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OPENSEQ.org
RPOA - DNA-directed RNA polymerase subunit alpha
UniProt: P0A7Z4 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG10893
Length: 329 (324)
Sequences: 1193
Seq/Len: 3.68
RPOA
Paralog alert: 0.02 [within 20: 0.01] - 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
205_M 217_I 4.578 1.00
56_V 88_L 4.496 1.00
87_G 128_H 4.169 1.00
100_L 146_V 3.57 1.00
23_H 206_E 3.101 1.00
56_V 85_L 3.026 1.00
115_I 144_I 2.89 1.00
109_P 129_V 2.811 1.00
89_A 208_N 2.736 1.00
147_Q 177_Y 2.733 1.00
104_K 108_G 2.733 1.00
59_V 85_L 2.722 1.00
23_H 204_E 2.561 1.00
62_D 141_S 2.541 1.00
25_K 204_E 2.501 1.00
158_R 175_A 2.49 1.00
129_V 132_H 2.488 1.00
105_S 139_S 2.363 1.00
98_V 118_D 2.354 1.00
103_N 141_S 2.339 1.00
57_T 147_Q 2.285 1.00
85_L 88_L 2.153 1.00
131_C 140_I 2.118 1.00
263_T 302_E 2.085 1.00
133_L 138_A 2.079 1.00
93_Q 122_E 2.041 1.00
88_L 113_A 2.039 1.00
286_E 304_K 2.019 1.00
89_A 210_T 2.004 1.00
59_V 82_L 1.989 1.00
104_K 114_D 1.979 1.00
188_E 202_V 1.963 1.00
60_E 143_R 1.945 1.00
107_I 136_E 1.928 1.00
124_V 210_T 1.919 1.00
91_R 122_E 1.915 1.00
81_I 130_I 1.886 1.00
125_K 128_H 1.792 0.99
74_V 81_I 1.771 0.99
295_L 303_I 1.74 0.99
158_R 162_E 1.669 0.99
192_V 196_T 1.663 0.99
42_A 224_L 1.651 0.99
296_G 299_S 1.61 0.98
257_V 267_A 1.608 0.98
104_K 133_L 1.587 0.98
82_L 171_L 1.556 0.98
203_I 217_I 1.525 0.97
85_L 144_I 1.509 0.97
99_I 143_R 1.503 0.97
92_V 121_V 1.494 0.97
54_C 148_R 1.486 0.97
225_A 232_V 1.422 0.96
278_I 310_R 1.419 0.96
28_L 231_F 1.414 0.96
64_V 71_K 1.402 0.95
100_L 144_I 1.397 0.95
153_V 177_Y 1.39 0.95
90_V 123_I 1.39 0.95
58_E 170_R 1.377 0.95
249_F 254_L 1.367 0.94
56_V 173_V 1.36 0.94
101_T 143_R 1.348 0.94
31_L 80_E 1.346 0.94
46_I 220_A 1.345 0.94
290_L 295_L 1.324 0.93
92_V 146_V 1.294 0.92
225_A 228_L 1.279 0.91
191_R 199_D 1.278 0.91
88_L 112_A 1.278 0.91
219_R 222_T 1.265 0.91
79_L 171_L 1.251 0.90
61_I 78_I 1.25 0.90
305_D 309_S 1.238 0.89
108_G 133_L 1.235 0.89
267_A 271_K 1.227 0.89
94_G 120_D 1.225 0.89
149_G 153_V 1.213 0.88
264_V 269_C 1.198 0.87
36_G 187_V 1.191 0.87
301_T 305_D 1.191 0.87
68_Y 187_V 1.182 0.86
269_C 294_N 1.18 0.86
163_E 166_R 1.179 0.86
303_I 314_L 1.161 0.85
284_R 288_E 1.16 0.85
46_I 224_L 1.147 0.84
177_Y 238_R 1.143 0.84
36_G 199_D 1.138 0.83
23_H 26_V 1.138 0.83
88_L 128_H 1.136 0.83
277_Y 281_L 1.134 0.83
58_E 145_K 1.127 0.82
255_R 278_I 1.127 0.82
101_T 141_S 1.119 0.82
294_N 299_S 1.1 0.80
264_V 294_N 1.099 0.80
104_K 140_I 1.093 0.80
79_L 82_L 1.087 0.79
93_Q 120_D 1.086 0.79
109_P 132_H 1.079 0.79
266_S 294_N 1.072 0.78
88_L 117_H 1.071 0.78
251_P 289_L 1.07 0.78
28_L 31_L 1.069 0.78
112_A 125_K 1.064 0.77
96_D 148_R 1.061 0.77
85_L 211_I 1.059 0.77
261_E 269_C 1.058 0.77
187_V 265_R 1.057 0.77
304_K 312_L 1.057 0.77
267_A 303_I 1.051 0.76
294_N 298_K 1.051 0.76
184_A 206_E 1.045 0.75
292_T 295_L 1.043 0.75
191_R 197_D 1.04 0.75
265_R 268_N 1.039 0.75
306_V 310_R 1.037 0.75
66_H 70_T 1.036 0.74
268_N 298_K 1.033 0.74
128_H 145_K 1.031 0.74
252_I 255_R 1.031 0.74
101_T 116_T 1.029 0.74
113_A 123_I 1.025 0.73
258_D 271_K 1.024 0.73
282_V 285_T 1.016 0.72
105_S 137_N 1.015 0.72
210_T 271_K 1.013 0.72
269_C 295_L 1.011 0.72
124_V 128_H 1.01 0.72
268_N 296_G 1.007 0.71
82_L 173_V 1.007 0.71
126_P 177_Y 1.004 0.71
258_D 267_A 1 0.71
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
4kn7A40.9971000.151Contact Map0.694
2a6hA40.93621000.189Contact Map0.821
1bdfA40.71121000.394Contact Map0.787
2pa8D10.66261000.53Contact Map0.494
4c2mC20.69911000.545Contact Map0.404
1twfC10.80851000.563Contact Map0.435
3h0gC20.75081000.568Contact Map0.394
3k4gA80.261499.90.798Contact Map0.539
3gfkB10.240199.90.818Contact Map0.442
1z3eB10.221999.80.82Contact Map0.475
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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