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OPENSEQ.org
PcrA vs UvrB (A, 10-650) (B, 20-530)
Genes: A B A+B
Length: 641 511 1142
Sequences: 6870 3234 1786
Seq/Len: 10.72 6.33 1.56
MirrorTree (Pazo et al. 2001) -0.02
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 0.06 0.04 0.01
2 0.06 0.04 0.01
5 0.06 0.04 0.03
10 0.07 0.04 0.05
20 0.07 0.04 0.10
100 0.14 0.04 0.40
∞ 0.24 0.13 1.55
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
383_I 182_E 0.97 0.42 0.00
119_I 388_M 0.93 0.38 0.00
80_I 425_R 0.90 0.35 0.00
200_V 190_E 0.87 0.33 0.00
347_I 424_E 0.87 0.32 0.00
20_L 241_I 0.84 0.30 0.00
569_L 96_I 0.80 0.26 0.00
250_W 393_I 0.78 0.24 0.00
342_L 119_I 0.75 0.22 0.00
610_T 183_I 0.73 0.21 0.00
198_P 469_I 0.73 0.21 0.00
199_E 181_V 0.72 0.21 0.00
549_D 110_A 0.72 0.20 0.00
405_I 450_G 0.72 0.20 0.00
19_L 511_S 0.72 0.20 0.00
347_I 148_I 0.72 0.20 0.00
383_I 388_M 0.71 0.20 0.00
228_K 107_A 0.71 0.19 0.00
90_I 142_L 0.70 0.19 0.00
80_I 140_V 0.70 0.19 0.00
347_I 466_I 0.70 0.19 0.00
69_S 250_E 0.69 0.18 0.00
358_I 481_V 0.69 0.18 0.00
199_E 89_F 0.68 0.18 0.00
115_V 181_V 0.68 0.18 0.00
423_S 183_I 0.67 0.17 0.00
71_L 316_I 0.67 0.17 0.00
238_C 197_F 0.67 0.17 0.00
21_M 439_S 0.66 0.17 0.00
450_N 3_E 0.66 0.17 0.00
605_Q 298_P 0.66 0.17 0.00
150_E 344_D 0.66 0.17 0.00
549_D 431_V 0.66 0.16 0.00
250_W 508_F 0.66 0.16 0.00
324_G 185_P 0.66 0.16 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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