May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
DDPD - Probable D,D-dipeptide transport ATP-binding protein DdpD
UniProt: P77268 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG13787
Length: 328 (319)
Sequences: 12593
Seq/Len: 39.48
DDPD
Paralog alert: 0.93 [within 20: 0.80] - 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
36_E 226_S 4.523 1.00
93_R 176_Q 3.904 1.00
9_Q 70_Q 3.495 1.00
7_D 31_Q 3.405 1.00
10_Q 27_N 3.396 1.00
137_L 172_S 3.021 1.00
239_G 244_V 2.906 1.00
140_E 206_S 2.848 1.00
39_G 224_C 2.805 1.00
13_L 54_L 2.759 1.00
38_V 228_Y 2.691 1.00
26_N 234_S 2.663 1.00
240_V 243_D 2.586 1.00
228_Y 235_V 2.58 1.00
226_S 238_S 2.573 1.00
201_H 205_A 2.563 1.00
70_Q 77_D 2.554 1.00
74_L 176_Q 2.515 1.00
34_R 176_Q 2.471 1.00
77_D 80_N 2.427 1.00
140_E 205_A 2.4 1.00
133_K 136_D 2.302 1.00
7_D 72_S 2.2 1.00
299_Q 302_N 2.185 1.00
57_R 86_L 2.15 1.00
126_S 129_E 2.14 1.00
82_R 85_Q 2.132 1.00
33_N 36_E 2.12 1.00
297_G 320_Y 2.119 1.00
133_K 174_E 2.112 1.00
12_H 27_N 2.111 1.00
76_E 85_Q 2.095 1.00
8_I 11_L 2.068 1.00
116_M 134_A 2.037 1.00
116_M 130_A 2.024 1.00
14_S 23_H 2.023 1.00
214_S 220_V 2.015 1.00
23_H 26_N 1.945 1.00
52_A 213_I 1.939 1.00
74_L 93_R 1.917 1.00
149_V 152_R 1.903 1.00
139_E 147_V 1.895 1.00
10_Q 29_S 1.879 1.00
199_L 210_V 1.85 1.00
8_I 30_L 1.849 1.00
102_M 162_R 1.839 1.00
15_F 50_V 1.806 1.00
115_M 138_L 1.782 1.00
39_G 220_V 1.781 1.00
135_I 150_M 1.756 1.00
157_L 165_V 1.721 1.00
97_I 180_A 1.719 1.00
37_I 203_A 1.693 1.00
174_E 206_S 1.674 1.00
4_P 33_N 1.655 1.00
136_D 140_E 1.637 1.00
243_D 247_H 1.621 1.00
308_A 311_D 1.62 1.00
196_L 219_V 1.598 1.00
32_I 211_L 1.568 1.00
40_L 211_L 1.566 1.00
149_V 157_L 1.562 1.00
32_I 177_L 1.56 1.00
9_Q 31_Q 1.56 1.00
180_A 210_V 1.558 1.00
200_K 203_A 1.552 1.00
112_G 150_M 1.546 1.00
120_R 130_A 1.514 1.00
228_Y 238_S 1.512 1.00
9_Q 72_S 1.51 1.00
12_H 68_R 1.508 1.00
86_L 90_R 1.476 1.00
130_A 134_A 1.463 1.00
290_R 301_E 1.453 1.00
26_N 288_A 1.428 1.00
30_L 51_T 1.416 1.00
112_G 151_S 1.414 1.00
81_A 85_Q 1.408 1.00
109_R 113_L 1.395 0.99
131_R 150_M 1.385 0.99
145_D 148_E 1.37 0.99
234_S 303_V 1.353 0.99
152_R 156_E 1.353 0.99
131_R 151_S 1.351 0.99
115_M 172_S 1.342 0.99
32_I 38_V 1.339 0.99
299_Q 319_W 1.33 0.99
76_E 81_A 1.319 0.99
