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OPENSEQ.org
IscAIscX
Genes: A B A+B
Length: 107 66 173
Sequences: 2921 320 190
Seq/Len: 27.3 4.85 1.1
MirrorTree (Pazo et al. 2001) 0.34
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 0.03
5 0.01 0.00 1.05
10 0.01 0.00 1.10
20 0.02 0.00 1.09
100 0.03 0.00 1.14
∞ 0.09 0.00 1.42
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
8_S 3_L 1.55 0.82 0.06
3_I 63_D 1.40 0.72 0.04
49_T 60_V 1.28 0.62 0.03
56_E 22_L 1.23 0.57 0.03
106_H 2_G 1.18 0.53 0.02
33_S 63_D 1.16 0.51 0.02
72_L 63_D 1.15 0.50 0.02
49_T 36_I 1.13 0.48 0.02
38_M 34_Q 1.13 0.48 0.02
106_H 45_D 1.12 0.48 0.02
11_A 19_Y 1.10 0.45 0.02
26_L 8_S 1.08 0.43 0.02
31_R 59_L 1.07 0.42 0.01
12_R 27_V 1.06 0.42 0.01
8_S 14_A 1.06 0.42 0.01
38_M 9_R 1.04 0.40 0.01
4_T 63_D 1.01 0.38 0.01
79_F 52_K 1.00 0.36 0.01
81_K 33_H 0.98 0.35 0.01
8_S 1_M 0.98 0.35 0.01
66_G 58_L 0.96 0.33 0.01
48_P 10_E 0.95 0.32 0.01
96_K 12_G 0.92 0.30 0.01
19_N 60_V 0.92 0.30 0.01
66_G 60_V 0.91 0.29 0.01
14_N 10_E 0.91 0.29 0.01
18_A 37_C 0.91 0.28 0.01
12_R 59_L 0.90 0.28 0.01
8_S 36_I 0.89 0.27 0.01
97_D 9_R 0.88 0.27 0.01
19_N 40_E 0.88 0.26 0.01
50_P 27_V 0.87 0.25 0.01
66_G 50_N 0.86 0.25 0.01
98_E 25_K 0.86 0.25 0.01
6_S 63_D 0.86 0.25 0.01
64_V 65_A 0.86 0.25 0.01
2_S 59_L 0.85 0.24 0.01
89_K 37_C 0.84 0.24 0.01
49_T 19_Y 0.84 0.24 0.01
89_K 40_E 0.83 0.23 0.01
65_D 52_K 0.83 0.23 0.01
8_S 59_L 0.82 0.22 0.01
63_V 59_L 0.82 0.22 0.01
87_G 11_I 0.81 0.22 0.01
85_N 31_D 0.81 0.22 0.01
75_T 43_D 0.81 0.22 0.01
80_V 53_I 0.81 0.21 0.01
63_V 58_L 0.81 0.21 0.01
95_V 21_D 0.80 0.21 0.01
95_V 57_I 0.80 0.21 0.01
95_V 14_A 0.80 0.21 0.01
19_N 48_A 0.80 0.21 0.01
72_L 49_S 0.78 0.20 0.01
6_S 13_E 0.78 0.20 0.01
5_L 50_N 0.77 0.19 0.01
7_D 35_W 0.77 0.19 0.01
5_L 60_V 0.76 0.19 0.01
31_R 36_I 0.76 0.18 0.01
45_V 25_K 0.76 0.18 0.01
3_I 41_D 0.76 0.18 0.01
79_F 46_P 0.76 0.18 0.01
80_V 37_C 0.75 0.18 0.01
68_S 24_P 0.75 0.18 0.01
72_L 33_H 0.75 0.18 0.01
17_L 33_H 0.75 0.18 0.01
2_S 19_Y 0.75 0.18 0.01
81_K 41_D 0.74 0.17 0.01
53_I 1_M 0.74 0.17 0.01
49_T 40_E 0.74 0.17 0.01
4_T 59_L 0.74 0.17 0.01
44_F 3_L 0.73 0.17 0.01
6_S 50_N 0.73 0.17 0.01
44_F 62_L 0.73 0.17 0.01
6_S 65_A 0.73 0.17 0.01
57_D 16_Y 0.73 0.17 0.01
26_L 28_R 0.73 0.17 0.00
79_F 32_M 0.72 0.16 0.00
98_E 19_Y 0.72 0.16 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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