GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GARS_N - Phosphoribosylglycinamide synthetase N domain
Pfam: PF02844 (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: 100
Sequences: 80082
Seq/Len: 800.82
HH_delta: 0.162 (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
83_R90_F4.604252.940
3_V65_L4.122492.632
86_G90_F4.035322.577
50_D53_E3.941992.517
83_R86_G3.789982.420
31_A46_I3.125511.996
2_K27_E3.089931.973
18_K22_S2.923091.866
13_H17_W2.74951.756
46_I53_E2.604661.663
51_P94_K2.518111.608
34_N37_T2.512131.604
2_K29_Y2.476341.581
8_S32_P2.424031.548
29_Y61_N2.415991.543
66_V95_E2.409131.538
3_V26_E2.37771.518
3_V19_L2.362211.508
44_V60_E2.351951.502
54_L95_E2.336741.492
35_P45_P2.281481.457
85_A89_V2.267811.448
51_P79_A2.267781.448
18_K21_Q2.248351.436
6_I68_V2.23841.429
53_E56_D2.16861.385
51_P55_A2.159851.379
26_E65_L2.153751.375
31_A57_F2.149581.372
56_D60_E2.125971.357
90_F94_K2.119441.353
35_P39_E2.033661.298
29_Y44_V1.960061.251
79_A94_K1.939191.238
27_E42_K1.938721.238
68_V96_A1.936791.237
2_K62_K1.931181.233
14_A17_W1.923921.228
78_L81_A1.921311.227
81_A84_A1.826811.166
46_I57_F1.810441.156
15_I67_V1.760371.124
9_G13_H1.753791.120
16_A30_V1.726151.102
4_L31_A1.719721.098
19_L26_E1.712151.093
55_A59_K1.703391.088
5_V16_A1.679481.072
38_A43_N1.672051.068
52_E56_D1.657681.058
56_D59_K1.644021.050
17_W21_Q1.633531.043
70_P84_A1.627781.039
73_P76_A1.623281.036
68_V95_E1.61581.032
85_A90_F1.607091.026
9_G37_T1.602361.023
51_P97_A1.537360.982
4_L63_I1.527390.975
14_A18_K1.519380.970
68_V92_P1.508850.963
49_T84_A1.480380.945
93_S97_A1.440850.920
46_I54_L1.43870.919
22_S26_E1.423310.909
44_V57_F1.398170.893
70_P81_A1.390.888
72_A81_A1.36530.872
49_T86_G1.364980.872
29_Y42_K1.350640.862
48_I91_G1.349410.862
87_I91_G1.334180.852
82_L90_F1.332510.851
92_P96_A1.322120.844
52_E55_A1.321890.844
90_F93_S1.31170.838
2_K64_D1.293320.826
19_L65_L1.287580.822
54_L94_K1.274490.814
11_R15_I1.26680.809
6_I95_E1.250760.799
23_P26_E1.248170.797
80_D84_A1.21980.779
4_L57_F1.210180.773
92_P95_E1.191370.761
79_A97_A1.176070.751
9_G34_N1.161430.742
10_G14_A1.155650.738
2_K61_N1.152230.736
17_W20_S1.150420.735
79_A90_F1.144890.731
49_T87_I1.10970.709
79_A83_R1.101710.703
30_V43_N1.099030.702
35_P43_N1.095260.699
15_I19_L1.091450.697
89_V93_S1.080410.690
77_G81_A1.070420.683
34_N38_A1.065480.680
36_G39_E1.062260.678
29_Y63_I1.060830.677
82_L89_V1.058530.676
4_L66_V1.057320.675
32_P43_N1.040360.664
44_V61_N1.030680.658
58_A61_N1.023340.653
35_P38_A1.01760.650
82_L93_S0.998190.637
45_P53_E0.994610.635
50_D54_L0.993210.634
9_G32_P0.976860.624
32_P38_A0.968460.618
57_F61_N0.952940.608
58_A66_V0.951050.607
66_V96_A0.949130.606
53_E57_F0.944410.603
8_S33_G0.922650.589
84_A87_I0.919340.587
15_I18_K0.912510.583
26_E64_D0.877330.560
29_Y60_E0.87290.557
74_L77_G0.871880.557
42_K61_N0.869910.555
16_A28_V0.86120.550
2_K63_I0.842760.538
47_D50_D0.838320.535
72_A78_L0.834850.533
94_K97_A0.830410.530
57_F95_E0.827060.528
16_A20_S0.820490.524
83_R94_K0.816720.521
32_P45_P0.809820.517
72_A77_G0.807680.516
72_A76_A0.803040.513
86_G94_K0.801750.512
20_S28_V0.797890.509
58_A95_E0.791290.505
69_G88_P0.78130.499
32_P35_P0.777270.496
79_A82_L0.770810.492
73_P77_G0.76750.490
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
2pzmA0.9699.10.162
3svtA0.9899.10.168
2z1mA0.9899.10.176
2q1wA0.9699.10.181
3pk0A0.98990.181
4dryA0.98990.182
3w1vA0.96990.183
4j2oA0.96990.183
2h7iA0.98990.183
3l6eA0.98990.185

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