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OPENSEQ.org
YFDR - Uncharacterized protein YfdR
UniProt: P76514 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG14140
Length: 178 (175)
Sequences: 253
Seq/Len: 1.45
YFDR
Paralog alert: 0.13 [within 20: 0.00] - ratio of genomes with paralogs
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
30_S 40_H 3.165 1.00
64_F 68_M 2.468 1.00
45_Y 125_T 1.933 0.97
24_I 168_F 1.74 0.94
76_C 101_I 1.698 0.93
172_S 175_R 1.675 0.92
55_S 167_R 1.663 0.92
155_L 160_A 1.635 0.91
38_A 41_L 1.625 0.91
24_I 165_M 1.622 0.91
62_F 65_E 1.616 0.90
66_A 115_V 1.613 0.90
6_T 75_Y 1.593 0.90
86_L 93_M 1.563 0.88
34_I 77_Q 1.547 0.88
2_S 5_K 1.546 0.88
12_F 97_I 1.542 0.88
165_M 168_F 1.491 0.85
45_Y 88_P 1.483 0.85
35_C 44_F 1.46 0.83
155_L 163_M 1.46 0.83
30_S 75_Y 1.42 0.81
143_G 175_R 1.416 0.81
83_L 124_A 1.412 0.80
49_Q 130_L 1.403 0.80
87_L 138_W 1.325 0.74
49_Q 122_M 1.297 0.72
59_P 88_P 1.271 0.70
13_Y 16_K 1.256 0.68
58_V 66_A 1.255 0.68
49_Q 128_R 1.255 0.68
62_F 111_M 1.254 0.68
49_Q 154_P 1.253 0.68
79_I 167_R 1.246 0.68
54_C 118_A 1.239 0.67
170_D 174_L 1.236 0.67
14_Y 77_Q 1.229 0.66
38_A 80_P 1.228 0.66
58_V 61_E 1.222 0.65
168_F 172_S 1.216 0.65
65_E 111_M 1.169 0.60
22_I 173_E 1.168 0.60
6_T 12_F 1.168 0.60
89_D 92_R 1.146 0.58
83_L 94_E 1.143 0.58
65_E 112_S 1.14 0.57
130_L 152_V 1.139 0.57
8_S 23_V 1.136 0.57
138_W 141_L 1.134 0.57
93_M 157_P 1.132 0.57
166_E 170_D 1.132 0.57
83_L 91_K 1.127 0.56
40_H 75_Y 1.122 0.56
61_E 175_R 1.122 0.56
33_N 94_E 1.112 0.55
98_D 163_M 1.099 0.53
25_N 51_A 1.096 0.53
8_S 15_D 1.096 0.53
66_A 79_I 1.092 0.53
8_S 26_D 1.087 0.52
144_I 171_L 1.085 0.52
91_K 173_E 1.085 0.52
6_T 74_A 1.084 0.52
99_A 117_Y 1.084 0.52
144_I 175_R 1.081 0.51
22_I 26_D 1.08 0.51
6_T 37_F 1.073 0.51
65_E 102_R 1.069 0.50
29_V 32_S 1.067 0.50
33_N 49_Q 1.065 0.50
56_Q 110_V 1.065 0.50
45_Y 161_Y 1.063 0.50
105_Y 109_P 1.06 0.49
83_L 93_M 1.055 0.49
13_Y 18_N 1.055 0.49
124_A 163_M 1.051 0.48
19_K 68_M 1.042 0.47
32_S 77_Q 1.039 0.47
140_V 174_L 1.039 0.47
92_R 96_K 1.038 0.47
37_F 123_L 1.019 0.45
20_D 75_Y 1.018 0.45
22_I 75_Y 1.014 0.45
37_F 80_P 1.013 0.44
47_V 84_K 1.013 0.44
102_R 115_V 1.011 0.44
70_D 84_K 1.009 0.44
155_L 161_Y 1.008 0.44
10_K 23_V 1.006 0.44
55_S 63_A 1.004 0.44
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
2gz4A40.99441000.416Contact Map0.453
1xx7A60.865299.70.742Contact Map0.315
4l1jA20.898999.70.755Contact Map0.291
3kh1A20.910199.60.776Contact Map0.251
2cqzA60.820299.50.779Contact Map0.353
3mzoA30.853999.50.782Contact Map0.314
2paqA20.870899.50.787Contact Map0.349
1ynbA30.80999.30.808Contact Map0.416
3ljxA10.949435.90.953Contact Map0.383
4mcjA100.589929.10.955Contact Map0.093
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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