GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
QRPTase_N - Quinolinate phosphoribosyl transferase N-terminal domain
Pfam: PF02749 (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: CL0105
Length: 88
Sequences: 2033
Seq/Len: 23.1
HH_delta: 0.02 (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
18_G70_A1.049722.683
52_K55_D1.028142.628
46_E67_E1.007212.574
51_V61_D0.939242.401
50_L65_E0.885362.263
40_F80_A0.882392.255
43_L76_A0.861162.201
19_T67_E0.832412.128
27_D58_E0.746911.909
48_E65_E0.736361.882
17_T67_E0.700621.791
30_L51_V0.697531.783
27_D59_P0.682591.745
30_L57_V0.662821.694
19_T65_E0.651071.664
15_D69_P0.624631.597
51_V55_D0.612681.566
38_E42_K0.573581.466
30_L33_L0.568671.453
30_L63_I0.567561.451
37_E41_E0.562971.439
22_I36_A0.527611.349
58_E61_D0.522821.336
45_L68_G0.519991.329
36_A64_L0.512671.310
21_T62_V0.512211.309
69_P72_A0.494371.264
62_V65_E0.488181.248
39_I79_T0.487721.247
36_A80_A0.477781.221
48_E67_E0.47311.209
37_E49_W0.466011.191
34_E53_D0.464911.188
45_L66_I0.457441.169
43_L72_A0.456351.166
44_G69_P0.454051.161
39_I76_A0.448331.146
21_T65_E0.442971.132
47_V64_L0.427041.091
38_E41_E0.425911.089
39_I83_F0.418071.069
27_D56_R0.417341.067
30_L84_L0.416851.065
17_T69_P0.405371.036
28_G57_V0.387580.991
77_E81_L0.385750.986
78_R81_L0.376850.963
14_P71_R0.373950.956
22_I81_L0.368320.941
74_L82_N0.365160.933
22_I84_L0.364530.932
35_E87_L0.359180.918
76_A80_A0.354610.906
45_L72_A0.35320.903
22_I66_I0.347710.889
33_L49_W0.340010.869
36_A39_I0.334520.855
18_G73_L0.333180.852
78_R82_N0.330570.845
33_L37_E0.323830.828
12_I70_A0.320380.819
29_V56_R0.316580.809
32_G88_S0.316430.809
39_I80_A0.313150.800
36_A47_V0.312240.798
16_K70_A0.310010.792
26_E59_P0.309170.790
74_L77_E0.306460.783
57_V63_I0.304520.778
34_E37_E0.302460.773
34_E38_E0.297670.761
28_G88_S0.297520.760
17_T46_E0.296430.758
74_L78_R0.295850.756
24_A57_V0.293590.750
40_F76_A0.292860.749
15_D71_R0.292830.748
20_A66_I0.287970.736
22_I64_L0.284860.728
6_L24_A0.282280.721
24_A28_G0.281140.719
30_L88_S0.275230.703
39_I42_K0.268870.687
83_F87_L0.2640.675
28_G61_D0.262990.672
33_L84_L0.262380.671
40_F66_I0.260390.666
40_F45_L0.25580.654
53_D77_E0.255580.653
33_L52_K0.249130.637
31_A87_L0.247940.634
13_P71_R0.247320.632
42_K83_F0.246610.630
77_E82_N0.238280.609
35_E83_F0.231640.592
22_I80_A0.231320.591
32_G87_L0.22770.582
5_D8_T0.227390.581
81_L86_R0.227190.581
12_I71_R0.224570.574
35_E39_I0.222950.570
24_A63_I0.222160.568
48_E52_K0.221090.565
20_A78_R0.218720.559
27_D57_V0.217670.556
19_T58_E0.216880.554
50_L56_R0.214610.549
46_E49_W0.2130.544
43_L75_T0.211530.541
20_A77_E0.209850.536
64_L84_L0.209010.534
37_E47_V0.207440.530
43_L73_L0.206580.528
49_W55_D0.206550.528
31_A85_Q0.206120.527
35_E86_R0.203780.521
44_G48_E0.203180.519
13_P16_K0.203150.519
75_T87_L0.202080.517
16_K69_P0.200280.512
16_K71_R0.199650.510
51_V57_V0.199560.510
7_T11_L0.198720.508
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
1x1oA199.90.02
3l0gA0.988699.90.046
1o4uA0.977399.90.047
3tqvA0.977399.90.055
1qpoA0.988699.90.055
3pajA0.988699.90.061
3gnnA0.988699.90.07
2b7nA0.988699.90.091
2jbmA0.977399.80.098
1qapA0.977399.80.109

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