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OPENSEQ.org
675
Genes: A B A+B
Length: 116 128 234
Sequences: 8581 7028 600
Seq/Len: 73.97 54.91 2.56
MirrorTree (Pazo et al. 2001) 0.26
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 0.03 0.01 2.46
2 0.04 0.02 2.65
5 0.06 0.03 2.97
10 0.07 0.03 3.22
20 0.08 0.04 3.50
100 0.13 0.06 4.89
∞ 0.17 0.15 8.20
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
29_S 101_Y 1.12 0.73 0.02
21_Q 8_Y 0.83 0.39 0.01
58_D 104_F 0.78 0.34 0.01
96_L 13_G 0.77 0.33 0.01
68_A 110_L 0.77 0.33 0.01
41_P 57_G 0.73 0.29 0.01
41_P 52_I 0.72 0.28 0.01
95_P 38_G 0.71 0.27 0.01
87_Q 44_D 0.71 0.27 0.01
8_I 46_H 0.70 0.27 0.01
44_E 18_F 0.69 0.25 0.01
97_T 29_F 0.69 0.25 0.01
93_G 118_M 0.69 0.25 0.01
26_L 85_L 0.67 0.23 0.01
38_T 103_R 0.66 0.23 0.01
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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