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OPENSEQ.org
YBDO - Uncharacterized HTH-type transcriptional regulator YbdO
UniProt: P77746 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG13534
Length: 300 (288)
Sequences: 37119
Seq/Len: 128.89
YBDO
Paralog alert: 0.88 [within 20: 0.50] - ratio of genomes with paralogs
Cluster includes: AAER ABGR ALLS CBL CYNR CYSB DMLR DSDC GCVA HCAR HDFR ICIA ILVY LEUO LRHA LYSR METR NAC NHAR OXYR PERR TDCA TTDR XAPR YAFC YAHB YBDO YBEF YBHD YCAN YCJZ YDCI YDHB YEEY YEIE YFER YFIE YGFI YHAJ YHJC YIAU YIDZ YJIE YNEJ YNFL
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
79_K 83_G 3.644 1.00
24_H 33_S 3.353 1.00
238_I 245_G 2.469 1.00
103_Y 149_A 2.398 1.00
166_M 297_N 2.384 1.00
29_K 32_E 2.342 1.00
76_H 90_I 2.272 1.00
172_R 249_Y 2.263 1.00
181_H 196_E 2.238 1.00
23_Q 78_E 2.214 1.00
189_T 192_Q 2.163 1.00
20_C 33_S 2.157 1.00
101_I 129_E 2.14 1.00
99_N 127_E 2.12 1.00
99_N 129_E 2.078 1.00
22_Y 66_P 2.067 1.00
167_P 170_T 2.058 1.00
80_N 84_L 2.05 1.00
170_T 274_K 2.037 1.00
27_I 45_L 1.997 1.00
235_I 255_Y 1.99 1.00
76_H 83_G 1.98 1.00
17_I 44_S 1.971 1.00
19_E 74_H 1.971 1.00
54_D 69_T 1.947 1.00
74_H 78_E 1.922 1.00
20_C 24_H 1.869 1.00
167_P 274_K 1.859 1.00
19_E 23_Q 1.855 1.00
19_E 78_E 1.846 1.00
20_C 23_Q 1.83 1.00
120_L 126_V 1.82 1.00
17_I 41_V 1.815 1.00
119_C 295_R 1.812 1.00
58_I 65_A 1.8 1.00
73_L 87_T 1.8 1.00
199_T 243_L 1.792 1.00
174_T 249_Y 1.736 1.00
239_A 255_Y 1.728 1.00
22_Y 74_H 1.714 1.00
239_A 260_N 1.702 1.00
142_E 146_H 1.689 1.00
18_F 74_H 1.68 1.00
68_T 71_L 1.667 1.00
140_A 152_V 1.659 1.00
23_Q 33_S 1.652 1.00
197_E 225_S 1.647 1.00
19_E 77_L 1.639 1.00
28_S 38_P 1.631 1.00
72_N 90_I 1.606 1.00
177_C 264_I 1.604 1.00
17_I 36_I 1.587 1.00
37_T 40_A 1.57 1.00
24_H 29_K 1.565 1.00
120_L 292_F 1.563 1.00
26_S 29_K 1.558 1.00
19_E 81_L 1.553 1.00
170_T 272_S 1.552 1.00
95_E 125_S 1.501 1.00
143_L 148_K 1.472 1.00
76_H 86_Q 1.459 1.00
199_T 234_I 1.457 1.00
165_C 276_Y 1.447 1.00
208_V 212_Q 1.443 1.00
110_C 232_L 1.433 1.00
80_N 87_T 1.429 1.00
20_C 34_L 1.425 1.00
14_L 47_R 1.422 1.00
55_P 58_I 1.421 1.00
174_T 263_E 1.415 1.00
14_L 44_S 1.41 1.00
14_L 51_Q 1.389 0.99
71_L 75_H 1.373 0.99
11_D 14_L 1.372 0.99
12_L 84_L 1.367 0.99
151_L 289_F 1.347 0.99
46_Q 50_A 1.344 0.99
133_I 139_N 1.341 0.99
196_E 244_L 1.331 0.99
119_C 123_D 1.329 0.99
73_L 88_I 1.327 0.99
119_C 122_Q 1.309 0.99
164_I 281_K 1.297 0.99
