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OPENSEQ.org
IscUIscX
Genes: A B A+B
Length: 128 66 192
Sequences: 2384 320 134
Seq/Len: 18.62 4.85 0.7
MirrorTree (Pazo et al. 2001) 0.41
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 0.00 0.01
2 0.00 0.00 0.01
5 0.00 0.00 0.64
10 0.00 0.00 0.69
20 0.01 0.00 0.71
100 0.01 0.00 0.73
∞ 0.02 0.00 0.94
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
73_V 63_D 1.95 0.90 0.37
108_I 17_D 1.70 0.80 0.22
108_I 63_D 1.69 0.79 0.21
108_I 13_E 1.57 0.72 0.15
108_I 58_L 1.56 0.71 0.15
108_I 59_L 1.52 0.68 0.13
91_T 9_R 1.48 0.65 0.12
86_Q 3_L 1.44 0.62 0.10
98_E 36_I 1.34 0.54 0.08
19_S 28_R 1.33 0.53 0.07
81_S 58_L 1.32 0.52 0.07
29_S 60_V 1.31 0.51 0.07
118_I 37_C 1.29 0.50 0.07
86_Q 1_M 1.26 0.47 0.06
28_G 21_D 1.21 0.43 0.05
88_I 35_W 1.19 0.41 0.04
45_I 21_D 1.18 0.40 0.04
8_I 53_I 1.17 0.39 0.04
104_I 60_V 1.15 0.38 0.04
47_V 21_D 1.14 0.37 0.04
87_A 25_K 1.09 0.34 0.03
45_I 52_K 1.09 0.33 0.03
26_N 52_K 1.08 0.33 0.03
13_N 63_D 1.08 0.33 0.03
22_N 3_L 1.05 0.31 0.03
42_K 28_R 1.04 0.30 0.03
8_I 3_L 1.04 0.30 0.03
118_I 53_I 1.02 0.28 0.02
19_S 30_T 1.01 0.27 0.02
73_V 28_R 1.00 0.27 0.02
92_D 50_N 0.99 0.26 0.02
28_G 63_D 0.98 0.26 0.02
95_E 12_G 0.98 0.26 0.02
123_S 10_E 0.98 0.26 0.02
27_V 38_D 0.97 0.25 0.02
119_A 63_D 0.97 0.25 0.02
119_A 62_L 0.96 0.24 0.02
50_E 48_A 0.92 0.22 0.02
19_S 8_S 0.92 0.22 0.02
95_E 48_A 0.91 0.21 0.01
22_N 30_T 0.91 0.21 0.01
92_D 10_E 0.91 0.21 0.01
83_D 41_D 0.91 0.21 0.01
84_E 49_S 0.91 0.21 0.01
116_A 44_D 0.90 0.21 0.01
83_D 65_A 0.89 0.20 0.01
26_N 33_H 0.88 0.20 0.01
50_E 38_D 0.88 0.20 0.01
29_S 8_S 0.88 0.20 0.01
57_R 35_W 0.88 0.20 0.01
45_I 48_A 0.88 0.19 0.01
92_D 9_R 0.87 0.19 0.01
119_A 53_I 0.87 0.19 0.01
119_A 59_L 0.87 0.19 0.01
5_E 60_V 0.86 0.18 0.01
28_G 59_L 0.84 0.18 0.01
122_K 38_D 0.84 0.17 0.01
52_I 36_I 0.84 0.17 0.01
52_I 22_L 0.84 0.17 0.01
47_V 13_E 0.83 0.17 0.01
42_K 30_T 0.82 0.17 0.01
61_Y 50_N 0.82 0.17 0.01
45_I 13_E 0.82 0.17 0.01
20_F 65_A 0.82 0.17 0.01
29_S 9_R 0.82 0.17 0.01
61_Y 25_K 0.82 0.17 0.01
50_E 25_K 0.82 0.17 0.01
123_S 48_A 0.81 0.17 0.01
95_E 47_Q 0.81 0.16 0.01
86_Q 41_D 0.81 0.16 0.01
11_Y 37_C 0.81 0.16 0.01
82_L 27_V 0.81 0.16 0.01
122_K 40_E 0.80 0.16 0.01
21_D 33_H 0.80 0.16 0.01
23_N 41_D 0.79 0.15 0.01
91_T 19_Y 0.79 0.15 0.01
55_D 12_G 0.79 0.15 0.01
73_V 26_T 0.78 0.15 0.01
31_M 48_A 0.77 0.15 0.01
51_G 53_I 0.77 0.15 0.01
88_I 22_L 0.77 0.14 0.01
28_G 49_S 0.77 0.14 0.01
87_A 49_S 0.77 0.14 0.01
46_K 16_Y 0.77 0.14 0.01
21_D 37_C 0.76 0.14 0.01
2_A 13_E 0.76 0.14 0.01
28_G 48_A 0.75 0.14 0.01
108_I 28_R 0.75 0.14 0.01
21_D 56_A 0.75 0.14 0.01
41_M 32_M 0.75 0.14 0.01
122_K 25_K 0.74 0.13 0.01
81_S 59_L 0.74 0.13 0.01
125_R 57_I 0.74 0.13 0.01
52_I 25_K 0.74 0.13 0.01
87_A 43_D 0.73 0.13 0.01
118_I 50_N 0.73 0.13 0.01
42_K 62_L 0.73 0.13 0.01
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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