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OPENSEQ.org
PcrA_RpoB
Genes: A B A+B
Length: 724 1048 1762
Sequences: 7778 438 321
Seq/Len: 10.74 0.42 0.18
MirrorTree (Pazo et al. 2001) 0.28
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.06 0.00 0.00
2 0.07 0.00 0.00
5 0.08 0.00 0.00
10 0.09 0.00 0.00
20 0.10 0.00 0.01
100 0.16 0.00 0.04
∞ 0.25 0.00 0.18
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
246_I 287_N 1.55 0.32 0.00
122_L 255_L 1.39 0.25 0.00
440_S 938_I 1.35 0.23 0.00
112_N 887_I 1.34 0.23 0.00
73_R 753_L 1.30 0.21 0.00
336_V 534_Y 1.28 0.20 0.00
259_W 111_V 1.25 0.19 0.00
411_L 67_I 1.20 0.17 0.00
354_F 655_A 1.20 0.17 0.00
392_I 386_S 1.18 0.17 0.00
259_W 631_N 1.18 0.17 0.00
203_F 987_I 1.16 0.16 0.00
554_A 395_V 1.15 0.16 0.00
217_F 220_T 1.12 0.15 0.00
222_I 655_A 1.12 0.15 0.00
351_Y 690_V 1.11 0.14 0.00
538_L 742_L 1.09 0.14 0.00
605_Y 563_Y 1.08 0.14 0.00
268_L 533_S 1.06 0.13 0.00
80_L 588_I 1.06 0.13 0.00
647_E 302_I 1.06 0.13 0.00
274_Y 655_A 1.05 0.13 0.00
274_Y 585_G 1.05 0.13 0.00
217_F 987_I 1.05 0.13 0.00
336_V 364_I 1.05 0.13 0.00
96_C 515_C 1.05 0.13 0.00
594_D 303_L 1.04 0.13 0.00
41_L 390_N 1.04 0.13 0.00
409_L 263_K 1.03 0.12 0.00
582_E 255_L 1.03 0.12 0.00
190_L 573_V 1.02 0.12 0.00
203_F 674_V 1.02 0.12 0.00
73_R 307_G 1.02 0.12 0.00
405_P 887_I 1.01 0.12 0.00
41_L 624_A 1.00 0.12 0.00
638_L 78_V 1.00 0.12 0.00
216_K 677_K 1.00 0.12 0.00
76_V 687_A 0.99 0.11 0.00
396_L 590_D 0.99 0.11 0.00
112_N 1037_M 0.98 0.11 0.00
39_R 573_V 0.98 0.11 0.00
193_D 432_R 0.98 0.11 0.00
274_Y 584_E 0.98 0.11 0.00
617_L 103_T 0.97 0.11 0.00
318_G 537_V 0.97 0.11 0.00
490_K 715_F 0.97 0.11 0.00
404_N 94_V 0.97 0.11 0.00
595_D 210_L 0.97 0.11 0.00
333_A 690_V 0.96 0.11 0.00
218_Q 738_K 0.96 0.11 0.00
441_L 987_I 0.96 0.11 0.00
72_M 853_E 0.96 0.11 0.00
205_R 887_I 0.95 0.10 0.00
411_L 812_D 0.95 0.10 0.00
626_F 87_T 0.95 0.10 0.00
119_T 892_V 0.94 0.10 0.00
616_V 431_V 0.94 0.10 0.00
72_M 530_S 0.94 0.10 0.00
99_I 971_V 0.94 0.10 0.00
240_A 60_G 0.93 0.10 0.00
373_K 784_D 0.93 0.10 0.00
14_K 537_V 0.93 0.10 0.00
94_S 586_A 0.92 0.10 0.00
235_L 121_D 0.92 0.10 0.00
465_R 887_I 0.92 0.10 0.00
104_I 238_E 0.92 0.10 0.00
209_V 1002_E 0.92 0.10 0.00
274_Y 781_L 0.92 0.10 0.00
543_D 537_V 0.92 0.10 0.00
217_F 795_Y 0.91 0.10 0.00
110_N 52_I 0.91 0.10 0.00
124_V 938_I 0.91 0.10 0.00
240_A 610_Y 0.91 0.10 0.00
78_S 364_I 0.91 0.10 0.00
