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OPENSEQ.org
narl
Genes: A B A+B
Length: 64 112 176
Sequences: 308 85878 246
Seq/Len: 4.81 766.77 1.4
MirrorTree (Pazo et al. 2001) 0.36
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.10 1.18
2 0.00 0.13 1.20
5 0.00 0.15 1.23
10 0.00 0.18 1.30
20 0.00 0.23 1.40
100 0.00 0.31 1.78
∞ 0.08 0.34 1.97
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
31_G 77_V 1.41 0.80 0.04
40_E 37_I 1.41 0.79 0.04
55_Q 87_V 1.40 0.79 0.04
22_M 1_I 1.35 0.75 0.04
37_S 19_S 1.27 0.69 0.03
3_A 111_A 1.26 0.68 0.03
5_I 14_V 1.19 0.61 0.02
28_Q 36_G 1.18 0.60 0.02
46_R 36_G 1.18 0.60 0.02
38_S 79_S 1.15 0.58 0.02
13_I 82_N 1.10 0.52 0.02
22_M 109_L 1.09 0.52 0.02
45_I 72_S 1.09 0.52 0.02
29_M 92_K 1.07 0.49 0.02
47_N 77_V 1.03 0.46 0.01
26_C 20_M 1.01 0.43 0.01
25_S 90_A 1.00 0.42 0.01
37_S 14_V 0.99 0.41 0.01
54_A 109_L 0.97 0.40 0.01
53_W 33_G 0.95 0.37 0.01
32_D 31_S 0.95 0.37 0.01
49_L 32_N 0.94 0.37 0.01
41_L 77_V 0.93 0.35 0.01
46_R 74_R 0.92 0.34 0.01
30_Q 75_I 0.91 0.34 0.01
30_Q 110_K 0.91 0.34 0.01
21_K 112_L 0.91 0.34 0.01
22_M 3_L 0.91 0.34 0.01
41_L 93_R 0.91 0.33 0.01
3_A 61_E 0.90 0.33 0.01
41_L 68_E 0.90 0.33 0.01
50_N 28_G 0.90 0.33 0.01
52_S 102_D 0.90 0.33 0.01
18_S 47_L 0.90 0.33 0.01
37_S 36_G 0.90 0.32 0.01
37_S 25_T 0.89 0.32 0.01
7_R 76_V 0.89 0.32 0.01
53_W 80_V 0.89 0.32 0.01
41_L 64_D 0.89 0.32 0.01
32_D 66_L 0.88 0.31 0.01
49_L 104_E 0.88 0.31 0.01
55_Q 10_L 0.87 0.30 0.01
43_S 68_E 0.86 0.30 0.01
42_L 50_L 0.86 0.29 0.01
55_Q 8_P 0.85 0.29 0.01
32_D 25_T 0.85 0.28 0.01
28_Q 54_M 0.85 0.28 0.01
18_S 96_D 0.85 0.28 0.01
31_G 86_D 0.84 0.28 0.01
4_T 31_S 0.84 0.28 0.01
56_L 102_D 0.83 0.27 0.01
47_N 110_K 0.83 0.27 0.01
60_L 48_I 0.82 0.26 0.01
44_Q 16_Q 0.82 0.26 0.01
12_S 94_G 0.82 0.26 0.01
58_E 45_P 0.82 0.26 0.01
55_Q 4_I 0.81 0.25 0.01
18_S 33_G 0.80 0.25 0.01
28_Q 23_D 0.80 0.25 0.01
59_L 11_R 0.80 0.25 0.01
29_M 37_I 0.80 0.24 0.01
38_S 109_L 0.80 0.24 0.01
3_A 47_L 0.80 0.24 0.01
1_E 51_D 0.80 0.24 0.01
1_E 59_G 0.80 0.24 0.01
1_E 101_K 0.80 0.24 0.01
10_H 51_D 0.80 0.24 0.01
10_H 59_G 0.80 0.24 0.01
10_H 101_K 0.80 0.24 0.01
11_D 51_D 0.80 0.24 0.01
11_D 59_G 0.80 0.24 0.01
11_D 101_K 0.80 0.24 0.01
15_Q 51_D 0.80 0.24 0.01
15_Q 59_G 0.80 0.24 0.01
15_Q 101_K 0.80 0.24 0.01
57_R 51_D 0.80 0.24 0.01
57_R 59_G 0.80 0.24 0.01
57_R 101_K 0.80 0.24 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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