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OPENSEQ.org
CXCR4 and Arrestin1
Genes: A B A+B
Length: 352 418 700
Sequences: 17000 629 163
Seq/Len: 48.3 1.5 0.23
MirrorTree (Pazo et al. 2001) 0.22
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 0.01
2 0.22 0.02 0.02
5 0.24 0.02 0.03
10 0.26 0.02 0.04
20 0.28 0.03 0.05
100 0.32 0.03 0.13
∞ 0.33 0.05 0.21
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
253_L 57_L 1.29 0.24 0.00
57_G 119_I 1.23 0.22 0.00
254_P 205_K 1.17 0.19 0.00
203_H 120_P 1.16 0.19 0.00
76_Y 102_E 1.09 0.16 0.00
57_G 233_I 1.09 0.16 0.00
53_I 134_E 1.05 0.15 0.00
114_V 57_L 1.04 0.14 0.00
91_L 43_V 1.01 0.14 0.00
226_L 232_K 1.00 0.13 0.00
228_H 50_E 0.97 0.12 0.00
297_L 120_P 0.95 0.12 0.00
135_Y 41_V 0.95 0.12 0.00
76_Y 233_I 0.94 0.12 0.00
112_V 123_L 0.93 0.12 0.00
77_R 41_V 0.92 0.11 0.00
315_H 157_K 0.91 0.11 0.00
312_S 37_V 0.91 0.11 0.00
53_I 106_K 0.90 0.11 0.00
300_I 205_K 0.90 0.11 0.00
186_C 39_G 0.90 0.11 0.00
115_I 46_E 0.90 0.11 0.00
153_E 231_I 0.89 0.11 0.00
145_Q 347_L 0.89 0.10 0.00
304_F 217_N 0.89 0.10 0.00
226_L 214_I 0.88 0.10 0.00
296_C 113_Y 0.87 0.10 0.00
52_G 305_L 0.86 0.10 0.00
69_L 28_V 0.86 0.10 0.00
52_G 218_V 0.86 0.10 0.00
65_Y 43_V 0.84 0.09 0.00
58_L 319_V 0.84 0.09 0.00
49_F 111_H 0.84 0.09 0.00
139_V 218_V 0.84 0.09 0.00
166_L 43_V 0.84 0.09 0.00
44_I 231_I 0.83 0.09 0.00
166_L 46_E 0.83 0.09 0.00
109_C 39_G 0.83 0.09 0.00
226_L 153_N 0.82 0.09 0.00
131_S 117_F 0.82 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
6106 0.23 CXCR4 and Arrestin1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
6076 0.03 CXCR4 and Arrestin1 Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
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