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OPENSEQ.org
TA_six
Genes: A B A+B
Length: 86 92 173
Sequences: 1328 2849 604
Seq/Len: 15.44 30.97 3.49
MirrorTree (Pazo et al. 2001) 0.63
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 0.01 0.01 3.39
2 0.01 0.03 3.40
5 0.02 0.04 3.44
10 0.03 0.05 3.50
20 0.03 0.06 3.58
100 0.05 0.08 3.80
∞ 0.08 0.12 4.38
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_T 83_R 1.92 1.00 0.97
83_K 8_Y 1.91 1.00 0.97
65_S 9_S 1.76 0.99 0.95
73_K 7_E 1.67 0.99 0.94
66_E 73_K 1.54 0.97 0.90
81_F 30_K 1.54 0.97 0.90
62_I 59_Y 1.46 0.96 0.87
57_L 11_Q 1.37 0.94 0.82
66_E 59_Y 1.19 0.86 0.69
78_D 30_K 1.17 0.84 0.67
84_L 16_V 1.15 0.83 0.65
80_L 8_Y 1.14 0.82 0.63
49_F 64_V 1.14 0.82 0.63
85_G 16_V 1.07 0.76 0.56
55_N 83_R 1.05 0.75 0.55
74_A 8_Y 1.02 0.72 0.51
65_S 80_R 1.02 0.71 0.50
78_D 48_K 1.01 0.71 0.50
58_T 15_D 1.01 0.70 0.49
66_E 58_G 1.00 0.69 0.48
65_S 82_E 0.97 0.65 0.44
68_G 9_S 0.96 0.65 0.43
75_K 5_D 0.95 0.64 0.43
78_D 34_T 0.90 0.57 0.36
55_N 15_D 0.90 0.57 0.36
20_A 27_N 0.85 0.51 0.31
64_N 9_S 0.85 0.51 0.31
72_H 16_V 0.84 0.50 0.30
59_I 56_W 0.83 0.48 0.28
34_V 86_T 0.81 0.46 0.26
57_L 83_R 0.81 0.46 0.26
85_G 20_Q 0.81 0.45 0.26
84_L 33_M 0.81 0.45 0.26
61_S 9_S 0.78 0.42 0.23
73_K 5_D 0.76 0.40 0.22
85_G 3_Q 0.75 0.39 0.21
80_L 7_E 0.75 0.38 0.21
7_V 75_T 0.75 0.38 0.20
50_D 41_L 0.72 0.34 0.18
77_A 34_T 0.71 0.34 0.17
77_A 16_V 0.71 0.34 0.17
36_I 72_Y 0.70 0.33 0.17
56_Q 48_K 0.70 0.33 0.17
85_G 30_K 0.69 0.31 0.15
63_K 55_S 0.67 0.29 0.14
81_F 86_T 0.67 0.28 0.14
31_S 59_Y 0.66 0.28 0.13
46_A 71_I 0.66 0.27 0.13
77_A 37_I 0.66 0.27 0.13
80_L 16_V 0.65 0.27 0.13
68_G 3_Q 0.65 0.27 0.13
14_D 34_T 0.65 0.27 0.12
76_D 13_S 0.64 0.26 0.12
14_D 58_G 0.64 0.26 0.12
71_V 9_S 0.63 0.24 0.11
51_L 31_Y 0.62 0.24 0.11
62_I 56_W 0.62 0.24 0.11
9_A 7_E 0.62 0.24 0.11
72_H 37_I 0.61 0.23 0.10
40_K 56_W 0.61 0.23 0.10
72_H 79_L 0.61 0.23 0.10
68_G 82_E 0.61 0.23 0.10
55_N 44_P 0.60 0.22 0.10
24_A 22_R 0.60 0.22 0.10
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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