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OPENSEQ.org
RIBD - Riboflavin biosynthesis protein RibD
UniProt: P25539 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG11321
Length: 367 (352)
Sequences: 1606
Seq/Len: 4.56
RIBD
Paralog alert: 0.02 [within 20: 0.00] - ratio of genomes with paralogs
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
9_R 40_E 4.619 1.00
99_S 131_A 4.576 1.00
68_A 88_L 4.11 1.00
86_D 114_R 3.68 1.00
268_R 291_Q 3.044 1.00
113_Y 117_Q 3.004 1.00
98_A 112_L 2.948 1.00
67_T 97_V 2.875 1.00
254_A 284_L 2.866 1.00
128_M 132_E 2.652 1.00
100_M 139_L 2.619 1.00
132_E 143_R 2.618 1.00
179_D 320_Y 2.593 1.00
86_D 90_A 2.59 1.00
150_Q 187_S 2.589 1.00
140_K 144_T 2.54 1.00
29_C 68_A 2.48 1.00
76_S 85_C 2.464 1.00
45_R 48_E 2.453 1.00
140_K 315_D 2.378 1.00
76_S 110_R 2.315 1.00
201_D 243_R 2.261 1.00
298_V 308_L 2.241 1.00
68_A 93_V 2.239 1.00
173_S 358_P 2.221 1.00
89_I 114_R 2.136 1.00
140_K 146_F 2.134 1.00
136_K 316_E 2.131 1.00
22_H 188_H 2.08 1.00
64_K 92_G 2.074 1.00
123_S 126_L 2.052 1.00
192_T 300_A 1.998 1.00
191_L 304_L 1.974 1.00
6_Y 37_I 1.955 1.00
228_I 252_W 1.916 1.00
156_S 324_K 1.893 1.00
195_A 199_A 1.888 1.00
324_K 347_Q 1.874 1.00
287_Q 291_Q 1.872 1.00
95_R 121_D 1.85 1.00
194_S 198_L 1.843 1.00
10_A 71_T 1.84 1.00
89_I 120_I 1.826 1.00
183_L 297_W 1.799 1.00
287_Q 290_K 1.781 1.00
36_E 62_K 1.78 1.00
285_M 308_L 1.777 1.00
189_A 230_I 1.773 1.00
85_C 89_I 1.767 1.00
281_L 313_L 1.766 1.00
88_L 93_V 1.755 1.00
232_I 304_L 1.731 0.99
170_W 177_R 1.722 0.99
46_A 80_R 1.721 0.99
29_C 88_L 1.7 0.99
192_T 197_V 1.678 0.99
173_S 176_A 1.667 0.99
87_A 91_A 1.652 0.99
198_L 237_R 1.647 0.99
172_T 176_A 1.645 0.99
149_I 285_M 1.626 0.99
31_I 68_A 1.612 0.99
101_Q 112_L 1.607 0.99
76_S 114_R 1.6 0.99
308_L 313_L 1.599 0.99
228_I 293_I 1.593 0.99
44_Q 54_H 1.588 0.99
158_D 327_G 1.585 0.99
60_G 63_A 1.572 0.99
104_N 142_M 1.571 0.99
56_L 63_A 1.564 0.99
95_R 123_S 1.553 0.99
324_K 345_A 1.551 0.99
151_L 305_A 1.545 0.99
318_I 361_C 1.538 0.99
161_T 302_P 1.528 0.98
78_H 86_D 1.5 0.98
194_S 238_V 1.476 0.98
56_L 87_A 1.473 0.98
242_H 245_V 1.471 0.98
153_L 319_V 1.467 0.98
167_E 342_L 1.463 0.98
173_S 359_D 1.458 0.98
203_A 243_R 1.45 0.98
148_Y 316_E 1.448 0.98
233_D 237_R 1.438 0.97
49_P 57_R 1.429 0.97
113_Y 116_Q 1.422 0.97
197_V 244_I 1.415 0.97
155_A 321_I 1.412 0.97
17_G 42_Y 1.408 0.97
146_F 286_M 1.407 0.97
21_T 46_A 1.403 0.97
316_E 363_H 1.399 0.97
156_S 326_L 1.395 0.97
326_L 342_L 1.394 0.97
136_K 148_Y 1.393 0.97
