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OPENSEQ.org
cgas-rragd (Q9NQL2) (B, 55-245)
Genes: A B A+B
Length: 362 191 535
Sequences: 515 33118 136
Seq/Len: 1.42 173.39 0.25
MirrorTree (Pazo et al. 2001) 0.31
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.05 0.04 0.00
2 0.06 0.05 0.00
5 0.07 0.06 0.01
10 0.07 0.08 0.02
20 0.07 0.11 0.05
100 0.07 0.22 0.15
∞ 0.08 0.27 0.25
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
128_I 163_Y 1.29 0.26 0.00
162_L 24_I 1.13 0.18 0.00
163_A 163_Y 1.03 0.15 0.00
163_A 134_H 1.02 0.15 0.00
28_G 89_F 1.00 0.14 0.00
288_Q 92_D 0.99 0.14 0.00
33_L 125_H 0.99 0.14 0.00
295_W 63_D 0.96 0.13 0.00
274_S 49_E 0.93 0.12 0.00
66_F 172_I 0.92 0.12 0.00
215_W 20_G 0.92 0.12 0.00
327_E 179_V 0.91 0.12 0.00
68_V 90_V 0.91 0.11 0.00
254_K 21_K 0.90 0.11 0.00
358_V 90_V 0.89 0.11 0.00
263_R 125_H 0.87 0.10 0.00
45_G 165_T 0.86 0.10 0.00
302_L 149_D 0.86 0.10 0.00
33_L 46_I 0.86 0.10 0.00
12_L 172_I 0.86 0.10 0.00
252_L 166_S 0.86 0.10 0.00
315_L 89_F 0.85 0.10 0.00
158_V 108_V 0.85 0.10 0.00
281_A 121_E 0.85 0.10 0.00
124_I 160_L 0.85 0.10 0.00
304_F 11_I 0.84 0.10 0.00
119_K 13_L 0.84 0.10 0.00
31_D 92_D 0.84 0.10 0.00
215_W 128_D 0.83 0.10 0.00
67_D 21_K 0.83 0.10 0.00
308_V 25_Q 0.83 0.10 0.00
138_M 174_E 0.82 0.09 0.00
283_F 12_L 0.82 0.09 0.00
307_C 125_H 0.81 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)
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