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OPENSEQ.org
YRDA - Protein YrdA
UniProt: P0A9W9 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG12838
Length: 184 (176)
Sequences: 2586
Seq/Len: 14.69
YRDA
Paralog alert: 0.62 [within 20: 0.02] - ratio of genomes with paralogs
Cluster includes: CAIE MAA PAAY THGA WBBJ WCAF YRDA
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
35_D 56_A 2.993 1.00
36_D 57_R 2.928 1.00
101_G 120_D 2.896 1.00
66_L 81_L 2.861 1.00
16_G 35_D 2.795 1.00
103_R 121_D 2.791 1.00
136_L 142_Y 2.678 1.00
57_R 86_D 2.663 1.00
14_Q 32_R 2.392 1.00
86_D 103_R 2.373 1.00
102_N 120_D 2.356 1.00
32_R 53_Q 2.349 1.00
125_G 143_L 2.332 1.00
18_R 36_D 2.293 1.00
121_D 139_G 2.232 1.00
84_G 102_N 2.117 1.00
117_I 135_R 2.079 1.00
79_N 115_G 2.046 1.00
34_A 56_A 1.996 1.00
41_P 175_Y 1.981 1.00
85_E 102_N 1.889 1.00
120_D 138_S 1.885 1.00
122_V 140_Y 1.742 1.00
56_A 85_E 1.734 1.00
95_L 98_C 1.733 1.00
11_L 30_D 1.722 1.00
24_S 42_L 1.669 1.00
112_L 116_A 1.663 1.00
15_I 19_V 1.651 1.00
57_R 169_V 1.647 1.00
131_P 134_K 1.604 1.00
65_M 92_K 1.595 1.00
99_T 117_I 1.573 1.00
101_G 117_I 1.546 1.00
119_E 135_R 1.541 1.00
27_V 31_V 1.535 1.00
7_P 10_D 1.514 1.00
42_L 63_G 1.513 1.00
119_E 138_S 1.503 1.00
119_E 137_E 1.496 1.00
22_D 41_P 1.491 1.00
27_V 33_L 1.48 1.00
9_R 174_E 1.471 1.00
128_S 147_V 1.463 1.00
17_Q 35_D 1.458 1.00
7_P 12_F 1.452 1.00
142_Y 149_Q 1.444 1.00
43_V 64_S 1.375 0.99
122_V 138_S 1.375 0.99
45_I 52_V 1.373 0.99
139_G 158_K 1.37 0.99
151_R 157_E 1.352 0.99
92_K 109_G 1.345 0.99
124_I 136_L 1.333 0.99
154_S 157_E 1.321 0.99
106_V 112_L 1.295 0.99
130_V 147_V 1.285 0.99
37_V 85_E 1.283 0.99
18_R 35_D 1.281 0.99
140_Y 152_P 1.261 0.99
114_D 132_Q 1.251 0.99
172_K 176_L 1.235 0.98
64_S 93_V 1.221 0.98
33_L 37_V 1.202 0.98
32_R 51_Y 1.162 0.97
111_I 127_G 1.134 0.97
100_I 106_V 1.12 0.96
113_L 126_A 1.111 0.96
143_L 150_I 1.102 0.96
159_A 162_R 1.095 0.96
82_T 99_T 1.084 0.96
33_L 39_I 1.075 0.95
31_V 47_G 1.07 0.95
93_V 110_S 1.058 0.95
166_N 170_K 1.057 0.95
105_L 123_M 1.049 0.94
66_L 98_C 1.044 0.94
37_V 58_T 1.043 0.94
149_Q 152_P 1.042 0.94
140_Y 149_Q 1.039 0.94
60_I 66_L 1.037 0.94
30_D 51_Y 1.032 0.94
137_E 149_Q 1.022 0.93
137_E 142_Y 1.007 0.93
104_V 122_V 1.006 0.93
8_Y 174_E 1 0.92
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
3r3rA111000.344Contact Map0.861
3r1wA30.98911000.373Contact Map0.902
1v3wA10.94021000.375Contact Map0.8
3ixcA10.92391000.376Contact Map0.816
1xhdA10.94021000.378Contact Map0.84
4mfgA40.9131000.4Contact Map0.855
3hsqA30.97831000.433Contact Map0.685
3c8vA40.90761000.436Contact Map0.639
2qiaA10.98911000.438Contact Map0.63
1j2zA10.98371000.445Contact Map0.618
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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