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OPENSEQ.org
wspAwspB
Genes: A B A+B
Length: 542 171 699
Sequences: 16042 3789 1230
Seq/Len: 29.6 22.16 1.76
MirrorTree (Pazo et al. 2001) 0.62
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 0.14 0.04 1.08
2 0.15 0.07 1.17
5 0.17 0.10 1.34
10 0.19 0.11 1.53
20 0.21 0.11 1.73
100 0.27 0.15 2.77
∞ 0.30 0.22 3.70
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
405_R 85_R 1.18 0.67 0.01
394_A 145_Q 1.06 0.55 0.01
382_V 44_K 1.03 0.51 0.01
379_I 31_A 1.00 0.49 0.00
408_A 88_L 1.00 0.48 0.00
169_E 140_P 0.99 0.48 0.00
408_A 60_R 0.93 0.41 0.00
387_N 85_R 0.92 0.40 0.00
230_A 88_L 0.88 0.36 0.00
253_F 131_R 0.87 0.35 0.00
391_L 65_P 0.87 0.35 0.00
541_K 79_L 0.85 0.33 0.00
388_L 16_L 0.85 0.33 0.00
433_R 82_T 0.82 0.30 0.00
21_M 76_R 0.82 0.30 0.00
135_E 141_R 0.81 0.29 0.00
506_G 152_L 0.80 0.28 0.00
12_A 133_L 0.80 0.28 0.00
288_Q 68_D 0.79 0.27 0.00
270_S 146_W 0.78 0.27 0.00
381_K 115_C 0.78 0.27 0.00
384_D 85_R 0.78 0.27 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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