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OPENSEQ.org
YPDB - Transcriptional regulatory protein YpdB
UniProt: P0AE39 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG14149
Length: 244 (243)
Sequences: 3119
Seq/Len: 12.84
YPDB
Paralog alert: 0.61 [within 20: 0.03] - ratio of genomes with paralogs
Cluster includes: YEHT YPDB
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
195_C 228_V 3.991 1.00
13_Q 31_T 3.594 1.00
2_K 27_E 3.138 1.00
184_C 194_R 3.131 1.00
17_S 31_T 2.887 1.00
60_D 63_L 2.862 1.00
92_E 107_R 2.843 1.00
6_V 38_V 2.786 1.00
32_F 41_F 2.767 1.00
13_Q 33_D 2.554 1.00
7_E 56_I 2.448 1.00
79_F 95_A 2.25 1.00
4_I 32_F 2.179 1.00
35_G 64_L 2.156 1.00
66_Q 89_E 2.108 1.00
65_A 79_F 2.009 1.00
231_S 234_K 1.981 1.00
141_L 167_V 1.976 1.00
78_V 111_M 1.937 1.00
5_I 17_S 1.934 1.00
49_A 115_L 1.93 1.00
80_I 103_Y 1.919 1.00
5_I 13_Q 1.916 1.00
17_S 21_K 1.912 1.00
34_D 37_D 1.889 1.00
193_F 238_F 1.843 1.00
158_A 165_T 1.829 1.00
235_V 239_R 1.795 1.00
146_R 208_E 1.792 1.00
184_C 200_C 1.753 1.00
169_T 174_Y 1.741 1.00
7_E 13_Q 1.692 1.00
151_P 154_D 1.663 1.00
15_E 19_L 1.626 1.00
196_H 199_F 1.622 1.00
94_E 114_K 1.607 1.00
22_E 105_E 1.604 1.00
35_G 59_L 1.604 1.00
55_N 83_W 1.586 1.00
3_V 26_M 1.548 1.00
223_D 226_F 1.544 1.00
196_H 229_P 1.516 1.00
97_D 107_R 1.487 1.00
42_L 47_V 1.485 1.00
9_E 12_A 1.482 1.00
201_V 219_L 1.474 1.00
41_F 45_N 1.464 1.00
65_A 77_I 1.457 1.00
156_Y 205_K 1.448 1.00
191_H 204_N 1.446 1.00
166_F 173_S 1.439 1.00
188_P 191_H 1.422 1.00
210_E 227_E 1.42 1.00
187_L 192_F 1.419 1.00
30_G 41_F 1.416 1.00
164_M 175_V 1.416 1.00
78_V 115_L 1.402 0.99
138_T 149_V 1.402 0.99
208_E 220_R 1.395 0.99
25_Q 116_E 1.388 0.99
157_Y 199_F 1.382 0.99
50_I 75_P 1.381 0.99
62_V 65_A 1.372 0.99
97_D 111_M 1.353 0.99
157_Y 228_V 1.352 0.99
42_L 64_L 1.349 0.99
33_D 37_D 1.344 0.99
193_F 203_L 1.337 0.99
170_R 205_K 1.318 0.99
199_F 228_V 1.314 0.99
140_N 149_V 1.312 0.99
39_L 64_L 1.31 0.99
4_I 47_V 1.307 0.99
178_M 182_E 1.3 0.99
105_E 109_T 1.281 0.99
108_I 112_L 1.278 0.99
188_P 200_C 1.247 0.99
209_I 238_F 1.241 0.98
83_W 86_H 1.235 0.98
8_D 53_D 1.234 0.98
154_D 170_R 1.233 0.98
201_V 206_I 1.218 0.98
51_F 80_I 1.206 0.98
236_K 240_Q 1.205 0.98
97_D 114_K 1.203 0.98
179_N 182_E 1.192 0.98
161_H 166_F 1.182 0.98
237_E 241_L 1.181 0.98
156_Y 223_D 1.175 0.98
56_I 59_L 1.173 0.98
157_Y 168_Y 1.171 0.98
59_L 67_N 1.166 0.97
10_F 14_Q 1.166 0.97
19_L 105_E 1.155 0.97
199_F 229_P 1.152 0.97
155_I 167_V 1.147 0.97
79_F 93_L 1.138 0.97
193_F 234_K 1.138 0.97
158_A 183_F 1.133 0.97
103_Y 108_I 1.124 0.97
62_V 93_L 1.119 0.96
218_I 227_E 1.111 0.96
52_L 65_A 1.11 0.96
51_F 78_V 1.108 0.96
3_V 49_A 1.105 0.96
202_N 205_K 1.104 0.96
160_A 197_R 1.101 0.96
111_M 115_L 1.097 0.96
96_F 111_M 1.096 0.96
159_E 168_Y 1.095 0.96
41_F 47_V 1.084 0.96
89_E 92_E 1.084 0.96
20_I 26_M 1.08 0.95
39_L 67_N 1.067 0.95
159_E 199_F 1.064 0.95
51_F 108_I 1.063 0.95
80_I 99_I 1.055 0.95
53_D 101_K 1.05 0.94
146_R 210_E 1.048 0.94
15_E 18_W 1.043 0.94
206_I 219_L 1.042 0.94
8_D 101_K 1.041 0.94
99_I 108_I 1.041 0.94
35_G 39_L 1.04 0.94
141_L 150_T 1.038 0.94
234_K 237_E 1.033 0.94
166_F 175_V 1.032 0.94
65_A 93_L 1.032 0.94
19_L 108_I 1.03 0.94
90_A 95_A 1.03 0.94
6_V 50_I 1.025 0.93
4_I 30_G 1.021 0.93
157_Y 226_F 1.018 0.93
92_E 110_G 1.016 0.93
76_F 115_L 1.012 0.93
32_F 35_G 1.005 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
3d6wA20.446799.90.57Contact Map0.859
1kgsA10.901699.90.593Contact Map0.663
4g4kA20.413999.90.606Contact Map0.845
3n0rA10.512399.80.61Contact Map0.595
1dz3A10.512399.80.641Contact Map0.577
4hyeA20.799299.80.641Contact Map0.767
1ny5A20.954999.80.641Contact Map0.72
2ayxA10.504199.80.642Contact Map0.504
3to5A10.483699.80.644Contact Map0.725
4l4uA10.95999.80.645Contact Map0.698
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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