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OPENSEQ.org
L4-vs-TsaA
Genes: A B A+B
Length: 201 231 428
Sequences: 3177 3108 1326
Seq/Len: 15.81 13.45 3.1
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 0.08 0.00 0.00
2 0.08 0.00 0.00
5 0.08 0.00 0.00
10 0.09 0.00 0.02
20 0.09 0.00 0.03
100 0.09 0.00 0.69
∞ 0.09 0.00 3.07
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
44_R 78_A 1.10 0.76 0.03
122_E 98_M 1.09 0.75 0.03
85_F 89_M 1.05 0.71 0.03
28_V 197_I 0.99 0.65 0.02
73_I 81_L 0.95 0.59 0.02
179_S 74_G 0.94 0.58 0.02
162_R 122_V 0.92 0.56 0.02
56_G 80_G 0.88 0.51 0.02
161_A 98_M 0.88 0.51 0.02
10_S 82_A 0.85 0.47 0.01
106_K 3_I 0.84 0.46 0.01
109_L 87_L 0.82 0.43 0.01
28_V 59_L 0.82 0.43 0.01
120_V 21_G 0.81 0.43 0.01
77_I 189_P 0.80 0.41 0.01
85_F 39_L 0.79 0.40 0.01
192_A 40_P 0.78 0.39 0.01
86_A 30_C 0.78 0.39 0.01
186_V 216_V 0.78 0.38 0.01
29_H 68_F 0.77 0.37 0.01
98_K 194_M 0.77 0.37 0.01
154_D 97_T 0.76 0.37 0.01
184_D 115_I 0.76 0.36 0.01
181_I 88_P 0.75 0.36 0.01
196_V 23_V 0.75 0.36 0.01
23_F 219_R 0.75 0.36 0.01
49_R 95_L 0.75 0.36 0.01
12_L 163_V 0.73 0.33 0.01
188_M 18_W 0.73 0.33 0.01
140_D 197_I 0.73 0.33 0.01
188_M 75_I 0.72 0.32 0.01
109_L 70_G 0.71 0.31 0.01
27_L 220_N 0.71 0.31 0.01
113_V 56_I 0.71 0.31 0.01
90_Q 119_M 0.71 0.30 0.01
82_G 125_A 0.71 0.30 0.01
17_T 87_L 0.70 0.30 0.01
136_Q 45_I 0.70 0.30 0.01
64_G 116_D 0.70 0.30 0.01
57_K 118_R 0.70 0.29 0.01
162_R 197_I 0.69 0.29 0.01
195_Q 218_L 0.69 0.29 0.01
187_V 219_R 0.69 0.29 0.01
37_A 116_D 0.69 0.28 0.01
136_Q 43_Q 0.69 0.28 0.01
124_F 225_K 0.68 0.28 0.01
28_V 94_T 0.68 0.28 0.01
188_M 74_G 0.68 0.28 0.01
6_K 6_I 0.68 0.28 0.01
150_T 198_A 0.68 0.28 0.01
56_G 224_W 0.68 0.27 0.01
148_I 197_I 0.68 0.27 0.01
132_K 143_V 0.68 0.27 0.01
46_Q 14_S 0.67 0.27 0.01
97_N 222_V 0.67 0.27 0.01
141_M 110_R 0.67 0.27 0.01
153_L 17_L 0.67 0.27 0.01
188_M 9_A 0.67 0.26 0.01
35_Y 222_V 0.67 0.26 0.01
11_A 128_Q 0.67 0.26 0.01
87_A 119_M 0.67 0.26 0.01
98_K 210_V 0.66 0.26 0.01
28_V 213_A 0.66 0.26 0.01
16_E 172_D 0.66 0.25 0.01
106_K 91_G 0.66 0.25 0.01
187_V 98_M 0.65 0.25 0.01
106_K 17_L 0.65 0.25 0.01
156_N 117_A 0.65 0.24 0.01
14_V 12_A 0.65 0.24 0.01
124_F 192_E 0.65 0.24 0.01
120_V 69_T 0.65 0.24 0.01
194_K 41_M 0.65 0.24 0.01
77_I 73_I 0.64 0.24 0.01
98_K 126_E 0.64 0.24 0.01
51_E 42_V 0.64 0.24 0.01
32_V 49_S 0.64 0.23 0.01
97_N 80_G 0.64 0.23 0.01
175_I 128_Q 0.63 0.23 0.01
90_Q 194_M 0.63 0.23 0.01
61_R 113_A 0.63 0.23 0.01
174_G 71_V 0.63 0.23 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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