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OPENSEQ.org
BipA, EF-G
Genes: A B A+B
Length: 195 285 441
Sequences: 22247 4048 860
Seq/Len: 114.09 14.2 1.95
MirrorTree (Pazo et al. 2001) 0.11
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 0.10 0.06 0.05
2 0.10 0.06 0.07
5 0.11 0.06 0.10
10 0.12 0.06 0.20
20 0.15 0.06 0.33
100 0.24 0.07 0.90
∞ 0.29 0.17 1.79
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
123_P 5_T 1.02 0.54 0.00
21_L 182_V 0.94 0.45 0.00
165_A 158_I 0.91 0.42 0.00
126_V 229_A 0.82 0.32 0.00
146_D 245_E 0.80 0.31 0.00
119_Y 244_T 0.80 0.30 0.00
183_M 230_S 0.77 0.28 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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