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OPENSEQ.org
MFD550RNAP650_ecoli
Genes: A B A+B
Length: 550 650 1175
Sequences: 4233 1187 876
Seq/Len: 7.7 1.83 0.75
MirrorTree (Pazo et al. 2001) 0.08
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 0.08 0.00
2 0.03 0.08 0.00
5 0.03 0.08 0.00
10 0.03 0.08 0.01
20 0.03 0.08 0.03
100 0.05 0.08 0.11
∞ 0.20 0.08 0.73
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
186_D 475_V 1.55 0.72 0.01
45_I 92_Y 1.52 0.70 0.01
171_L 138_I 1.28 0.50 0.00
169_L 92_Y 1.07 0.34 0.00
169_L 603_I 1.07 0.34 0.00
547_G 329_G 1.03 0.30 0.00
410_Q 376_P 1.02 0.30 0.00
248_V 380_A 0.99 0.28 0.00
273_F 624_D 0.98 0.27 0.00
344_L 147_S 0.96 0.25 0.00
521_V 650_V 0.95 0.25 0.00
304_E 211_R 0.95 0.25 0.00
232_R 75_L 0.93 0.24 0.00
374_L 209_I 0.93 0.23 0.00
170_D 28_L 0.93 0.23 0.00
397_A 180_R 0.92 0.23 0.00
481_Q 459_M 0.91 0.22 0.00
209_I 335_T 0.91 0.22 0.00
297_A 641_E 0.91 0.22 0.00
107_I 616_I 0.90 0.22 0.00
184_F 429_M 0.90 0.21 0.00
395_R 442_V 0.89 0.21 0.00
184_F 67_E 0.88 0.20 0.00
248_V 137_V 0.88 0.20 0.00
264_F 184_L 0.87 0.20 0.00
187_D 426_I 0.87 0.20 0.00
179_P 375_P 0.87 0.20 0.00
165_R 134_G 0.87 0.20 0.00
189_I 423_D 0.87 0.20 0.00
371_L 101_R 0.87 0.20 0.00
146_D 587_L 0.87 0.20 0.00
194_V 479_L 0.86 0.20 0.00
412_I 447_H 0.85 0.19 0.00
250_K 70_Y 0.85 0.19 0.00
186_D 464_F 0.85 0.19 0.00
374_L 80_F 0.85 0.19 0.00
284_N 209_I 0.84 0.18 0.00
282_L 650_V 0.84 0.18 0.00
271_P 610_E 0.83 0.18 0.00
481_Q 518_N 0.83 0.18 0.00
137_S 603_I 0.83 0.18 0.00
62_F 347_I 0.83 0.18 0.00
60_S 476_K 0.82 0.18 0.00
327_L 211_R 0.82 0.17 0.00
39_A 394_R 0.81 0.17 0.00
277_P 473_R 0.81 0.17 0.00
409_P 508_S 0.81 0.17 0.00
141_L 476_K 0.81 0.17 0.00
119_P 137_V 0.81 0.17 0.00
180_Y 650_V 0.81 0.17 0.00
34_I 132_D 0.80 0.17 0.00
105_V 317_L 0.80 0.17 0.00
387_F 91_T 0.80 0.16 0.00
81_F 138_I 0.80 0.16 0.00
92_L 476_K 0.80 0.16 0.00
338_Q 648_D 0.79 0.16 0.00
143_T 176_I 0.79 0.16 0.00
186_D 348_S 0.79 0.16 0.00
184_F 403_M 0.78 0.16 0.00
195_F 166_S 0.78 0.16 0.00
379_E 578_Y 0.78 0.16 0.00
191_S 631_E 0.78 0.16 0.00
508_Y 318_S 0.78 0.16 0.00
161_E 123_Y 0.78 0.16 0.00
44_L 383_S 0.78 0.16 0.00
321_W 379_E 0.78 0.16 0.00
106_L 493_I 0.78 0.15 0.00
442_A 98_V 0.78 0.15 0.00
16_Q 477_E 0.78 0.15 0.00
255_A 473_R 0.78 0.15 0.00
521_V 616_I 0.78 0.15 0.00
171_L 612_G 0.78 0.15 0.00
57_D 409_L 0.78 0.15 0.00
42_V 379_E 0.77 0.15 0.00
384_P 449_G 0.77 0.15 0.00
399_G 106_E 0.77 0.15 0.00
374_L 518_N 0.77 0.15 0.00
321_W 593_K 0.77 0.15 0.00
344_L 464_F 0.76 0.15 0.00
135_R 145_I 0.76 0.15 0.00
263_L 553_T 0.76 0.15 0.00
89_S 539_T 0.76 0.15 0.00
189_I 627_G 0.76 0.15 0.00
165_R 180_R 0.76 0.15 0.00
92_L 398_S 0.76 0.15 0.00
105_V 379_E 0.76 0.14 0.00
100_T 584_Y 0.76 0.14 0.00
283_V 209_I 0.75 0.14 0.00
215_H 468_L 0.75 0.14 0.00
59_I 122_V 0.75 0.14 0.00
62_F 172_Y 0.75 0.14 0.00
376_K 423_D 0.75 0.14 0.00
59_I 176_I 0.75 0.14 0.00
406_K 492_M 0.75 0.14 0.00
45_I 426_I 0.75 0.14 0.00
197_V 398_S 0.75 0.14 0.00
190_D 347_I 0.74 0.14 0.00
400_E 601_D 0.74 0.14 0.00
444_I 427_D 0.74 0.14 0.00
165_R 567_P 0.74 0.14 0.00
184_F 14_D 0.74 0.14 0.00
169_L 360_L 0.74 0.14 0.00
36_E 412_E 0.74 0.14 0.00
417_E 470_R 0.74 0.14 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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