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OPENSEQ.org
2NUU-3
Genes: A B A+B
Length: 409 112 509
Sequences: 4091 2544 1446
Seq/Len: 10 22.71 2.84
MirrorTree (Pazo et al. 2001) 0.26
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 0.02 0.04 2.69
2 0.04 0.06 2.76
5 0.04 0.06 2.75
10 0.05 0.06 2.77
20 0.05 0.06 2.78
100 0.06 0.07 2.85
∞ 0.13 0.19 3.28
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
391_E 85_K 1.36 0.91 0.40
245_I 8_I 0.90 0.51 0.10
301_G 99_V 0.82 0.41 0.07
308_L 79_K 0.80 0.39 0.07
252_E 44_E 0.74 0.32 0.05
127_R 18_E 0.71 0.29 0.04
317_V 55_F 0.70 0.29 0.04
286_G 96_L 0.69 0.27 0.04
120_G 108_D 0.69 0.27 0.04
33_L 76_I 0.68 0.26 0.04
378_K 61_I 0.67 0.25 0.04
246_L 93_V 0.67 0.25 0.04
389_P 61_I 0.67 0.25 0.04
41_G 48_G 0.66 0.24 0.04
375_I 107_A 0.66 0.24 0.04
378_K 59_V 0.65 0.23 0.03
253_W 40_K 0.65 0.23 0.03
46_S 17_R 0.63 0.22 0.03
70_A 110_A 0.63 0.22 0.03
378_K 85_K 0.63 0.22 0.03
57_L 75_D 0.63 0.21 0.03
162_L 100_I 0.63 0.21 0.03
270_A 62_D 0.62 0.21 0.03
187_K 14_E 0.62 0.21 0.03
41_G 31_T 0.62 0.21 0.03
72_G 96_L 0.62 0.21 0.03
313_D 44_E 0.62 0.21 0.03
196_F 61_I 0.61 0.20 0.03
129_S 8_I 0.61 0.20 0.03
120_G 90_K 0.61 0.20 0.03
320_V 28_L 0.61 0.20 0.03
262_L 46_Y 0.61 0.20 0.03
330_I 74_I 0.61 0.20 0.03
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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