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OPENSEQ.org
Thiomonas ssuA acRAFb
Genes: A B A+B
Length: 109 88 188
Sequences: 555 1990 52
Seq/Len: 5.09 22.61 0.28
MirrorTree (Pazo et al. 2001) 0.80
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 0.04 0.01 0.01
2 0.04 0.01 0.01
5 0.09 0.01 0.02
10 0.09 0.01 0.22
20 0.10 0.01 0.26
100 0.10 0.02 0.35
∞ 0.17 0.04 0.93
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
77_L 61_L 1.59 0.45 0.00
5_Q 49_N 1.44 0.36 0.00
88_M 46_H 1.40 0.34 0.00
36_A 65_D 1.32 0.29 0.00
78_E 83_L 1.31 0.29 0.00
89_V 57_V 1.27 0.27 0.00
35_I 69_L 1.25 0.26 0.00
88_M 54_T 1.24 0.25 0.00
77_L 22_A 1.17 0.22 0.00
25_E 73_E 1.17 0.22 0.00
27_V 28_Q 1.16 0.21 0.00
59_M 37_A 1.16 0.21 0.00
42_A 49_N 1.14 0.20 0.00
48_K 46_H 1.11 0.19 0.00
42_A 38_A 1.10 0.19 0.00
79_A 14_P 1.09 0.18 0.00
73_V 21_F 1.09 0.18 0.00
22_M 65_D 1.06 0.17 0.00
98_A 65_D 1.06 0.17 0.00
35_I 22_A 1.05 0.17 0.00
22_M 7_S 1.02 0.16 0.00
89_V 29_T 1.02 0.16 0.00
50_T 84_A 1.01 0.15 0.00
12_K 71_E 1.01 0.15 0.00
96_N 37_A 1.01 0.15 0.00
4_V 36_L 1.00 0.15 0.00
73_V 79_R 1.00 0.15 0.00
22_M 54_T 0.99 0.15 0.00
73_V 25_S 0.98 0.14 0.00
4_V 51_N 0.98 0.14 0.00
53_R 21_F 0.97 0.14 0.00
45_H 14_P 0.97 0.14 0.00
43_V 78_A 0.97 0.14 0.00
73_V 69_L 0.96 0.14 0.00
91_F 19_K 0.96 0.14 0.00
32_A 53_G 0.96 0.14 0.00
42_A 66_G 0.95 0.14 0.00
94_Y 26_Y 0.95 0.14 0.00
88_M 64_A 0.95 0.14 0.00
73_V 34_D 0.95 0.13 0.00
104_A 39_L 0.95 0.13 0.00
75_A 69_L 0.94 0.13 0.00
56_F 78_A 0.93 0.13 0.00
45_H 52_F 0.93 0.13 0.00
72_A 46_H 0.92 0.12 0.00
102_G 23_F 0.92 0.12 0.00
93_A 46_H 0.91 0.12 0.00
4_V 73_E 0.90 0.12 0.00
70_V 39_L 0.90 0.12 0.00
34_T 43_T 0.90 0.12 0.00
81_H 58_N 0.90 0.12 0.00
22_M 21_F 0.90 0.12 0.00
32_A 56_Y 0.90 0.12 0.00
29_R 18_F 0.90 0.12 0.00
91_F 50_I 0.90 0.12 0.00
46_T 15_P 0.89 0.12 0.00
37_Q 39_L 0.89 0.12 0.00
23_T 36_L 0.89 0.12 0.00
35_I 63_A 0.89 0.12 0.00
9_A 18_F 0.89 0.12 0.00
7_Y 20_R 0.89 0.12 0.00
82_R 26_Y 0.89 0.12 0.00
100_S 6_A 0.89 0.12 0.00
86_D 10_E 0.89 0.12 0.00
89_V 60_T 0.89 0.12 0.00
32_A 58_N 0.88 0.11 0.00
8_K 12_G 0.88 0.11 0.00
94_Y 52_F 0.87 0.11 0.00
7_Y 14_P 0.87 0.11 0.00
34_T 84_A 0.87 0.11 0.00
102_G 52_F 0.87 0.11 0.00
46_T 61_L 0.86 0.11 0.00
96_N 15_P 0.86 0.11 0.00
106_V 5_T 0.86 0.11 0.00
56_F 61_L 0.86 0.11 0.00
73_V 82_A 0.86 0.11 0.00
50_T 27_A 0.86 0.11 0.00
23_T 85_G 0.85 0.11 0.00
106_V 49_N 0.85 0.11 0.00
27_V 35_A 0.85 0.11 0.00
45_H 17_L 0.85 0.11 0.00
6_A 46_H 0.85 0.11 0.00
11_K 73_E 0.85 0.11 0.00
103_L 25_S 0.85 0.11 0.00
108_Y 59_I 0.85 0.11 0.00
97_Y 58_N 0.85 0.10 0.00
40_N 55_T 0.84 0.10 0.00
87_H 17_L 0.84 0.10 0.00
77_L 9_R 0.84 0.10 0.00
21_Q 73_E 0.83 0.10 0.00
83_E 51_N 0.83 0.10 0.00
56_F 81_D 0.83 0.10 0.00
55_S 71_E 0.83 0.10 0.00
45_H 20_R 0.83 0.10 0.00
78_E 23_F 0.82 0.10 0.00
47_E 34_D 0.82 0.10 0.00
59_M 46_H 0.82 0.10 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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