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OPENSEQ.org
IscRIscU
Genes: A B A+B
Length: 162 128 272
Sequences: 5205 2384 592
Seq/Len: 32.13 18.62 2.18
MirrorTree (Pazo et al. 2001) 0.68
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 0.14
2 0.01 0.00 1.32
5 0.01 0.00 1.95
10 0.02 0.00 2.04
20 0.02 0.01 2.09
100 0.03 0.01 2.46
∞ 0.10 0.02 4.68
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
123_N 84_E 1.02 0.58 0.00
78_E 108_I 0.99 0.54 0.00
82_A 56_A 0.98 0.53 0.00
82_A 47_V 0.96 0.51 0.00
39_L 13_N 0.94 0.48 0.00
75_A 81_S 0.92 0.46 0.00
36_G 49_D 0.92 0.46 0.00
66_L 22_N 0.90 0.43 0.00
125_T 104_I 0.89 0.42 0.00
9_Y 108_I 0.84 0.37 0.00
56_S 55_D 0.84 0.37 0.00
102_D 20_F 0.84 0.37 0.00
35_Q 116_A 0.83 0.36 0.00
125_T 87_A 0.82 0.35 0.00
134_E 125_R 0.81 0.34 0.00
26_V 119_A 0.81 0.34 0.00
12_T 31_M 0.80 0.33 0.00
99_Q 54_E 0.79 0.32 0.00
139_S 52_I 0.78 0.31 0.00
17_V 86_Q 0.78 0.31 0.00
32_S 19_S 0.78 0.30 0.00
51_K 124_K 0.77 0.30 0.00
31_I 82_L 0.77 0.30 0.00
22_E 88_I 0.77 0.30 0.00
37_I 82_L 0.76 0.29 0.00
133_Q 111_E 0.76 0.29 0.00
122_N 45_I 0.75 0.28 0.00
45_L 2_A 0.75 0.28 0.00
84_D 91_T 0.75 0.28 0.00
32_S 119_A 0.75 0.28 0.00
118_T 73_V 0.74 0.28 0.00
121_L 114_I 0.74 0.27 0.00
46_F 72_L 0.74 0.27 0.00
108_A 20_F 0.74 0.27 0.00
52_N 21_D 0.73 0.26 0.00
70_D 49_D 0.72 0.26 0.00
24_G 119_A 0.72 0.26 0.00
55_V 114_I 0.72 0.26 0.00
109_L 72_L 0.72 0.25 0.00
78_E 77_V 0.72 0.25 0.00
113_L 53_I 0.71 0.25 0.00
34_R 95_E 0.71 0.25 0.00
52_N 84_E 0.71 0.25 0.00
50_R 10_H 0.71 0.24 0.00
22_E 50_E 0.71 0.24 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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