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OPENSEQ.org
ACKR3 and Gi alpha 2
Genes: A B A+B
Length: 362 355 678
Sequences: 15749 2249 355
Seq/Len: 43.51 6.34 0.52
MirrorTree (Pazo et al. 2001) 0.21
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 0.01 0.02
2 0.23 0.01 0.03
5 0.25 0.02 0.06
10 0.27 0.02 0.09
20 0.29 0.02 0.16
100 0.33 0.02 0.35
∞ 0.33 0.03 0.50
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
261_F 70_R 1.21 0.35 0.00
174_C 171_T 1.16 0.32 0.00
173_F 164_S 1.07 0.26 0.00
57_I 78_V 1.04 0.24 0.00
140_V 222_I 1.03 0.24 0.00
146_I 141_L 1.01 0.23 0.00
202_E 279_I 0.92 0.18 0.00
58_G 26_D 0.92 0.18 0.00
99_V 98_P 0.92 0.18 0.00
175_V 149_L 0.90 0.17 0.00
143_Y 78_V 0.88 0.17 0.00
88_I 27_G 0.87 0.16 0.00
262_L 62_S 0.86 0.16 0.00
306_V 115_E 0.85 0.15 0.00
294_F 160_L 0.84 0.15 0.00
244_D 240_E 0.84 0.15 0.00
126_I 54_K 0.83 0.14 0.00
260_V 11_A 0.83 0.14 0.00
157_K 303_Y 0.81 0.14 0.00
86_L 157_L 0.81 0.14 0.00
166_I 304_I 0.80 0.13 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
6388 0.04 ACKR3 and Gi alpha 2 Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2016_06b) Killed - Shared
6158 0.52 ACKR3 and Gi alpha 2 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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