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OPENSEQ.org
DI1200006_5D0O
Genes: A B A+B
Length: 56 245 297
Sequences: 318 5804 112
Seq/Len: 5.68 23.69 0.38
MirrorTree (Pazo et al. 2001) 0.41
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 0.02 0.00
2 0.00 0.02 0.00
5 0.00 0.02 0.00
10 0.00 0.02 0.00
20 0.00 0.02 0.01
100 0.00 0.02 0.04
∞ 0.00 0.05 0.37
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
6_V 194_V 1.35 0.38 0.00
9_D 183_E 1.19 0.28 0.00
49_K 23_S 1.19 0.28 0.00
49_K 103_P 1.19 0.28 0.00
8_G 121_D 1.18 0.27 0.00
55_P 172_D 1.17 0.27 0.00
1_R 83_A 1.17 0.26 0.00
37_A 239_A 1.17 0.26 0.00
45_G 43_L 1.12 0.24 0.00
14_E 48_W 1.11 0.23 0.00
36_Y 36_Y 1.10 0.23 0.00
15_A 102_H 1.09 0.23 0.00
45_G 28_P 1.09 0.22 0.00
47_V 50_Q 1.08 0.22 0.00
47_V 184_Y 1.08 0.22 0.00
52_D 59_D 1.06 0.21 0.00
10_E 53_T 1.06 0.21 0.00
52_D 137_P 1.06 0.21 0.00
55_P 170_L 1.05 0.20 0.00
8_G 82_N 1.04 0.20 0.00
13_L 237_I 1.02 0.19 0.00
21_L 214_A 1.01 0.18 0.00
3_K 194_V 0.99 0.18 0.00
52_D 29_D 0.99 0.18 0.00
26_G 187_E 0.99 0.17 0.00
7_S 58_L 0.99 0.17 0.00
55_P 67_Y 0.98 0.17 0.00
55_P 206_P 0.98 0.17 0.00
11_A 205_Y 0.98 0.17 0.00
39_P 113_G 0.98 0.17 0.00
38_I 105_I 0.97 0.17 0.00
25_A 37_A 0.97 0.17 0.00
21_L 66_P 0.97 0.17 0.00
1_R 126_G 0.97 0.17 0.00
49_K 14_S 0.96 0.17 0.00
39_P 36_Y 0.96 0.16 0.00
5_Q 29_D 0.94 0.16 0.00
21_L 88_A 0.94 0.16 0.00
36_Y 180_S 0.94 0.16 0.00
47_V 82_N 0.94 0.16 0.00
54_R 78_A 0.94 0.15 0.00
45_G 29_D 0.94 0.15 0.00
21_L 15_L 0.93 0.15 0.00
45_G 118_A 0.93 0.15 0.00
10_E 89_Q 0.93 0.15 0.00
38_I 32_P 0.92 0.15 0.00
21_L 191_W 0.92 0.15 0.00
4_R 199_E 0.92 0.15 0.00
31_V 218_M 0.91 0.15 0.00
51_L 50_Q 0.91 0.15 0.00
5_Q 122_S 0.91 0.15 0.00
13_L 33_N 0.91 0.15 0.00
18_L 33_N 0.91 0.15 0.00
36_Y 109_M 0.91 0.14 0.00
44_S 41_Q 0.90 0.14 0.00
44_S 19_G 0.90 0.14 0.00
25_A 130_V 0.89 0.14 0.00
23_A 18_A 0.88 0.14 0.00
21_L 107_Y 0.88 0.14 0.00
9_D 11_A 0.88 0.14 0.00
38_I 172_D 0.87 0.13 0.00
4_R 210_A 0.87 0.13 0.00
47_V 103_P 0.87 0.13 0.00
46_A 161_T 0.86 0.13 0.00
53_I 238_I 0.86 0.13 0.00
38_I 191_W 0.86 0.13 0.00
4_R 84_D 0.86 0.13 0.00
26_G 24_K 0.86 0.13 0.00
6_V 201_M 0.86 0.13 0.00
9_D 96_I 0.86 0.13 0.00
55_P 120_D 0.85 0.13 0.00
5_Q 21_S 0.85 0.13 0.00
21_L 211_T 0.85 0.13 0.00
8_G 165_K 0.85 0.12 0.00
24_P 194_V 0.84 0.12 0.00
14_E 141_R 0.84 0.12 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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