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OPENSEQ.org
4eb7_C_A
Genes: A B A+B
Length: 153 382 491
Sequences: 1952 19192 1705
Seq/Len: 12.76 50.24 3.47
MirrorTree (Pazo et al. 2001) 0.81
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 0.01 0.03 3.06
2 0.01 0.03 3.11
5 0.01 0.05 3.16
10 0.01 0.06 3.16
20 0.01 0.07 3.19
100 0.01 0.12 3.31
∞ 0.03 0.21 3.57
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
96_P 31_P 0.81 0.45 0.00
53_F 203_P 0.78 0.42 0.00
52_K 57_N 0.74 0.36 0.00
51_I 53_A 0.73 0.36 0.00
97_K 238_P 0.72 0.35 0.00
32_V 327_Q 0.69 0.30 0.00
43_V 22_P 0.68 0.29 0.00
68_A 17_L 0.65 0.27 0.00
34_G 302_E 0.63 0.25 0.00
42_K 357_E 0.63 0.24 0.00
68_A 322_S 0.62 0.24 0.00
26_G 317_T 0.62 0.24 0.00
34_G 300_E 0.61 0.23 0.00
43_V 70_T 0.61 0.23 0.00
14_R 52_V 0.60 0.22 0.00
30_N 99_M 0.60 0.22 0.00
66_S 34_V 0.60 0.22 0.00
10_F 369_V 0.59 0.21 0.00
32_V 337_L 0.59 0.21 0.00
13_P 203_P 0.58 0.20 0.00
81_L 35_H 0.58 0.20 0.00
12_N 183_V 0.57 0.19 0.00
45_D 64_V 0.57 0.19 0.00
47_R 15_R 0.56 0.19 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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