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OPENSEQ.org
DI1200003_1QFN
Genes: A B A+B
Length: 30 85 111
Sequences: 205 10186 177
Seq/Len: 6.83 119.84 1.59
MirrorTree (Pazo et al. 2001) 0.04
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.01 0.01
2 0.00 0.01 0.01
5 0.00 0.01 0.09
10 0.00 0.01 0.16
20 0.00 0.01 0.20
100 0.00 0.03 0.47
∞ 0.00 0.08 1.54
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
10_A 52_A 1.29 0.74 0.02
21_D 30_D 1.17 0.64 0.01
9_D 68_H 1.07 0.53 0.01
25_S 16_R 1.02 0.48 0.01
29_K 73_T 0.98 0.44 0.01
14_L 18_K 0.92 0.38 0.01
21_D 12_P 0.92 0.37 0.01
14_L 32_Q 0.92 0.37 0.01
9_D 30_D 0.92 0.37 0.01
16_P 69_I 0.89 0.35 0.01
14_L 22_E 0.87 0.32 0.01
25_S 65_D 0.86 0.32 0.01
22_G 12_P 0.85 0.31 0.01
8_E 20_L 0.83 0.29 0.01
19_Q 44_T 0.82 0.28 0.01
22_G 32_Q 0.82 0.28 0.01
18_I 38_I 0.82 0.28 0.01
26_G 30_D 0.81 0.27 0.01
1_Q 57_E 0.80 0.27 0.01
25_S 79_V 0.80 0.27 0.01
27_A 73_T 0.80 0.27 0.01
20_D 32_Q 0.79 0.26 0.00
13_D 54_K 0.79 0.26 0.00
25_S 22_E 0.79 0.26 0.00
12_D 19_D 0.76 0.24 0.00
1_Q 46_E 0.75 0.23 0.00
12_D 23_K 0.74 0.22 0.00
25_S 3_T 0.72 0.20 0.00
11_Q 17_A 0.72 0.20 0.00
12_D 36_V 0.71 0.20 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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