May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
SAPD - Peptide transport system ATP-binding protein SapD
UniProt: P0AAH4 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG12304
Length: 330 (315)
Sequences: 10808
Seq/Len: 34.31
SAPD
Paralog alert: 0.92 [within 20: 0.76] - ratio of genomes with paralogs
Cluster includes: ARTP BTUD CCMA CYSA DDPD DDPF DPPD DPPF FBPC FECE FEPC FHUC FTSE GLNQ GLTL HISP LIVF LIVG LOLD LPTB MALK METN MLAF MODC NIKD NIKE OPPD OPPF PHNC PHNK PHNL POTA POTG PROV PSTB SAPD SAPF SSUB SUFC TAUB THIQ UGPC YADG YBBA YBBL YCJV YDCT YECC YEHX YHDZ YNJD ZNUC
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
34_E 228_K 4.463 1.00
90_N 178_R 3.885 1.00
7_R 67_R 3.378 1.00
5_D 29_T 3.338 1.00
8_N 25_R 3.223 1.00
139_L 174_A 2.987 1.00
241_A 246_L 2.908 1.00
142_R 208_S 2.888 1.00
11_I 52_A 2.777 1.00
37_G 226_A 2.774 1.00
71_D 178_R 2.675 1.00
36_R 230_N 2.652 1.00
230_N 237_T 2.571 1.00
242_P 245_E 2.551 1.00
228_K 240_T 2.526 1.00
67_R 74_D 2.513 1.00
74_D 77_R 2.497 1.00
203_R 207_N 2.482 1.00
142_R 207_N 2.474 1.00
32_E 178_R 2.448 1.00
24_D 236_Q 2.385 1.00
135_R 138_E 2.338 1.00
302_Q 323_F 2.31 1.00
304_E 307_V 2.29 1.00
55_G 83_R 2.152 1.00
31_T 34_E 2.131 1.00
79_S 82_E 2.105 1.00
12_E 21_K 2.099 1.00
122_K 127_Q 2.096 1.00
10_T 25_R 2.074 1.00
73_I 82_E 2.052 1.00
5_D 69_R 2.026 1.00
135_R 176_Q 2.022 1.00
113_M 136_A 1.999 1.00
71_D 90_N 1.991 1.00
6_I 9_L 1.963 1.00
216_S 222_L 1.956 1.00
151_A 154_S 1.931 1.00
6_I 28_M 1.908 1.00
113_M 132_R 1.901 1.00
99_Q 164_C 1.899 1.00
201_L 212_I 1.889 1.00
21_K 24_D 1.86 1.00
50_A 215_I 1.859 1.00
13_F 48_L 1.825 1.00
8_N 27_S 1.819 1.00
137_I 152_M 1.816 1.00
112_L 140_L 1.809 1.00
37_G 222_L 1.766 1.00
141_H 149_K 1.764 1.00
94_I 182_A 1.738 1.00
295_G 306_I 1.704 1.00
176_Q 208_S 1.694 1.00
35_I 205_N 1.668 1.00
30_L 213_L 1.665 1.00
2_P 31_T 1.659 1.00
245_E 249_M 1.639 1.00
117_P 132_R 1.622 1.00
38_L 213_L 1.605 1.00
159_L 167_V 1.605 1.00
202_T 205_N 1.604 1.00
30_L 179_L 1.604 1.00
10_T 65_A 1.592 1.00
151_A 159_L 1.579 1.00
138_E 142_R 1.566 1.00
147_D 150_D 1.562 1.00
109_G 152_M 1.554 1.00
198_F 221_M 1.544 1.00
7_R 29_T 1.514 1.00
132_R 136_A 1.489 1.00
301_A 306_I 1.481 1.00
236_Q 308_T 1.47 1.00
24_D 293_R 1.463 1.00
7_R 69_R 1.459 1.00
182_A 212_I 1.445 1.00
154_S 158_E 1.441 1.00
230_N 240_T 1.437 1.00
78_L 82_E 1.428 1.00
304_E 322_H 1.418 1.00
28_M 49_I 1.416 1.00
106_E 110_R 1.413 1.00
133_K 152_M 1.402 0.99
73_I 78_L 1.399 0.99
83_R 87_V 1.396 0.99
