GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Gluconate_2-dh3 - Gluconate 2-dehydrogenase subunit 3
Pfam: PF13618 (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: 131
Sequences: 764
Seq/Len: 5.83
HH_delta: 0.899 (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
14_T77_E0.388543.088
72_S75_Q0.384953.059
4_E50_R0.377783.002
18_A26_D0.349872.780
14_T76_R0.338622.691
16_I113_Y0.265142.107
52_G101_F0.242951.931
67_S70_E0.223311.775
49_F108_L0.223161.774
15_I106_R0.214781.707
12_A109_T0.207781.651
66_K70_E0.207431.648
73_P77_E0.20691.644
68_F76_R0.197711.571
14_T80_L0.195651.555
32_F112_G0.189941.509
7_T53_L0.185781.476
3_E57_D0.181931.446
28_G31_E0.179691.428
9_A30_P0.179451.426
11_I80_L0.175191.392
114_Y123_K0.17131.361
4_E54_A0.165971.319
5_A30_P0.162191.289
7_T69_A0.160291.274
27_A113_Y0.157861.255
43_P47_R0.155321.234
63_R82_A0.154921.231
64_Y78_A0.149711.190
23_G26_D0.145971.160
57_D67_S0.144281.147
75_Q78_A0.14411.145
13_D25_S0.142031.129
32_F116_S0.140991.120
7_T56_L0.140831.119
78_A82_A0.140081.113
59_Y63_R0.138831.103
84_E106_R0.138421.100
56_L105_L0.137711.094
9_A25_S0.137531.093
36_M39_D0.13631.083
8_L12_A0.135381.076
30_P34_D0.134361.068
32_F122_N0.13421.067
67_S81_D0.12991.032
38_A46_R0.128681.023
31_E34_D0.128671.023
73_P76_R0.128051.018
47_R51_A0.128041.018
77_E81_D0.12771.015
81_D84_E0.127011.009
7_T11_I0.126981.009
5_A34_D0.125540.998
37_L49_F0.125260.995
24_A29_V0.124520.990
46_R52_G0.124110.986
11_I53_L0.123570.982
36_M112_G0.123290.980
111_Q116_S0.122180.971
117_P122_N0.121950.969
10_A14_T0.121820.968
43_P50_R0.121470.965
57_D61_Q0.120320.956
14_T73_P0.118480.942
19_D122_N0.118230.940
102_F121_G0.117790.936
24_A109_T0.115910.921
16_I106_R0.11580.920
57_D69_A0.115170.915
109_T112_G0.115020.914
36_M43_P0.11490.913
3_E69_A0.114090.907
111_Q122_N0.113920.905
56_L100_R0.113840.905
27_A112_G0.112890.897
104_Q107_N0.11240.893
59_Y70_E0.112310.893
58_A74_A0.111240.884
19_D22_P0.109930.874
83_L99_A0.109190.868
2_A66_K0.108930.866
53_L57_D0.108770.864
10_A76_R0.108110.859
36_M108_L0.108050.859
38_A56_L0.107930.858
27_A118_E0.107890.857
16_I110_L0.10760.855
10_A25_S0.107520.854
39_D116_S0.107480.854
13_D97_P0.10660.847
6_A67_S0.106460.846
116_S122_N0.1060.842
2_A78_A0.105280.837
82_A87_E0.104370.829
47_R70_E0.104190.828
63_R79_L0.104120.827
97_P100_R0.103480.822
114_Y124_N0.103420.822
55_A83_L0.103050.819
20_D81_D0.102690.816
8_L37_L0.102640.816
25_S30_P0.10190.810
3_E7_T0.101750.809
2_A9_A0.100820.801
11_I100_R0.10030.797
2_A45_D0.10.795
43_P78_A0.099960.794
67_S79_L0.099920.794
55_A86_S0.099290.789
18_A113_Y0.099250.789
68_F71_L0.099150.788
42_M48_A0.098930.786
55_A87_E0.098740.785
74_A77_E0.098370.782
84_E101_F0.098280.781
4_E43_P0.09820.780
68_F80_L0.098160.780
13_D76_R0.097080.772
75_Q79_L0.096760.769
28_G112_G0.096620.768
51_A97_P0.096620.768
16_I32_F0.095570.760
78_A81_D0.095530.759
81_D85_K0.095390.758
106_R117_P0.095190.756
114_Y121_G0.09510.756
17_P116_S0.094870.754
56_L79_L0.094360.750
32_F36_M0.093450.743
111_Q114_Y0.093170.740
13_D18_A0.093020.739
52_G60_A0.092940.739
114_Y122_N0.09290.738
8_L105_L0.092660.736
14_T68_F0.092230.733
5_A9_A0.09220.733
59_Y107_N0.092090.732
17_P24_A0.091690.729
16_I108_L0.091590.728
42_M45_D0.091580.728
58_A61_Q0.09090.722
44_E78_A0.090780.721
64_Y75_Q0.090620.720
5_A53_L0.090490.719
79_L82_A0.090370.718
41_Y56_L0.090360.718
52_G105_L0.090250.717
28_G32_F0.089940.715
84_E102_F0.089490.711
38_A47_R0.089350.710
22_P29_V0.089190.709
118_E121_G0.089180.709
46_R50_R0.088860.706
6_A69_A0.088430.703
15_I37_L0.088240.701
26_D124_N0.08810.700
49_F105_L0.087990.699
111_Q117_P0.087910.699
73_P78_A0.087580.696
99_A103_Q0.087560.696
63_R72_S0.087190.693
35_R38_A0.086850.690
6_A70_E0.086660.689
7_T79_L0.086090.684
58_A62_K0.085830.682
121_G124_N0.085790.682
116_S123_K0.085740.681
6_A105_L0.085720.681
29_V33_I0.085630.681
6_A29_V0.085180.677
61_Q67_S0.085180.677
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
4ksaA0.908433.30.899
4ksfA0.908424.30.906
3plsA0.519121.90.908
2pvfA0.557317.80.911
1c7cA0.839715.60.913
4gk0E0.694715.10.914
2yb5A0.847314.70.914
2y8nA0.580214.40.914
2w9yA0.6641130.916
1h16A0.603112.70.916
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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