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OPENSEQ.org
DI1210006_4ZOU
Genes: A B A+B
Length: 30 155 180
Sequences: 199 12080 56
Seq/Len: 6.63 77.94 0.31
MirrorTree (Pazo et al. 2001) 0.42
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 0.02 0.01
10 0.00 0.02 0.01
20 0.00 0.02 0.01
100 0.00 0.02 0.04
∞ 0.01 0.04 0.30
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
14_A 117_K 1.50 0.42 0.00
17_S 110_A 1.29 0.29 0.00
4_A 142_M 1.27 0.29 0.00
18_N 69_T 1.23 0.26 0.00
14_A 94_D 1.13 0.21 0.00
15_A 65_V 1.12 0.21 0.00
14_A 36_S 1.09 0.20 0.00
17_S 57_E 1.07 0.19 0.00
18_N 143_N 1.06 0.18 0.00
5_Q 25_I 1.04 0.17 0.00
13_P 132_R 1.02 0.17 0.00
4_A 84_N 1.01 0.16 0.00
12_A 147_E 1.00 0.16 0.00
26_D 16_N 1.00 0.16 0.00
14_A 92_T 1.00 0.16 0.00
17_S 106_R 0.99 0.16 0.00
3_G 39_Y 0.97 0.15 0.00
7_R 58_A 0.97 0.15 0.00
21_P 121_V 0.96 0.15 0.00
15_A 76_Q 0.96 0.15 0.00
9_Q 128_P 0.95 0.14 0.00
15_A 55_A 0.94 0.14 0.00
23_D 121_V 0.92 0.13 0.00
2_G 111_L 0.91 0.13 0.00
4_A 110_A 0.91 0.13 0.00
16_P 125_A 0.90 0.13 0.00
24_F 87_K 0.90 0.13 0.00
12_A 30_G 0.89 0.12 0.00
2_G 147_E 0.89 0.12 0.00
15_A 89_G 0.88 0.12 0.00
17_S 25_I 0.88 0.12 0.00
9_Q 96_K 0.87 0.12 0.00
8_P 136_L 0.86 0.12 0.00
13_P 117_K 0.86 0.12 0.00
10_Q 60_K 0.86 0.12 0.00
12_A 5_V 0.83 0.11 0.00
1_S 110_A 0.83 0.11 0.00
26_D 17_P 0.83 0.11 0.00
26_D 38_G 0.83 0.11 0.00
26_D 78_I 0.83 0.11 0.00
26_D 46_R 0.82 0.10 0.00
26_D 77_G 0.82 0.10 0.00
26_D 141_A 0.82 0.10 0.00
13_P 64_E 0.82 0.10 0.00
1_S 61_E 0.82 0.10 0.00
26_D 13_C 0.82 0.10 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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