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OPENSEQ.org
SYW - Tryptophan--tRNA ligase
UniProt: P00954 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG11030
Length: 334 (329)
Sequences: 3807
Seq/Len: 11.57
SYW
Paralog alert: 0.88 [within 20: 0.02] - 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
212_D 215_S 3.688 1.00
140_Q 323_A 3.204 1.00
87_E 314_S 3.084 1.00
61_L 303_Q 2.883 1.00
87_E 318_S 2.835 1.00
38_I 316_H 2.794 1.00
301_F 304_Q 2.672 1.00
5_I 36_H 2.664 1.00
286_T 290_E 2.542 1.00
291_R 294_R 2.536 1.00
171_I 327_A 2.402 1.00
75_E 308_D 2.361 1.00
260_E 264_Q 2.325 1.00
259_P 262_E 2.308 1.00
290_E 294_R 2.296 1.00
263_K 267_G 2.273 1.00
101_F 126_F 2.259 1.00
7_F 40_C 2.219 1.00
259_P 263_K 2.212 1.00
140_Q 320_T 2.132 1.00
36_H 78_T 2.131 1.00
38_I 78_T 2.102 1.00
217_V 221_K 2.083 1.00
38_I 141_T 2.035 1.00
12_P 46_A 1.995 1.00
301_F 305_V 1.948 1.00
224_V 227_S 1.937 1.00
216_V 282_S 1.915 1.00
308_D 311_E 1.914 1.00
7_F 42_V 1.875 1.00
65_A 68_L 1.829 1.00
65_A 302_L 1.808 1.00
262_E 266_E 1.801 1.00
283_G 288_L 1.8 1.00
265_F 276_E 1.796 1.00
257_S 260_E 1.793 1.00
105_S 126_F 1.786 1.00
65_A 296_R 1.778 1.00
283_G 286_T 1.759 1.00
142_N 173_K 1.739 1.00
263_K 266_E 1.736 1.00
151_K 177_P 1.703 1.00
29_V 33_D 1.7 1.00
260_E 263_K 1.693 1.00
211_E 219_K 1.684 1.00
137_L 161_A 1.674 1.00
58_K 62_D 1.662 1.00
315_A 319_R 1.655 1.00
33_D 76_K 1.638 1.00
94_A 328_I 1.632 1.00
191_E 194_K 1.623 1.00
217_V 278_A 1.609 1.00
161_A 176_E 1.609 1.00
298_D 301_F 1.606 1.00
213_P 282_S 1.58 1.00
140_Q 173_K 1.577 1.00
250_L 277_V 1.561 1.00
64_L 306_M 1.552 1.00
294_R 298_D 1.55 1.00
8_S 23_G 1.547 1.00
137_L 164_F 1.546 1.00
5_I 38_I 1.544 1.00
253_V 280_A 1.538 1.00
55_K 59_A 1.537 1.00
91_L 324_V 1.531 1.00
80_F 84_H 1.522 1.00
256_Q 260_E 1.504 1.00
68_L 295_F 1.494 1.00
221_K 275_G 1.492 1.00
300_A 304_Q 1.486 1.00
72_I 77_S 1.483 1.00
256_Q 264_Q 1.48 1.00
244_S 262_E 1.472 1.00
288_L 292_Y 1.466 1.00
44_Q 86_P 1.464 1.00
211_E 215_S 1.45 1.00
90_Q 325_Y 1.44 1.00
73_D 76_K 1.424 1.00
228_D 240_K 1.409 1.00
88_H 91_L 1.404 0.99
307_K 311_E 1.403 0.99
8_S 145_P 1.402 0.99
27_Q 30_N 1.4 0.99
318_S 322_K 1.379 0.99
220_I 281_V 1.375 0.99
298_D 304_Q 1.359 0.99
70_C 288_L 1.357 0.99
276_E 280_A 1.354 0.99
10_A 23_G 1.345 0.99
279_D 283_G 1.337 0.99
