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OPENSEQ.org
YDHB - Uncharacterized HTH-type transcriptional regulator YdhB
UniProt: P0ACR2 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG12140
Length: 310 (290)
Sequences: 36779
Seq/Len: 126.82
YDHB
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
71_S 75_K 3.703 1.00
16_N 25_E 3.351 1.00
231_I 238_G 2.469 1.00
97_A 142_V 2.401 1.00
21_A 24_Q 2.36 1.00
68_E 82_Q 2.327 1.00
161_R 289_G 2.306 1.00
167_S 242_T 2.26 1.00
15_R 70_R 2.198 1.00
186_S 189_T 2.193 1.00
12_A 25_E 2.177 1.00
95_A 124_L 2.147 1.00
176_H 193_W 2.143 1.00
93_Q 122_E 2.133 1.00
93_Q 124_L 2.119 1.00
72_V 76_M 2.111 1.00
162_D 165_M 2.083 1.00
165_M 267_A 2.062 1.00
14_A 58_L 2.057 1.00
68_E 75_K 2.03 1.00
228_A 248_W 2.008 1.00
113_D 287_Y 2 1.00
9_V 36_T 1.978 1.00
11_D 66_L 1.975 1.00
66_L 70_R 1.931 1.00
19_F 37_V 1.93 1.00
46_V 61_A 1.923 1.00
162_D 267_A 1.887 1.00
12_A 16_N 1.886 1.00
11_D 70_R 1.859 1.00
11_D 15_R 1.853 1.00
12_A 15_R 1.833 1.00
9_V 33_V 1.813 1.00
114_F 121_V 1.807 1.00
50_E 57_E 1.792 1.00
65_F 79_T 1.79 1.00
169_S 242_T 1.767 1.00
196_L 236_C 1.767 1.00
135_D 139_D 1.764 1.00
232_S 248_W 1.751 1.00
232_S 253_K 1.745 1.00
14_A 66_L 1.703 1.00
60_A 63_A 1.692 1.00
172_V 257_L 1.686 1.00
64_W 82_Q 1.661 1.00
10_V 66_L 1.65 1.00
11_D 69_G 1.644 1.00
20_S 30_P 1.637 1.00
15_R 25_E 1.636 1.00
133_V 145_A 1.601 1.00
18_S 21_A 1.595 1.00
165_M 265_D 1.591 1.00
29_V 32_A 1.581 1.00
9_V 28_R 1.581 1.00
11_D 73_V 1.578 1.00
16_N 21_A 1.571 1.00
89_G 120_D 1.565 1.00
169_S 256_A 1.562 1.00
160_F 269_C 1.512 1.00
136_A 141_R 1.505 1.00
68_E 78_I 1.471 1.00
104_P 225_E 1.449 1.00
12_A 26_L 1.44 1.00
72_V 79_T 1.433 1.00
196_L 227_S 1.431 1.00
47_P 50_E 1.422 1.00
6_S 39_Q 1.416 1.00
6_S 36_T 1.397 0.99
194_P 218_R 1.395 0.99
113_D 117_H 1.391 0.99
6_S 43_W 1.389 0.99
63_A 67_K 1.378 0.99
65_F 80_R 1.371 0.99
114_F 284_L 1.36 0.99
172_V 237_I 1.352 0.99
113_D 291_S 1.345 0.99
193_W 237_I 1.339 0.99
128_E 132_G 1.339 0.99
38_R 42_E 1.338 0.99
91_R 120_D 1.323 0.99
68_E 71_S 1.321 0.99
113_D 116_R 1.321 0.99
159_A 272_W 1.321 0.99
246_K 250_N 1.32 0.99
283_W 286_E 1.303 0.99
144_L 281_L 1.295 0.99
137_L 145_A 1.282 0.99
159_A 274_Q 1.281 0.99
4_E 76_M 1.28 0.99
248_W 253_K 1.276 0.99
112_V 116_R 1.271 0.99
136_A 142_V 1.268 0.99
227_S 238_G 1.267 0.99
181_M 189_T 1.253 0.99
43_W 80_R 1.23 0.98
144_L 270_L 1.23 0.98
161_R 272_W 1.227 0.98
13_V 37_V 1.225 0.98
282_T 286_E 1.216 0.98
183_G 255_V 1.214 0.98
174_S 253_K 1.214 0.98
10_V 14_A 1.211 0.98
177_P 193_W 1.209 0.98
285_L 289_G 1.208 0.98
221_V 227_S 1.203 0.98
229_T 232_S 1.201 0.98
115_Y 194_P 1.199 0.98
35_Y 38_R 1.192 0.98
67_K 71_S 1.191 0.98
64_W 67_K 1.187 0.98
3_S 6_S 1.186 0.98
10_V 49_F 1.185 0.98
242_T 246_K 1.183 0.98
28_R 32_A 1.181 0.98
95_A 126_F 1.18 0.98
52_R 57_E 1.179 0.98
68_E 79_T 1.172 0.98
138_S 157_R 1.171 0.98
13_V 22_A 1.161 0.97
117_H 287_Y 1.158 0.97
14_A 49_F 1.158 0.97
205_L 209_I 1.157 0.97
75_K 78_I 1.156 0.97
103_R 127_Q 1.155 0.97
10_V 48_L 1.153 0.97
19_F 56_V 1.152 0.97
34_S 38_R 1.141 0.97
242_T 256_A 1.136 0.97
8_E 77_Q 1.13 0.97
58_L 62_G 1.129 0.97
283_W 287_Y 1.123 0.97
185_F 189_T 1.112 0.96
114_F 118_F 1.109 0.96
147_G 271_T 1.101 0.96
5_Y 8_E 1.093 0.96
12_A 22_A 1.092 0.96
172_V 176_H 1.089 0.96
247_P 251_E 1.088 0.96
112_V 233_A 1.087 0.96
36_T 39_Q 1.085 0.96
94_L 284_L 1.085 0.96
166_L 243_H 1.08 0.95
162_D 269_C 1.078 0.95
229_T 233_A 1.074 0.95
171_V 245_A 1.072 0.95
173_A 234_G 1.071 0.95
270_L 285_L 1.068 0.95
64_W 68_E 1.068 0.95
35_Y 39_Q 1.063 0.95
7_L 69_G 1.062 0.95
176_H 194_P 1.062 0.95
174_S 255_V 1.061 0.95
160_F 271_T 1.058 0.95
286_E 289_G 1.055 0.95
277_M 281_L 1.048 0.94
161_R 285_L 1.047 0.94
170_C 237_I 1.046 0.94
49_F 56_V 1.04 0.94
272_W 285_L 1.039 0.94
28_R 33_V 1.036 0.94
72_V 75_K 1.036 0.94
228_A 232_S 1.028 0.94
71_S 78_I 1.025 0.93
149_T 269_C 1.023 0.93
77_Q 81_Q 1.021 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
3fxqA20.95811000.208Contact Map0.782
2esnA40.94521000.214Contact Map0.763
3fzvA40.95481000.22Contact Map0.718
1uthA10.95161000.22Contact Map0.74
2h98A20.9711000.222Contact Map0.761
1ixcA20.9291000.226Contact Map0.753
1al3A10.98711000.228Contact Map0.783
2h9bA20.96451000.235Contact Map0.769
3hhgA80.96131000.24Contact Map0.919
3szpA20.92261000.241Contact Map0.765
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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