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OPENSEQ.org
mfd (570) rnap (670) ecoli
Genes: A B A+B
Length: 570 670 1222
Sequences: 3809 1571 1150
Seq/Len: 6.68 2.34 0.94
MirrorTree (Pazo et al. 2001) 0.17
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 0.04
100 0.05 0.08 0.17
∞ 0.19 0.08 0.93
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 1.68 0.85 0.12
189_I 541_E 1.29 0.59 0.04
274_S 23_D 1.28 0.57 0.04
45_I 92_Y 1.19 0.49 0.03
41_P 379_E 1.13 0.44 0.02
45_I 666_S 1.11 0.42 0.02
374_L 176_I 1.08 0.40 0.02
189_I 650_V 1.05 0.37 0.02
338_Q 663_V 1.04 0.36 0.02
180_Y 195_F 1.01 0.33 0.02
493_Y 623_L 0.98 0.31 0.01
189_I 42_D 0.97 0.31 0.01
529_I 347_I 0.96 0.30 0.01
321_W 379_E 0.94 0.28 0.01
308_V 480_S 0.93 0.27 0.01
42_V 429_M 0.93 0.27 0.01
45_I 615_V 0.92 0.27 0.01
169_L 16_G 0.91 0.26 0.01
481_Q 459_M 0.91 0.26 0.01
490_V 624_D 0.91 0.26 0.01
168_L 35_F 0.90 0.25 0.01
277_P 473_R 0.88 0.24 0.01
152_H 379_E 0.88 0.24 0.01
70_L 382_E 0.88 0.24 0.01
325_D 379_E 0.87 0.23 0.01
363_V 650_V 0.86 0.23 0.01
171_L 138_I 0.86 0.23 0.01
496_M 157_F 0.85 0.22 0.01
549_A 496_K 0.85 0.22 0.01
188_E 453_I 0.84 0.22 0.01
562_R 501_A 0.84 0.21 0.01
189_I 577_V 0.84 0.21 0.01
159_H 580_Q 0.84 0.21 0.01
130_M 157_F 0.84 0.21 0.01
107_I 392_E 0.84 0.21 0.01
330_E 666_S 0.83 0.21 0.01
108_V 97_R 0.83 0.21 0.01
189_I 641_E 0.83 0.21 0.01
70_L 361_S 0.83 0.20 0.01
499_L 23_D 0.83 0.20 0.01
163_A 650_V 0.83 0.20 0.01
171_L 218_E 0.82 0.20 0.01
387_F 132_D 0.82 0.20 0.01
409_P 508_S 0.82 0.20 0.01
274_S 650_V 0.82 0.20 0.01
508_Y 318_S 0.82 0.20 0.01
190_D 430_K 0.81 0.20 0.01
569_L 93_S 0.81 0.19 0.01
180_Y 650_V 0.81 0.19 0.01
244_I 576_S 0.81 0.19 0.01
70_L 550_V 0.81 0.19 0.01
162_Y 589_T 0.80 0.19 0.01
106_L 433_I 0.80 0.19 0.01
493_Y 500_A 0.80 0.19 0.01
162_Y 117_I 0.79 0.19 0.01
318_Q 92_Y 0.79 0.19 0.01
531_R 581_T 0.79 0.18 0.01
542_L 648_D 0.79 0.18 0.01
186_D 604_H 0.79 0.18 0.01
374_L 80_F 0.79 0.18 0.01
560_K 100_L 0.79 0.18 0.01
306_R 502_V 0.79 0.18 0.01
476_E 163_K 0.79 0.18 0.01
45_I 426_I 0.79 0.18 0.01
499_L 117_I 0.79 0.18 0.01
184_F 14_D 0.78 0.18 0.01
547_G 329_G 0.78 0.18 0.01
395_R 442_V 0.78 0.18 0.01
195_F 374_E 0.78 0.18 0.01
387_F 91_T 0.77 0.17 0.01
190_D 56_V 0.77 0.17 0.01
172_F 490_Q 0.77 0.17 0.01
105_V 379_E 0.77 0.17 0.01
516_D 132_D 0.77 0.17 0.01
391_S 553_T 0.77 0.17 0.01
182_L 310_I 0.76 0.17 0.01
184_F 386_E 0.76 0.17 0.01
389_V 83_Q 0.76 0.17 0.01
300_L 376_P 0.76 0.17 0.01
169_L 176_I 0.76 0.17 0.01
192_L 108_E 0.76 0.17 0.01
195_F 400_V 0.75 0.16 0.01
479_I 23_D 0.75 0.16 0.01
45_I 100_L 0.75 0.16 0.01
274_S 663_V 0.75 0.16 0.01
372_D 200_R 0.74 0.16 0.01
432_H 648_D 0.74 0.16 0.01
282_L 596_D 0.74 0.16 0.01
553_A 545_F 0.74 0.16 0.01
381_F 589_T 0.74 0.16 0.01
449_L 429_M 0.74 0.16 0.01
189_I 374_E 0.74 0.16 0.01
506_G 581_T 0.74 0.16 0.01
497_T 176_I 0.74 0.16 0.01
563_D 7_E 0.74 0.16 0.01
530_S 35_F 0.73 0.16 0.01
441_L 176_I 0.73 0.16 0.01
184_F 67_E 0.73 0.15 0.01
184_F 346_Y 0.73 0.15 0.01
514_A 500_A 0.73 0.15 0.01
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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