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OPENSEQ.org
TsaD-vs-L5
Genes: A B A+B
Length: 337 179 511
Sequences: 3839 2042 1261
Seq/Len: 11.39 11.41 2.47
MirrorTree (Pazo et al. 2001) 0.36
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 0.09 0.00
2 0.07 0.09 0.00
5 0.08 0.09 0.00
10 0.08 0.09 0.00
20 0.08 0.09 0.03
100 0.08 0.09 0.54
∞ 0.11 0.09 2.44
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
270_S 83_Y 0.96 0.54 0.00
18_Y 74_V 0.95 0.54 0.00
264_V 74_V 0.90 0.46 0.00
114_G 102_R 0.88 0.45 0.00
50_D 46_D 0.88 0.45 0.00
29_L 55_A 0.88 0.45 0.00
118_A 129_S 0.87 0.44 0.00
207_L 25_V 0.87 0.43 0.00
293_A 20_F 0.85 0.41 0.00
239_F 70_A 0.83 0.38 0.00
48_S 117_L 0.82 0.38 0.00
277_A 21_N 0.82 0.38 0.00
141_Q 46_D 0.81 0.37 0.00
151_Y 143_Y 0.81 0.37 0.00
293_A 162_S 0.81 0.36 0.00
261_K 21_N 0.80 0.35 0.00
270_S 69_K 0.79 0.35 0.00
236_A 135_Q 0.79 0.34 0.00
157_S 3_K 0.78 0.33 0.00
92_A 69_K 0.78 0.33 0.00
157_S 20_F 0.78 0.33 0.00
220_N 12_V 0.76 0.32 0.00
39_Y 129_S 0.76 0.32 0.00
48_S 178_R 0.76 0.32 0.00
263_L 66_L 0.75 0.31 0.00
48_S 43_A 0.75 0.31 0.00
214_L 115_R 0.75 0.30 0.00
74_D 121_S 0.74 0.30 0.00
104_V 159_T 0.73 0.28 0.00
224_D 59_A 0.71 0.27 0.00
25_L 75_A 0.71 0.27 0.00
92_A 159_T 0.71 0.27 0.00
149_G 143_Y 0.71 0.27 0.00
120_M 97_W 0.71 0.27 0.00
24_L 27_Q 0.71 0.26 0.00
153_L 95_R 0.70 0.26 0.00
128_F 24_S 0.70 0.26 0.00
222_I 61_S 0.69 0.25 0.00
81_G 53_A 0.69 0.25 0.00
255_L 112_R 0.69 0.24 0.00
265_M 100_F 0.69 0.24 0.00
150_Q 31_V 0.68 0.24 0.00
275_L 64_K 0.68 0.24 0.00
97_S 104_I 0.68 0.23 0.00
151_Y 83_Y 0.67 0.23 0.00
293_A 22_Y 0.67 0.23 0.00
162_A 27_Q 0.67 0.23 0.00
266_A 111_I 0.66 0.22 0.00
195_F 117_L 0.66 0.22 0.00
131_V 47_K 0.66 0.22 0.00
143_I 40_V 0.66 0.22 0.00
32_Q 139_P 0.65 0.22 0.00
25_L 129_S 0.65 0.21 0.00
110_H 152_L 0.65 0.21 0.00
73_I 147_D 0.64 0.21 0.00
24_L 98_E 0.64 0.21 0.00
97_S 57_L 0.64 0.21 0.00
85_V 93_G 0.64 0.21 0.00
96_R 60_I 0.64 0.21 0.00
287_R 154_I 0.64 0.20 0.00
256_D 17_M 0.64 0.20 0.00
148_I 175_F 0.63 0.20 0.00
171_K 150_R 0.63 0.20 0.00
78_Y 136_I 0.63 0.20 0.00
73_I 146_V 0.63 0.20 0.00
130_F 149_V 0.63 0.20 0.00
192_A 106_I 0.63 0.20 0.00
238_A 9_K 0.62 0.19 0.00
112_M 145_K 0.62 0.19 0.00
48_S 26_M 0.62 0.19 0.00
20_D 132_V 0.62 0.19 0.00
78_Y 24_S 0.62 0.19 0.00
58_L 148_R 0.62 0.19 0.00
181_P 153_D 0.62 0.19 0.00
173_L 118_S 0.62 0.19 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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