45_I 741_I 0.90 0.10 0.00
94_S 106_V 0.90 0.10 0.00
216_K 597_R 0.90 0.09 0.00
209_V 690_V 0.90 0.09 0.00
347_G 545_T 0.90 0.09 0.00
42_T 126_I 0.90 0.09 0.00
564_L 953_I 0.90 0.09 0.00
445_L 894_N 0.90 0.09 0.00
325_E 938_I 0.89 0.09 0.00
486_E 655_A 0.89 0.09 0.00
27_L 478_A 0.89 0.09 0.00
473_Q 655_A 0.89 0.09 0.00
461_L 273_Y 0.89 0.09 0.00
216_K 230_D 0.89 0.09 0.00
221_H 987_I 0.89 0.09 0.00
15_E 662_M 0.89 0.09 0.00
96_C 110_D 0.89 0.09 0.00
484_V 222_D 0.88 0.09 0.00
216_K 358_E 0.88 0.09 0.00
689_V 946_Y 0.88 0.09 0.00
314_E 385_I 0.88 0.09 0.00
445_L 655_A 0.88 0.09 0.00
134_I 762_G 0.88 0.09 0.00
590_S 255_L 0.88 0.09 0.00
196_I 146_F 0.88 0.09 0.00
486_E 855_T 0.88 0.09 0.00
580_M 395_V 0.88 0.09 0.00
54_V 361_I 0.87 0.09 0.00
44_R 873_R 0.87 0.09 0.00
221_H 532_S 0.87 0.09 0.00
383_G 217_L 0.87 0.09 0.00
165_A 146_F 0.87 0.09 0.00
480_V 497_E 0.87 0.09 0.00
138_K 664_Y 0.87 0.09 0.00
259_W 236_I 0.87 0.09 0.00
543_D 613_V 0.87 0.09 0.00
259_W 184_I 0.87 0.09 0.00
246_I 148_G 0.87 0.09 0.00
445_L 82_K 0.87 0.09 0.00
70_R 239_R 0.86 0.09 0.00
440_S 738_K 0.86 0.09 0.00
409_L 935_I 0.86 0.09 0.00
484_V 25_E 0.86 0.09 0.00
76_V 431_V 0.86 0.09 0.00
190_L 604_S 0.86 0.09 0.00
409_L 762_G 0.86 0.09 0.00
195_L 48_M 0.86 0.09 0.00
235_L 771_Y 0.86 0.09 0.00
288_S 718_S 0.85 0.09 0.00
56_P 383_S 0.85 0.09 0.00
613_E 338_V 0.85 0.09 0.00
580_M 232_A 0.85 0.09 0.00
530_S 812_D 0.85 0.09 0.00
217_F 935_I 0.85 0.09 0.00
483_L 289_R 0.85 0.09 0.00
209_V 734_D 0.85 0.09 0.00
290_K 740_E 0.85 0.08 0.00
20_V 594_A 0.85 0.08 0.00
559_V 655_A 0.85 0.08 0.00
291_R 775_I 0.84 0.08 0.00
295_A 281_I 0.84 0.08 0.00
392_I 681_I 0.84 0.08 0.00
39_R 715_F 0.84 0.08 0.00
49_M 158_F 0.84 0.08 0.00
284_Q 249_E 0.84 0.08 0.00
617_L 202_G 0.84 0.08 0.00
19_A 890_V 0.84 0.08 0.00
280_I 1002_E 0.84 0.08 0.00
263_D 172_Y 0.84 0.08 0.00
441_L 709_K 0.83 0.08 0.00
246_I 610_Y 0.83 0.08 0.00
335_F 1030_V 0.83 0.08 0.00
557_D 385_I 0.83 0.08 0.00
597_M 227_E 0.83 0.08 0.00
258_R 641_A 0.83 0.08 0.00
274_Y 12_R 0.83 0.08 0.00
274_Y 305_E 0.83 0.08 0.00
576_F 610_Y 0.83 0.08 0.00
336_V 556_K 0.82 0.08 0.00
347_G 539_R 0.82 0.08 0.00
105_D 784_D 0.82 0.08 0.00
246_I 841_L 0.82 0.08 0.00
154_E 302_I 0.82 0.08 0.00
689_V 112_F 0.82 0.08 0.00
131_E 202_G 0.82 0.08 0.00
546_E 34_T 0.82 0.08 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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