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OPENSEQ.org
MFD550RNAP1342_ecoli
Genes: A B A+B
Length: 550 692 1219
Sequences: 4233 1062 862
Seq/Len: 7.7 1.53 0.71
MirrorTree (Pazo et al. 2001) 0.11
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.03 0.09 0.00
2 0.03 0.09 0.00
5 0.03 0.09 0.00
10 0.03 0.09 0.00
20 0.03 0.09 0.02
100 0.05 0.09 0.09
∞ 0.20 0.09 0.69
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
190_D 404_L 1.44 0.62 0.00
186_D 187_A 1.19 0.42 0.00
197_V 33_A 1.19 0.41 0.00
93_S 667_P 1.19 0.41 0.00
271_P 463_L 1.17 0.39 0.00
169_L 574_P 1.14 0.38 0.00
89_S 162_F 1.10 0.34 0.00
162_Y 175_E 1.08 0.33 0.00
528_L 140_D 1.05 0.31 0.00
183_D 232_I 1.05 0.30 0.00
179_P 588_L 1.04 0.30 0.00
507_E 23_H 1.03 0.29 0.00
108_V 429_I 1.02 0.29 0.00
18_L 23_H 1.01 0.28 0.00
184_F 221_V 1.00 0.27 0.00
186_D 42_T 0.98 0.26 0.00
296_Q 462_I 0.97 0.25 0.00
188_E 459_I 0.96 0.25 0.00
150_Y 237_V 0.94 0.23 0.00
338_Q 429_I 0.94 0.23 0.00
189_I 439_E 0.94 0.23 0.00
329_S 437_Y 0.93 0.23 0.00
272_L 133_L 0.91 0.21 0.00
283_V 208_G 0.90 0.21 0.00
481_Q 660_D 0.89 0.20 0.00
195_F 636_T 0.89 0.20 0.00
184_F 237_V 0.89 0.20 0.00
185_F 154_F 0.88 0.20 0.00
121_S 217_E 0.88 0.20 0.00
451_G 33_A 0.88 0.20 0.00
190_D 483_K 0.88 0.20 0.00
42_V 45_A 0.87 0.20 0.00
369_A 43_L 0.87 0.19 0.00
277_P 84_I 0.87 0.19 0.00
479_I 208_G 0.87 0.19 0.00
172_F 5_V 0.86 0.19 0.00
353_L 118_M 0.86 0.19 0.00
187_D 13_V 0.86 0.19 0.00
119_P 593_M 0.85 0.19 0.00
186_D 186_L 0.85 0.18 0.00
93_S 285_T 0.85 0.18 0.00
208_A 221_V 0.85 0.18 0.00
374_L 680_I 0.85 0.18 0.00
183_D 250_K 0.85 0.18 0.00
165_R 245_L 0.85 0.18 0.00
517_A 120_C 0.84 0.18 0.00
275_Y 148_Q 0.84 0.18 0.00
141_L 175_E 0.84 0.18 0.00
321_W 44_R 0.84 0.18 0.00
487_E 46_D 0.83 0.18 0.00
93_S 636_T 0.83 0.17 0.00
215_H 23_H 0.83 0.17 0.00
400_E 634_A 0.83 0.17 0.00
427_I 250_K 0.83 0.17 0.00
214_A 18_I 0.83 0.17 0.00
404_R 258_E 0.83 0.17 0.00
283_V 429_I 0.83 0.17 0.00
197_V 404_L 0.82 0.17 0.00
526_L 150_M 0.82 0.17 0.00
372_D 658_I 0.82 0.17 0.00
410_Q 394_P 0.82 0.17 0.00
407_I 269_R 0.82 0.17 0.00
45_I 127_V 0.82 0.17 0.00
188_E 23_H 0.82 0.17 0.00
220_D 410_I 0.82 0.17 0.00
105_V 223_I 0.82 0.17 0.00
423_R 16_S 0.82 0.17 0.00
500_E 132_V 0.82 0.17 0.00
444_I 162_F 0.81 0.17 0.00
151_R 269_R 0.81 0.16 0.00
153_V 278_V 0.81 0.16 0.00
154_D 600_S 0.81 0.16 0.00
39_A 74_V 0.81 0.16 0.00
282_L 563_Y 0.81 0.16 0.00
199_S 680_I 0.81 0.16 0.00
220_D 168_V 0.80 0.16 0.00
165_R 243_T 0.80 0.16 0.00
192_L 635_Y 0.80 0.16 0.00
192_L 175_E 0.80 0.16 0.00
192_L 648_V 0.79 0.16 0.00
378_L 269_R 0.79 0.15 0.00
481_Q 656_K 0.79 0.15 0.00
283_V 133_L 0.79 0.15 0.00
481_Q 600_S 0.79 0.15 0.00
532_Y 473_G 0.79 0.15 0.00
367_Q 459_I 0.79 0.15 0.00
226_L 79_A 0.78 0.15 0.00
39_A 79_A 0.78 0.15 0.00
331_L 127_V 0.78 0.15 0.00
100_T 64_V 0.78 0.15 0.00
159_H 588_L 0.78 0.15 0.00
402_L 570_Q 0.78 0.15 0.00
481_Q 586_N 0.78 0.15 0.00
97_Q 171_R 0.78 0.15 0.00
217_F 79_A 0.78 0.15 0.00
71_A 634_A 0.78 0.15 0.00
165_R 238_T 0.78 0.15 0.00
531_R 156_P 0.78 0.15 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
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