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OPENSEQ.org
2B3T-2
Genes: A B A+B
Length: 274 355 607
Sequences: 4481 3375 2086
Seq/Len: 16.35 9.51 3.44
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 0.01 0.08 3.06
2 0.01 0.08 3.21
5 0.01 0.08 3.28
10 0.01 0.08 3.31
20 0.01 0.08 3.32
100 0.02 0.10 3.43
∞ 0.11 0.14 4.08
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
223_S 215_P 0.87 0.53 0.00
266_N 235_T 0.84 0.49 0.00
113_L 240_I 0.83 0.48 0.00
165_S 22_A 0.78 0.41 0.00
38_I 173_F 0.77 0.41 0.00
93_D 217_D 0.73 0.35 0.00
75_E 261_K 0.71 0.33 0.00
229_S 326_D 0.71 0.33 0.00
273_R 285_A 0.65 0.26 0.00
190_D 173_F 0.64 0.26 0.00
125_A 260_H 0.64 0.25 0.00
116_G 232_H 0.62 0.24 0.00
138_V 97_L 0.62 0.24 0.00
197_D 293_L 0.62 0.23 0.00
87_T 92_L 0.58 0.20 0.00
261_R 223_F 0.58 0.20 0.00
29_H 263_K 0.58 0.20 0.00
58_L 125_G 0.58 0.20 0.00
77_W 261_K 0.57 0.20 0.00
60_R 336_L 0.56 0.18 0.00
96_C 113_A 0.55 0.18 0.00
208_A 152_H 0.55 0.17 0.00
265_D 352_L 0.54 0.17 0.00
129_E 96_L 0.54 0.17 0.00
254_Y 114_G 0.54 0.17 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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