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OPENSEQ.org
2qam_X_T
Genes: A B A+B
Length: 63 100 157
Sequences: 1921 2676 1811
Seq/Len: 30.49 26.76 11.54
MirrorTree (Pazo et al. 2001) 0.62
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 0.09 0.08 0.01
2 0.09 0.08 0.02
5 0.09 0.08 0.72
10 0.09 0.08 11.04
20 0.09 0.08 11.11
100 0.09 0.08 11.15
∞ 0.09 0.08 11.34
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
22_L 9_K 2.23 1.00 0.99
34_S 95_F 1.20 0.98 0.79
23_R 8_L 1.13 0.97 0.73
26_F 51_F 0.93 0.88 0.51
30_M 14_P 0.82 0.78 0.38
38_Q 89_E 0.81 0.77 0.36
21_L 43_I 0.81 0.77 0.36
3_A 11_L 0.75 0.68 0.28
54_K 33_K 0.75 0.68 0.28
29_R 12_R 0.70 0.60 0.23
26_F 11_L 0.69 0.59 0.22
44_K 24_M 0.69 0.59 0.22
57_L 82_K 0.68 0.57 0.21
34_S 96_V 0.66 0.54 0.19
40_S 25_E 0.62 0.48 0.16
27_N 50_L 0.62 0.48 0.16
47_R 18_E 0.61 0.46 0.15
34_S 69_R 0.60 0.43 0.14
31_Q 69_R 0.57 0.38 0.12
25_Q 12_R 0.56 0.38 0.12
32_A 13_A 0.56 0.37 0.11
34_S 91_Q 0.56 0.37 0.11
10_S 41_A 0.55 0.36 0.11
49_D 11_L 0.55 0.36 0.11
14_L 34_V 0.55 0.35 0.10
6_L 17_S 0.53 0.33 0.10
32_A 29_T 0.53 0.32 0.09
22_L 11_L 0.52 0.30 0.09
44_K 44_K 0.52 0.30 0.09
33_A 40_K 0.51 0.30 0.09
19_L 49_K 0.51 0.30 0.08
35_G 68_K 0.51 0.29 0.08
48_R 76_R 0.51 0.29 0.08
5_E 80_W 0.51 0.29 0.08
49_D 49_K 0.51 0.29 0.08
44_K 13_A 0.50 0.28 0.08
38_Q 96_V 0.50 0.28 0.08
31_Q 51_F 0.49 0.27 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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