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OPENSEQ.org
TsaB-vs-L5
Genes: A B A+B
Length: 231 179 406
Sequences: 3108 2042 1265
Seq/Len: 13.45 11.41 3.12
MirrorTree (Pazo et al. 2001) 0.69
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 0.09 0.00
2 0.00 0.09 0.00
5 0.00 0.09 0.00
10 0.00 0.09 0.00
20 0.00 0.09 0.02
100 0.00 0.09 0.71
∞ 0.00 0.09 3.09
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
68_F 147_D 1.08 0.74 0.03
34_H 73_S 1.08 0.74 0.03
79_Q 175_F 1.02 0.68 0.02
59_L 133_R 0.97 0.63 0.02
34_H 167_R 0.96 0.62 0.02
93_S 120_K 0.93 0.57 0.02
10_T 78_K 0.91 0.55 0.02
227_L 27_Q 0.88 0.52 0.01
142_A 71_R 0.88 0.51 0.01
207_T 75_A 0.85 0.47 0.01
66_G 22_Y 0.85 0.47 0.01
211_E 102_R 0.85 0.47 0.01
215_P 153_D 0.84 0.47 0.01
71_V 178_R 0.84 0.46 0.01
59_L 168_A 0.82 0.44 0.01
130_D 12_V 0.82 0.43 0.01
224_W 50_L 0.81 0.43 0.01
223_A 133_R 0.81 0.43 0.01
66_G 29_P 0.81 0.42 0.01
86_E 57_L 0.80 0.41 0.01
26_H 71_R 0.80 0.41 0.01
119_M 157_T 0.79 0.40 0.01
120_G 152_L 0.77 0.38 0.01
76_G 24_S 0.77 0.38 0.01
225_K 51_D 0.77 0.38 0.01
227_L 102_R 0.77 0.38 0.01
5_A 152_L 0.77 0.37 0.01
55_D 12_V 0.76 0.36 0.01
90_I 166_G 0.75 0.36 0.01
91_G 103_L 0.75 0.35 0.01
109_T 146_V 0.75 0.35 0.01
23_V 61_S 0.74 0.35 0.01
151_E 28_V 0.74 0.35 0.01
74_G 81_Q 0.74 0.34 0.01
35_T 162_S 0.74 0.34 0.01
213_A 35_T 0.73 0.34 0.01
45_I 174_D 0.73 0.34 0.01
71_V 76_G 0.73 0.33 0.01
53_L 34_I 0.73 0.33 0.01
219_R 38_M 0.73 0.33 0.01
162_T 111_I 0.72 0.33 0.01
121_E 43_A 0.72 0.32 0.01
213_A 51_D 0.72 0.32 0.01
20_D 34_I 0.72 0.32 0.01
8_T 142_D 0.72 0.32 0.01
221_N 46_D 0.71 0.31 0.01
219_R 87_C 0.71 0.31 0.01
56_I 45_A 0.71 0.31 0.01
130_D 67_I 0.71 0.31 0.01
99_A 68_T 0.71 0.31 0.01
46_L 57_L 0.71 0.31 0.01
34_H 103_L 0.70 0.30 0.01
46_L 105_T 0.70 0.30 0.01
61_Y 83_Y 0.70 0.30 0.01
73_I 32_E 0.69 0.29 0.01
80_G 42_E 0.69 0.29 0.01
124_W 71_R 0.69 0.29 0.01
68_F 24_S 0.69 0.29 0.01
85_A 87_C 0.69 0.29 0.01
12_A 153_D 0.69 0.29 0.01
218_L 32_E 0.69 0.29 0.01
167_W 163_D 0.69 0.29 0.01
11_E 34_I 0.69 0.28 0.01
218_L 153_D 0.68 0.28 0.01
5_A 156_I 0.68 0.28 0.01
115_I 78_K 0.68 0.28 0.01
113_A 175_F 0.68 0.28 0.01
45_I 79_I 0.68 0.28 0.01
13_C 134_E 0.68 0.28 0.01
53_L 171_A 0.68 0.28 0.01
11_E 35_T 0.68 0.28 0.01
73_I 94_E 0.68 0.27 0.01
219_R 132_V 0.67 0.27 0.01
125_A 22_Y 0.67 0.27 0.01
116_D 38_M 0.67 0.27 0.01
13_C 88_K 0.67 0.27 0.01
219_R 153_D 0.67 0.27 0.01
31_P 42_E 0.67 0.27 0.01
164_G 47_K 0.67 0.26 0.01
59_L 47_K 0.67 0.26 0.01
126_E 159_T 0.66 0.26 0.01
1_M 167_R 0.66 0.26 0.01
7_D 74_V 0.66 0.26 0.01
75_I 76_G 0.66 0.26 0.01
91_G 37_N 0.66 0.26 0.01
46_L 84_P 0.66 0.26 0.01
112_L 171_A 0.66 0.26 0.01
218_L 74_V 0.66 0.26 0.01
189_P 88_K 0.66 0.26 0.01
230_K 100_F 0.66 0.26 0.01
161_V 119_A 0.66 0.25 0.01
49_S 56_D 0.66 0.25 0.01
50_G 104_I 0.65 0.25 0.01
188_L 12_V 0.65 0.25 0.01
165_T 104_I 0.65 0.25 0.01
90_I 84_P 0.65 0.25 0.01
74_G 111_I 0.65 0.25 0.01
76_G 132_V 0.65 0.25 0.01
56_I 129_S 0.65 0.25 0.01
163_V 94_E 0.65 0.25 0.01
88_P 84_P 0.65 0.24 0.01
123_Y 152_L 0.65 0.24 0.01
173_L 154_I 0.65 0.24 0.01
119_M 175_F 0.64 0.24 0.01
192_E 25_V 0.64 0.24 0.01
219_R 73_S 0.64 0.24 0.01
73_I 156_I 0.64 0.24 0.01
56_I 67_I 0.64 0.24 0.01
28_E 68_T 0.64 0.24 0.01
163_V 4_L 0.64 0.24 0.01
100_Q 57_L 0.64 0.24 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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