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OPENSEQ.org
TsaB-TsaD
Genes: A B A+B
Length: 231 337 555
Sequences: 3108 3839 1861
Seq/Len: 13.45 11.39 3.35
MirrorTree (Pazo et al. 2001) 0.40
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.07 0.08
2 0.00 0.07 1.21
5 0.00 0.08 1.57
10 0.00 0.08 1.63
20 0.00 0.08 1.66
100 0.00 0.08 1.80
∞ 0.00 0.11 3.28
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
43_Q 100_F 3.17 1.00 1.00
83_L 60_Q 2.26 1.00 0.99
84_G 101_A 1.69 0.99 0.95
81_L 101_A 1.57 0.97 0.93
39_L 97_S 1.51 0.97 0.91
43_Q 103_D 1.51 0.97 0.91
83_L 56_V 1.40 0.94 0.87
214_E 53_R 1.35 0.93 0.84
80_G 59_I 1.35 0.93 0.84
80_G 94_V 1.34 0.92 0.83
211_E 60_Q 1.29 0.90 0.80
53_L 100_F 1.26 0.89 0.78
86_E 60_Q 1.18 0.84 0.71
84_G 98_L 1.14 0.81 0.68
84_G 97_S 1.14 0.81 0.68
77_I 93_T 1.12 0.80 0.66
39_L 100_F 1.11 0.79 0.65
227_L 38_D 1.00 0.68 0.52
35_T 89_L 0.97 0.64 0.48
74_G 234_D 0.95 0.63 0.47
123_Y 31_S 0.93 0.60 0.44
46_L 100_F 0.92 0.58 0.42
80_G 97_S 0.91 0.57 0.41
76_G 93_T 0.90 0.56 0.40
227_L 39_Y 0.90 0.55 0.39
47_T 284_K 0.89 0.55 0.39
75_I 52_V 0.87 0.52 0.36
79_Q 116_L 0.87 0.52 0.36
76_G 94_V 0.84 0.48 0.33
81_L 97_S 0.84 0.48 0.32
81_L 100_F 0.83 0.47 0.32
83_L 59_I 0.82 0.46 0.31
77_I 97_S 0.82 0.46 0.31
53_L 103_D 0.79 0.42 0.27
84_G 102_W 0.79 0.42 0.27
35_T 158_I 0.79 0.42 0.27
83_L 94_V 0.77 0.40 0.25
2_R 61_A 0.77 0.39 0.25
66_G 240_E 0.76 0.38 0.23
60_A 265_M 0.75 0.37 0.23
66_G 269_V 0.74 0.36 0.22
52_S 103_D 0.74 0.35 0.21
172_D 280_A 0.73 0.35 0.21
219_R 108_P 0.72 0.34 0.20
96_M 152_E 0.71 0.32 0.19
9_A 19_D 0.70 0.32 0.18
69_T 89_L 0.70 0.32 0.18
39_L 93_T 0.70 0.31 0.18
54_T 71_K 0.70 0.31 0.18
3_I 98_L 0.69 0.30 0.17
115_I 154_L 0.69 0.30 0.17
59_L 218_A 0.69 0.30 0.17
87_L 73_I 0.69 0.30 0.17
54_T 103_D 0.68 0.29 0.16
81_L 275_L 0.67 0.28 0.16
86_E 72_D 0.67 0.28 0.16
119_M 50_D 0.67 0.28 0.16
10_T 89_L 0.67 0.28 0.16
15_V 233_A 0.67 0.28 0.16
221_N 46_L 0.67 0.28 0.15
89_M 108_P 0.67 0.28 0.15
53_L 101_A 0.66 0.27 0.15
24_N 46_L 0.66 0.27 0.15
145_K 17_I 0.66 0.27 0.15
87_L 226_G 0.66 0.27 0.14
206_K 72_D 0.65 0.26 0.14
80_G 98_L 0.64 0.25 0.14
76_G 52_V 0.64 0.25 0.13
81_L 290_V 0.63 0.24 0.13
89_M 142_L 0.63 0.24 0.13
211_E 39_Y 0.63 0.24 0.13
12_A 99_A 0.63 0.24 0.13
5_A 75_A 0.63 0.24 0.13
81_L 90_V 0.63 0.24 0.13
23_V 216_T 0.63 0.24 0.12
71_V 93_T 0.63 0.24 0.12
90_I 92_A 0.63 0.24 0.12
97_T 310_M 0.62 0.24 0.12
114_A 176_D 0.62 0.23 0.12
44_D 71_K 0.62 0.23 0.12
53_L 16_A 0.62 0.23 0.12
118_R 113_E 0.61 0.23 0.12
59_L 279_L 0.61 0.23 0.12
73_I 85_V 0.61 0.22 0.11
198_A 283_M 0.61 0.22 0.11
68_F 262_R 0.61 0.22 0.11
75_I 236_A 0.61 0.22 0.11
96_M 207_L 0.61 0.22 0.11
68_F 50_D 0.61 0.22 0.11
17_L 17_I 0.61 0.22 0.11
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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