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OPENSEQ.org
Y_vs_A
Genes: A B A+B
Length: 118 105 220
Sequences: 88238 1448 941
Seq/Len: 747.78 13.79 4.28
MirrorTree (Pazo et al. 2001) 0.59
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 0.11 0.00 1.70
2 0.13 0.00 2.74
5 0.16 0.00 3.29
10 0.19 0.01 3.84
20 0.23 0.01 4.22
100 0.31 0.02 4.59
∞ 0.34 0.09 4.72
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
60_L 20_L 1.12 0.85 0.09
9_S 66_T 1.11 0.84 0.09
68_A 82_Q 0.98 0.73 0.06
99_G 53_G 0.95 0.70 0.06
36_A 91_F 0.94 0.68 0.05
64_K 80_E 0.93 0.67 0.05
98_S 71_N 0.90 0.64 0.05
93_A 21_A 0.89 0.62 0.04
38_N 103_D 0.87 0.60 0.04
116_K 29_V 0.85 0.57 0.04
91_A 64_E 0.84 0.55 0.04
47_F 105_Y 0.81 0.52 0.03
114_L 5_I 0.81 0.51 0.03
73_S 55_G 0.80 0.51 0.03
14_I 56_T 0.80 0.50 0.03
50_S 90_L 0.73 0.41 0.03
101_V 68_L 0.73 0.41 0.03
51_D 45_R 0.73 0.40 0.02
49_I 90_L 0.72 0.40 0.02
102_V 23_M 0.72 0.40 0.02
25_N 36_D 0.72 0.40 0.02
114_L 68_L 0.71 0.39 0.02
63_L 71_N 0.71 0.39 0.02
77_V 93_E 0.71 0.38 0.02
100_Y 11_T 0.71 0.38 0.02
61_E 86_D 0.70 0.37 0.02
36_A 50_I 0.70 0.37 0.02
24_F 58_G 0.70 0.36 0.02
10_T 56_T 0.70 0.36 0.02
101_V 25_Q 0.69 0.36 0.02
79_M 47_A 0.69 0.36 0.02
81_T 15_E 0.69 0.36 0.02
35_D 75_E 0.69 0.35 0.02
52_W 40_L 0.69 0.35 0.02
36_A 89_N 0.68 0.35 0.02
35_D 10_Q 0.68 0.34 0.02
90_I 7_D 0.67 0.34 0.02
58_D 13_F 0.67 0.33 0.02
5_V 49_S 0.67 0.32 0.02
49_I 21_A 0.66 0.32 0.02
36_A 30_L 0.66 0.32 0.02
81_T 50_I 0.65 0.31 0.02
110_L 58_G 0.65 0.30 0.02
48_V 32_P 0.65 0.30 0.02
80_V 24_E 0.65 0.30 0.02
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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