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OPENSEQ.org
ACKR3 and Gi alpha 1
Genes: A B A+B
Length: 362 354 677
Sequences: 15749 2169 350
Seq/Len: 43.51 6.13 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 0.01 0.06
10 0.27 0.01 0.09
20 0.29 0.01 0.16
100 0.33 0.02 0.35
∞ 0.33 0.02 0.49
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
174_C 170_T 1.26 0.39 0.00
261_F 70_K 1.15 0.31 0.00
140_V 221_I 1.06 0.26 0.00
173_F 163_S 1.04 0.25 0.00
57_I 78_I 1.00 0.22 0.00
165_C 273_L 0.96 0.20 0.00
262_L 62_S 0.94 0.19 0.00
175_V 148_L 0.91 0.18 0.00
171_L 104_A 0.91 0.17 0.00
58_G 26_D 0.90 0.17 0.00
146_I 140_F 0.89 0.17 0.00
143_Y 78_I 0.88 0.16 0.00
308_C 54_K 0.85 0.15 0.00
59_M 168_V 0.84 0.15 0.00
126_I 54_K 0.82 0.14 0.00
202_E 278_I 0.81 0.14 0.00
157_K 302_Y 0.81 0.14 0.00
294_F 159_L 0.81 0.14 0.00
88_I 264_I 0.80 0.13 0.00
244_D 239_E 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)
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