GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GMP_synt_C - GMP synthase C terminal domain
Pfam: PF00958 (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: 93
Sequences: 945
Seq/Len: 10.16
HH_delta: -0.074 (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_W49_F1.035523.503
46_S49_F0.844712.858
14_W46_S0.791342.677
68_R72_E0.770622.607
39_V76_V0.73812.497
45_E55_A0.733672.482
84_T89_A0.726462.458
61_L65_I0.722932.446
56_R63_E0.626772.120
34_T77_N0.600352.031
10_Y16_A0.592482.004
44_V91_I0.551121.865
7_A64_E0.544171.841
5_K10_Y0.540851.830
2_E6_K0.535871.813
29_Q34_T0.527791.786
57_L61_L0.499861.691
38_V80_V0.496761.681
63_E67_S0.488051.651
54_W59_W0.487411.649
29_Q70_T0.472721.599
36_G75_G0.446091.509
3_E6_K0.443651.501
70_T84_T0.443321.500
21_L40_V0.417761.413
12_K45_E0.398721.349
19_V93_W0.394681.335
13_I55_A0.385061.303
3_E68_R0.376681.274
9_L61_L0.3751.269
56_R60_E0.372051.259
53_D85_S0.364751.234
3_E72_E0.347831.177
43_A55_A0.345331.168
3_E64_E0.338051.144
4_L16_A0.333221.127
9_L12_K0.331441.121
64_E67_S0.329081.113
24_R37_Y0.328351.111
13_I57_L0.327421.108
18_A39_V0.309351.047
78_R82_D0.308391.043
41_L65_I0.306831.038
2_E68_R0.303681.027
4_L13_I0.299091.012
39_V79_V0.299081.012
4_L7_A0.298831.011
45_E53_D0.297591.007
54_W66_S0.295531.000
5_K11_D0.290270.982
62_L83_I0.280010.947
64_E68_R0.279210.945
80_V93_W0.27650.935
38_V93_W0.276490.935
54_W63_E0.274420.928
43_A57_L0.272060.920
21_L38_V0.270950.917
9_L13_I0.270710.916
6_K64_E0.269750.913
7_A61_L0.264720.896
63_E85_S0.264130.894
28_V31_D0.259230.877
36_G70_T0.254880.862
8_G11_D0.251770.852
36_G74_P0.238760.808
22_P38_V0.23330.789
82_D93_W0.232620.787
3_E7_A0.232580.787
29_Q77_N0.22990.778
44_V52_A0.228120.772
18_A76_V0.227350.769
40_V80_V0.226260.765
8_G13_I0.223240.755
66_S84_T0.222810.754
25_S38_V0.221220.748
29_Q36_G0.221020.748
36_G84_T0.219220.742
34_T73_V0.218680.740
13_I43_A0.210830.713
66_S83_I0.210680.713
38_V89_A0.207180.701
8_G12_K0.204970.693
36_G47_E0.203650.689
53_D63_E0.201020.680
4_L8_G0.197490.668
44_V89_A0.197090.667
16_A23_V0.196240.664
24_R36_G0.195430.661
6_K72_E0.188910.639
2_E72_E0.187940.636
12_K55_A0.187660.635
23_V93_W0.187240.633
25_S78_R0.18670.632
5_K16_A0.186450.631
86_K92_E0.186240.630
18_A41_L0.186070.630
67_S85_S0.184320.624
55_A58_P0.184240.623
10_Y22_P0.183270.620
86_K90_T0.182380.617
54_W58_P0.182250.617
22_P93_W0.181640.615
18_A36_G0.17970.608
25_S35_Y0.17810.603
31_D71_N0.176050.596
26_V33_R0.172870.585
27_G33_R0.172310.583
32_Q74_P0.171510.580
13_I47_E0.170310.576
63_E66_S0.169730.574
42_R50_M0.168960.572
6_K37_Y0.168650.571
47_E70_T0.167640.567
3_E17_F0.166750.564
47_E51_T0.163260.552
46_S53_D0.16290.551
30_G88_P0.162540.550
83_I93_W0.162030.548
20_L29_Q0.1610.545
59_W74_P0.159680.540
18_A47_E0.159130.538
64_E72_E0.158460.536
66_S70_T0.157790.534
80_V83_I0.156790.530
70_T75_G0.156120.528
34_T74_P0.156080.528
31_D35_Y0.15510.525
19_V23_V0.153690.520
56_R59_W0.153450.519
40_V43_A0.153080.518
5_K9_L0.152260.515
19_V52_A0.15160.513
3_E48_D0.151050.511
54_W83_I0.150470.509
50_M87_P0.149980.507
11_D16_A0.149610.506
13_I61_L0.148790.503
28_V33_R0.148410.502
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
3uowA1100-0.074
3tqiA1100-0.067
1gpmA1100-0.025
2ywbA1100-0.014
2vxoA0.98921000.033
2dplA0.97851000.085
2vxoA195.70.86
2wcuA0.419447.60.92
3e7nA0.419434.60.926
2wcvA0.419433.30.927

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