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OPENSEQ.org
2b3t_B_A
Genes: A B A+B
Length: 360 276 609
Sequences: 3364 4434 2063
Seq/Len: 9.34 16.07 3.39
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 0.01 3.01
2 0.08 0.01 3.15
5 0.08 0.01 3.20
10 0.08 0.01 3.23
20 0.08 0.01 3.24
100 0.10 0.02 3.34
∞ 0.14 0.11 4.01
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
239_T 267_N 0.88 0.53 0.00
219_P 224_S 0.87 0.52 0.00
244_I 114_L 0.81 0.45 0.00
265_K 76_E 0.78 0.41 0.00
221_D 94_D 0.74 0.36 0.00
177_F 191_D 0.73 0.35 0.00
177_F 39_I 0.72 0.34 0.00
330_D 230_S 0.68 0.29 0.00
26_A 166_S 0.65 0.27 0.00
236_H 117_G 0.64 0.25 0.00
297_L 198_D 0.63 0.24 0.00
267_K 30_H 0.62 0.24 0.00
264_H 126_A 0.62 0.23 0.00
156_H 209_A 0.61 0.23 0.00
101_L 139_V 0.61 0.23 0.00
23_L 160_N 0.61 0.22 0.00
328_R 94_D 0.60 0.22 0.00
289_A 274_R 0.60 0.21 0.00
221_D 187_I 0.59 0.21 0.00
91_Q 104_A 0.57 0.19 0.00
227_F 262_R 0.56 0.18 0.00
340_L 61_R 0.56 0.18 0.00
96_L 88_T 0.56 0.18 0.00
98_V 187_I 0.55 0.18 0.00
118_G 255_Y 0.55 0.18 0.00
118_G 62_R 0.55 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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