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OPENSEQ.org
5201
Genes: A B A+B
Length: 96 73 150
Sequences: 3934 1989 745
Seq/Len: 40.98 27.25 4.97
MirrorTree (Pazo et al. 2001) 0.65
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 4.41
2 0.02 0.02 4.43
5 0.02 0.03 4.47
10 0.03 0.03 4.51
20 0.03 0.04 4.58
100 0.06 0.06 4.88
∞ 0.11 0.10 6.16
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
84_H 52_Q 1.21 0.93 0.27
55_Q 29_Y 1.12 0.88 0.21
46_Q 49_T 1.08 0.86 0.19
43_S 44_Q 1.08 0.85 0.19
53_V 70_K 1.06 0.84 0.18
21_E 20_D 1.03 0.81 0.16
27_A 29_Y 1.01 0.80 0.15
39_Q 49_T 0.98 0.77 0.14
77_M 14_N 0.94 0.72 0.12
16_T 63_K 0.91 0.69 0.11
56_P 40_L 0.86 0.63 0.09
63_R 56_D 0.85 0.62 0.09
29_L 14_N 0.84 0.60 0.09
10_W 65_L 0.84 0.60 0.09
52_G 36_A 0.83 0.58 0.08
73_K 28_M 0.82 0.58 0.08
85_I 38_Y 0.82 0.57 0.08
63_R 33_F 0.81 0.57 0.08
46_Q 46_K 0.80 0.55 0.07
54_T 39_V 0.80 0.55 0.07
53_V 13_Y 0.80 0.55 0.07
67_Q 39_V 0.78 0.52 0.07
70_S 29_Y 0.78 0.51 0.07
80_H 58_A 0.77 0.50 0.06
5_T 55_V 0.76 0.49 0.06
64_G 50_T 0.76 0.49 0.06
18_E 56_D 0.76 0.48 0.06
45_A 25_Y 0.75 0.48 0.06
62_A 17_A 0.75 0.47 0.06
19_Q 13_Y 0.74 0.47 0.06
36_W 14_N 0.74 0.46 0.06
37_I 17_A 0.73 0.45 0.06
56_P 41_H 0.73 0.44 0.05
32_I 29_Y 0.72 0.44 0.05
35_N 60_R 0.72 0.43 0.05
49_S 16_A 0.72 0.43 0.05
7_D 57_L 0.71 0.42 0.05
44_Q 29_Y 0.71 0.41 0.05
55_Q 16_A 0.71 0.41 0.05
18_E 68_E 0.71 0.41 0.05
18_E 60_R 0.70 0.40 0.05
51_L 25_Y 0.69 0.39 0.04
51_L 6_F 0.69 0.39 0.04
59_S 60_R 0.69 0.39 0.04
47_A 11_S 0.69 0.39 0.04
59_S 61_R 0.69 0.39 0.04
32_I 54_D 0.69 0.39 0.04
69_F 28_M 0.69 0.38 0.04
28_E 22_D 0.68 0.38 0.04
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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