GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
P-mevalo_kinase - Phosphomevalonate kinase
Pfam: PF04275 (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: 116
Sequences: 2502
Seq/Len: 21.57
HH_delta: 0.172 (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
61_P65_A0.687332.828
10_D95_S0.610782.513
31_S35_K0.548942.258
36_R40_E0.540922.225
79_C97_M0.525562.162
34_I78_F0.521672.146
36_R85_E0.514462.116
38_Y64_I0.472521.944
62_D66_W0.464031.909
83_V109_N0.458561.886
31_S98_R0.454581.870
1_F13_A0.443771.826
15_I18_S0.418091.720
37_E84_E0.413531.701
63_M75_P0.397281.634
8_G11_Y0.391971.613
80_R83_V0.378521.557
104_A107_R0.374851.542
105_W108_E0.37441.540
35_K98_R0.366971.510
14_D17_A0.362651.492
26_R85_E0.328011.349
79_C105_W0.322781.328
14_D27_I0.312941.287
101_T104_A0.311711.282
104_A108_E0.31151.281
14_D18_S0.310621.278
63_M68_E0.309381.273
100_K104_A0.302121.243
59_Y62_D0.291821.201
25_C91_V0.288551.187
102_D106_F0.283521.166
1_F16_L0.273461.125
76_G99_R0.26741.100
20_L25_C0.266921.098
77_F80_R0.257711.060
44_L80_R0.255981.053
87_A90_D0.247721.019
97_M103_V0.246511.014
32_D35_K0.245081.008
24_N90_D0.240280.988
79_C83_V0.237960.979
31_S96_D0.235110.967
62_D65_A0.23480.966
37_E40_E0.233690.961
1_F17_A0.233320.960
13_A27_I0.232760.958
59_Y63_M0.22910.943
3_G9_K0.228450.940
34_I38_Y0.22660.932
15_I19_R0.224310.923
26_R88_D0.223210.918
10_D29_S0.22310.918
20_L24_N0.217810.896
17_A27_I0.214880.884
29_S32_D0.213290.877
84_E89_V0.211510.870
13_A93_I0.210350.865
3_G8_G0.209010.860
4_K106_F0.20880.859
58_Q62_D0.207960.856
17_A24_N0.207160.852
67_G98_R0.206220.848
28_V85_E0.204920.843
88_D100_K0.204230.840
63_M66_W0.203910.839
79_C82_A0.202530.833
33_P82_A0.201280.828
33_P37_E0.200780.826
105_W109_N0.199570.821
17_A26_R0.197910.814
89_V92_W0.195480.804
18_S26_R0.194620.801
38_Y41_A0.193530.796
18_S24_N0.191640.788
37_E41_A0.18920.778
76_G105_W0.187880.773
62_D108_E0.183520.755
29_S95_S0.183430.755
32_D36_R0.183110.753
61_P108_E0.18290.752
1_F93_I0.181520.747
84_E87_A0.181030.745
10_D35_K0.179880.740
5_R78_F0.179560.739
33_P96_D0.177940.732
24_N108_E0.177940.732
20_L93_I0.17650.726
43_G59_Y0.175840.723
5_R95_S0.174640.718
99_R106_F0.173370.713
25_C87_A0.173040.712
31_S99_R0.172520.710
15_I107_R0.172030.708
87_A108_E0.169760.698
93_I109_N0.169710.698
37_E81_A0.16970.698
5_R30_I0.168480.693
96_D99_R0.168130.692
20_L28_V0.167670.690
100_K108_E0.167590.689
13_A30_I0.167090.687
19_R24_N0.167080.687
43_G62_D0.166780.686
76_G80_R0.165290.680
37_E44_L0.163920.674
28_V81_A0.163260.672
5_R81_A0.16270.669
5_R96_D0.16250.669
69_E103_V0.162420.668
79_C109_N0.162160.667
2_S77_F0.160170.659
63_M77_F0.160090.659
35_K96_D0.159780.657
31_S94_I0.158570.652
30_I99_R0.156230.643
10_D98_R0.156180.643
26_R90_D0.155730.641
99_R102_D0.155260.639
36_R101_T0.154520.636
69_E84_E0.154430.635
90_D104_A0.151970.625
38_Y61_P0.151230.622
67_G70_Q0.150640.620
78_F99_R0.149420.615
68_E89_V0.148930.613
43_G100_K0.148370.610
14_D101_T0.147490.607
83_V108_E0.147270.606
64_I81_A0.146990.605
41_A99_R0.14430.594
5_R31_S0.143290.589
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
3ch4B0.991499.70.172
3sr0A0.844899.30.37
3umfA0.844899.30.384
3gmtA0.844899.20.41
1dekA0.974199.20.413
3lw7A0.8362990.475
3tlxA0.844898.90.479
3dl0A0.844898.90.49
3fb4A0.844898.90.491
1e4vA0.844898.90.491

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