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OPENSEQ.org
GNAS2-Rho2
Genes: A B A+B
Length: 394 348 684
Sequences: 2903 19329 449
Seq/Len: 7.37 55.54 0.66
MirrorTree (Pazo et al. 2001) 0.16
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 0.01 0.20 0.03
2 0.01 0.23 0.04
5 0.01 0.25 0.07
10 0.01 0.27 0.10
20 0.01 0.29 0.17
100 0.02 0.33 0.40
∞ 0.02 0.34 0.61
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
185_I 57_L 1.04 0.28 0.00
276_I 306_Y 1.00 0.26 0.00
150_A 172_L 0.98 0.24 0.00
315_F 255_I 0.97 0.24 0.00
18_A 260_A 0.95 0.23 0.00
163_Y 139_V 0.88 0.19 0.00
244_I 133_I 0.87 0.18 0.00
131_I 66_K 0.83 0.17 0.00
160_R 126_W 0.83 0.17 0.00
150_A 85_F 0.83 0.17 0.00
332_P 88_L 0.81 0.16 0.00
33_D 249_E 0.80 0.15 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
5687 0.66 GNAS2-Rho2 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5680 0.24 GNAS2-Rho Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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