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DDPB - Probable D,D-dipeptide transport system permease protein DdpB
UniProt: P77308 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG13789
Length: 340 (324)
Sequences: 6421
Seq/Len: 19.82
DDPB
Paralog alert: 0.81 [within 20: 0.11] - ratio of genomes with paralogs
Cluster includes: DDPB DDPC DPPB DPPC GSIC GSID NIKB NIKC OPPB OPPC SAPB SAPC YEJB YEJE
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
55_Q 60_D 3.847 1.00
61_Q 65_V 3.805 1.00
30_H 66_Q 3.593 1.00
61_Q 69_R 3.515 1.00
22_C 67_F 3.415 1.00
72_S 76_H 3.348 1.00
35_D 54_R 3.275 1.00
47_D 51_E 3.217 1.00
68_Y 72_S 3.069 1.00
240_R 246_G 2.899 1.00
23_V 67_F 2.84 1.00
99_A 286_W 2.716 1.00
227_M 254_A 2.692 1.00
236_I 254_A 2.69 1.00
248_Y 252_C 2.681 1.00
263_I 330_I 2.586 1.00
64_Y 68_Y 2.496 1.00
106_G 208_A 2.48 1.00
164_L 205_I 2.366 1.00
92_E 292_W 2.269 1.00
267_G 323_V 2.19 1.00
291_A 295_T 2.157 1.00
110_L 212_A 2.155 1.00
238_T 242_S 2.142 1.00
164_L 202_Q 2.107 1.00
21_V 313_S 2.087 1.00
231_L 254_A 1.997 1.00
264_T 327_Y 1.996 1.00
73_D 78_D 1.988 1.00
5_S 9_Q 1.917 1.00
88_P 91_E 1.882 1.00
74_L 79_L 1.854 1.00
51_E 55_Q 1.854 1.00
52_N 56_Q 1.832 1.00
129_W 133_L 1.832 1.00
125_W 128_R 1.831 1.00
22_C 70_Y 1.814 1.00
18_V 314_F 1.798 1.00
230_Q 235_Y 1.797 1.00
65_V 69_R 1.778 1.00
49_I 52_N 1.769 1.00
50_V 54_R 1.768 1.00
113_L 117_P 1.765 1.00
153_V 210_T 1.756 1.00
326_L 329_W 1.741 1.00
85_T 92_E 1.719 1.00
87_R 91_E 1.716 1.00
245_P 248_Y 1.711 1.00
19_A 23_V 1.709 1.00
12_W 16_L 1.663 1.00
124_V 250_V 1.656 1.00
118_L 134_V 1.652 1.00
89_V 307_G 1.639 1.00
90_L 94_R 1.634 1.00
114_I 117_P 1.629 1.00
296_S 304_A 1.594 1.00
51_E 54_R 1.586 1.00
230_Q 233_E 1.585 1.00
14_L 317_V 1.58 1.00
158_Y 166_G 1.573 1.00
46_S 49_I 1.544 1.00
156_L 160_H 1.543 1.00
87_R 95_I 1.538 1.00
123_A 228_L 1.537 1.00
148_W 152_G 1.534 1.00
247_W 251_L 1.529 1.00
235_Y 257_N 1.528 1.00
155_V 160_H 1.522 1.00
212_A 216_L 1.518 1.00
69_R 72_S 1.517 1.00
230_Q 236_I 1.515 1.00
65_V 68_Y 1.514 1.00
37_A 50_V 1.509 1.00
242_S 253_Y 1.502 1.00
152_G 156_L 1.501 1.00
121_L 125_W 1.499 1.00
19_A 67_F 1.491 1.00
127_N 131_D 1.486 1.00
234_D 237_R 1.453 1.00
131_D 224_R 1.453 1.00
164_L 206_L 1.452 1.00
58_G 61_Q 1.445 1.00
62_P 65_V 1.43 1.00
19_A 71_V 1.428 1.00
141_G 217_G 1.419 1.00
