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OPENSEQ.org
YBHD - Uncharacterized HTH-type transcriptional regulator YbhD
UniProt: P52696 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG13230
Length: 317 (293)
Sequences: 36973
Seq/Len: 126.19
YBHD
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
72_E 76_K 3.744 1.00
17_S 26_L 3.378 1.00
160_T 291_I 2.602 1.00
233_V 240_S 2.467 1.00
22_N 25_K 2.348 1.00
98_A 143_S 2.343 1.00
69_E 83_N 2.34 1.00
184_E 187_E 2.217 1.00
166_P 244_G 2.212 1.00
13_I 26_L 2.212 1.00
16_E 71_R 2.174 1.00
96_T 125_R 2.166 1.00
94_M 123_K 2.155 1.00
94_M 125_R 2.135 1.00
175_H 191_Y 2.121 1.00
161_P 164_N 2.12 1.00
73_L 77_F 2.097 1.00
114_K 293_L 2.079 1.00
69_E 76_K 2.06 1.00
164_N 268_T 2.055 1.00
15_A 59_L 2.022 1.00
12_V 67_L 1.997 1.00
10_A 37_R 1.973 1.00
230_L 250_A 1.958 1.00
47_V 62_A 1.958 1.00
67_L 71_R 1.937 1.00
13_I 17_S 1.928 1.00
114_K 289_L 1.888 1.00
161_P 268_T 1.875 1.00
20_F 38_I 1.866 1.00
12_V 71_R 1.855 1.00
12_V 16_E 1.843 1.00
51_E 58_T 1.839 1.00
13_I 16_E 1.836 1.00
66_L 80_T 1.8 1.00
194_I 238_G 1.785 1.00
168_V 244_G 1.777 1.00
10_A 34_L 1.771 1.00
115_F 122_I 1.764 1.00
15_A 67_L 1.744 1.00
192_K 220_F 1.706 1.00
61_K 64_K 1.691 1.00
65_R 83_N 1.667 1.00
136_E 140_C 1.661 1.00
11_F 67_L 1.639 1.00
12_V 70_A 1.636 1.00
16_E 26_L 1.633 1.00
164_N 266_R 1.615 1.00
21_N 31_Q 1.592 1.00
134_C 146_G 1.587 1.00
17_S 22_N 1.583 1.00
234_E 250_A 1.575 1.00
90_Y 121_N 1.564 1.00
30_T 33_A 1.564 1.00
19_S 22_N 1.563 1.00
115_F 286_F 1.56 1.00
12_V 74_I 1.545 1.00
10_A 29_I 1.533 1.00
180_K 187_E 1.497 1.00
159_F 270_G 1.495 1.00
69_E 79_E 1.489 1.00
137_S 142_E 1.482 1.00
105_F 227_S 1.462 1.00
13_I 27_L 1.45 1.00
73_L 80_T 1.434 1.00
114_K 118_L 1.428 1.00
48_Q 51_E 1.428 1.00
7_S 40_K 1.418 1.00
194_I 229_S 1.403 0.99
64_K 68_P 1.39 0.99
145_F 283_A 1.382 0.99
7_S 44_D 1.379 0.99
5_L 77_F 1.379 0.99
7_S 37_R 1.377 0.99
92_R 121_N 1.363 0.99
191_Y 239_I 1.355 0.99
66_L 81_L 1.348 0.99
114_K 117_E 1.345 0.99
158_D 273_R 1.334 0.99
285_R 288_A 1.334 0.99
39_K 43_E 1.332 0.99
158_D 275_K 1.328 0.99
171_C 239_I 1.323 0.99
203_R 207_E 1.313 0.99
257_G 260_L 1.307 0.99
69_E 72_E 1.307 0.99
271_I 287_F 1.304 0.99
137_S 143_S 1.299 0.99
279_L 283_A 1.299 0.99
4_E 7_S 1.294 0.99
113_G 117_E 1.291 0.99
229_S 240_S 1.29 0.99
287_F 291_I 1.278 0.99
129_Q 133_N 1.272 0.99
116_N 192_K 1.238 0.98
160_T 273_R 1.23 0.98
223_V 229_S 1.229 0.98
11_F 15_A 1.224 0.98
231_G 234_E 1.223 0.98
176_P 191_Y 1.218 0.98
69_E 80_T 1.217 0.98
68_P 72_E 1.217 0.98
116_N 220_F 1.213 0.98
115_F 289_L 1.212 0.98
44_D 81_L 1.207 0.98
118_L 289_L 1.205 0.98
53_T 58_T 1.204 0.98
96_T 127_L 1.198 0.98
36_R 39_K 1.193 0.98
65_R 68_P 1.192 0.98
255_I 261_V 1.185 0.98
244_G 248_P 1.178 0.98
171_C 258_I 1.173 0.98
29_I 33_A 1.173 0.98
11_F 50_F 1.171 0.98
14_L 38_I 1.167 0.97
251_P 254_S 1.166 0.97
288_A 291_I 1.166 0.97
95_V 286_F 1.155 0.97
76_K 79_E 1.155 0.97
35_T 39_K 1.148 0.97
15_A 50_F 1.146 0.97
248_P 252_Y 1.14 0.97
273_R 287_F 1.139 0.97
14_L 23_A 1.134 0.97
11_F 49_L 1.133 0.97
168_V 257_G 1.132 0.97
139_L 156_S 1.131 0.97
173_R 254_S 1.129 0.97
20_F 57_V 1.125 0.97
148_N 272_I 1.123 0.97
9_K 78_D 1.117 0.96
145_F 271_I 1.117 0.96
59_L 63_G 1.11 0.96
113_G 235_A 1.109 0.96
284_E 288_A 1.107 0.96
210_L 215_W 1.103 0.96
172_R 236_G 1.102 0.96
118_L 292_N 1.096 0.96
37_R 40_K 1.092 0.96
13_I 23_A 1.09 0.96
230_L 234_E 1.086 0.96
65_R 69_E 1.081 0.95
161_P 270_G 1.08 0.95
169_L 239_I 1.074 0.95
231_G 235_A 1.068 0.95
36_R 40_K 1.064 0.95
159_F 272_I 1.063 0.95
247_M 250_A 1.063 0.95
8_M 70_A 1.061 0.95
6_S 9_K 1.061 0.95
165_E 245_L 1.059 0.95
171_C 175_H 1.059 0.95
119_Y 285_R 1.059 0.95
150_N 270_G 1.056 0.95
115_F 119_Y 1.051 0.94
29_I 34_L 1.046 0.94
192_K 218_D 1.034 0.94
50_F 57_V 1.03 0.94
73_L 76_K 1.027 0.94
160_T 287_F 1.025 0.93
72_E 79_E 1.024 0.93
78_D 82_F 1.024 0.93
183_V 187_E 1.023 0.93
256_I 260_L 1.015 0.93
129_Q 137_S 1.012 0.93
110_L 235_A 1.008 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
2esnA40.94011000.186Contact Map0.758
3fzvA40.94951000.192Contact Map0.719
1ixcA20.92111000.194Contact Map0.758
3fxqA20.94951000.196Contact Map0.779
1uthA10.95271000.198Contact Map0.721
1al3A10.98111000.202Contact Map0.731
2h9bA20.96851000.209Contact Map0.766
2h98A20.96851000.212Contact Map0.765
3szpA20.91481000.219Contact Map0.756
3hhgA80.95271000.221Contact Map0.92
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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