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OPENSEQ.org
6151
Genes: A B A+B
Length: 83 95 170
Sequences: 2210 4400 1162
Seq/Len: 26.63 46.32 6.84
MirrorTree (Pazo et al. 2001) 0.73
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 0.02 6.53
2 0.01 0.03 6.60
5 0.02 0.04 6.71
10 0.03 0.05 6.76
20 0.03 0.06 6.87
100 0.05 0.08 7.17
∞ 0.10 0.13 8.10
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
70_S 65_Q 2.26 1.00 0.99
81_S 2_T 2.19 1.00 0.99
79_L 7_F 1.30 0.97 0.85
76_D 4_T 1.26 0.97 0.82
63_V 47_L 1.23 0.96 0.81
69_R 76_V 1.21 0.96 0.80
72_Q 10_D 1.15 0.94 0.75
76_D 6_K 1.06 0.90 0.66
63_V 50_C 0.98 0.84 0.56
69_R 50_C 0.97 0.83 0.55
70_S 50_C 0.92 0.79 0.50
57_L 46_G 0.92 0.79 0.49
79_L 31_K 0.91 0.78 0.48
61_E 13_K 0.89 0.76 0.45
74_L 8_R 0.87 0.73 0.42
67_T 50_C 0.86 0.73 0.42
65_L 77_A 0.86 0.72 0.41
56_A 52_K 0.83 0.68 0.38
62_L 63_V 0.81 0.66 0.35
55_D 37_P 0.80 0.65 0.34
62_L 80_K 0.79 0.63 0.33
14_S 14_E 0.79 0.63 0.33
17_K 54_K 0.79 0.63 0.33
64_K 10_D 0.79 0.62 0.33
54_L 62_L 0.79 0.62 0.33
64_K 8_R 0.75 0.57 0.28
68_E 10_D 0.74 0.56 0.27
46_P 75_V 0.72 0.53 0.25
6_L 83_R 0.72 0.52 0.25
78_D 4_T 0.71 0.51 0.24
16_L 37_P 0.70 0.49 0.22
29_G 25_Q 0.69 0.47 0.22
70_S 9_D 0.68 0.46 0.21
55_D 47_L 0.68 0.46 0.21
69_R 8_R 0.68 0.46 0.21
79_L 27_V 0.68 0.45 0.20
66_V 63_V 0.68 0.45 0.20
21_M 81_R 0.66 0.44 0.19
17_K 75_V 0.66 0.43 0.19
43_Y 15_W 0.66 0.43 0.19
68_E 17_K 0.66 0.43 0.19
62_L 55_L 0.66 0.43 0.19
62_L 81_R 0.65 0.42 0.18
55_D 44_L 0.65 0.42 0.18
29_G 66_V 0.65 0.41 0.18
77_V 7_F 0.65 0.41 0.18
20_P 54_K 0.65 0.41 0.17
15_E 4_T 0.64 0.41 0.17
36_N 78_V 0.64 0.40 0.17
8_D 86_V 0.63 0.39 0.17
46_P 23_Q 0.63 0.39 0.17
17_K 64_Y 0.63 0.39 0.16
38_N 33_C 0.63 0.39 0.16
40_P 81_R 0.63 0.38 0.16
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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