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RFFA - Lipopolysaccharide biosynthesis protein RffA
UniProt: P27833 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG11456
Length: 376 (359)
Sequences: 35244
Seq/Len: 98.17
RFFA
Paralog alert: 0.93 [within 20: 0.55] - ratio of genomes with paralogs
Cluster includes: AAT ALAA ALAC ARNB AVTA CSDA HIS8 ISCS MALY RFFA SERC SUFS TYRB YBDL YDCR YJIR
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
263_N 365_R 3.411 1.00
113_E 144_K 3.273 1.00
18_Q 22_G 3.141 1.00
267_A 368_I 3.119 1.00
73_E 96_V 3.071 1.00
313_A 373_N 3.048 1.00
73_E 117_T 2.804 1.00
39_W 243_L 2.799 1.00
263_N 361_P 2.765 1.00
73_E 94_K 2.731 1.00
11_G 15_D 2.648 1.00
134_E 137_T 2.622 1.00
366_T 370_T 2.579 1.00
259_A 361_P 2.525 1.00
72_D 121_R 2.377 1.00
258_L 262_Q 2.294 1.00
111_L 114_A 2.247 1.00
109_E 141_L 2.202 1.00
15_D 19_S 2.187 1.00
278_E 296_K 2.175 1.00
52_T 58_S 2.16 1.00
73_E 120_T 2.156 1.00
262_Q 266_D 2.134 1.00
360_S 363_N 2.124 1.00
139_M 149_V 2.093 1.00
111_L 115_A 2.085 1.00
68_I 93_A 2.084 1.00
165_A 168_T 2.079 1.00
309_F 312_E 2.061 1.00
263_N 267_A 2.031 1.00
73_E 119_K 2.025 1.00
240_A 243_L 2.022 1.00
136_D 140_A 2.007 1.00
113_E 145_H 1.969 1.00
267_A 270_P 1.965 1.00
109_E 137_T 1.941 1.00
366_T 369_A 1.939 1.00
122_V 150_V 1.937 1.00
140_A 144_K 1.935 1.00
302_D 305_A 1.923 1.00
108_D 111_L 1.919 1.00
313_A 370_T 1.904 1.00
139_M 143_K 1.879 1.00
14_L 18_Q 1.858 1.00
62_A 172_I 1.855 1.00
47_A 197_K 1.839 1.00
38_Q 42_Q 1.837 1.00
137_T 140_A 1.836 1.00
48_K 197_K 1.819 1.00
98_V 115_A 1.808 1.00
99_D 111_L 1.788 1.00
113_E 141_L 1.77 1.00
78_S 99_D 1.752 1.00
256_Q 259_A 1.733 1.00
60_E 64_L 1.722 1.00
267_A 365_R 1.718 1.00
296_K 349_R 1.692 1.00
143_K 171_H 1.685 1.00
267_A 372_L 1.681 1.00
255_Q 259_A 1.679 1.00
69_Q 72_D 1.667 1.00
309_F 374_Y 1.645 1.00
34_R 38_Q 1.628 1.00
305_A 309_F 1.623 1.00
19_S 23_S 1.603 1.00
153_A 173_G 1.595 1.00
15_D 18_Q 1.584 1.00
116_I 141_L 1.583 1.00
142_A 149_V 1.578 1.00
353_L 367_V 1.562 1.00
110_T 114_A 1.555 1.00
14_L 22_G 1.55 1.00
271_L 372_L 1.547 1.00
270_P 372_L 1.54 1.00
142_A 147_L 1.531 1.00
251_D 255_Q 1.53 1.00
55_C 174_C 1.524 1.00
35_R 239_Q 1.492 1.00
256_Q 260_L 1.482 1.00
110_T 113_E 1.48 1.00
39_W 239_Q 1.47 1.00
141_L 145_H 1.463 1.00
101_R 104_T 1.452 1.00
265_Y 293_F 1.443 1.00
266_D 270_P 1.435 1.00
63_A 88_F 1.434 1.00
177_F 238_L 1.429 1.00
96_V 115_A 1.424 1.00
361_P 365_R 1.423 1.00
75_I 115_A 1.419 1.00
123_I 147_L 1.41 1.00
110_T 137_T 1.398 0.99
62_A 150_V 1.394 0.99
123_I 142_A 1.392 0.99
96_V 117_T 1.39 0.99
78_S 97_F 1.39 0.99
53_P 57_A 1.388 0.99
74_V 88_F 1.384 0.99
