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OPENSEQ.org
IscSIscU
Genes: A B A+B
Length: 404 128 508
Sequences: 31466 2384 1925
Seq/Len: 77.89 18.62 3.79
MirrorTree (Pazo et al. 2001) 0.81
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 0.07 0.00 3.52
2 0.09 0.00 3.58
5 0.11 0.00 3.62
10 0.12 0.00 3.66
20 0.15 0.01 3.70
100 0.25 0.01 4.01
∞ 0.29 0.02 4.52
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
36_P 100_P 0.71 0.35 0.00
309_E 38_G 0.62 0.26 0.00
97_I 5_E 0.62 0.26 0.00
21_E 84_E 0.62 0.25 0.00
148_V 88_I 0.61 0.24 0.00
25_Q 47_V 0.60 0.24 0.00
311_E 38_G 0.60 0.23 0.00
346_D 34_A 0.59 0.23 0.00
105_K 38_G 0.56 0.20 0.00
20_A 73_V 0.56 0.20 0.00
152_H 77_V 0.55 0.19 0.00
98_I 120_D 0.55 0.19 0.00
196_K 51_G 0.55 0.19 0.00
309_E 3_Y 0.54 0.18 0.00
287_V 77_V 0.54 0.18 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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