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OPENSEQ.org
D3_GNAI1
Genes: A B A+B
Length: 400 354 723
Sequences: 1636 1662 79
Seq/Len: 4.09 4.69 0.11
MirrorTree (Pazo et al. 2001) 0.02
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 0.06 0.08 0.00
2 0.06 0.09 0.00
5 0.07 0.09 0.01
10 0.07 0.09 0.01
20 0.08 0.10 0.01
100 0.10 0.12 0.05
∞ 0.13 0.15 0.10
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
58_R 20_D 1.31 0.16 0.00
395_L 122_E 1.21 0.13 0.00
160_L 174_V 1.12 0.11 0.00
128_R 76_N 1.11 0.11 0.00
72_A 20_D 1.10 0.11 0.00
188_F 291_A 1.04 0.10 0.00
47_N 76_N 1.02 0.09 0.00
154_I 151_S 1.00 0.09 0.00
340_V 120_T 0.97 0.09 0.00
126_I 299_A 0.97 0.09 0.00
383_Y 267_F 0.96 0.08 0.00
383_Y 269_N 0.96 0.08 0.00
383_Y 272_D 0.96 0.08 0.00
202_G 122_E 0.96 0.08 0.00
354_H 166_N 0.93 0.08 0.00
335_L 61_Y 0.93 0.08 0.00
383_Y 76_N 0.87 0.07 0.00
188_F 4_T 0.86 0.07 0.00
398_L 165_P 0.86 0.07 0.00
188_F 77_T 0.86 0.07 0.00
105_V 85_I 0.85 0.07 0.00
77_L 256_N 0.85 0.07 0.00
121_L 26_D 0.85 0.07 0.00
181_C 174_V 0.84 0.07 0.00
391_R 302_Y 0.84 0.07 0.00
375_N 150_D 0.84 0.07 0.00
71_L 267_F 0.83 0.07 0.00
71_L 269_N 0.83 0.07 0.00
71_L 272_D 0.83 0.07 0.00
170_F 198_M 0.83 0.06 0.00
337_A 71_A 0.83 0.06 0.00
45_F 247_M 0.82 0.06 0.00
38_A 64_E 0.82 0.06 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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