110_R 151_S 1.318 0.99
131_R 135_I 1.316 0.99
293_C 300_C 1.306 0.99
8_I 55_I 1.304 0.99
15_F 24_A 1.295 0.99
9_Q 29_S 1.293 0.99
287_C 293_C 1.291 0.99
178_I 210_V 1.29 0.99
140_E 201_H 1.29 0.99
234_S 317_A 1.289 0.99
51_T 230_M 1.284 0.99
142_Q 201_H 1.273 0.99
5_V 177_L 1.269 0.99
28_V 51_T 1.264 0.99
14_S 67_H 1.25 0.99
38_V 238_S 1.25 0.99
306_L 317_A 1.246 0.98
30_L 228_Y 1.246 0.98
17_G 20_G 1.244 0.98
132_A 136_D 1.244 0.98
52_A 179_I 1.24 0.98
34_R 207_G 1.232 0.98
112_G 131_R 1.231 0.98
227_V 241_T 1.23 0.98
296_A 301_E 1.222 0.98
12_H 23_H 1.216 0.98
135_I 147_V 1.215 0.98
138_L 150_M 1.209 0.98
73_L 93_R 1.206 0.98
234_S 288_A 1.203 0.98
37_I 210_V 1.199 0.98
89_W 94_V 1.198 0.98
115_M 134_A 1.198 0.98
28_V 235_V 1.193 0.98
123_Q 133_K 1.19 0.98
10_Q 68_R 1.19 0.98
242_A 246_H 1.182 0.98
72_S 77_D 1.176 0.98
5_V 73_L 1.173 0.98
148_E 152_R 1.173 0.98
73_L 177_L 1.171 0.98
285_D 290_R 1.163 0.97
56_M 96_M 1.16 0.97
212_F 223_L 1.157 0.97
37_I 224_C 1.156 0.97
251_P 254_I 1.15 0.97
298_A 301_E 1.148 0.97
143_I 149_V 1.147 0.97
12_H 26_N 1.143 0.97
13_L 59_L 1.141 0.97
105_L 165_V 1.127 0.97
110_R 113_L 1.116 0.96
287_C 300_C 1.115 0.96
57_R 60_P 1.109 0.96
136_D 139_E 1.107 0.96
4_P 7_D 1.104 0.96
81_A 86_L 1.094 0.96
14_S 26_N 1.092 0.96
142_Q 194_Q 1.091 0.96
105_L 162_R 1.089 0.96
128_R 132_A 1.084 0.96
238_S 315_R 1.082 0.96
203_A 225_D 1.081 0.95
34_R 74_L 1.07 0.95
40_L 228_Y 1.063 0.95
13_L 25_L 1.059 0.95
129_E 132_A 1.059 0.95
14_S 21_D 1.057 0.95
287_C 318_C 1.046 0.94
6_L 177_L 1.045 0.94
254_I 295_A 1.04 0.94
85_Q 88_Q 1.03 0.94
34_R 209_A 1.026 0.94
178_I 208_T 1.023 0.93
94_V 177_L 1.022 0.93
59_L 64_Y 1.022 0.93
217_M 245_I 1.013 0.93
308_A 313_N 1.009 0.93
119_I 172_S 1.006 0.93
254_I 258_Q 1.006 0.93
300_C 318_C 1.004 0.93
113_L 116_M 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
4fwiB10.98781000.102Contact Map0.763
3tuiC40.94821000.332Contact Map0.865
2it1A20.92381000.352Contact Map0.802
2yyzA10.92381000.355Contact Map0.748
1oxxK10.94511000.357Contact Map0.771
1g29120.94511000.359Contact Map0.835
1v43A10.92991000.366Contact Map0.779
3rlfA20.92681000.371Contact Map0.789
1z47A20.92381000.377Contact Map0.8
1b0uA10.76221000.381Contact Map0.785
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 0.0262 seconds.