52_D 55_K 1.333 0.99
103_E 159_D 1.319 0.99
293_H 297_N 1.313 0.99
123_A 127_D 1.308 0.99
62_D 66_L 1.307 0.99
10_A 16_L 1.301 0.99
4_P 142_N 1.301 0.99
80_F 139_Y 1.298 0.99
154_L 178_F 1.298 0.99
304_Q 308_D 1.286 0.99
100_Y 103_E 1.283 0.99
213_P 286_T 1.281 0.99
322_K 326_E 1.276 0.99
133_A 157_S 1.275 0.99
319_R 322_K 1.244 0.98
10_A 25_L 1.241 0.98
258_I 262_E 1.241 0.98
275_G 279_D 1.235 0.98
32_Q 77_S 1.23 0.98
26_R 30_N 1.227 0.98
55_K 58_K 1.227 0.98
104_L 123_A 1.222 0.98
6_V 28_W 1.217 0.98
308_D 312_K 1.214 0.98
189_L 194_K 1.213 0.98
94_A 324_V 1.21 0.98
236_D 239_N 1.206 0.98
320_T 324_V 1.198 0.98
261_L 265_F 1.191 0.98
244_S 248_D 1.188 0.98
6_V 31_M 1.186 0.98
47_I 330_F 1.186 0.98
137_L 165_N 1.184 0.98
23_G 181_K 1.181 0.98
289_Q 293_H 1.181 0.98
268_K 272_H 1.173 0.98
216_V 285_L 1.16 0.97
272_H 275_G 1.157 0.97
97_C 124_G 1.152 0.97
88_H 139_Y 1.148 0.97
293_H 296_R 1.143 0.97
56_L 59_A 1.136 0.97
5_I 141_T 1.132 0.97
296_R 302_L 1.122 0.97
162_Q 174_V 1.117 0.96
278_A 282_S 1.115 0.96
66_L 292_Y 1.113 0.96
133_A 156_L 1.112 0.96
95_L 137_L 1.112 0.96
12_P 41_I 1.109 0.96
314_S 318_S 1.104 0.96
10_A 20_N 1.095 0.96
28_W 39_Y 1.086 0.96
277_V 280_A 1.081 0.95
311_E 315_A 1.072 0.95
280_A 283_G 1.069 0.95
8_S 20_N 1.064 0.95
151_K 179_I 1.064 0.95
30_N 34_D 1.064 0.95
16_L 67_Y 1.063 0.95
41_I 64_L 1.061 0.95
10_A 67_Y 1.051 0.94
101_F 105_S 1.051 0.94
83_S 87_E 1.048 0.94
321_L 325_Y 1.047 0.94
96_N 127_D 1.036 0.94
189_L 205_N 1.036 0.94
319_R 323_A 1.036 0.94
271_G 275_G 1.033 0.94
20_N 23_G 1.032 0.94
61_L 65_A 1.029 0.94
244_S 265_F 1.026 0.94
194_K 203_R 1.025 0.93
123_A 130_V 1.021 0.93
247_L 261_L 1.018 0.93
57_R 61_L 1.011 0.93
257_S 276_E 1.008 0.93
217_V 282_S 1.008 0.93
311_E 322_K 1.007 0.93
84_H 310_A 1.004 0.93
15_E 62_D 1.002 0.92
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
3n9iA211000.068Contact Map0.664
2yy5A40.9821000.078Contact Map0.645
3sz3A111000.079Contact Map0.585
3prhA20.9881000.082Contact Map0.65
1i6kA10.9821000.085Contact Map0.613
2el7A20.96711000.123Contact Map0.674
2g36A10.96711000.179Contact Map0.642
1yi8B30.97311000.182Contact Map0.663
3tzlA20.95511000.193Contact Map0.664
2cycA20.86531000.267Contact Map0.663
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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