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OPENSEQ.org
ACKR3 and Arrestin1
Genes: A B A+B
Length: 362 418 716
Sequences: 15749 629 140
Seq/Len: 43.51 1.5 0.2
MirrorTree (Pazo et al. 2001) 0.23
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 0.20 0.02 0.01
2 0.23 0.02 0.02
5 0.25 0.02 0.03
10 0.27 0.02 0.04
20 0.29 0.03 0.05
100 0.33 0.03 0.12
∞ 0.33 0.05 0.18
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
63_S 119_I 1.34 0.24 0.00
266_L 57_L 1.25 0.21 0.00
244_D 199_L 1.24 0.20 0.00
116_T 43_V 1.12 0.16 0.00
309_C 113_Y 1.06 0.14 0.00
82_Y 102_E 1.04 0.13 0.00
196_C 330_S 1.01 0.13 0.00
241_A 50_E 1.01 0.12 0.00
325_E 37_V 0.99 0.12 0.00
323_R 214_I 0.98 0.12 0.00
241_A 42_L 0.97 0.12 0.00
310_V 120_P 0.96 0.11 0.00
226_S 18_L 0.94 0.11 0.00
219_L 55_V 0.91 0.10 0.00
130_G 113_Y 0.91 0.10 0.00
57_I 241_I 0.89 0.10 0.00
78_D 86_S 0.89 0.10 0.00
122_L 57_L 0.89 0.10 0.00
263_V 119_I 0.88 0.10 0.00
233_F 37_V 0.85 0.09 0.00
87_A 173_Y 0.85 0.09 0.00
140_V 329_V 0.85 0.09 0.00
172_A 231_I 0.85 0.09 0.00
86_L 124_P 0.84 0.09 0.00
310_V 274_L 0.84 0.09 0.00
120_T 123_L 0.83 0.09 0.00
146_I 124_P 0.83 0.09 0.00
231_F 220_V 0.83 0.09 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
6107 0.2 ACKR3 and Arrestin1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
6077 0.02 ACKR3 and Arrestin1 Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
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