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OPENSEQ.org
DivK-DivLHK
Genes: A B A+B
Length: 125 249 357
Sequences: 89670 83656 33527
Seq/Len: 717.36 335.97 93.91
MirrorTree (Pazo et al. 2001) 1.03
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 0.11 0.04 72.84
2 0.13 0.07 77.42
5 0.16 0.11 81.34
10 0.19 0.14 85.26
20 0.23 0.18 89.64
100 0.31 0.28 99.99
∞ 0.34 0.32 102.53
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
17_L 41_G 1.92 1.00 0.98
13_L 66_A 1.66 1.00 0.95
14_N 37_T 1.62 1.00 0.95
16_K 62_A 1.50 1.00 0.92
16_K 58_N 1.50 1.00 0.92
20_D 59_H 1.49 1.00 0.92
13_L 65_A 1.44 1.00 0.90
13_L 62_A 1.30 0.99 0.84
109_V 44_E 1.16 0.97 0.74
24_A 49_A 1.14 0.97 0.71
108_S 44_E 1.09 0.96 0.67
13_L 38_T 1.06 0.95 0.64
21_L 45_L 1.00 0.92 0.57
17_L 42_Y 0.95 0.89 0.51
24_A 48_R 0.94 0.89 0.49
110_V 48_R 0.90 0.86 0.45
20_D 55_R 0.89 0.85 0.44
108_S 68_T 0.84 0.80 0.37
11_N 38_T 0.82 0.78 0.35
23_E 55_R 0.79 0.74 0.32
20_D 45_L 0.72 0.64 0.24
11_N 69_Q 0.71 0.62 0.23
14_N 38_T 0.68 0.58 0.20
16_K 42_Y 0.67 0.56 0.19
109_V 48_R 0.64 0.51 0.16
110_V 44_E 0.63 0.49 0.16
108_S 40_I 0.61 0.45 0.14
25_Q 48_R 0.58 0.41 0.12
17_L 38_T 0.55 0.35 0.10
17_L 45_L 0.54 0.34 0.09
21_L 48_R 0.54 0.33 0.09
86_A 75_D 0.52 0.31 0.08
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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