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AMPD - 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD
UniProt: P13016 Sequence
Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG10041
Length: 183 (179)
Sequences: 810
Seq/Len: 4.53

AMPD
Paralog alert: 0.05 [within 20: 0.00] - ratio of genomes with paralogs
GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Scaled Score Prob
18_H 54_G 3.962 1.00
31_L 137_T 3.451 1.00
48_I 77_L 3.389 1.00
127_D 173_R 3.093 1.00
134_A 177_L 2.928 1.00
137_T 174_F 2.915 1.00
76_C 90_F 2.909 1.00
117_L 133_L 2.686 1.00
49_D 87_Y 2.68 1.00
89_P 92_K 2.61 1.00
19_Y 92_K 2.581 1.00
76_C 136_V 2.549 1.00
130_Y 170_D 2.461 1.00
7_W 13_R 2.448 1.00
84_I 132_Q 2.445 1.00
20_D 107_R 2.443 1.00
79_R 85_V 2.05 1.00
12_R 83_E 2.014 1.00
58_P 67_I 1.999 1.00
21_C 92_K 1.855 1.00
121_D 163_T 1.844 1.00
20_D 71_R 1.84 1.00
35_N 121_D 1.806 1.00
88_V 94_A 1.799 1.00
125_Y 168_A 1.766 1.00
78_I 133_L 1.754 1.00
79_R 83_E 1.733 0.99
63_F 66_E 1.701 0.99
46_P 50_A 1.695 0.99
47_W 50_A 1.679 0.99
93_R 110_D 1.675 0.99
78_I 117_L 1.644 0.99
19_Y 89_P 1.627 0.99
46_P 79_R 1.597 0.99
63_F 67_I 1.557 0.99
33_V 174_F 1.546 0.99
41_G 120_T 1.538 0.98
31_L 174_F 1.531 0.98
40_P 63_F 1.517 0.98
47_W 64_F 1.515 0.98
90_F 140_L 1.453 0.98
100_S 157_I 1.445 0.97
120_T 123_L 1.423 0.97
58_P 68_A 1.37 0.96
32_V 157_I 1.363 0.96
103_Q 150_N 1.348 0.96
12_R 85_V 1.327 0.95
40_P 67_I 1.317 0.95
50_A 53_T 1.315 0.95
139_A 143_C 1.307 0.95
54_G 76_C 1.286 0.94
57_D 60_A 1.277 0.94
127_D 131_Q 1.267 0.94
65_A 68_A 1.265 0.93
42_E 61_H 1.257 0.93
14_V 53_T 1.239 0.92
29_T 150_N 1.237 0.92
90_F 144_Y 1.219 0.92
32_V 152_T 1.213 0.91
158_A 161_R 1.159 0.89
102_Y 150_N 1.148 0.88
18_H 76_C 1.143 0.88
3_L 8_L 1.139 0.88
101_Q 104_G 1.137 0.87
20_D 93_R 1.137 0.87
35_N 166_G 1.123 0.87
8_L 136_V 1.104 0.85
35_N 125_Y 1.063 0.82
90_F 136_V 1.06 0.82
172_A 176_V 1.043 0.81
173_R 177_L 1.032 0.80
50_A 70_L 1.014 0.78
43_F 123_L 1.013 0.78
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.
HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov P(%) HHΔ   Acc
1j3gA111000.292Contact Map0.465
4bxjA20.83611000.407Contact Map0.787
3d2yA10.85791000.413Contact Map0.584
4bolA20.86341000.423Contact Map0.789
3latA20.87431000.477Contact Map0.473
3hmaA20.83611000.517Contact Map0.603
1yb0A30.83611000.524Contact Map0.615
1ohtA10.88521000.537Contact Map0.435
2rkqA10.8471000.541Contact Map0.495
2cb3A40.87431000.543Contact Map0.499

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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