GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CHMI - 5-carboxymethyl-2-hydroxymuconate isomerase
Pfam: PF02962 (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: CL0082
Length: 124
Sequences: 1370
Seq/Len: 11.05
HH_delta: 0.081 (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
72_S75_Q0.394982.437
23_A90_H0.360412.224
30_A82_A0.344922.128
80_S106_I0.337892.085
73_E112_A0.33622.075
85_A89_A0.31271.930
84_L102_L0.305751.887
26_D30_A0.298051.839
26_D36_E0.249211.538
78_A82_A0.249081.537
17_I48_H0.246671.522
81_E85_A0.246041.518
88_K95_F0.237081.463
6_E44_I0.236681.461
80_S115_F0.226651.399
6_E42_R0.222011.370
25_H41_V0.221661.368
21_L41_V0.221461.367
109_M114_Y0.220691.362
76_K108_E0.214871.326
10_N13_D0.213431.317
70_G108_E0.209571.293
35_P38_G0.208871.289
25_H29_L0.208061.284
32_G67_I0.201261.242
82_A85_A0.199881.233
26_D86_V0.195871.209
72_S76_K0.193411.194
42_R47_D0.19021.174
66_R107_R0.188781.165
73_E77_K0.188091.161
69_A111_P0.186351.150
22_R26_D0.185281.143
23_A89_A0.184191.137
21_L50_R0.182541.126
27_A86_V0.180681.115
73_E108_E0.180581.114
21_L31_S0.180431.113
64_T107_R0.177321.094
115_F118_N0.177091.093
45_R48_H0.175051.080
57_D101_Q0.174431.076
66_R105_E0.173891.073
36_E54_G0.173821.073
40_K103_S0.173671.072
21_L43_A0.173141.068
23_A86_V0.170221.050
59_A101_Q0.169771.048
105_E109_M0.169121.044
27_A82_A0.167951.036
16_D59_A0.167411.033
79_L83_L0.167191.032
78_A81_E0.166411.027
54_G81_E0.166191.026
55_Q101_Q0.16561.022
49_Y60_F0.165421.021
62_H105_E0.16381.011
23_A91_L0.160530.991
78_A89_A0.159180.982
76_K80_S0.158080.976
25_H36_E0.155980.963
33_L75_Q0.155870.962
64_T105_E0.153390.947
7_Y43_A0.153250.946
22_R85_A0.152680.942
67_I76_K0.152510.941
6_E71_R0.149450.922
85_A93_P0.14850.916
16_D19_A0.148160.914
88_K91_L0.147190.908
17_I43_A0.146530.904
30_A86_V0.146520.904
21_L38_G0.145930.901
19_A23_A0.144970.895
45_R107_R0.144770.893
68_L109_M0.144690.893
22_R39_I0.144250.890
29_L111_P0.144030.889
68_L111_P0.143690.887
21_L24_L0.143630.886
77_K81_E0.142680.880
86_V90_H0.142350.878
26_D90_H0.141780.875
21_L39_I0.140770.869
38_G103_S0.139630.862
18_P50_R0.139060.858
25_H53_D0.139060.858
40_K62_H0.13870.856
77_K83_L0.137740.850
88_K92_A0.13750.849
82_A86_V0.136910.845
13_D19_A0.136670.843
29_L36_E0.135720.838
40_K114_Y0.135580.837
68_L80_S0.135230.835
18_P22_R0.134510.830
74_E78_A0.134080.827
20_L86_V0.134010.827
33_L78_A0.133480.824
31_S82_A0.133470.824
66_R109_M0.133370.823
55_Q115_F0.133030.821
61_V65_L0.133020.821
19_A57_D0.133010.821
55_Q58_D0.132770.819
110_D114_Y0.132460.817
25_H28_L0.131060.809
34_F67_I0.1310.808
87_L95_F0.130990.808
47_D51_V0.130650.806
32_G39_I0.12980.801
78_A85_A0.129540.799
74_E77_K0.129230.797
12_E45_R0.128690.794
26_D77_K0.127770.788
19_A86_V0.127360.786
26_D78_A0.126690.782
76_K106_I0.125510.775
7_Y71_R0.125440.774
39_I67_I0.123810.764
23_A26_D0.122570.756
92_A95_F0.1220.753
86_V89_A0.121830.752
74_E96_A0.121820.752
46_C96_A0.12170.751
43_A50_R0.121670.751
17_I45_R0.12150.750
42_R103_S0.121410.749
58_D101_Q0.121370.749
30_A112_A0.120810.746
93_P106_I0.120130.741
75_Q78_A0.120070.741
16_D90_H0.119680.739
12_E24_L0.119260.736
34_F103_S0.118920.734
106_I115_F0.118680.732
38_G116_K0.118640.732
28_L75_Q0.11850.731
28_L65_L0.117620.726
40_K44_I0.11760.726
51_V93_P0.117520.725
84_L104_V0.116990.722
26_D29_L0.116750.720
40_K51_V0.116110.717
28_L72_S0.115690.714
17_I20_L0.115660.714
68_L105_E0.115390.712
22_R36_E0.11490.709
40_K66_R0.114640.707
23_A27_A0.114390.706
46_C49_Y0.113950.703
71_R79_L0.113840.703
61_V103_S0.113530.701
19_A78_A0.113360.700
33_L36_E0.113190.698
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
4dh4A0.919499.90.081
3t5sA0.911399.90.097
2wkbA0.943599.90.101
3djhA0.919499.90.103
3kanA0.935599.80.115
3fwtA0.903299.80.117
3fwuA0.903299.80.117
1uizA0.919499.80.122
2xczA0.919499.80.123
1hfoA0.911399.80.125

Page generated in 0.0175 seconds.