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OPENSEQ.org
5208
Genes: A B A+B
Length: 80 96 165
Sequences: 1342 4470 660
Seq/Len: 16.77 46.56 4
MirrorTree (Pazo et al. 2001) 0.62
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 0.01 3.75
2 0.01 0.03 3.79
5 0.02 0.04 3.82
10 0.03 0.05 3.83
20 0.03 0.06 3.90
100 0.05 0.08 4.22
∞ 0.09 0.13 4.86
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
55_E 77_A 1.54 0.98 0.85
59_L 50_C 1.51 0.98 0.84
65_R 8_D 1.39 0.96 0.77
63_R 65_S 1.34 0.94 0.72
54_S 10_R 1.30 0.93 0.70
63_R 50_C 1.29 0.93 0.69
62_V 76_I 1.16 0.87 0.56
73_I 6_A 1.03 0.77 0.42
62_V 8_D 1.03 0.76 0.42
56_E 47_L 1.00 0.73 0.39
52_S 14_E 0.92 0.64 0.30
52_S 77_A 0.92 0.64 0.30
46_V 20_V 0.89 0.60 0.27
72_A 15_W 0.86 0.56 0.24
63_R 49_D 0.84 0.54 0.23
8_L 9_P 0.83 0.53 0.23
62_V 74_L 0.83 0.53 0.22
22_K 30_L 0.83 0.52 0.22
56_E 63_V 0.82 0.51 0.21
68_N 8_D 0.82 0.51 0.21
26_T 22_V 0.81 0.49 0.20
17_Y 24_E 0.76 0.43 0.16
45_P 64_Y 0.75 0.41 0.16
28_T 5_L 0.75 0.41 0.16
76_R 9_P 0.74 0.41 0.15
33_L 33_V 0.74 0.40 0.15
26_T 71_L 0.73 0.39 0.15
64_E 48_P 0.71 0.37 0.13
22_K 69_K 0.70 0.35 0.13
73_I 31_E 0.69 0.33 0.12
46_V 55_L 0.69 0.33 0.12
66_L 8_D 0.68 0.33 0.11
33_L 64_Y 0.68 0.33 0.11
64_E 28_K 0.68 0.32 0.11
75_V 5_L 0.68 0.32 0.11
15_E 30_L 0.67 0.32 0.11
57_A 3_Y 0.67 0.32 0.11
14_N 5_L 0.67 0.32 0.11
29_E 71_L 0.66 0.31 0.10
65_R 14_E 0.66 0.30 0.10
9_D 73_V 0.64 0.29 0.10
78_D 27_K 0.64 0.28 0.09
42_G 66_V 0.64 0.28 0.09
3_T 82_E 0.63 0.27 0.09
20_L 7_F 0.63 0.27 0.09
44_M 72_L 0.62 0.27 0.09
78_D 5_L 0.62 0.26 0.09
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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