GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ADK - Adenylate kinase
Pfam: PF00406 (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: CL0023
Length: 151
Sequences: 9935
Seq/Len: 65.79
HH_delta: 0.056 (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
115_T118_E1.77514.046
125_E129_K1.288522.937
44_Q47_E1.218762.778
113_D136_R1.163362.652
117_I129_K1.070282.439
133_E137_E1.063682.424
117_I121_S1.020852.327
47_E51_N1.01352.310
46_Q50_D0.999872.279
67_R70_Q0.941392.146
15_R18_K0.909732.074
121_S125_E0.882732.012
65_K69_E0.845391.927
14_K18_K0.829861.891
1_I13_A0.811561.850
134_E138_N0.764771.743
59_L62_E0.757311.726
7_S111_C0.75411.719
31_L60_V0.725041.653
14_K17_A0.695851.586
48_Y53_E0.691741.577
66_E70_Q0.682121.555
118_E122_Q0.675061.539
124_N127_V0.670861.529
130_K134_E0.638721.456
111_C116_L0.617191.407
30_L33_E0.614691.401
90_E93_E0.614611.401
33_E37_S0.614021.400
35_I38_D0.60991.390
134_E137_E0.591311.348
15_R19_R0.585721.335
61_I82_F0.584381.332
129_K133_E0.566081.290
67_R71_P0.562971.283
3_G7_S0.558851.274
6_G120_L0.554461.264
34_E42_G0.552561.259
4_P116_L0.54951.252
87_E90_E0.544921.242
113_D117_I0.543251.238
132_L136_R0.541161.233
48_Y56_P0.540911.233
113_D133_E0.535551.221
130_K133_E0.535171.220
114_E118_E0.534451.218
91_A94_E0.524421.195
35_I42_G0.524081.195
29_D64_L0.522471.191
40_E43_K0.521021.188
13_A17_A0.511021.165
34_E66_E0.51071.164
47_E50_D0.508071.158
127_V130_K0.494661.127
120_L128_I0.494581.127
39_S42_G0.491581.120
8_G11_T0.489391.115
111_C115_T0.48511.106
34_E39_S0.483791.103
62_E65_K0.482381.099
86_L90_E0.472321.077
116_L120_L0.470511.072
13_A24_H0.469651.070
28_G32_R0.468711.068
44_Q48_Y0.467091.065
43_K47_E0.462871.055
25_I30_L0.462171.053
69_E99_E0.460731.050
40_E44_Q0.460531.050
38_D43_K0.460291.049
112_P115_T0.450911.028
57_D61_I0.450361.026
17_A24_H0.448091.021
111_C119_R0.445271.015
61_I91_A0.444641.013
61_I134_E0.440241.003
133_E136_R0.439131.001
10_G80_D0.435560.993
90_E94_E0.434670.991
34_E37_S0.433120.987
36_K42_G0.424190.967
56_P60_V0.419640.956
4_P7_S0.416880.950
113_D129_K0.416130.948
38_D42_G0.413220.942
34_E63_L0.40910.932
70_Q73_C0.406490.926
45_I49_L0.406290.926
2_L106_V0.40460.922
35_I39_S0.400280.912
135_Y139_T0.400020.912
12_Q15_R0.399760.911
85_T88_Q0.39910.910
65_K99_E0.397270.905
126_E130_K0.396550.904
71_P74_N0.395990.903
42_G46_Q0.39570.902
86_L89_A0.387780.884
115_T119_R0.384690.877
43_K46_Q0.377910.861
46_Q49_L0.37160.847
7_S110_D0.369420.842
56_P59_L0.367280.837
3_G10_G0.362530.826
35_I49_L0.361280.823
123_D127_V0.358610.817
81_G84_R0.357110.814
34_E38_D0.350660.799
8_G119_R0.350520.799
123_D128_I0.350280.798
36_K39_S0.348790.795
5_P116_L0.344560.785
3_G8_G0.343620.783
22_L76_G0.343140.782
4_P135_Y0.342770.781
84_R88_Q0.342340.780
45_I48_Y0.340410.776
30_L34_E0.337440.769
10_G28_G0.337240.769
12_Q109_L0.336060.766
65_K68_L0.333460.760
85_T92_L0.332730.758
29_D33_E0.332650.758
120_L132_L0.331020.754
11_T119_R0.328810.749
66_E69_E0.327320.746
11_T15_R0.322640.735
61_I65_K0.317870.725
87_E91_A0.315910.720
61_I64_L0.315160.718
17_A21_G0.315150.718
44_Q62_E0.314880.718
3_G9_K0.308950.704
49_L57_D0.306510.699
79_L92_L0.303710.692
64_L67_R0.302420.689
57_D60_V0.301490.687
33_E67_R0.300910.686
114_E117_I0.299870.683
81_G88_Q0.298250.680
127_V131_R0.297860.679
24_H75_R0.294960.672
73_C76_G0.294790.672
26_S29_D0.294170.670
7_S10_G0.294110.670
126_E129_K0.292790.667
12_Q16_L0.29260.667
74_N77_F0.29150.664
2_L108_F0.291150.664
1_I16_L0.289350.660
69_E72_P0.288710.658
37_S40_E0.284930.649
52_G55_V0.283860.647
64_L68_L0.283480.646
58_E62_E0.280110.638
67_R72_P0.27950.637
16_L20_Y0.279470.637
7_S109_L0.279250.636
89_A92_L0.279220.636
10_G13_A0.278880.636
4_P113_D0.278580.635
88_Q92_L0.276520.630
33_E36_K0.274830.626
99_E102_P0.274510.626
48_Y51_N0.274210.625
124_N130_K0.268860.613
13_A25_I0.268760.613
4_P108_F0.268210.611
104_D107_I0.26720.609
13_A23_V0.266890.608
131_R135_Y0.26620.607
81_G85_T0.265040.604
57_D85_T0.264290.602
128_I132_L0.263440.600
69_E100_G0.261620.596
68_L71_P0.260280.593
21_G75_R0.260250.593
110_D113_D0.259740.592
1_I109_L0.258850.590
5_P120_L0.255360.582
71_P76_G0.255090.581
29_D32_R0.254270.580
14_K24_H0.253780.578
124_N132_L0.252950.577
20_Y23_V0.252460.575
17_A23_V0.248430.566
7_S116_L0.247260.564
44_Q51_N0.24630.561
3_G13_A0.245650.560
121_S124_N0.245550.560
60_V85_T0.245160.559
12_Q119_R0.24480.558
35_I43_K0.244460.557
77_F80_D0.244420.557
31_L35_I0.244030.556
58_E61_I0.242140.552
32_R35_I0.240950.549
82_F89_A0.240530.548
55_V60_V0.239660.546
57_D87_E0.239560.546
13_A80_D0.238920.545
37_S45_I0.23820.543
54_L131_R0.236580.539
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
3sr0A0.980199.90.056
3umfA0.973599.90.066
3gmtA0.973599.90.086
3tlxA199.90.139
3dl0A199.80.171
3fb4A199.80.179
3be4A199.80.193
1akyA199.80.212
1ak2A199.80.213
2xb4A0.993499.80.229

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