77_L100_V0.138090.682
7_S15_A0.137660.680
95_N100_V0.136360.674
105_E108_I0.13590.671
89_L105_E0.134760.666
102_E105_E0.134530.665
20_P40_L0.133060.657
75_M100_V0.132960.657
106_E109_E0.132910.657
55_A72_A0.131260.649
28_R46_K0.131160.648
46_K92_E0.13110.648
104_I108_I0.130680.646
38_E91_R0.130580.645
51_L73_H0.130560.645
13_G57_R0.129780.641
89_L94_K0.129720.641
31_D35_A0.129690.641
111_F119_L0.129340.639
50_E54_L0.129170.638
23_P90_I0.129040.638
51_L70_F0.128960.637
18_L74_L0.128840.637
6_V104_I0.128180.633
34_E42_Q0.128120.633
68_A110_Q0.128020.633
10_I111_F0.12740.629
69_I79_D0.12730.629
28_R31_D0.127130.628
6_V77_L0.127020.628
44_L100_V0.126670.626
36_E97_E0.126650.626
77_L108_I0.126330.624
50_E80_P0.125790.622
13_G24_E0.125090.618
28_R62_L0.125030.618
69_I108_I0.124180.614
85_E89_L0.123570.611
63_G73_H0.123460.610
40_L87_E0.123220.609
62_L70_F0.122510.605
70_F121_E0.122420.605
86_V103_V0.122390.605
38_E46_K0.12230.604
33_I91_R0.122160.604
43_A83_I0.122120.603
33_I37_I0.121730.601
73_H84_D0.12160.601
76_M108_I0.120470.595
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
1zymA11000.037
2wqdA199.90.125
2hwgA199.90.127
3p7mA0.471533.50.903
7mdhA0.617927.50.906
3craA0.81325.80.908
1nm8A0.577222.60.91
4ixoA0.422822.50.91
2d4aB0.471521.40.911
1ez4A0.479719.80.912

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