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OPENSEQ.org
TA_three
Genes: A B A+B
Length: 122 124 233
Sequences: 152 123 131
Seq/Len: 1.25 0.99 0.56
MirrorTree (Pazo et al. 2001) 0.48
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 0.02 0.01 0.53
2 0.02 0.01 0.55
5 0.02 0.01 0.57
10 0.03 0.01 0.57
20 0.03 0.03 0.57
100 0.05 0.04 0.57
∞ 0.09 0.08 0.56
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
90_V 23_Q 1.31 0.45 0.00
103_T 42_P 1.31 0.44 0.00
103_T 116_T 1.28 0.43 0.00
55_S 5_P 1.17 0.34 0.00
107_C 15_R 1.15 0.33 0.00
103_T 70_Y 1.11 0.30 0.00
49_G 32_Q 1.11 0.30 0.00
87_Q 108_N 1.09 0.29 0.00
18_P 86_S 1.07 0.28 0.00
107_C 7_L 1.05 0.26 0.00
65_A 20_E 1.03 0.25 0.00
114_V 2_K 1.03 0.25 0.00
98_T 66_L 1.03 0.25 0.00
63_D 57_I 1.02 0.25 0.00
85_R 111_T 1.02 0.24 0.00
14_N 16_P 1.01 0.24 0.00
107_C 32_Q 1.01 0.24 0.00
117_T 2_K 1.00 0.23 0.00
60_Y 86_S 1.00 0.23 0.00
116_P 22_W 1.00 0.23 0.00
116_P 43_F 1.00 0.23 0.00
116_P 59_L 1.00 0.23 0.00
96_G 81_S 0.98 0.22 0.00
76_M 45_D 0.98 0.22 0.00
116_P 55_A 0.96 0.21 0.00
83_N 27_S 0.96 0.21 0.00
29_C 99_R 0.94 0.20 0.00
117_T 46_E 0.94 0.20 0.00
81_E 37_T 0.93 0.20 0.00
100_K 75_T 0.93 0.20 0.00
98_T 4_L 0.93 0.20 0.00
56_D 12_A 0.93 0.20 0.00
14_N 82_A 0.93 0.19 0.00
26_V 117_L 0.92 0.19 0.00
112_L 119_K 0.92 0.19 0.00
117_T 7_L 0.91 0.19 0.00
112_L 105_T 0.90 0.18 0.00
89_T 32_Q 0.90 0.18 0.00
12_D 21_I 0.88 0.17 0.00
103_T 63_V 0.87 0.17 0.00
36_Q 30_L 0.87 0.17 0.00
53_L 99_R 0.86 0.16 0.00
30_F 50_E 0.86 0.16 0.00
51_R 31_D 0.86 0.16 0.00
24_C 79_G 0.85 0.16 0.00
87_Q 88_L 0.85 0.16 0.00
103_T 58_S 0.84 0.15 0.00
110_V 90_N 0.84 0.15 0.00
117_T 12_A 0.84 0.15 0.00
86_H 71_A 0.84 0.15 0.00
112_L 6_V 0.84 0.15 0.00
53_L 8_P 0.83 0.15 0.00
118_P 47_R 0.83 0.15 0.00
116_P 65_F 0.83 0.15 0.00
71_K 50_E 0.83 0.15 0.00
53_L 7_L 0.83 0.15 0.00
30_F 22_W 0.83 0.15 0.00
30_F 43_F 0.83 0.15 0.00
30_F 59_L 0.83 0.15 0.00
50_I 9_G 0.82 0.15 0.00
69_L 44_A 0.82 0.15 0.00
26_V 24_I 0.82 0.14 0.00
57_A 12_A 0.81 0.14 0.00
37_E 70_Y 0.81 0.14 0.00
109_Y 33_H 0.81 0.14 0.00
75_L 32_Q 0.80 0.14 0.00
65_A 57_I 0.80 0.14 0.00
24_C 32_Q 0.79 0.14 0.00
49_G 44_A 0.79 0.14 0.00
110_V 78_P 0.79 0.13 0.00
118_P 13_S 0.79 0.13 0.00
17_R 31_D 0.79 0.13 0.00
55_S 12_A 0.79 0.13 0.00
116_P 62_A 0.78 0.13 0.00
83_N 81_S 0.78 0.13 0.00
97_L 61_D 0.78 0.13 0.00
107_C 11_A 0.78 0.13 0.00
92_L 22_W 0.78 0.13 0.00
92_L 43_F 0.78 0.13 0.00
92_L 59_L 0.78 0.13 0.00
118_P 88_L 0.78 0.13 0.00
95_K 51_Q 0.77 0.13 0.00
86_H 14_S 0.77 0.13 0.00
31_G 3_T 0.77 0.13 0.00
76_M 61_D 0.77 0.13 0.00
27_T 5_P 0.76 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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