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OPENSEQ.org
L14-vs-TsaD
Genes: A B A+B
Length: 123 337 456
Sequences: 1778 3839 1393
Seq/Len: 14.46 11.39 3.05
MirrorTree (Pazo et al. 2001) 0.39
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 0.09 0.07 0.00
2 0.09 0.07 0.00
5 0.09 0.08 0.00
10 0.09 0.08 0.00
20 0.09 0.08 0.04
100 0.09 0.08 0.68
∞ 0.10 0.11 3.03
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
67_K 52_V 0.99 0.65 0.01
93_Q 157_S 0.95 0.59 0.01
83_A 181_P 0.94 0.58 0.01
68_G 52_V 0.89 0.52 0.01
62_V 297_F 0.87 0.50 0.01
97_T 173_L 0.87 0.49 0.01
34_G 146_T 0.86 0.48 0.01
86_L 53_R 0.85 0.47 0.01
99_I 242_A 0.84 0.45 0.01
94_P 198_P 0.82 0.44 0.01
52_V 243_V 0.82 0.43 0.00
87_L 270_S 0.80 0.40 0.00
72_P 235_I 0.79 0.40 0.00
31_R 153_L 0.79 0.39 0.00
94_P 275_L 0.78 0.38 0.00
59_K 131_V 0.74 0.34 0.00
62_V 120_M 0.74 0.34 0.00
77_I 271_A 0.73 0.33 0.00
94_P 217_F 0.73 0.32 0.00
87_L 250_K 0.72 0.32 0.00
88_N 283_M 0.72 0.32 0.00
94_P 242_A 0.72 0.32 0.00
62_V 322_G 0.71 0.31 0.00
88_N 290_V 0.71 0.30 0.00
57_V 205_P 0.71 0.30 0.00
112_F 69_T 0.71 0.30 0.00
84_C 162_A 0.70 0.30 0.00
123_L 3_V 0.70 0.29 0.00
93_Q 120_M 0.69 0.28 0.00
84_C 308_A 0.69 0.28 0.00
21_C 113_E 0.69 0.28 0.00
43_I 256_D 0.69 0.28 0.00
84_C 108_P 0.68 0.28 0.00
60_A 140_T 0.68 0.27 0.00
87_L 264_V 0.68 0.27 0.00
75_S 149_G 0.68 0.27 0.00
68_G 266_A 0.68 0.27 0.00
99_I 264_V 0.67 0.26 0.00
88_N 110_H 0.67 0.26 0.00
86_L 119_P 0.67 0.26 0.00
24_V 89_L 0.67 0.26 0.00
62_V 38_D 0.66 0.26 0.00
47_I 197_F 0.66 0.26 0.00
32_Y 35_L 0.66 0.26 0.00
51_K 134_L 0.66 0.25 0.00
19_V 128_F 0.66 0.25 0.00
39_I 59_I 0.66 0.25 0.00
116_I 176_D 0.65 0.25 0.00
118_L 114_G 0.65 0.25 0.00
17_R 65_E 0.65 0.25 0.00
99_I 187_A 0.65 0.25 0.00
30_R 171_K 0.65 0.24 0.00
80_D 309_G 0.64 0.23 0.00
14_S 102_W 0.64 0.23 0.00
66_K 34_K 0.64 0.23 0.00
14_S 253_R 0.63 0.23 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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