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OPENSEQ.org
L4-vs-TsaD
Genes: A B A+B
Length: 201 337 534
Sequences: 3177 3839 1458
Seq/Len: 15.81 11.39 2.73
MirrorTree (Pazo et al. 2001) 0.46
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 0.07 0.00
2 0.08 0.07 0.00
5 0.08 0.08 0.01
10 0.09 0.08 0.02
20 0.09 0.08 0.04
100 0.09 0.08 0.62
∞ 0.09 0.11 2.71
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
162_R 73_I 0.97 0.58 0.00
175_I 275_L 0.85 0.43 0.00
44_R 110_H 0.81 0.39 0.00
193_V 169_T 0.80 0.38 0.00
175_I 140_T 0.79 0.37 0.00
123_K 146_T 0.78 0.36 0.00
156_N 152_E 0.78 0.36 0.00
200_L 183_L 0.78 0.36 0.00
196_V 107_I 0.77 0.35 0.00
164_L 284_K 0.76 0.33 0.00
26_A 120_M 0.74 0.31 0.00
116_D 97_S 0.74 0.31 0.00
106_K 216_T 0.74 0.31 0.00
144_E 76_V 0.73 0.30 0.00
165_H 23_G 0.73 0.30 0.00
15_S 216_T 0.71 0.28 0.00
38_G 17_I 0.70 0.27 0.00
50_A 20_D 0.69 0.27 0.00
20_G 143_I 0.69 0.26 0.00
80_S 97_S 0.68 0.25 0.00
193_V 64_K 0.67 0.24 0.00
189_T 94_V 0.67 0.24 0.00
30_Q 134_L 0.67 0.24 0.00
139_K 61_A 0.66 0.24 0.00
115_Q 281_E 0.66 0.24 0.00
199_M 114_G 0.66 0.24 0.00
22_D 147_G 0.66 0.23 0.00
105_L 131_V 0.66 0.23 0.00
97_N 246_T 0.65 0.23 0.00
18_T 238_A 0.65 0.23 0.00
110_S 293_A 0.65 0.23 0.00
158_F 185_K 0.65 0.23 0.00
157_L 153_L 0.65 0.23 0.00
118_L 76_V 0.64 0.22 0.00
164_L 327_P 0.64 0.22 0.00
187_V 283_M 0.64 0.22 0.00
187_V 64_K 0.64 0.22 0.00
28_V 59_I 0.64 0.22 0.00
41_Q 184_S 0.63 0.21 0.00
85_F 231_T 0.62 0.20 0.00
142_A 112_M 0.61 0.20 0.00
160_A 158_I 0.61 0.20 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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