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OPENSEQ.org
4A-4Gmin
Genes: A B A+B
Length: 406 350 728
Sequences: 51436 513 264
Seq/Len: 126.69 1.47 0.36
MirrorTree (Pazo et al. 2001) 0.11
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 0.10 0.10 0.01
2 0.12 0.11 0.01
5 0.14 0.18 0.05
10 0.16 0.18 0.08
20 0.20 0.19 0.14
100 0.27 0.19 0.35
∞ 0.29 0.20 0.48
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
345_I 307_K 1.03 0.19 0.00
336_I 78_L 1.01 0.18 0.00
322_S 65_Q 0.95 0.15 0.00
180_V 198_A 0.92 0.14 0.00
325_V 249_I 0.90 0.14 0.00
81_G 250_G 0.90 0.14 0.00
82_K 250_G 0.90 0.14 0.00
182_D 250_G 0.90 0.14 0.00
183_E 250_G 0.90 0.14 0.00
105_V 92_Q 0.89 0.14 0.00
292_M 245_L 0.89 0.13 0.00
211_L 253_L 0.88 0.13 0.00
146_K 254_D 0.84 0.12 0.00
211_L 296_N 0.83 0.12 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)
ID Seq/Len Name Options I_Prob Status
4215 0.15 4A-4Gmin Δgene:(1, 100) A:(1E-80, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4064 0.36 4A-4Gmin Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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