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OPENSEQ.org
CXCR4 and Arrestin 2
Genes: A B A+B
Length: 352 409 713
Sequences: 17000 1084 225
Seq/Len: 48.3 2.65 0.32
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 0.19 0.02 0.02
2 0.22 0.03 0.03
5 0.24 0.03 0.04
10 0.26 0.03 0.05
20 0.28 0.03 0.08
100 0.32 0.04 0.18
∞ 0.33 0.06 0.30
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
85_L 290_L 1.19 0.25 0.00
114_V 58_L 1.14 0.22 0.00
134_R 223_N 1.09 0.20 0.00
297_L 19_L 1.07 0.19 0.00
80_L 125_P 1.06 0.18 0.00
111_A 226_T 1.06 0.18 0.00
166_L 356_P 1.04 0.18 0.00
76_Y 234_V 1.03 0.17 0.00
57_G 120_I 1.02 0.17 0.00
43_T 330_V 1.01 0.17 0.00
134_R 213_E 0.98 0.15 0.00
228_H 51_D 0.97 0.15 0.00
56_N 223_N 0.96 0.15 0.00
310_K 127_S 0.96 0.15 0.00
88_V 326_V 0.93 0.14 0.00
228_H 273_Y 0.93 0.14 0.00
215_I 358_P 0.91 0.13 0.00
302_Y 344_L 0.90 0.13 0.00
59_V 127_S 0.89 0.13 0.00
84_D 143_V 0.89 0.13 0.00
54_V 179_P 0.89 0.12 0.00
134_R 238_Q 0.88 0.12 0.00
159_G 362_A 0.86 0.12 0.00
169_I 36_D 0.86 0.12 0.00
136_L 111_Q 0.86 0.12 0.00
146_R 301_L 0.86 0.12 0.00
63_M 353_I 0.85 0.12 0.00
81_S 200_L 0.85 0.11 0.00
212_G 38_V 0.85 0.11 0.00
213_I 265_P 0.84 0.11 0.00
317_L 275_I 0.84 0.11 0.00
104_F 114_H 0.84 0.11 0.00
170_P 318_I 0.84 0.11 0.00
91_L 44_V 0.84 0.11 0.00
314_Q 265_P 0.84 0.11 0.00
49_F 112_H 0.84 0.11 0.00
254_P 215_L 0.83 0.11 0.00
248_F 223_N 0.83 0.11 0.00
310_K 215_L 0.82 0.11 0.00
128_A 303_S 0.82 0.11 0.00
53_I 135_E 0.82 0.11 0.00
111_A 114_H 0.82 0.10 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
6109 0.32 CXCR4 and Arrestin 2 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
6079 0.03 CXCR4 and Arrestin 2 Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
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