May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
YPHF - ABC transporter periplasmic-binding protein YphF
UniProt: P77269 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG13467
Length: 327 (284)
Sequences: 14990
Seq/Len: 52.78
YPHF
Paralog alert: 0.90 [within 20: 0.53] - ratio of genomes with paralogs
Cluster includes: ALSB ARAF ASCG CRA CYTR DGAL EBGR GALR GALS GNTR IDNR LACI LSRB MALI PURR RBSB RBSR TORT TRER XYLF YCJW YPHF YTFQ
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
140_L 184_E 3.846 1.00
161_Q 222_N 3.628 1.00
90_A 288_T 2.907 1.00
255_M 274_D 2.727 1.00
146_L 251_F 2.696 1.00
179_R 183_E 2.696 1.00
239_V 248_I 2.477 1.00
161_Q 249_A 2.455 1.00
54_A 286_A 2.336 1.00
50_G 281_G 2.32 1.00
208_I 241_N 2.292 1.00
144_K 184_E 2.284 1.00
54_A 57_D 2.258 1.00
283_A 286_A 2.247 1.00
133_A 291_V 2.158 1.00
144_K 185_V 2.136 1.00
142_F 253_S 2.08 1.00
55_A 285_F 2.069 1.00
212_E 242_Q 2.021 1.00
216_I 242_Q 1.982 1.00
54_A 282_N 1.978 1.00
290_K 295_Q 1.96 1.00
144_K 189_R 1.956 1.00
211_G 224_I 1.952 1.00
141_E 145_K 1.947 1.00
53_D 278_K 1.927 1.00
207_A 234_G 1.914 1.00
140_L 180_K 1.893 1.00
244_Q 247_K 1.891 1.00
212_E 238_A 1.874 1.00
143_G 225_M 1.825 1.00
208_I 238_A 1.777 1.00
276_S 279_K 1.772 1.00
274_D 307_D 1.767 1.00
147_G 151_A 1.707 1.00
34_G 88_V 1.702 1.00
141_E 144_K 1.702 1.00
180_K 184_E 1.699 1.00
211_G 235_A 1.674 1.00
163_K 220_D 1.669 1.00
118_Y 284_V 1.664 1.00
148_N 152_D 1.662 1.00
165_A 221_L 1.645 1.00
251_F 271_A 1.629 1.00
54_A 285_F 1.612 1.00
279_K 282_N 1.61 1.00
138_D 141_E 1.603 1.00
50_G 278_K 1.584 1.00
269_L 312_T 1.583 1.00
226_G 235_A 1.574 1.00
143_G 147_G 1.558 1.00
34_G 83_L 1.558 1.00
167_I 235_A 1.554 1.00
33_I 55_A 1.548 1.00
58_S 289_L 1.535 1.00
145_K 306_I 1.534 1.00
286_A 290_K 1.524 1.00
181_G 185_V 1.523 1.00
143_G 181_G 1.517 1.00
238_A 242_Q 1.509 1.00
212_E 241_N 1.504 1.00
279_K 283_A 1.487 1.00
166_V 227_E 1.485 1.00
144_K 148_N 1.47 1.00
106_R 110_E 1.47 1.00
163_K 194_Q 1.47 1.00
54_A 58_S 1.451 1.00
35_A 51_V 1.448 1.00
240_R 268_V 1.436 1.00
165_A 214_L 1.434 1.00
238_A 241_N 1.431 1.00
177_Q 180_K 1.429 1.00
239_V 244_Q 1.427 1.00
255_M 311_K 1.418 1.00
211_G 239_V 1.416 1.00
289_L 293_N 1.415 1.00
150_A 223_A 1.411 1.00
236_V 250_V 1.405 0.99
161_Q 223_A 1.382 0.99
205_D 209_S 1.368 0.99
183_E 187_K 1.365 0.99
152_D 156_A 1.365 0.99
148_N 185_V 1.363 0.99
163_K 222_N 1.35 0.99
52_Q 56_K 1.334 0.99
67_T 83_L 1.307 0.99
229_G 272_V 1.302 0.99
234_G 238_A 1.298 0.99
142_F 306_I 1.284 0.99
51_V 92_I 1.282 0.99
140_L 144_K 1.281 0.99
31_M 89_D 1.279 0.99
208_I 212_E 1.272 0.99
202_T 206_K 1.266 0.99
81_D 107_R 1.264 0.99
182_F 186_L 1.262 0.99
147_G 182_F 1.26 0.99
264_E 268_V 1.251 0.99
209_S 213_K 1.251 0.99
31_M 60_V 1.243 0.98
208_I 237_K 1.241 0.98
224_I 235_A 1.23 0.98
218_T 221_L 1.223 0.98
51_V 285_F 1.22 0.98
67_T 79_F 1.216 0.98
140_L 181_G 1.209 0.98
151_A 155_I 1.206 0.98
147_G 181_G 1.196 0.98
276_S 304_V 1.192 0.98
92_I 284_V 1.177 0.98
240_R 264_E 1.175 0.98
140_L 177_Q 1.173 0.98
252_G 272_V 1.168 0.97
164_I 186_L 1.166 0.97
226_G 232_T 1.158 0.97
148_N 189_R 1.152 0.97
211_G 215_I 1.141 0.97
281_G 285_F 1.139 0.97
229_G 252_G 1.137 0.97
166_V 179_R 1.133 0.97
239_V 250_V 1.122 0.97
182_F 225_M 1.108 0.96
58_S 286_A 1.106 0.96
164_I 223_A 1.103 0.96
282_N 286_A 1.09 0.96
265_N 268_V 1.078 0.95
151_A 185_V 1.069 0.95
51_V 281_G 1.067 0.95
147_G 185_V 1.066 0.95
201_G 231_A 1.064 0.95
283_A 287_Q 1.063 0.95
75_K 78_T 1.062 0.95
186_L 193_A 1.062 0.95
48_R 52_Q 1.054 0.95
169_C 203_V 1.053 0.95
150_A 251_F 1.052 0.95
206_K 209_S 1.051 0.94
55_A 64_L 1.051 0.94
137_G 275_I 1.05 0.94
226_G 231_A 1.043 0.94
278_K 282_N 1.042 0.94
229_G 232_T 1.041 0.94
283_A 302_I 1.038 0.94
162_P 222_N 1.038 0.94
180_K 183_E 1.034 0.94
155_I 191_P 1.028 0.94
207_A 211_G 1.022 0.93
288_T 292_I 1.009 0.93
163_K 196_V 1.007 0.93
176_V 180_K 1.002 0.92
184_E 187_K 1.001 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
4kvfA10.88071000.24Contact Map0.612
4kzkA10.9481000.249Contact Map0.634
2driA10.81961000.257Contact Map0.712
3d02A10.85631000.265Contact Map0.611
1tjyA10.85931000.27Contact Map0.628
2rjoA10.87771000.272Contact Map0.631
2hsgA10.89911000.273Contact Map0.788
2h3hA20.86851000.278Contact Map0.728
3uugA20.8931000.281Contact Map0.676
3h5oA20.91741000.281Contact Map0.79
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.
Page generated in 0.72 seconds.