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OPENSEQ.org
4XGQ
Genes: A B A+B
Length: 84 131 209
Sequences: 263 9053 234
Seq/Len: 3.13 69.11 1.12
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 0.02 0.04 1.09
2 0.03 0.05 1.09
5 0.04 0.08 1.09
10 0.04 0.09 1.10
20 0.06 0.11 1.13
100 0.07 0.15 1.18
∞ 0.12 0.20 1.21
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
57_R 22_E 1.65 0.87 0.19
52_E 63_R 1.58 0.84 0.16
72_E 86_Y 1.40 0.73 0.10
59_R 56_E 1.28 0.62 0.07
56_I 63_R 1.17 0.53 0.05
26_T 1_M 1.13 0.48 0.04
28_A 45_I 1.09 0.45 0.04
59_R 59_L 1.08 0.44 0.04
2_A 61_L 1.06 0.42 0.03
29_V 116_K 1.05 0.41 0.03
61_A 18_A 1.04 0.40 0.03
17_L 77_D 1.01 0.38 0.03
51_D 78_A 1.01 0.38 0.03
46_V 86_Y 1.01 0.37 0.03
62_A 42_A 1.00 0.36 0.03
53_L 88_K 0.99 0.36 0.03
43_R 8_L 0.98 0.35 0.03
54_A 52_P 0.98 0.35 0.03
35_E 92_R 0.98 0.35 0.02
49_L 64_A 0.98 0.35 0.02
18_A 89_G 0.97 0.34 0.02
62_A 17_D 0.97 0.34 0.02
19_A 25_V 0.94 0.32 0.02
47_V 73_A 0.94 0.31 0.02
75_L 44_V 0.93 0.30 0.02
5_I 90_R 0.92 0.30 0.02
38_A 118_E 0.92 0.30 0.02
77_Y 75_Q 0.91 0.29 0.02
22_G 105_L 0.91 0.29 0.02
34_R 102_S 0.89 0.27 0.02
67_D 72_H 0.89 0.27 0.02
7_H 91_H 0.89 0.27 0.02
58_H 60_W 0.88 0.27 0.02
59_R 17_D 0.88 0.27 0.02
15_R 85_T 0.87 0.26 0.02
71_A 49_F 0.86 0.25 0.01
76_G 94_G 0.86 0.25 0.01
45_R 121_Q 0.85 0.25 0.01
53_L 22_E 0.85 0.25 0.01
24_T 63_R 0.84 0.24 0.01
2_A 81_A 0.84 0.24 0.01
39_R 57_L 0.84 0.24 0.01
22_G 7_A 0.84 0.24 0.01
53_L 9_V 0.84 0.24 0.01
63_L 53_G 0.83 0.23 0.01
25_L 18_A 0.83 0.23 0.01
25_L 66_V 0.83 0.23 0.01
61_A 45_I 0.83 0.23 0.01
66_V 48_R 0.82 0.23 0.01
78_D 9_V 0.82 0.23 0.01
48_P 63_R 0.82 0.22 0.01
24_T 102_S 0.82 0.22 0.01
37_L 90_R 0.81 0.22 0.01
75_L 47_A 0.81 0.22 0.01
21_T 116_K 0.81 0.21 0.01
9_E 98_G 0.80 0.21 0.01
14_A 1_M 0.80 0.21 0.01
54_A 72_H 0.79 0.20 0.01
36_R 24_A 0.79 0.20 0.01
55_A 31_R 0.79 0.20 0.01
61_A 17_D 0.79 0.20 0.01
70_S 16_P 0.79 0.20 0.01
83_P 68_L 0.79 0.20 0.01
20_R 42_A 0.78 0.20 0.01
53_L 69_V 0.78 0.20 0.01
31_T 70_A 0.78 0.20 0.01
2_A 94_G 0.78 0.20 0.01
29_V 12_L 0.77 0.19 0.01
18_A 97_Y 0.76 0.19 0.01
35_E 94_G 0.76 0.19 0.01
18_A 3_I 0.76 0.18 0.01
63_L 56_E 0.76 0.18 0.01
18_A 39_L 0.76 0.18 0.01
57_R 14_D 0.75 0.18 0.01
29_V 49_F 0.75 0.18 0.01
1_M 93_A 0.75 0.18 0.01
10_A 93_A 0.75 0.18 0.01
21_T 39_L 0.75 0.18 0.01
62_A 74_D 0.75 0.18 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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