GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GARS_C - Phosphoribosylglycinamide synthetase C domain
Pfam: PF02843 (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: 2111
Seq/Len: 22.7
HH_delta: 0.101 (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
4_G55_T1.663594.547
21_P45_Q1.361563.722
36_H39_V1.244583.402
17_E20_F1.130433.090
7_L82_M0.954422.609
3_V67_R0.803162.195
23_T78_D0.720411.969
3_V89_G0.676291.849
40_K47_V0.671581.836
62_T65_E0.667731.825
75_E86_K0.642031.755
7_L74_I0.635051.736
67_R90_H0.622421.701
9_S20_F0.600441.641
64_E68_E0.587351.605
42_E45_Q0.582441.592
32_V73_A0.575961.574
20_F80_P0.573871.569
67_R89_G0.569331.556
4_G57_V0.564551.543
58_A70_A0.553861.514
74_I84_Y0.543481.486
41_K46_L0.541061.479
20_F48_T0.530871.451
61_D65_E0.521421.425
10_K17_E0.514841.407
18_K49_N0.500481.368
9_S16_Y0.499691.366
69_K72_E0.489011.337
25_E46_L0.481931.317
74_I82_M0.475921.301
73_A76_K0.475371.299
40_K49_N0.469491.283
5_V71_Y0.46721.277
5_V74_I0.464121.269
79_F82_M0.461571.262
60_G65_E0.460111.258
72_E75_E0.459581.256
10_K81_G0.457711.251
6_V37_A0.443581.213
21_P47_V0.426171.165
8_A83_F0.423711.158
68_E72_E0.421561.152
63_L92_A0.410911.123
48_T79_F0.406171.110
2_S59_L0.402311.100
1_A63_L0.401121.096
16_Y83_F0.399461.092
65_E68_E0.39931.091
10_K80_P0.37511.025
72_E76_K0.372561.018
63_L93_L0.367541.005
10_K16_Y0.366271.001
10_K20_F0.364310.996
65_E69_K0.356690.975
56_V73_A0.353660.967
42_E47_V0.34680.948
56_V77_I0.342140.935
11_G16_Y0.338920.926
22_I54_L0.330270.903
20_F81_G0.324670.887
67_R93_L0.322640.882
60_G69_K0.320650.876
15_S18_K0.317340.867
3_V66_A0.306110.837
2_S57_V0.29830.815
85_R88_I0.295610.808
17_E81_G0.287560.786
48_T82_M0.285150.779
36_H46_L0.279750.765
31_G69_K0.276850.757
11_G15_S0.276480.756
75_E84_Y0.276380.755
6_V54_L0.275020.752
1_A62_T0.266610.729
12_Y52_R0.260340.712
60_G71_Y0.259420.709
30_E69_K0.254540.696
58_A73_A0.252250.690
9_S51_G0.251380.687
41_K45_Q0.250840.686
38_G53_V0.24780.677
9_S53_V0.24750.677
32_V69_K0.243250.665
33_H59_L0.24030.657
68_E75_E0.239320.654
35_F55_T0.238460.652
53_V79_F0.234790.642
67_R91_R0.234270.640
3_V70_A0.229980.629
29_P32_V0.229290.627
38_G51_G0.228420.624
6_V51_G0.225650.617
34_V54_L0.222080.607
33_H57_V0.218680.598
58_A69_K0.218490.597
7_L54_L0.215460.589
8_A91_R0.214470.586
38_G49_N0.213030.582
78_D82_M0.21180.579
2_S22_I0.211020.577
10_K48_T0.210990.577
7_L84_Y0.21070.576
5_V51_G0.209520.573
64_E93_L0.207310.567
51_G71_Y0.20710.566
4_G56_V0.207080.566
7_L79_F0.203580.556
71_Y74_I0.20310.555
85_R89_G0.202070.552
34_V56_V0.199120.544
28_E34_V0.196250.536
45_Q69_K0.196210.536
35_F48_T0.19490.533
70_A77_I0.193610.529
3_V63_L0.193360.529
1_A61_D0.192440.526
61_D64_E0.191160.523
38_G52_R0.190520.521
4_G7_L0.189940.519
26_E73_A0.188670.516
19_G49_N0.188460.515
24_G77_I0.18770.513
5_V70_A0.187160.512
27_E31_G0.185540.507
5_V56_V0.184870.505
1_A58_A0.184320.504
27_E76_K0.183920.503
32_V58_A0.182770.500
75_E78_D0.182630.499
25_E28_E0.182580.499
35_F50_G0.182340.498
19_G47_V0.181620.496
6_V9_S0.180360.493
9_S38_G0.180270.493
56_V89_G0.178510.488
22_I77_I0.178170.487
23_T80_P0.177920.486
69_K76_K0.177920.486
28_E31_G0.177380.485
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
3mjfA199.90.101
3lp8A199.90.132
2xclA199.70.367
2yrxA199.60.387
2ip4A0.989299.60.4
2qk4A199.60.402
2yw2A199.60.406
1vkzA0.924799.60.421
2dzdA0.967798.80.615
1w96A0.95798.70.625

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