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OPENSEQ.org
PcrA-beta
Genes: A B A+B
Length: 58 49 102
Sequences: 765 4190 1011
Seq/Len: 13.19 85.51 9.91
MirrorTree (Pazo et al. 2001) 0.25
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 0.00 0.01
2 0.09 0.00 0.01
5 0.09 0.00 0.03
10 0.09 0.01 0.09
20 0.09 0.01 0.21
100 0.09 0.09 1.74
∞ 0.09 0.19 9.45
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
17_R 27_T 1.07 0.95 0.08
45_I 37_A 1.07 0.95 0.08
29_E 40_P 0.95 0.89 0.06
38_P 13_L 0.89 0.85 0.05
52_N 37_A 0.81 0.77 0.04
4_V 42_D 0.80 0.74 0.03
10_T 6_I 0.79 0.74 0.03
33_T 24_F 0.77 0.71 0.03
46_H 10_E 0.77 0.71 0.03
40_G 7_T 0.77 0.70 0.03
21_A 37_A 0.76 0.70 0.03
1_V 13_L 0.73 0.65 0.03
17_R 30_N 0.70 0.61 0.02
54_E 15_L 0.68 0.56 0.02
29_E 44_L 0.67 0.56 0.02
48_V 12_E 0.67 0.55 0.02
52_N 19_K 0.66 0.54 0.02
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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