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OPENSEQ.org
YBIS - Probable L,D-transpeptidase YbiS
UniProt: P0AAX8 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG13324
Length: 306 (301)
Sequences: 310
Seq/Len: 1.03
YBIS
Paralog alert: 0.67 [within 20: 0.01] - ratio of genomes with paralogs
Cluster includes: ERFK YBIS YCFS YNHG
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
144_R 186_Y 2.603 1.00
107_E 239_K 2.501 0.99
96_T 234_I 2.319 0.99
58_A 67_M 2.258 0.98
131_G 207_S 2.165 0.98
152_T 174_A 2.07 0.97
27_Y 37_V 2.068 0.97
111_Y 239_K 1.965 0.95
160_E 208_H 1.961 0.95
36_L 92_I 1.837 0.92
155_A 159_A 1.784 0.91
250_I 305_L 1.783 0.91
101_I 142_V 1.651 0.86
152_T 171_V 1.619 0.84
91_L 122_V 1.606 0.84
126_G 207_S 1.567 0.82
107_E 111_Y 1.545 0.80
37_V 91_L 1.517 0.79
132_K 208_H 1.516 0.79
250_I 291_L 1.515 0.78
58_A 216_E 1.507 0.78
92_I 241_T 1.503 0.78
56_F 157_M 1.494 0.77
242_T 246_G 1.47 0.75
105_S 187_I 1.467 0.75
215_N 219_K 1.463 0.75
159_A 163_A 1.445 0.74
142_V 185_L 1.441 0.73
140_T 188_G 1.427 0.72
201_G 206_V 1.414 0.71
294_A 303_V 1.405 0.71
212_R 239_K 1.402 0.70
150_T 174_A 1.389 0.69
58_A 199_N 1.389 0.69
242_T 248_R 1.387 0.69
154_T 190_L 1.369 0.68
67_M 85_L 1.367 0.68
161_Y 166_E 1.357 0.67
125_I 211_V 1.346 0.66
219_K 223_E 1.339 0.65
138_W 199_N 1.329 0.64
31_T 98_H 1.315 0.63
14_A 17_G 1.306 0.63
187_I 192_A 1.306 0.63
12_A 15_V 1.302 0.62
3_M 8_L 1.301 0.62
155_A 170_A 1.301 0.62
53_L 301_M 1.3 0.62
201_G 204_L 1.297 0.62
3_M 9_F 1.289 0.61
140_T 256_L 1.277 0.60
110_L 197_N 1.263 0.59
180_M 192_A 1.254 0.58
75_D 78_L 1.242 0.57
7_T 16_V 1.24 0.57
4_K 7_T 1.238 0.56
158_H 168_L 1.231 0.56
75_D 200_F 1.225 0.55
52_P 77_F 1.219 0.55
148_G 228_G 1.217 0.54
54_E 214_R 1.215 0.54
57_A 250_I 1.214 0.54
156_K 208_H 1.213 0.54
145_K 237_P 1.212 0.54
162_R 172_V 1.208 0.54
80_K 83_T 1.206 0.53
153_P 158_H 1.205 0.53
199_N 202_I 1.196 0.52
63_G 201_G 1.194 0.52
123_L 220_F 1.194 0.52
8_L 12_A 1.191 0.52
4_K 17_G 1.19 0.52
25_V 61_Q 1.18 0.51
11_A 16_V 1.178 0.51
183_Y 219_K 1.168 0.50
143_E 186_Y 1.162 0.49
5_L 13_F 1.162 0.49
250_I 294_A 1.161 0.49
235_D 256_L 1.155 0.49
106_A 202_I 1.154 0.49
62_M 202_I 1.146 0.48
6_K 9_F 1.145 0.48
43_I 60_Y 1.145 0.48
153_P 191_Y 1.138 0.47
156_K 190_L 1.132 0.47
9_F 16_V 1.128 0.46
226_P 229_T 1.123 0.46
162_R 167_P 1.122 0.46
35_R 241_T 1.114 0.45
28_P 31_T 1.11 0.44
107_E 212_R 1.109 0.44
36_L 90_Q 1.107 0.44
157_M 208_H 1.104 0.44
78_L 200_F 1.102 0.44
12_A 18_F 1.1 0.44
12_A 17_G 1.099 0.43
9_F 15_V 1.098 0.43
132_K 160_E 1.094 0.43
124_P 217_D 1.094 0.43
11_A 14_A 1.092 0.43
186_Y 192_A 1.089 0.43
168_L 302_P 1.089 0.43
147_A 193_I 1.088 0.42
116_G 142_V 1.088 0.42
84_V 236_E 1.085 0.42
128_G 191_Y 1.085 0.42
6_K 16_V 1.077 0.41
288_Q 291_L 1.077 0.41
7_T 11_A 1.077 0.41
55_Y 250_I 1.073 0.41
184_A 192_A 1.072 0.41
6_K 18_F 1.071 0.41
30_P 256_L 1.07 0.41
4_K 8_L 1.069 0.41
30_P 140_T 1.068 0.41
99_E 163_A 1.064 0.40
32_D 101_I 1.062 0.40
57_A 90_Q 1.061 0.40
9_F 12_A 1.06 0.40
7_T 17_G 1.057 0.40
7_T 18_F 1.056 0.40
72_P 213_L 1.055 0.39
93_L 120_V 1.054 0.39
5_L 11_A 1.05 0.39
9_F 13_F 1.049 0.39
60_Y 177_D 1.047 0.39
229_T 249_Y 1.047 0.39
101_I 110_L 1.046 0.39
32_D 98_H 1.046 0.39
101_I 225_V 1.045 0.39
12_A 16_V 1.044 0.38
4_K 15_V 1.043 0.38
154_T 157_M 1.041 0.38
66_N 204_L 1.04 0.38
239_K 251_E 1.039 0.38
271_I 295_I 1.038 0.38
76_T 131_G 1.037 0.38
7_T 12_A 1.036 0.38
15_V 18_F 1.032 0.37
30_P 228_G 1.03 0.37
30_P 33_G 1.028 0.37
186_Y 305_L 1.028 0.37
206_V 252_V 1.025 0.37
48_G 81_G 1.025 0.37
5_L 12_A 1.022 0.37
108_M 186_Y 1.022 0.37
240_A 280_V 1.022 0.37
92_I 113_Y 1.021 0.36
150_T 293_E 1.018 0.36
34_S 244_P 1.017 0.36
96_T 113_Y 1.017 0.36
115_K 226_P 1.017 0.36
74_V 79_P 1.014 0.36
203_G 231_V 1.012 0.36
6_K 15_V 1.007 0.35
187_I 191_Y 1.006 0.35
80_K 241_T 1.005 0.35
78_L 115_K 1.001 0.35
8_L 18_F 1.001 0.35
127_I 235_D 1.001 0.35
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
4lzhA10.93141000.41Contact Map0.477
4jmnA10.65361000.671Contact Map0.285
4k73A10.71241000.688Contact Map0.284
4a1kA10.53591000.695Contact Map0.436
3vynA20.79741000.753Contact Map0.3
3vypA20.76141000.76Contact Map0.328
1zatA10.68951000.776Contact Map0.325
4lpqA10.581799.90.802Contact Map0.246
1e0gA10.156997.90.932Contact Map0.358
4b8vA10.290897.50.937Contact Map0.5
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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