230_Q 258_A 1.405 0.99
92_E 304_A 1.404 0.99
292_W 304_A 1.401 0.99
34_G 300_L 1.395 0.99
79_L 307_G 1.394 0.99
23_V 63_L 1.39 0.99
114_I 216_L 1.387 0.99
293_V 308_F 1.38 0.99
18_V 317_V 1.371 0.99
130_L 134_V 1.362 0.99
156_L 161_L 1.356 0.99
260_I 327_Y 1.354 0.99
236_I 249_I 1.351 0.99
208_A 212_A 1.35 0.99
14_L 321_L 1.346 0.99
112_L 266_L 1.342 0.99
119_G 223_I 1.337 0.99
8_R 12_W 1.337 0.99
121_L 130_L 1.337 0.99
99_A 102_E 1.333 0.99
144_T 149_L 1.331 0.99
111_A 215_H 1.316 0.99
149_L 213_F 1.313 0.99
58_G 69_R 1.307 0.99
134_V 220_A 1.3 0.99
120_I 227_M 1.291 0.99
308_F 312_V 1.279 0.99
22_C 310_V 1.269 0.99
69_R 73_D 1.269 0.99
322_V 326_L 1.261 0.99
153_V 206_L 1.259 0.99
53_I 57_L 1.246 0.98
325_L 329_W 1.244 0.98
110_L 208_A 1.234 0.98
115_G 219_V 1.224 0.98
30_H 63_L 1.219 0.98
157_F 161_L 1.218 0.98
125_W 130_L 1.215 0.98
150_G 210_T 1.202 0.98
123_A 227_M 1.191 0.98
201_L 205_I 1.177 0.98
23_V 27_I 1.176 0.98
127_N 132_H 1.174 0.98
146_A 280_T 1.158 0.97
91_E 94_R 1.151 0.97
105_F 109_L 1.145 0.97
169_R 286_W 1.127 0.97
7_L 325_L 1.122 0.97
108_L 266_L 1.12 0.96
119_G 123_A 1.118 0.96
95_I 98_P 1.114 0.96
102_E 204_L 1.114 0.96
277_A 280_T 1.112 0.96
67_F 71_V 1.106 0.96
205_I 209_L 1.106 0.96
115_G 223_I 1.094 0.96
6_I 10_R 1.093 0.96
319_V 323_V 1.089 0.96
27_I 63_L 1.076 0.95
72_S 75_F 1.072 0.95
82_S 301_D 1.071 0.95
61_Q 64_Y 1.071 0.95
123_A 231_L 1.066 0.95
87_R 92_E 1.063 0.95
150_G 283_V 1.063 0.95
244_L 249_I 1.049 0.94
223_I 262_S 1.043 0.94
157_F 163_I 1.041 0.94
41_A 53_I 1.041 0.94
53_I 56_Q 1.037 0.94
11_C 321_L 1.035 0.94
246_G 249_I 1.031 0.94
4_W 8_R 1.024 0.93
222_Q 265_V 1.024 0.93
79_L 90_L 1.014 0.93
74_L 310_V 1.014 0.93
271_G 316_Y 1.011 0.93
55_Q 61_Q 1.01 0.93
146_A 213_F 1.004 0.93
30_H 302_F 1.002 0.92
244_L 248_Y 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
3tuiA40.617699.90.767Contact Map0.724
2onkC40.785399.80.784Contact Map0.561
3rlfF10.855999.80.785Contact Map0.537
3d31C20.791299.70.798Contact Map0.536
3rlfG10.832499.60.822Contact Map0.398
3s82A20.255910.80.971Contact Map0.232
1n0uA10.18828.70.972Contact Map0.33
2yevC20.09418.10.973Contact Map0.632
3arcI20.11186.80.974Contact Map0.671
2p02A10.256.10.974Contact Map0.207
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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