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OPENSEQ.org
JJY
Genes: A B A+B
Length: 333 327 622
Sequences: 3770 21361 885
Seq/Len: 11.32 65.32 1.42
MirrorTree (Pazo et al. 2001) 0.05
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 0.02 0.05 0.09
2 0.03 0.08 0.21
5 0.04 0.12 0.45
10 0.05 0.16 0.81
20 0.07 0.22 1.34
100 0.14 0.31 2.97
∞ 0.24 0.35 3.38
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
308_T 146_I 1.04 0.47 0.00
271_V 145_G 1.02 0.45 0.00
271_V 296_D 0.90 0.33 0.00
295_V 79_L 0.79 0.24 0.00
163_G 293_D 0.75 0.21 0.00
298_C 230_H 0.73 0.20 0.00
195_E 211_S 0.73 0.20 0.00
156_N 295_L 0.73 0.20 0.00
190_V 39_V 0.72 0.20 0.00
308_T 209_M 0.72 0.19 0.00
89_H 168_I 0.71 0.18 0.00
113_N 146_I 0.69 0.18 0.00
116_Y 61_I 0.69 0.17 0.00
163_G 219_M 0.69 0.17 0.00
271_V 162_L 0.69 0.17 0.00
300_P 61_I 0.68 0.17 0.00
73_Y 299_L 0.68 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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