GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AIRS - AIR synthase related protein N-terminal domain
Pfam: PF00586 (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: 96
Sequences: 5566
Seq/Len: 57.98
HH_delta: 0.019 (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
34_Y82_E1.468923.020
38_W83_A1.259362.589
34_Y75_E1.198812.464
75_E78_K1.121332.305
16_V53_A1.089852.240
81_A85_R1.039382.137
48_L53_A1.006482.069
34_Y78_K0.950631.954
59_L93_G0.943881.940
82_E86_E0.880051.809
62_L73_L0.877141.803
4_A51_M0.86571.780
60_D80_I0.856311.760
17_V59_L0.843781.734
82_E85_R0.826541.699
83_A86_E0.802541.650
57_A92_V0.797091.639
2_D51_M0.790811.626
6_V16_V0.784741.613
35_D79_G0.779221.602
19_T61_S0.773521.590
32_D35_D0.730741.502
35_D38_W0.720641.481
41_V58_I0.709841.459
69_S72_E0.699441.438
42_A83_A0.680471.399
10_P13_K0.680071.398
38_W42_A0.679871.398
41_V80_I0.679141.396
64_L73_L0.676491.391
84_C91_I0.655621.348
5_A92_V0.652191.341
57_A90_P0.646511.329
45_L87_F0.644791.325
84_C89_I0.638271.312
45_L89_I0.637941.311
4_A16_V0.616621.268
18_S48_L0.615571.265
21_G61_S0.61211.258
38_W86_E0.601831.237
64_L76_I0.600841.235
21_G63_G0.585431.203
38_W82_E0.555711.142
33_P72_E0.509531.047
37_G79_G0.504741.038
37_G80_I0.504081.036
8_R14_R0.489561.006
78_K82_E0.481980.991
68_E72_E0.477930.982
41_V45_L0.466470.959
74_K78_K0.457370.940
6_V51_M0.456140.938
8_R12_G0.455320.936
9_I13_K0.454830.935
7_I57_A0.441760.908
17_V57_A0.435370.895
45_L49_A0.4340.892
41_V84_C0.42920.882
76_I80_I0.424180.872
71_E75_E0.419830.863
58_I80_I0.416740.857
39_K43_E0.414950.853
60_D77_V0.414290.852
45_L83_A0.412890.849
55_P89_I0.408960.841
41_V83_A0.405340.833
3_D50_A0.404750.832
58_I84_C0.402370.827
16_V48_L0.401440.825
70_P74_K0.400260.823
54_K88_G0.394140.810
34_Y79_G0.386270.794
20_D47_D0.382740.787
2_D50_A0.376650.774
22_F43_E0.373070.767
71_E74_K0.372650.766
42_A87_F0.368080.757
22_F40_A0.366740.754
72_E75_E0.363720.748
72_E76_I0.362210.745
64_L72_E0.362060.744
79_G83_A0.356430.733
19_T59_L0.354150.728
59_L92_V0.35040.720
61_S95_D0.347760.715
60_D91_I0.347010.713
32_D75_E0.344070.707
25_S39_K0.342060.703
3_D20_D0.337610.694
7_I10_P0.334850.688
6_V14_R0.332980.684
9_I15_L0.331380.681
80_I83_A0.329260.677
15_L56_L0.3280.674
68_E73_L0.325550.669
40_A76_I0.32460.667
78_K81_A0.323250.664
37_G76_I0.321790.661
58_I91_I0.315680.649
77_V80_I0.312310.642
31_M36_G0.309820.637
4_A50_A0.309190.636
7_I15_L0.308990.635
33_P75_E0.306880.631
26_V76_I0.304840.627
22_F95_D0.300890.619
44_A58_I0.300680.618
43_E47_D0.298590.614
42_A45_L0.29780.612
66_N69_S0.291280.599
35_D75_E0.287620.591
40_A62_L0.28260.581
42_A46_S0.281170.578
8_R13_K0.271670.558
10_P14_R0.270050.555
63_G95_D0.268710.552
25_S46_S0.266830.549
85_R88_G0.266770.548
92_V96_T0.265020.545
77_V81_A0.263580.542
31_M88_G0.263290.541
75_E79_G0.260590.536
26_V31_M0.257560.529
18_S44_A0.255430.525
23_G39_K0.25530.525
7_I92_V0.255120.524
23_G63_G0.249210.512
20_D37_G0.248720.511
7_I13_K0.248580.511
73_L77_V0.245350.504
71_E78_K0.244350.502
7_I17_V0.243130.500
83_A87_F0.241450.496
65_P72_E0.24120.496
56_L90_P0.240750.495
9_I12_G0.239460.492
84_C90_P0.236140.485
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
3mcqA0.989699.80.019
3c9uA0.989699.80.042
2zodA0.947999.80.046
2yydA0.947999.80.049
3u0oA0.958399.80.054
3fd5A0.958399.80.061
2yxzA0.989699.80.065
2z1uA0.958399.80.075
2rb9A0.979299.80.078
3vtiC0.937599.80.096

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