112_L 174_A 1.395 0.99
236_Q 320_A 1.393 0.99
109_G 153_R 1.368 0.99
133_K 153_R 1.352 0.99
298_C 305_C 1.351 0.99
107_R 153_R 1.349 0.99
26_V 49_I 1.346 0.99
142_R 203_R 1.344 0.99
32_E 209_N 1.336 0.99
6_I 53_I 1.317 0.99
292_C 298_C 1.316 0.99
133_K 137_I 1.304 0.99
7_R 27_S 1.301 0.99
303_R 306_I 1.295 0.99
12_E 64_T 1.29 0.99
144_G 203_R 1.28 0.99
236_Q 293_R 1.277 0.99
49_I 232_L 1.276 0.99
13_F 22_A 1.275 0.99
30_L 36_R 1.272 0.99
145_I 151_A 1.259 0.99
311_L 320_A 1.258 0.99
180_L 212_I 1.257 0.99
290_I 295_G 1.252 0.99
244_K 248_T 1.246 0.98
15_T 18_E 1.235 0.98
86_L 91_V 1.231 0.98
8_N 65_A 1.221 0.98
69_R 74_D 1.216 0.98
112_L 136_A 1.21 0.98
3_L 179_L 1.206 0.98
36_R 240_T 1.206 0.98
26_V 237_T 1.205 0.98
134_R 138_E 1.202 0.98
137_I 149_K 1.199 0.98
256_Q 300_Y 1.198 0.98
214_L 225_W 1.195 0.98
3_L 70_F 1.192 0.98
10_T 21_K 1.19 0.98
70_F 90_N 1.184 0.98
240_T 318_L 1.184 0.98
109_G 133_K 1.183 0.98
150_D 154_S 1.18 0.98
35_I 212_I 1.176 0.98
229_I 243_S 1.148 0.97
12_E 24_D 1.146 0.97
140_L 152_M 1.146 0.97
78_L 83_R 1.136 0.97
102_L 164_C 1.136 0.97
107_R 110_R 1.133 0.97
138_E 141_H 1.132 0.97
28_M 230_N 1.13 0.97
10_T 24_D 1.129 0.97
144_G 196_Q 1.123 0.97
50_A 181_I 1.118 0.96
12_E 19_W 1.108 0.96
102_L 167_V 1.103 0.96
256_Q 260_R 1.103 0.96
38_L 230_N 1.098 0.96
57_N 61_W 1.096 0.96
55_G 58_K 1.091 0.96
70_F 179_L 1.089 0.96
82_E 85_K 1.085 0.96
292_C 321_C 1.077 0.95
32_E 71_D 1.073 0.95
2_P 5_D 1.072 0.95
253_P 256_Q 1.071 0.95
35_I 226_A 1.063 0.95
292_C 305_C 1.061 0.95
57_N 60_N 1.057 0.95
54_C 93_M 1.055 0.95
116_I 174_A 1.052 0.95
313_G 318_L 1.051 0.94
313_G 316_N 1.049 0.94
11_I 23_V 1.049 0.94
205_N 227_D 1.048 0.94
180_L 210_T 1.045 0.94
53_I 68_M 1.043 0.94
54_C 91_V 1.041 0.94
120_T 135_R 1.03 0.94
124_R 134_R 1.029 0.94
307_V 322_H 1.029 0.94
75_L 91_V 1.029 0.94
127_Q 134_R 1.028 0.94
246_L 255_T 1.02 0.93
4_L 53_I 1.013 0.93
293_R 308_T 1.01 0.93
11_I 57_N 1.008 0.93
32_E 211_T 1.007 0.93
219_L 247_V 1.003 0.93
305_C 321_C 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
4fwiB10.96971000.124Contact Map0.757
3tuiC40.93641000.351Contact Map0.862
2it1A20.92121000.367Contact Map0.781
2yyzA10.92121000.373Contact Map0.738
1g29120.93641000.373Contact Map0.826
1oxxK10.93331000.374Contact Map0.752
1v43A10.90911000.38Contact Map0.765
3rlfA20.92121000.384Contact Map0.771
1z47A20.90611000.394Contact Map0.796
3fvqA20.93331000.401Contact Map0.697
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 1.4765 seconds.