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OPENSEQ.org
CXCR4 and Gi alpha 2
Genes: A B A+B
Length: 352 355 671
Sequences: 17000 2249 403
Seq/Len: 48.3 6.34 0.6
MirrorTree (Pazo et al. 2001) 0.18
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 0.19 0.01 0.03
2 0.22 0.01 0.03
5 0.24 0.02 0.06
10 0.26 0.02 0.09
20 0.28 0.02 0.16
100 0.32 0.02 0.39
∞ 0.33 0.03 0.57
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
247_A 11_A 1.19 0.37 0.00
166_L 171_T 1.11 0.31 0.00
80_L 157_L 1.00 0.24 0.00
70_R 93_L 0.96 0.22 0.00
85_L 276_E 0.95 0.21 0.00
54_V 265_I 0.93 0.20 0.00
69_L 290_E 0.92 0.20 0.00
52_G 26_D 0.91 0.20 0.00
86_L 123_E 0.90 0.19 0.00
311_T 274_L 0.88 0.18 0.00
254_P 84_I 0.88 0.18 0.00
158_V 304_I 0.86 0.17 0.00
315_H 85_I 0.86 0.17 0.00
248_F 70_R 0.86 0.17 0.00
232_H 171_T 0.85 0.17 0.00
300_I 20_D 0.84 0.16 0.00
166_L 232_D 0.84 0.16 0.00
99_V 160_L 0.84 0.16 0.00
78_L 9_D 0.81 0.15 0.00
41_L 138_Q 0.80 0.14 0.00
132_L 222_I 0.80 0.14 0.00
86_L 138_Q 0.80 0.14 0.00
47_I 98_P 0.80 0.14 0.00
165_L 135_S 0.80 0.14 0.00
182_D 163_I 0.80 0.14 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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