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OPENSEQ.org
DDPA - Probable D,D-dipeptide-binding periplasmic protein DdpA
UniProt: P76128 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG13790
Length: 516 (480)
Sequences: 9486
Seq/Len: 19.76
DDPA
Paralog alert: 0.87 [within 20: 0.29] - ratio of genomes with paralogs
Cluster includes: DDPA DPPA GSIB MPPA NIKA OPPA SAPA SGRR YBAE YEJA YGIS
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
201_K 212_V 4.506 1.00
144_D 147_T 3.836 1.00
305_Q 309_N 3.815 1.00
143_P 149_K 3.686 1.00
141_D 149_K 3.65 1.00
101_D 146_H 3.444 1.00
343_K 346_A 3.439 1.00
293_D 350_K 3.4 1.00
199_M 212_V 3.295 1.00
457_T 462_Q 3.294 1.00
449_K 453_N 3.246 1.00
442_Y 477_D 3.103 1.00
117_K 121_E 3.079 1.00
357_S 386_I 3.013 1.00
117_K 142_A 2.967 1.00
85_S 98_T 2.922 1.00
298_I 380_L 2.895 1.00
303_D 306_G 2.835 1.00
287_A 290_N 2.809 1.00
446_E 449_K 2.781 1.00
87_K 98_T 2.764 1.00
114_E 142_A 2.718 1.00
300_W 343_K 2.651 1.00
357_S 388_K 2.598 1.00
292_A 296_R 2.573 1.00
462_Q 465_R 2.495 1.00
293_D 296_R 2.491 1.00
111_V 195_S 2.458 1.00
65_V 86_W 2.429 1.00
444_N 477_D 2.404 1.00
444_N 473_I 2.381 1.00
94_E 149_K 2.334 1.00
89_S 93_K 2.33 1.00
141_D 151_T 2.323 1.00
430_S 443_E 2.314 1.00
381_N 386_I 2.309 1.00
346_A 350_K 2.295 1.00
173_P 177_K 2.294 1.00
446_E 469_Q 2.275 1.00
293_D 347_E 2.266 1.00
120_F 150_F 2.259 1.00
94_E 151_T 2.259 1.00
459_D 462_Q 2.255 1.00
96_T 149_K 2.252 1.00
359_T 388_K 2.224 1.00
199_M 215_P 2.223 1.00
84_S 101_D 2.204 1.00
106_A 214_N 2.204 1.00
98_T 147_T 2.19 1.00
88_A 95_W 2.174 1.00
103_A 111_V 2.165 1.00
359_T 390_E 2.155 1.00
453_N 466_D 2.146 1.00
104_K 110_P 2.143 1.00
198_F 224_F 2.125 1.00
104_K 216_H 2.119 1.00
116_V 148_V 2.099 1.00
430_S 448_D 2.096 1.00
210_V 226_R 2.081 1.00
465_R 469_Q 2.051 1.00
68_K 79_E 2.04 1.00
282_L 481_V 1.978 1.00
31_M 226_R 1.974 1.00
286_K 407_D 1.974 1.00
112_T 115_A 1.97 1.00
289_L 358_L 1.944 1.00
447_V 470_A 1.93 1.00
282_L 408_I 1.921 1.00
472_K 476_D 1.907 1.00
296_R 343_K 1.901 1.00
44_D 122_R 1.895 1.00
68_K 77_D 1.89 1.00
62_Q 81_D 1.883 1.00
454_A 467_Y 1.867 1.00
241_Q 246_D 1.864 1.00
102_N 110_P 1.855 1.00
204_Q 207_Q 1.825 1.00
347_E 350_K 1.822 1.00
450_L 469_Q 1.819 1.00
114_E 145_E 1.81 1.00
31_M 228_S 1.81 1.00
114_E 117_K 1.808 1.00
298_I 385_I 1.796 1.00
202_S 210_V 1.78 1.00
454_A 466_D 1.723 1.00
469_Q 472_K 1.723 1.00
138_L 153_S 1.716 1.00
466_D 469_Q 1.714 1.00
84_S 98_T 1.713 1.00
86_W 97_F 1.706 1.00
299_S 478_A 1.693 1.00
212_V 226_R 1.691 1.00
377_Q 381_N 1.689 1.00
107_D 172_N 1.682 1.00
445_S 449_K 1.675 1.00
35_G 247_I 1.667 1.00
319_M 485_Q 1.665 1.00
302_T 376_T 1.661 1.00
289_L 298_I 1.642 1.00
114_E 173_P 1.641 1.00
33_V 228_S 1.632 1.00
89_S 96_T 1.632 1.00
201_K 226_R 1.629 1.00
202_S 208_Q 1.629 1.00
213_P 225_K 1.629 1.00
292_A 477_D 1.624 1.00
266_K 494_K 1.614 1.00
139_K 151_T 1.609 1.00
453_N 462_Q 1.609 1.00
243_S 260_A 1.605 1.00
109_T 174_A 1.599 1.00
204_Q 208_Q 1.582 1.00
50_D 53_D 1.572 1.00
113_A 142_A 1.571 1.00
399_D 403_K 1.571 1.00
65_V 97_F 1.563 1.00
103_A 195_S 1.561 1.00
340_D 343_K 1.548 1.00
446_E 473_I 1.541 1.00
115_A 173_P 1.538 1.00
89_S 94_E 1.53 1.00
301_S 383_L 1.527 1.00
450_L 466_D 1.525 1.00
112_T 145_E 1.52 1.00
342_T 345_K 1.511 1.00
