GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PRA-CH - Phosphoribosyl-AMP cyclohydrolase
Pfam: PF01502 (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: 75
Sequences: 1431
Seq/Len: 19.08
HH_delta: -0.03 (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
13_T42_V1.319332.978
18_R31_R1.204832.719
5_M56_F1.157222.612
43_V59_E1.068062.411
69_R74_Y1.028392.321
20_T31_R1.017952.298
19_A56_F0.997072.250
41_K61_V0.994912.246
44_E57_K0.974082.199
2_L53_A0.968242.185
12_K15_E0.920542.078
28_R34_E0.915812.067
16_T20_T0.890162.009
7_K11_E0.849141.917
11_E15_E0.845371.908
41_K59_E0.844121.905
22_Y27_N0.8191.849
45_I56_F0.817691.846
21_Y40_Q0.784091.770
28_R35_T0.743661.678
18_R41_K0.736461.662
39_T61_V0.728581.644
31_R34_E0.66821.508
19_A42_V0.640871.446
60_Q63_P0.639041.442
3_A64_A0.618651.396
18_R39_T0.61861.396
12_K20_T0.615111.388
46_R57_K0.600281.355
6_N29_L0.564221.273
12_K29_L0.551261.244
67_T74_Y0.496051.120
48_D52_D0.492661.112
21_Y60_Q0.481631.087
38_N60_Q0.477661.078
12_K16_T0.47741.078
40_Q58_V0.462241.043
6_N9_A0.457281.032
22_Y29_L0.423290.955
12_K31_R0.421960.952
21_Y58_V0.417640.943
60_Q64_A0.415970.939
31_R39_T0.406270.917
6_N22_Y0.399110.901
8_E12_K0.379890.857
40_Q60_Q0.378560.854
14_L45_I0.37340.843
18_R34_E0.344430.777
8_E11_E0.341850.772
47_L51_G0.340340.768
5_M9_A0.332440.750
42_V73_F0.328780.742
1_M53_A0.326330.737
20_T29_L0.3210.725
3_A19_A0.31780.717
11_E27_N0.311550.703
40_Q64_A0.311090.702
47_L74_Y0.308050.695
1_M55_L0.301320.680
5_M13_T0.299030.675
22_Y26_R0.293520.662
37_G58_V0.292480.660
16_T31_R0.281120.635
42_V56_F0.280180.632
38_N68_G0.279450.631
8_E29_L0.279310.630
63_P69_R0.275770.622
26_R30_W0.274620.620
17_G41_K0.271110.612
25_S53_A0.269030.607
23_S30_W0.268820.607
3_A49_C0.268750.607
10_L54_L0.265320.599
9_A20_T0.262780.593
2_L24_R0.257970.582
6_N27_N0.252110.569
46_R55_L0.252070.569
38_N63_P0.246540.556
10_L45_I0.24650.556
19_A40_Q0.243340.549
49_C52_D0.241920.546
7_K70_R0.241110.544
38_N61_V0.237910.537
57_K70_R0.225480.509
4_Y47_L0.225390.509
47_L70_R0.22440.506
53_A73_F0.220480.498
42_V45_I0.219590.496
5_M42_V0.219010.494
32_K66_H0.218550.493
1_M50_D0.216140.488
5_M55_L0.214050.483
24_R53_A0.211530.477
1_M30_W0.208330.470
22_Y25_S0.207770.469
7_K51_G0.207410.468
43_V61_V0.206890.467
38_N49_C0.206220.465
7_K10_L0.20290.458
20_T63_P0.202590.457
14_L17_G0.202360.457
9_A29_L0.202020.456
46_R67_T0.201930.456
45_I54_L0.200570.453
38_N62_G0.199250.450
26_R35_T0.197940.447
10_L51_G0.196110.443
46_R74_Y0.195860.442
11_E61_V0.195710.442
57_K74_Y0.192730.435
25_S51_G0.190360.430
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
1zpsA1100-0.03
3tixA0.826746.30.912
3kydD0.653342.40.913
2ekeC0.666734.70.918
1wz0A0.7226.30.922
3pgeA0.826721.60.925
1yiiA0.6817.50.928
2d07B0.6667170.928
1n00A0.6815.50.93
2zhjA0.6814.90.93

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