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OPENSEQ.org
TsaD-vs-L20
Genes: A B A+B
Length: 337 118 446
Sequences: 3839 1984 1286
Seq/Len: 11.39 16.81 2.88
MirrorTree (Pazo et al. 2001) 0.22
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 0.07 0.10 0.00
2 0.07 0.10 0.00
5 0.08 0.10 0.02
10 0.08 0.10 0.04
20 0.08 0.10 0.09
100 0.08 0.10 0.43
∞ 0.11 0.10 2.83
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
52_V 25_Y 1.12 0.76 0.03
46_L 12_A 1.01 0.64 0.02
265_M 88_V 0.98 0.61 0.02
166_F 28_R 0.96 0.58 0.02
108_P 109_L 0.91 0.53 0.02
183_L 17_I 0.89 0.50 0.02
236_A 84_K 0.89 0.50 0.02
245_D 52_Q 0.87 0.48 0.02
94_V 38_A 0.81 0.40 0.01
108_P 12_A 0.79 0.38 0.01
114_G 35_A 0.78 0.36 0.01
70_A 79_F 0.77 0.36 0.01
198_P 24_Y 0.75 0.33 0.01
171_K 40_I 0.74 0.33 0.01
76_V 109_L 0.74 0.33 0.01
20_D 59_Q 0.74 0.32 0.01
166_F 8_V 0.74 0.32 0.01
142_L 114_K 0.74 0.32 0.01
263_L 63_A 0.73 0.32 0.01
171_K 94_I 0.72 0.30 0.01
235_I 18_L 0.71 0.30 0.01
96_R 90_I 0.71 0.29 0.01
290_V 19_K 0.71 0.29 0.01
19_D 24_Y 0.71 0.29 0.01
197_F 40_I 0.68 0.27 0.01
171_K 91_D 0.68 0.27 0.01
63_L 110_V 0.68 0.27 0.01
235_I 108_A 0.67 0.26 0.01
299_T 14_H 0.67 0.26 0.01
237_R 113_A 0.66 0.25 0.01
103_D 79_F 0.66 0.25 0.01
169_T 71_Q 0.65 0.24 0.01
149_G 14_H 0.65 0.24 0.01
220_N 109_L 0.65 0.23 0.01
50_D 43_G 0.65 0.23 0.01
259_G 90_I 0.65 0.23 0.01
219_A 79_F 0.64 0.23 0.01
48_S 77_S 0.64 0.23 0.01
236_A 51_R 0.63 0.22 0.01
150_Q 98_I 0.63 0.22 0.01
290_V 31_V 0.62 0.21 0.01
187_A 1_M 0.62 0.21 0.01
251_C 68_A 0.62 0.21 0.01
48_S 31_V 0.62 0.21 0.01
59_I 53_R 0.62 0.21 0.01
34_K 17_I 0.62 0.21 0.01
216_T 51_R 0.62 0.21 0.01
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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