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OPENSEQ.org
3ABO-2
Genes: A B A+B
Length: 249 122 354
Sequences: 83500 89235 33924
Seq/Len: 335.34 731.43 95.83
MirrorTree (Pazo et al. 2001) 1.07
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 0.04 0.11 74.52
2 0.07 0.13 79.23
5 0.11 0.16 83.12
10 0.14 0.19 86.99
20 0.18 0.23 91.44
100 0.28 0.31 101.65
∞ 0.32 0.34 104.12
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
40_A 17_I 1.96 1.00 0.98
67_Q 13_V 1.68 1.00 0.96
36_T 14_L 1.61 1.00 0.95
59_E 16_K 1.51 1.00 0.93
63_V 16_K 1.45 1.00 0.91
60_F 20_F 1.43 1.00 0.90
66_D 13_V 1.41 0.99 0.89
63_V 13_V 1.25 0.98 0.81
48_S 24_K 1.16 0.97 0.74
43_E 108_S 1.14 0.97 0.72
43_E 109_P 1.11 0.96 0.69
44_T 21_N 1.03 0.94 0.61
37_A 13_V 1.02 0.93 0.60
47_N 24_K 1.02 0.93 0.60
41_Y 17_I 0.95 0.89 0.51
47_N 110_S 0.93 0.88 0.49
37_A 11_S 0.84 0.80 0.38
56_T 20_F 0.83 0.79 0.37
69_N 108_S 0.82 0.78 0.36
56_T 23_K 0.81 0.76 0.34
70_H 11_S 0.77 0.72 0.30
37_A 14_L 0.72 0.64 0.24
44_T 20_F 0.69 0.58 0.21
43_E 110_S 0.67 0.55 0.19
41_Y 16_K 0.65 0.53 0.18
39_K 108_S 0.58 0.40 0.12
47_N 109_P 0.58 0.40 0.12
36_T 107_F 0.55 0.35 0.10
37_A 17_I 0.54 0.34 0.10
47_N 25_E 0.54 0.34 0.10
47_N 21_N 0.53 0.33 0.09
32_R 84_A 0.53 0.32 0.09
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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