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OPENSEQ.org
DI1200001_1R1R
Genes: A B A+B
Length: 30 395 424
Sequences: 364 6946 329
Seq/Len: 12.13 17.58 0.78
MirrorTree (Pazo et al. 2001) 0.65
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 0.00 0.00 0.68
2 0.00 0.00 0.72
5 0.00 0.00 0.73
10 0.00 0.00 0.73
20 0.00 0.00 0.74
100 0.00 0.00 0.75
∞ 0.00 0.04 0.77
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
28_F 385_L 1.53 0.72 0.01
13_V 146_E 1.27 0.51 0.00
25_L 330_D 1.24 0.48 0.00
8_V 338_M 1.23 0.47 0.00
27_N 68_M 1.22 0.47 0.00
20_V 271_S 1.15 0.40 0.00
14_G 82_N 1.09 0.36 0.00
16_I 384_L 1.08 0.35 0.00
13_V 310_I 1.02 0.31 0.00
29_Q 349_G 1.01 0.30 0.00
23_D 228_Q 1.01 0.29 0.00
1_V 306_G 1.00 0.29 0.00
25_L 11_T 0.99 0.28 0.00
18_S 40_E 0.99 0.28 0.00
25_L 13_L 0.99 0.28 0.00
15_Q 133_F 0.98 0.27 0.00
29_Q 20_T 0.98 0.27 0.00
24_D 338_M 0.94 0.25 0.00
12_L 135_L 0.93 0.24 0.00
17_D 133_F 0.93 0.24 0.00
18_S 70_Q 0.92 0.23 0.00
25_L 7_K 0.92 0.23 0.00
14_G 76_G 0.87 0.21 0.00
12_L 372_S 0.87 0.20 0.00
9_S 185_N 0.86 0.20 0.00
12_L 347_L 0.86 0.20 0.00
25_L 174_M 0.86 0.20 0.00
8_V 68_M 0.85 0.20 0.00
15_Q 135_L 0.85 0.19 0.00
6_V 325_Y 0.84 0.19 0.00
30_L 184_I 0.83 0.18 0.00
26_S 372_S 0.83 0.18 0.00
15_Q 148_A 0.82 0.18 0.00
15_Q 210_F 0.82 0.18 0.00
29_Q 69_M 0.81 0.17 0.00
24_D 378_Q 0.80 0.17 0.00
13_V 348_V 0.80 0.17 0.00
9_S 101_Q 0.80 0.17 0.00
13_V 181_I 0.79 0.16 0.00
12_L 210_F 0.79 0.16 0.00
6_V 213_I 0.79 0.16 0.00
15_Q 350_I 0.78 0.16 0.00
30_L 334_L 0.78 0.16 0.00
13_V 64_L 0.78 0.16 0.00
20_V 37_D 0.77 0.15 0.00
14_G 150_L 0.77 0.15 0.00
8_V 319_R 0.76 0.15 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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