177_C 244_L 1.293 0.99
76_H 79_K 1.29 0.99
97_K 125_S 1.289 0.99
164_I 279_Y 1.287 0.99
234_I 245_G 1.275 0.99
277_I 293_I 1.274 0.99
285_N 289_F 1.263 0.99
255_Y 260_N 1.261 0.99
118_R 122_Q 1.259 0.99
228_G 234_I 1.253 0.99
144_L 152_V 1.248 0.99
18_F 22_Y 1.244 0.98
166_M 279_Y 1.243 0.98
43_Q 46_Q 1.229 0.98
21_I 45_L 1.225 0.98
291_R 294_D 1.223 0.98
143_L 149_A 1.223 0.98
51_Q 88_I 1.201 0.98
121_R 197_E 1.2 0.98
179_N 260_N 1.198 0.98
209_D 213_M 1.194 0.98
151_L 277_I 1.193 0.98
109_S 132_D 1.193 0.98
18_F 56_L 1.189 0.98
101_I 131_H 1.189 0.98
100_F 292_F 1.187 0.98
182_P 196_E 1.186 0.98
18_F 57_F 1.186 0.98
75_H 79_K 1.185 0.98
215_I 220_M 1.182 0.98
27_I 64_I 1.177 0.98
145_V 162_S 1.175 0.98
36_I 40_A 1.173 0.98
253_N 257_D 1.168 0.97
76_H 87_T 1.163 0.97
236_N 239_A 1.163 0.97
42_S 46_Q 1.159 0.97
22_Y 57_F 1.158 0.97
72_N 75_H 1.156 0.97
21_I 30_A 1.155 0.97
66_P 70_G 1.152 0.97
83_G 86_Q 1.142 0.97
16_V 85_E 1.142 0.97
123_D 295_R 1.139 0.97
60_S 65_A 1.138 0.97
120_L 295_R 1.134 0.97
121_R 225_S 1.131 0.97
120_L 124_S 1.131 0.97
249_Y 253_N 1.126 0.97
188_S 192_Q 1.122 0.97
171_I 250_E 1.112 0.96
20_C 30_A 1.112 0.96
293_I 297_N 1.111 0.96
154_T 278_S 1.106 0.96
279_Y 293_I 1.091 0.96
178_S 241_T 1.078 0.95
43_Q 47_R 1.078 0.95
290_S 294_D 1.078 0.95
15_L 77_L 1.075 0.95
177_C 181_H 1.074 0.95
44_S 47_R 1.07 0.95
176_I 252_Y 1.063 0.95
13_N 16_V 1.062 0.95
179_N 262_K 1.061 0.95
235_I 239_A 1.057 0.95
103_Y 154_T 1.057 0.95
181_H 197_E 1.056 0.95
167_P 276_Y 1.053 0.95
156_M 276_Y 1.053 0.95
72_N 76_H 1.051 0.94
236_N 240_V 1.049 0.94
175_L 244_L 1.048 0.94
165_C 278_S 1.043 0.94
36_I 41_V 1.038 0.94
249_Y 263_E 1.038 0.94
186_D 262_K 1.036 0.94
280_N 283_S 1.032 0.94
118_R 240_V 1.029 0.94
22_Y 70_G 1.025 0.93
80_N 83_G 1.017 0.93
85_E 89_N 1.016 0.93
57_F 64_I 1.01 0.93
129_E 227_R 1.006 0.93
254_S 258_F 1.006 0.93
79_K 86_Q 1.006 0.93
73_L 77_L 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
1uthA10.99331000.105Contact Map0.725
2esnA40.98671000.109Contact Map0.759
3fzvA40.971000.122Contact Map0.722
3fxqA20.96331000.126Contact Map0.775
1ixcA20.95331000.132Contact Map0.755
1al3A10.961000.134Contact Map0.767
2h98A20.951000.139Contact Map0.74
2h9bA20.951000.147Contact Map0.743
3szpA20.951000.156Contact Map0.77
3hhgA80.95671000.168Contact Map0.927
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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