179_D 361_C 1.392 0.97
198_L 239_T 1.386 0.97
8_A 130_E 1.376 0.96
127_M 130_E 1.375 0.96
112_L 124_H 1.356 0.96
16_R 42_Y 1.348 0.96
39_G 58_M 1.347 0.96
309_L 334_C 1.337 0.96
9_R 13_L 1.335 0.96
179_D 354_R 1.314 0.95
191_L 232_I 1.313 0.95
18_R 186_Q 1.307 0.95
100_M 132_E 1.301 0.95
175_Q 357_G 1.279 0.94
85_C 114_R 1.279 0.94
254_A 287_Q 1.271 0.94
101_Q 124_H 1.265 0.94
191_L 308_L 1.263 0.93
141_R 294_N 1.26 0.93
43_H 48_E 1.256 0.93
8_A 127_M 1.248 0.93
231_V 244_I 1.228 0.92
6_Y 32_V 1.219 0.92
13_L 40_E 1.21 0.91
139_L 143_R 1.209 0.91
110_R 114_R 1.208 0.91
144_T 289_G 1.206 0.91
40_E 58_M 1.201 0.91
89_I 118_A 1.2 0.91
133_Q 136_K 1.197 0.91
78_H 82_P 1.197 0.91
32_V 69_Y 1.196 0.91
183_L 318_I 1.194 0.91
155_A 333_L 1.183 0.90
197_V 238_V 1.181 0.90
43_H 134_L 1.179 0.90
230_I 288_L 1.176 0.90
293_I 296_I 1.17 0.89
191_L 296_I 1.16 0.89
43_H 46_A 1.158 0.89
194_S 233_D 1.155 0.89
54_H 57_R 1.151 0.88
3_D 97_V 1.148 0.88
320_Y 361_C 1.147 0.88
18_R 26_N 1.146 0.88
38_V 62_K 1.146 0.88
32_V 66_A 1.121 0.87
198_L 233_D 1.12 0.87
162_A 170_W 1.118 0.86
125_G 128_M 1.116 0.86
254_A 270_L 1.113 0.86
153_L 333_L 1.109 0.86
194_S 237_R 1.109 0.86
352_E 363_H 1.104 0.85
17_G 20_T 1.104 0.85
229_R 251_T 1.103 0.85
319_V 333_L 1.091 0.85
279_L 284_L 1.089 0.84
3_D 123_S 1.082 0.84
77_H 107_V 1.079 0.84
194_S 245_V 1.075 0.83
98_A 124_H 1.073 0.83
188_H 294_N 1.073 0.83
353_I 360_V 1.069 0.83
53_V 57_R 1.069 0.83
132_E 139_L 1.065 0.83
58_M 63_A 1.065 0.83
304_L 308_L 1.06 0.82
9_R 12_K 1.057 0.82
232_I 284_L 1.041 0.81
185_A 206_V 1.037 0.80
26_N 135_N 1.036 0.80
14_A 134_L 1.035 0.80
298_V 304_L 1.035 0.80
114_R 118_A 1.03 0.80
179_D 318_I 1.03 0.80
31_I 55_A 1.02 0.79
56_L 91_A 1.017 0.78
17_G 21_T 1.016 0.78
54_H 58_M 1.016 0.78
350_F 362_L 1.015 0.78
17_G 43_H 1.014 0.78
168_S 177_R 1.013 0.78
39_G 53_V 1.012 0.78
97_V 126_L 1.011 0.78
160_R 332_G 1.009 0.78
236_N 255_R 1.006 0.77
135_N 139_L 1.004 0.77
141_R 289_G 1.003 0.77
151_L 298_V 1.002 0.77
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
2g6vA211000.235Contact Map0.836
2b3zA40.96191000.249Contact Map0.875
3zpgA10.95911000.266Contact Map0.752
2hxvA10.92921000.284Contact Map0.787
2p4gA10.6731000.641Contact Map0.555
3g8qA40.7331000.653Contact Map0.47
4ha7A20.62941000.658Contact Map0.67
2aznA60.56951000.658Contact Map0.798
1z3aA20.4061000.716Contact Map0.686
2nx8A10.41691000.719Contact Map0.596
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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