GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Amidase_2 - N-acetylmuramoyl-L-alanine amidase
Pfam: PF01510 (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: 132
Sequences: 3008
Seq/Len: 22.79
HH_delta: 0.118 (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
61_H73_G1.206284.093
41_Y99_L0.946583.212
41_Y55_E0.920343.123
76_L96_L0.894843.036
12_I100_I0.838072.844
17_T75_E0.744862.527
49_I95_A0.734642.493
11_G71_S0.666142.260
39_Y75_E0.618562.099
13_V121_V0.59152.007
53_V59_A0.564751.916
44_D50_Y0.557221.891
117_G120_D0.541441.837
90_D94_E0.536091.819
102_D106_R0.505891.717
54_P57_R0.491661.668
10_K70_R0.482871.638
43_I96_L0.462551.569
14_I96_L0.456391.549
97_A101_A0.44451.508
72_I103_L0.441581.498
14_I100_I0.433131.470
55_E106_R0.424721.441
58_V69_A0.422881.435
47_G95_A0.415181.409
44_D48_T0.399021.354
16_H79_N0.396971.347
13_V116_V0.395491.342
13_V62_A0.381971.296
42_V52_G0.373271.267
16_H80_G0.371091.259
15_H128_C0.370671.258
11_G116_V0.357971.215
41_Y49_I0.351811.194
103_L107_Y0.351351.192
55_E103_L0.350541.189
30_F33_R0.342261.161
91_A95_A0.339521.152
44_D77_V0.337031.144
109_I114_G0.335031.137
16_H78_G0.329241.117
122_S125_R0.323961.099
94_E98_R0.321281.090
101_A104_C0.320731.088
15_H75_E0.313841.065
67_A121_V0.312481.060
116_V121_V0.309161.049
79_N85_D0.304171.032
76_L92_Q0.30311.028
22_S28_V0.299591.017
88_P93_I0.299231.015
98_R102_D0.298711.014
16_H88_P0.290960.987
27_A44_D0.288730.980
43_I74_I0.287160.974
39_Y42_V0.285130.967
62_A121_V0.28380.963
118_H128_C0.283010.960
55_E107_Y0.281980.957
42_V77_V0.281410.955
59_A73_G0.280180.951
15_H118_H0.278120.944
29_W32_W0.276370.938
38_S53_V0.27290.926
104_C109_I0.268790.912
19_G23_A0.267050.906
55_E99_L0.265540.901
74_I103_L0.264930.899
72_I107_Y0.261640.888
103_L106_R0.261590.888
125_R128_C0.259320.880
13_V71_S0.259310.880
10_K114_G0.25930.880
11_G67_A0.259280.880
110_P114_G0.259230.880
23_A26_N0.255610.867
74_I99_L0.25380.861
78_G130_G0.252930.858
104_C111_P0.251950.855
21_S26_N0.250980.852
32_W35_S0.24960.847
116_V120_D0.248330.843
55_E72_I0.246710.837
78_G89_T0.246540.837
56_N108_G0.244920.831
62_A67_A0.243650.827
14_I74_I0.242130.822
102_D105_R0.241290.819
100_I115_I0.238140.808
62_A73_G0.237930.807
124_T128_C0.234150.794
43_I76_L0.23270.790
75_E118_H0.232120.788
93_I97_A0.231460.785
117_G124_T0.230310.781
49_I99_L0.229860.780
63_G122_S0.229360.778
12_I103_L0.227270.771
9_P107_Y0.225670.766
28_V50_Y0.224010.760
42_V50_Y0.2230.757
74_I100_I0.221730.752
67_A70_R0.220970.750
24_A77_V0.219610.745
22_S44_D0.219260.744
122_S128_C0.21820.740
47_G89_T0.218010.740
62_A71_S0.217820.739
104_C115_I0.216610.735
11_G70_R0.215180.730
39_Y52_G0.213510.724
23_A27_A0.21340.724
76_L88_P0.213250.724
12_I72_I0.212850.722
41_Y72_I0.212830.722
111_P114_G0.21260.721
7_R10_K0.211290.717
21_S32_W0.210560.714
24_A28_V0.210180.713
68_N73_G0.208750.708
51_Q55_E0.208560.708
89_T92_Q0.20790.705
100_I104_C0.207850.705
20_P23_A0.206820.702
95_A98_R0.205070.696
53_V60_W0.204560.694
13_V73_G0.203620.691
11_G121_V0.20340.690
15_H61_H0.202660.688
97_A100_I0.202630.688
31_Y34_S0.202480.687
104_C110_P0.201490.684
37_A52_G0.201410.683
79_N86_D0.200460.680
16_H130_G0.19740.670
119_R122_S0.196790.668
14_I76_L0.195770.664
45_R77_V0.194370.660
38_S60_W0.19320.656
48_T85_D0.191820.651
88_P92_Q0.190870.648
79_N130_G0.19030.646
18_A125_R0.190250.646
109_I121_V0.189780.644
117_G130_G0.189360.643
99_L103_L0.188510.640
62_A128_C0.186390.632
17_T42_V0.185420.629
61_H68_N0.185380.629
9_P56_N0.18410.625
62_A122_S0.183620.623
19_G35_S0.183510.623
103_L108_G0.182860.620
21_S24_A0.182580.620
125_R130_G0.182070.618
22_S79_N0.181250.615
43_I99_L0.180970.614
40_H118_H0.178560.606
18_A79_N0.177980.604
29_W35_S0.177960.604
60_W68_N0.177760.603
116_V119_R0.177240.601
40_H96_L0.176610.599
94_E97_A0.176310.598
12_I74_I0.175160.594
26_N44_D0.174790.593
98_R105_R0.174220.591
40_H59_A0.174180.591
104_C107_Y0.174020.590
87_P90_D0.173840.590
96_L100_I0.172410.585
60_W75_E0.172280.585
80_G130_G0.172220.584
22_S25_A0.171410.582
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
1j3gA0.962199.90.118
3d2yA0.962199.90.155
3hmaA0.931899.90.157
1yb0A0.94799.90.162
3latA0.954599.90.192
2rkqA0.94799.90.195
2cb3A0.94799.90.198
1ohtA0.94799.90.2
2xz4A0.94799.90.203
1sk4A0.94799.90.203

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