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OPENSEQ.org
PcrA_FL vs beta 1st half
Genes: A B A+B
Length: 739 600 1193
Sequences: 3698 1433 1078
Seq/Len: 5 2.39 0.9
MirrorTree (Pazo et al. 2001) 0.27
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 0.09 0.09 0.00
2 0.09 0.09 0.00
5 0.09 0.09 0.01
10 0.09 0.09 0.03
20 0.09 0.09 0.04
100 0.10 0.09 0.11
∞ 0.16 0.09 0.81
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
558_D 549_R 1.15 0.44 0.00
323_Y 127_I 1.08 0.38 0.00
76_V 549_R 1.07 0.37 0.00
337_A 592_I 1.00 0.32 0.00
323_Y 126_I 0.98 0.30 0.00
613_E 126_I 0.96 0.29 0.00
509_L 257_S 0.94 0.27 0.00
59_I 534_Y 0.94 0.27 0.00
498_K 126_I 0.93 0.26 0.00
375_G 88_Y 0.92 0.26 0.00
598_M 31_E 0.92 0.26 0.00
220_I 545_T 0.92 0.26 0.00
371_L 88_Y 0.91 0.25 0.00
229_N 162_V 0.91 0.25 0.00
246_L 478_A 0.90 0.24 0.00
600_E 501_M 0.89 0.24 0.00
419_K 581_L 0.89 0.24 0.00
125_I 179_V 0.89 0.24 0.00
337_A 20_I 0.88 0.23 0.00
272_K 585_G 0.88 0.23 0.00
89_I 231_K 0.86 0.22 0.00
461_L 535_A 0.85 0.21 0.00
355_A 375_N 0.85 0.21 0.00
337_A 534_Y 0.84 0.21 0.00
290_K 549_R 0.84 0.21 0.00
356_I 205_Q 0.84 0.21 0.00
557_K 436_S 0.84 0.21 0.00
562_L 545_T 0.84 0.20 0.00
74_E 88_Y 0.83 0.20 0.00
421_G 459_K 0.83 0.20 0.00
356_I 88_Y 0.83 0.20 0.00
185_L 385_I 0.83 0.20 0.00
642_I 574_V 0.83 0.20 0.00
376_L 126_I 0.83 0.20 0.00
536_T 454_V 0.82 0.20 0.00
356_I 558_T 0.82 0.20 0.00
398_Y 449_I 0.82 0.20 0.00
248_V 250_N 0.82 0.19 0.00
174_S 262_P 0.82 0.19 0.00
96_C 182_V 0.81 0.19 0.00
221_H 579_A 0.81 0.19 0.00
55_A 192_V 0.80 0.19 0.00
356_I 540_F 0.80 0.18 0.00
517_S 537_V 0.80 0.18 0.00
632_M 158_F 0.80 0.18 0.00
81_G 49_F 0.79 0.18 0.00
399_L 578_N 0.79 0.18 0.00
160_E 552_P 0.79 0.18 0.00
184_L 162_V 0.79 0.18 0.00
512_I 37_Y 0.79 0.18 0.00
270_F 537_V 0.79 0.18 0.00
143_S 549_R 0.79 0.18 0.00
426_S 19_R 0.79 0.18 0.00
20_V 537_V 0.78 0.17 0.00
522_F 195_L 0.78 0.17 0.00
621_A 146_F 0.78 0.17 0.00
352_S 68_D 0.78 0.17 0.00
178_A 221_L 0.77 0.17 0.00
109_I 540_F 0.77 0.17 0.00
560_I 146_F 0.77 0.17 0.00
52_K 126_I 0.77 0.17 0.00
279_V 537_V 0.77 0.17 0.00
380_I 574_V 0.77 0.17 0.00
410_S 497_E 0.77 0.17 0.00
622_K 126_I 0.77 0.17 0.00
29_L 77_P 0.77 0.17 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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