84_S 100_K 1.504 1.00
400_R 405_D 1.49 1.00
232_I 241_Q 1.488 1.00
109_T 172_N 1.485 1.00
285_S 441_F 1.479 1.00
465_R 468_Q 1.461 1.00
345_K 349_D 1.46 1.00
443_E 448_D 1.455 1.00
208_Q 228_S 1.454 1.00
106_A 199_M 1.44 1.00
393_A 396_T 1.436 1.00
462_Q 466_D 1.429 1.00
96_T 147_T 1.424 1.00
308_V 318_Q 1.419 1.00
259_N 262_K 1.417 1.00
150_F 159_F 1.41 1.00
268_N 494_K 1.404 0.99
110_P 146_H 1.394 0.99
143_P 147_T 1.393 0.99
172_N 175_V 1.392 0.99
305_Q 318_Q 1.389 0.99
30_D 225_K 1.387 0.99
100_K 103_A 1.387 0.99
98_T 146_H 1.37 0.99
464_T 468_Q 1.361 0.99
292_A 476_D 1.361 0.99
457_T 466_D 1.357 0.99
296_R 478_A 1.349 0.99
370_E 374_L 1.342 0.99
210_V 228_S 1.34 0.99
174_A 178_E 1.33 0.99
473_I 477_D 1.322 0.99
211_L 229_V 1.31 0.99
450_L 473_I 1.307 0.99
419_D 463_R 1.305 0.99
294_L 348_W 1.303 0.99
142_A 145_E 1.3 0.99
241_Q 247_I 1.291 0.99
104_K 214_N 1.291 0.99
442_Y 447_V 1.285 0.99
347_E 351_V 1.281 0.99
113_A 143_P 1.27 0.99
62_Q 195_S 1.26 0.99
106_A 200_L 1.257 0.99
98_T 101_D 1.254 0.99
95_W 159_F 1.252 0.99
379_S 382_K 1.237 0.98
62_Q 218_P 1.236 0.98
117_K 140_I 1.233 0.98
362_Y 389_L 1.223 0.98
294_L 351_V 1.217 0.98
248_D 493_N 1.215 0.98
80_G 86_W 1.212 0.98
341_E 345_K 1.209 0.98
375_A 379_S 1.195 0.98
212_V 215_P 1.193 0.98
446_E 450_L 1.179 0.98
348_W 351_V 1.179 0.98
213_P 222_P 1.179 0.98
82_L 195_S 1.178 0.98
237_S 241_Q 1.172 0.98
404_G 441_F 1.168 0.97
286_K 290_N 1.162 0.97
268_N 492_M 1.157 0.97
360_F 387_V 1.156 0.97
201_K 210_V 1.156 0.97
106_A 216_H 1.155 0.97
390_E 400_R 1.154 0.97
358_L 408_I 1.151 0.97
300_W 337_Y 1.151 0.97
154_Q 456_A 1.149 0.97
449_K 452_R 1.133 0.97
341_E 383_L 1.129 0.97
89_S 92_Q 1.129 0.97
110_P 145_E 1.126 0.97
450_L 453_N 1.123 0.97
377_Q 389_L 1.115 0.96
308_V 316_G 1.114 0.96
98_T 144_D 1.112 0.96
140_I 148_V 1.111 0.96
312_L 316_G 1.109 0.96
242_L 491_A 1.104 0.96
348_W 352_T 1.097 0.96
84_S 146_H 1.097 0.96
97_F 150_F 1.094 0.96
248_D 495_E 1.089 0.96
96_T 143_P 1.088 0.96
282_L 298_I 1.087 0.96
453_N 469_Q 1.087 0.96
306_G 379_S 1.086 0.96
307_M 372_I 1.086 0.96
453_N 457_T 1.08 0.95
35_G 238_R 1.08 0.95
213_P 221_K 1.078 0.95
33_V 230_K 1.073 0.95
380_L 387_V 1.065 0.95
299_S 304_Y 1.063 0.95
243_S 264_E 1.06 0.95
376_T 380_L 1.059 0.95
442_Y 479_A 1.059 0.95
301_S 380_L 1.053 0.95
32_L 496_V 1.053 0.95
68_K 72_D 1.048 0.94
116_V 170_I 1.045 0.94
322_P 482_Y 1.044 0.94
39_D 203_W 1.043 0.94
296_R 347_E 1.042 0.94
292_A 478_A 1.041 0.94
358_L 387_V 1.04 0.94
121_E 142_A 1.035 0.94
461_T 464_T 1.035 0.94
281_Y 409_A 1.03 0.94
325_E 485_Q 1.026 0.94
117_K 148_V 1.025 0.93
95_W 160_L 1.021 0.93
461_T 465_R 1.02 0.93
429_E 452_R 1.019 0.93
394_N 398_R 1.016 0.93
32_L 249_I 1.015 0.93
29_K 225_K 1.009 0.93
32_L 224_F 1.006 0.93
63_R 81_D 1.005 0.93
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
1uqwA20.96711000.163Contact Map0.769
1dpeA10.93411000.164Contact Map0.795
3m8uA10.9381000.166Contact Map0.788
3tpaA10.94771000.169Contact Map0.759
1xocA10.95741000.17Contact Map0.758
3o9pA10.94571000.171Contact Map0.746
4fajA10.95931000.173Contact Map0.735
3zs6A10.92441000.175Contact Map0.768
1jetA10.93991000.184Contact Map0.806
4gl8A20.96711000.184Contact Map0.801
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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