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OPENSEQ.org
YBEF - Uncharacterized HTH-type transcriptional regulator YbeF
UniProt: P30979 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG11594
Length: 317 (288)
Sequences: 36503
Seq/Len: 126.75
YBEF
Paralog alert: 0.88 [within 20: 0.49] - 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
98_Q 102_S 3.741 1.00
43_H 52_V 3.409 1.00
254_V 261_A 2.505 1.00
122_A 165_T 2.425 1.00
48_N 51_K 2.365 1.00
182_H 314_R 2.303 1.00
95_Y 109_I 2.302 1.00
188_N 265_S 2.265 1.00
197_N 212_A 2.264 1.00
42_V 97_S 2.223 1.00
205_D 208_T 2.212 1.00
39_A 52_V 2.209 1.00
118_T 147_L 2.177 1.00
183_V 186_T 2.109 1.00
186_T 291_D 2.089 1.00
99_G 103_I 2.081 1.00
120_T 149_R 2.052 1.00
95_Y 102_S 2.041 1.00
41_Y 85_P 2.041 1.00
36_I 63_S 1.991 1.00
38_E 93_H 1.986 1.00
73_D 88_F 1.981 1.00
46_I 64_I 1.979 1.00
138_A 312_V 1.968 1.00
251_A 271_F 1.962 1.00
118_T 149_R 1.942 1.00
93_H 97_S 1.92 1.00
39_A 43_H 1.919 1.00
183_V 291_D 1.903 1.00
38_E 97_S 1.881 1.00
38_E 42_V 1.88 1.00
39_A 42_V 1.867 1.00
255_A 276_P 1.838 1.00
158_N 162_Q 1.836 1.00
36_I 60_I 1.812 1.00
77_I 84_T 1.812 1.00
92_L 106_A 1.807 1.00
139_I 146_L 1.803 1.00
215_V 259_M 1.771 1.00
190_V 265_S 1.77 1.00
255_A 271_F 1.725 1.00
41_Y 93_H 1.714 1.00
87_A 90_M 1.685 1.00
91_H 109_I 1.674 1.00
38_E 96_I 1.673 1.00
37_F 93_H 1.654 1.00
47_V 57_P 1.653 1.00
193_C 280_L 1.648 1.00
42_V 52_V 1.646 1.00
213_A 241_N 1.641 1.00
56_T 59_A 1.603 1.00
43_H 48_N 1.6 1.00
156_A 168_I 1.592 1.00
45_G 48_N 1.588 1.00
36_I 55_L 1.572 1.00
186_T 289_Q 1.568 1.00
38_E 100_L 1.539 1.00
95_Y 105_G 1.505 1.00
33_L 66_K 1.472 1.00
190_V 279_K 1.467 1.00
215_V 250_I 1.465 1.00
181_H 293_S 1.464 1.00
159_Q 164_Q 1.461 1.00
129_A 248_L 1.454 1.00
39_A 53_L 1.448 1.00
99_G 106_A 1.438 1.00
74_P 77_I 1.429 1.00
224_F 228_R 1.417 1.00
139_I 309_V 1.414 1.00
33_L 63_S 1.406 0.99
33_L 70_I 1.401 0.99
212_A 260_L 1.401 0.99
92_L 107_L 1.393 0.99
167_L 306_L 1.389 0.99
90_M 94_E 1.387 0.99
31_L 103_I 1.386 0.99
138_A 142_H 1.37 0.99
116_Q 145_Q 1.355 0.99
65_Q 69_V 1.351 0.99
30_D 33_L 1.34 0.99
138_A 141_T 1.333 0.99
271_F 276_P 1.332 0.99
193_C 260_L 1.33 0.99
195_E 276_P 1.326 0.99
180_Q 298_K 1.324 0.99
180_Q 296_Y 1.317 0.99
95_Y 98_Q 1.315 0.99
308_G 311_D 1.305 0.99
250_I 261_A 1.3 0.99
137_R 141_T 1.282 0.99
244_S 250_I 1.258 0.99
308_G 312_V 1.257 0.99
159_Q 165_T 1.248 0.99
160_L 168_I 1.248 0.99
182_H 296_Y 1.245 0.98
269_N 273_R 1.239 0.98
37_F 41_Y 1.23 0.98
62_Q 65_Q 1.224 0.98
302_R 306_L 1.222 0.98
198_P 212_A 1.219 0.98
140_K 213_A 1.209 0.98
70_I 107_L 1.206 0.98
167_L 294_I 1.206 0.98
55_L 59_A 1.204 0.98
94_E 98_Q 1.204 0.98
46_I 83_V 1.2 0.98
95_Y 106_A 1.191 0.98
231_V 236_P 1.188 0.98
91_H 94_E 1.182 0.98
37_F 76_F 1.181 0.98
161_S 178_T 1.179 0.98
40_V 64_I 1.174 0.98
37_F 75_L 1.174 0.98
252_A 255_A 1.165 0.97
114_D 145_Q 1.163 0.97
40_V 49_A 1.162 0.97
265_S 269_N 1.154 0.97
102_S 105_G 1.151 0.97
140_K 241_N 1.15 0.97
79_K 84_T 1.15 0.97
41_Y 76_F 1.148 0.97
61_S 65_Q 1.147 0.97
294_I 310_I 1.145 0.97
119_I 309_V 1.142 0.97
204_D 208_T 1.131 0.97
139_I 143_Y 1.127 0.97
35_T 104_L 1.126 0.97
85_P 89_A 1.122 0.97
170_D 295_H 1.119 0.96
39_A 49_A 1.118 0.96
142_H 312_V 1.118 0.96
187_D 266_R 1.114 0.96
183_V 293_S 1.113 0.96
307_H 311_D 1.1 0.96
296_Y 310_I 1.096 0.96
122_A 170_D 1.091 0.96
195_E 278_E 1.09 0.96
32_N 35_T 1.084 0.96
194_R 257_S 1.084 0.96
251_A 255_A 1.084 0.96
62_Q 66_K 1.083 0.96
270_L 274_C 1.08 0.95
193_C 197_N 1.077 0.95
197_N 213_A 1.076 0.95
137_R 256_N 1.075 0.95
252_A 256_N 1.075 0.95
139_I 312_V 1.074 0.95
181_H 295_H 1.071 0.95
202_L 278_E 1.068 0.95
191_L 260_L 1.067 0.95
91_H 95_Y 1.066 0.95
297_N 300_S 1.062 0.95
63_S 66_K 1.06 0.95
192_I 268_Y 1.059 0.95
55_L 60_I 1.058 0.95
265_S 279_K 1.057 0.95
34_L 96_I 1.054 0.95
99_G 102_S 1.047 0.94
104_L 108_D 1.042 0.94
121_I 167_L 1.02 0.93
172_M 293_S 1.016 0.93
76_F 83_V 1.005 0.93
41_Y 89_A 1.004 0.93
98_Q 105_G 1.004 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
1uthA10.94951000.202Contact Map0.746
2esnA40.93061000.213Contact Map0.765
3fzvA40.91481000.219Contact Map0.721
3fxqA20.90851000.229Contact Map0.783
1ixcA20.89911000.231Contact Map0.762
1al3A10.90541000.233Contact Map0.789
2h98A20.89591000.234Contact Map0.755
2h9bA20.89911000.242Contact Map0.751
3szpA20.90221000.243Contact Map0.763
3hhgA80.91171000.248Contact Map0.922
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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