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OPENSEQ.org
1GRN
Genes: A B A+B
Length: 245 122 352
Sequences: 64784 54266 25129
Seq/Len: 264.42 444.8 71.39
MirrorTree (Pazo et al. 2001) 1.10
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 0.03 0.04 60.24
2 0.05 0.06 62.92
5 0.07 0.09 65.06
10 0.10 0.12 66.82
20 0.13 0.16 68.47
100 0.23 0.25 72.82
∞ 0.28 0.30 73.92
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
27_A 17_I 2.17 1.00 0.99
46_E 16_K 1.86 1.00 0.98
23_T 14_L 1.76 1.00 0.97
54_Q 13_V 1.69 1.00 0.96
30_E 108_S 1.69 1.00 0.96
53_D 13_V 1.62 1.00 0.95
47_F 20_F 1.48 1.00 0.92
50_V 13_V 1.29 0.99 0.84
31_T 21_N 1.26 0.99 0.83
35_S 24_K 1.25 0.98 0.82
50_V 16_K 1.12 0.96 0.72
43_T 23_K 1.00 0.92 0.59
24_A 11_S 0.98 0.92 0.57
34_N 110_S 0.98 0.92 0.57
28_Y 17_I 0.97 0.91 0.56
43_T 20_F 0.93 0.88 0.51
30_E 109_P 0.92 0.88 0.50
34_N 24_K 0.90 0.85 0.46
24_A 13_V 0.88 0.84 0.45
24_A 14_L 0.88 0.84 0.44
23_T 107_F 0.83 0.79 0.38
56_N 108_S 0.79 0.74 0.33
34_N 25_E 0.76 0.70 0.30
70_R 86_G 0.73 0.65 0.26
57_H 11_S 0.70 0.61 0.23
34_N 21_N 0.65 0.53 0.18
19_R 104_R 0.65 0.52 0.18
43_T 24_K 0.64 0.50 0.17
26_K 108_S 0.63 0.49 0.17
30_E 110_S 0.60 0.43 0.14
31_T 20_F 0.58 0.41 0.13
24_A 17_I 0.57 0.39 0.12
34_N 113_I 0.52 0.31 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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