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OPENSEQ.org
IscRIscA
Genes: A B A+B
Length: 162 107 257
Sequences: 5205 2921 425
Seq/Len: 32.13 27.3 1.65
MirrorTree (Pazo et al. 2001) 0.67
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 0.01 0.00 0.06
2 0.01 0.00 0.17
5 0.01 0.01 1.16
10 0.02 0.01 1.58
20 0.02 0.02 1.63
100 0.03 0.03 2.14
∞ 0.10 0.09 4.69
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_M 75_T 1.52 0.89 0.30
80_I 62_V 1.41 0.83 0.23
89_A 42_L 1.22 0.69 0.13
9_Y 41_V 1.19 0.66 0.12
36_G 97_D 1.14 0.61 0.10
52_N 79_F 1.13 0.61 0.10
125_T 47_E 1.12 0.59 0.10
78_E 14_N 1.12 0.59 0.10
61_P 77_L 1.11 0.59 0.09
76_V 49_T 1.09 0.56 0.09
24_G 107_V 1.09 0.56 0.09
5_S 12_R 1.06 0.53 0.08
82_A 63_V 0.97 0.44 0.06
57_S 68_S 0.97 0.43 0.06
88_D 83_G 0.94 0.41 0.05
70_D 50_P 0.93 0.40 0.05
23_A 28_L 0.92 0.39 0.05
29_A 27_R 0.91 0.38 0.04
56_S 47_E 0.91 0.38 0.04
115_D 79_F 0.89 0.36 0.04
6_K 22_K 0.89 0.35 0.04
4_T 69_L 0.88 0.35 0.04
117_L 106_H 0.88 0.34 0.04
116_R 26_L 0.88 0.34 0.04
100_G 7_D 0.88 0.34 0.04
51_K 72_L 0.87 0.34 0.04
19_L 6_S 0.87 0.33 0.04
137_D 64_V 0.86 0.33 0.04
14_M 5_L 0.86 0.32 0.04
117_L 3_I 0.85 0.32 0.04
17_V 28_L 0.85 0.31 0.03
136_L 56_E 0.84 0.31 0.03
140_G 50_P 0.83 0.30 0.03
79_V 8_S 0.83 0.30 0.03
146_D 6_S 0.83 0.30 0.03
128_E 16_F 0.83 0.30 0.03
91_R 63_V 0.83 0.30 0.03
108_A 28_L 0.82 0.29 0.03
96_G 62_V 0.82 0.29 0.03
146_D 18_A 0.82 0.29 0.03
79_V 44_F 0.82 0.29 0.03
72_S 2_S 0.82 0.29 0.03
125_T 44_F 0.81 0.28 0.03
134_E 72_L 0.81 0.28 0.03
40_S 103_E 0.81 0.28 0.03
23_A 11_A 0.80 0.28 0.03
15_L 95_V 0.80 0.28 0.03
48_R 80_V 0.80 0.27 0.03
65_Y 79_F 0.80 0.27 0.03
85_E 85_N 0.80 0.27 0.03
146_D 79_F 0.79 0.27 0.03
53_G 25_G 0.79 0.26 0.03
97_G 58_K 0.79 0.26 0.03
23_A 59_G 0.78 0.26 0.03
117_L 41_V 0.78 0.26 0.03
136_L 67_K 0.78 0.25 0.03
122_N 15_T 0.78 0.25 0.03
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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