GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UPF0079 - Uncharacterised P-loop hydrolase UPF0079
Pfam: PF02367 (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: 123
Sequences: 3598
Seq/Len: 29.25
HH_delta: 0.267 (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
31_F35_L0.733652.686
21_S110_E0.678012.482
32_V93_V0.638392.337
13_K16_D0.620762.272
98_E103_L0.60092.200
21_S112_E0.572062.094
21_S98_E0.571812.093
5_A31_F0.546272.000
12_L35_L0.543671.990
12_L18_I0.534781.958
5_A34_G0.530861.943
36_A63_L0.497991.823
6_K37_R0.494641.811
117_D120_R0.490451.795
116_L119_N0.485561.777
69_Y95_E0.485011.775
35_L93_V0.447441.638
81_G84_E0.444141.626
8_L31_F0.443941.625
67_D70_R0.436581.598
46_T49_T0.42921.571
19_L97_P0.424651.555
34_G38_A0.407491.492
21_S97_P0.404011.479
68_L100_L0.396521.452
46_T54_N0.389541.426
36_A45_V0.38471.408
6_K10_Q0.38181.398
92_C96_W0.368721.350
64_Y90_G0.368521.349
7_K10_Q0.364541.334
88_E92_C0.354981.299
36_A41_I0.349941.281
68_L97_P0.34521.264
76_E79_D0.331171.212
55_E64_Y0.330981.212
108_R111_I0.327311.198
116_L120_R0.318961.168
111_I115_I0.317541.162
20_L32_V0.306921.124
69_Y94_I0.291861.068
47_S95_E0.291431.067
5_A9_A0.28671.050
96_W100_L0.28561.045
53_V66_F0.283841.039
48_P56_Y0.283151.037
112_E115_I0.276751.013
33_R39_L0.275441.008
91_I95_E0.274841.006
41_I45_V0.272180.996
80_L86_L0.271670.994
50_F53_V0.268570.983
29_T64_Y0.263740.965
86_L94_I0.263210.964
74_P102_E0.261160.956
75_E78_E0.261070.956
72_E76_E0.260770.955
23_D115_I0.260640.954
47_S50_F0.259610.950
9_A38_A0.259460.950
75_E79_D0.259150.949
49_T56_Y0.258320.946
19_L108_R0.25550.935
99_R106_E0.25420.931
103_L119_N0.251820.922
48_P54_N0.251110.919
77_L82_L0.249990.915
34_G41_I0.249740.914
48_P95_E0.248730.911
50_F56_Y0.247050.904
30_T119_N0.245940.900
47_S56_Y0.245890.900
93_V96_W0.245580.899
69_Y73_D0.245150.897
53_V64_Y0.244750.896
31_F113_I0.244580.895
34_G40_G0.243990.893
36_A65_H0.243760.892
7_K11_I0.243220.890
86_L92_C0.242990.890
36_A54_N0.241670.885
66_F92_C0.239650.877
80_L84_E0.238220.872
9_A35_L0.238040.871
92_C97_P0.235930.864
95_E109_L0.235570.862
22_G27_G0.23550.862
66_F82_L0.233990.857
10_Q13_K0.233530.855
22_G25_G0.232720.852
55_E85_Y0.229110.839
9_A39_L0.225540.826
77_L100_L0.224980.824
89_D92_C0.224260.821
12_L16_D0.223740.819
29_T94_I0.223390.818
46_T50_F0.220580.807
18_I67_D0.219320.803
47_S69_Y0.219050.802
98_E101_K0.217090.795
70_R96_W0.21570.790
76_E90_G0.215460.789
73_D94_I0.215220.788
61_I91_I0.2130.780
16_D91_I0.212460.778
47_S96_W0.21240.778
6_K11_I0.212120.777
116_L121_R0.210760.772
51_S56_Y0.210670.771
65_H70_R0.210270.770
20_L69_Y0.209380.766
51_S54_N0.208970.765
78_E83_E0.20790.761
67_D95_E0.206970.758
49_T52_L0.206030.754
103_L116_L0.205960.754
65_H69_Y0.205310.752
49_T53_V0.202990.743
53_V57_E0.202390.741
34_G45_V0.202150.740
65_H96_W0.20.732
49_T59_G0.199650.731
46_T53_V0.199570.731
71_L77_L0.199160.729
107_D120_R0.198970.728
90_G94_I0.198630.727
71_L80_L0.197760.724
11_I14_P0.196930.721
47_S65_H0.195240.715
19_L26_A0.194070.710
56_Y67_D0.19250.705
33_R38_A0.19180.702
83_E87_F0.190650.698
43_E117_D0.188940.692
81_G85_Y0.188410.690
8_L109_L0.188080.689
77_L80_L0.188010.688
80_L85_Y0.186670.683
62_P90_G0.186550.683
71_L113_I0.186180.682
115_I119_N0.185580.679
19_L110_E0.185460.679
40_G43_E0.18520.678
22_G28_K0.18480.676
103_L108_R0.184710.676
53_V56_Y0.183240.671
48_P96_W0.182990.670
72_E98_E0.182760.669
25_G28_K0.182310.667
91_I94_I0.181810.666
6_K9_A0.180480.661
82_L86_L0.180180.660
86_L91_I0.179740.658
51_S55_E0.179020.655
11_I119_N0.178930.655
72_E99_R0.178670.654
69_Y109_L0.177810.651
52_L56_Y0.177110.648
29_T87_F0.176630.647
49_T67_D0.176580.646
67_D96_W0.176330.645
66_F74_P0.176040.644
41_I44_E0.176020.644
96_W99_R0.175510.642
46_T51_S0.174950.640
33_R37_R0.174620.639
20_L95_E0.174550.639
101_K110_E0.174490.639
15_G117_D0.173740.636
20_L25_G0.173420.635
73_D86_L0.170470.624
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
3fvqA0.951299.80.267
3rlfA0.951299.80.277
4hluD0.951299.80.283
3tuiC0.951299.80.284
1v43A0.951299.80.288
1z47A0.951299.80.289
2yyzA0.951299.80.289
1g2910.951299.80.29
2it1A0.951299.80.29
1oxxK0.951299.80.292

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