GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PP_kinase_N - Polyphosphate kinase N-terminal domain
Pfam: PF13089 (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: 109
Sequences: 1193
Seq/Len: 10.94
HH_delta: -0.02 (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
11_S80_R0.495832.622
21_A87_E0.457172.418
11_S14_E0.450982.385
68_L76_A0.445552.357
49_V77_I0.433122.291
14_E87_E0.406452.150
19_E25_V0.391132.069
90_E94_E0.361651.913
21_A91_I0.352541.865
101_A106_H0.349971.851
30_R91_I0.348821.845
99_E102_E0.33891.792
78_R82_H0.32771.733
80_R83_E0.323661.712
87_E90_E0.317581.680
9_W13_N0.316621.675
38_S88_Q0.303131.603
85_V89_Y0.301641.595
47_V50_A0.297741.575
52_L73_Q0.296241.567
14_E80_R0.295851.565
37_F84_L0.295181.561
92_Y97_L0.28271.495
23_E95_E0.271151.434
35_A54_R0.268231.419
37_F88_Q0.267671.416
4_N73_Q0.264951.401
71_Q75_D0.262891.390
23_E99_E0.256271.355
9_W35_A0.255221.350
92_Y107_L0.23591.248
46_M73_Q0.231031.222
75_D79_K0.226311.197
37_F89_Y0.221751.173
76_A79_K0.219551.161
20_A91_I0.219081.159
99_E103_E0.217921.153
4_N55_Q0.21241.123
34_L107_L0.206041.090
32_K81_V0.205581.087
10_L81_V0.204681.083
69_T73_Q0.203331.075
27_L96_L0.201791.067
89_Y93_N0.200551.061
72_E76_A0.197871.047
79_K83_E0.197631.045
32_K35_A0.194451.028
86_E102_E0.191881.015
34_L96_L0.190311.007
83_E87_E0.1880.994
6_E52_L0.186140.984
35_A46_M0.181920.962
38_S85_V0.181380.959
55_Q60_V0.181170.958
4_N66_D0.179710.950
56_I74_L0.179560.950
7_L80_R0.178860.946
14_E84_L0.178280.943
35_A93_N0.176840.935
9_W46_M0.176440.933
12_F16_V0.172920.915
80_R84_L0.17140.907
90_E98_P0.170660.903
11_S103_E0.170220.900
45_F85_V0.169580.897
59_G70_P0.168690.892
19_E88_Q0.167870.888
97_L107_L0.167560.886
49_V52_L0.166860.883
55_Q70_P0.166760.882
9_W33_F0.166350.880
98_P102_E0.165940.878
30_R105_I0.164290.869
7_L76_A0.162850.861
6_E73_Q0.16220.858
90_E93_N0.162160.858
34_L88_Q0.16150.854
69_T72_E0.161260.853
81_V84_L0.160320.848
46_M89_Y0.158810.840
54_R65_P0.158460.838
50_A78_R0.157920.835
18_E21_A0.156820.829
98_P101_A0.15470.818
56_I71_Q0.154520.817
41_L85_V0.153430.811
78_R81_V0.151790.803
87_E91_I0.151680.802
10_L31_L0.151460.801
52_L68_L0.151090.799
53_K57_E0.150820.798
53_K56_I0.150810.798
94_E98_P0.149980.793
86_E106_H0.149810.792
16_V81_V0.148350.785
49_V74_L0.148110.783
39_S107_L0.147040.778
23_E97_L0.146450.775
85_V88_Q0.145310.769
74_L78_R0.145150.768
9_W47_V0.145070.767
32_K73_Q0.143580.759
15_R50_A0.142530.754
4_N51_G0.142060.751
4_N69_T0.140920.745
17_L37_F0.140640.744
8_S72_E0.140560.743
39_S47_V0.140080.741
10_L93_N0.139780.739
3_F71_Q0.139450.738
94_E101_A0.139260.737
27_L99_E0.139170.736
58_A107_L0.139010.735
27_L105_I0.138910.735
86_E104_G0.138340.732
93_N96_L0.1380.730
10_L85_V0.137770.729
25_V35_A0.137440.727
93_N109_N0.137230.726
46_M60_V0.137170.725
37_F45_F0.137130.725
68_L72_E0.136730.723
17_L45_F0.136380.721
72_E86_E0.136350.721
51_G55_Q0.13610.720
21_A94_E0.136070.720
29_E100_L0.13520.715
10_L41_L0.135070.714
10_L16_V0.1350.714
63_R72_E0.134510.711
61_K72_E0.134260.710
10_L22_D0.134250.710
47_V54_R0.133930.708
18_E25_V0.133760.707
4_N68_L0.132790.702
10_L77_I0.132670.702
58_A61_K0.132530.701
64_D67_G0.132340.700
53_K64_D0.131360.695
55_Q59_G0.131260.694
103_E106_H0.130650.691
53_K77_I0.130620.691
81_V85_V0.130350.689
21_A95_E0.130230.689
21_A45_F0.130020.688
56_I61_K0.12940.684
56_I96_L0.128760.681
10_L15_R0.128680.681
77_I84_L0.128150.678
19_E73_Q0.127770.676
8_S51_G0.127470.674
31_L35_A0.12710.672
54_R57_E0.126540.669
99_E106_H0.125840.666
21_A106_H0.125590.664
83_E109_N0.125410.663
7_L52_L0.125120.662
31_L60_V0.125120.662
8_S47_V0.124930.661
22_D34_L0.124740.660
92_Y109_N0.123930.655
88_Q92_Y0.123810.655
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
2o8rA1100-0.02
1xdpA0.97251000.004
1zj8A0.8807550.924
3ivzA0.477115.60.942
1th5A0.266114.40.943
3b0gA0.880712.40.944
1ekjA0.440411.20.945
2akjA0.880711.10.945
3cx8B0.871610.60.946
3nufA0.385310.60.946

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