175_F 190_G 1.375 0.99
113_E 137_T 1.374 0.99
263_N 364_Q 1.368 0.99
125_P 138_I 1.355 0.99
265_Y 269_A 1.352 0.99
88_F 93_A 1.35 0.99
88_F 95_I 1.346 0.99
197_K 201_E 1.341 0.99
193_L 200_I 1.341 0.99
75_I 120_T 1.333 0.99
278_E 298_R 1.331 0.99
12_T 240_A 1.323 0.99
369_A 373_N 1.319 0.99
267_A 369_A 1.317 0.99
150_V 174_C 1.316 0.99
116_I 147_L 1.31 0.99
39_W 42_Q 1.309 0.99
41_E 49_V 1.308 0.99
58_S 174_C 1.3 0.99
117_T 120_T 1.285 0.99
308_N 312_E 1.284 0.99
72_D 119_K 1.278 0.99
40_L 51_L 1.277 0.99
127_H 156_G 1.276 0.99
63_A 124_V 1.276 0.99
188_E 238_L 1.275 0.99
365_R 369_A 1.272 0.99
305_A 308_N 1.269 0.99
261_W 265_Y 1.268 0.99
252_R 255_Q 1.262 0.99
267_A 271_L 1.261 0.99
113_E 117_T 1.253 0.99
263_N 266_D 1.246 0.98
256_Q 361_P 1.238 0.98
52_T 61_M 1.237 0.98
309_F 313_A 1.233 0.98
136_D 168_T 1.225 0.98
266_D 269_A 1.221 0.98
12_T 244_W 1.207 0.98
295_I 353_L 1.206 0.98
17_M 237_D 1.196 0.98
101_R 108_D 1.195 0.98
317_A 351_L 1.184 0.98
85_A 89_V 1.183 0.98
16_Y 19_S 1.182 0.98
16_Y 240_A 1.179 0.98
172_I 199_L 1.172 0.98
260_L 361_P 1.157 0.97
36_C 51_L 1.155 0.97
255_Q 258_L 1.154 0.97
14_L 21_M 1.148 0.97
112_I 138_I 1.136 0.97
40_L 190_G 1.133 0.97
50_L 200_I 1.132 0.97
64_L 91_R 1.125 0.97
140_A 143_K 1.124 0.97
59_L 83_S 1.123 0.97
236_S 239_Q 1.12 0.96
265_Y 281_S 1.113 0.96
307_I 317_A 1.112 0.96
15_D 22_G 1.107 0.96
94_K 117_T 1.098 0.96
11_G 14_L 1.094 0.96
75_I 98_V 1.092 0.96
259_A 263_N 1.091 0.96
35_R 243_L 1.09 0.96
66_L 148_F 1.086 0.96
116_I 145_H 1.084 0.96
315_I 370_T 1.076 0.95
294_Y 350_L 1.076 0.95
269_A 279_L 1.072 0.95
11_G 22_G 1.067 0.95
39_W 244_W 1.067 0.95
68_I 74_V 1.064 0.95
154_A 176_S 1.056 0.95
194_I 200_I 1.049 0.94
313_A 323_P 1.047 0.94
45_G 165_A 1.046 0.94
252_R 256_Q 1.042 0.94
35_R 39_W 1.04 0.94
76_M 95_I 1.04 0.94
76_M 88_F 1.04 0.94
109_E 113_E 1.036 0.94
362_V 365_R 1.033 0.94
264_Y 353_L 1.033 0.94
42_Q 243_L 1.031 0.94
310_L 317_A 1.027 0.94
39_W 246_Q 1.023 0.93
306_L 374_Y 1.019 0.93
264_Y 267_A 1.019 0.93
70_P 92_G 1.019 0.93
245_A 248_E 1.018 0.93
315_I 367_V 1.016 0.93
47_A 195_N 1.01 0.93
297_L 306_L 1.009 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
3frkA20.95481000.3Contact Map0.679
4lc3A20.97871000.302Contact Map0.686
2fnuA20.96811000.309Contact Map0.687
1o69A20.95741000.323Contact Map0.632
3dr4A40.96281000.327Contact Map0.684
1mdoA10.98141000.331Contact Map0.581
2c81A10.98941000.334Contact Map0.65
3b8xA20.97071000.339Contact Map0.662
3nytA10.94681000.34Contact Map0.63
3bb8A20.98671000.341Contact Map0.663
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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