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OPENSEQ.org
2807
Genes: A B A+B
Length: 138 56 157
Sequences: 1041 259 259
Seq/Len: 7.54 4.62 1.65
MirrorTree (Pazo et al. 2001) 0.70
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 0.00 1.34
2 0.01 0.00 1.34
5 0.02 0.00 1.34
10 0.02 0.00 1.34
20 0.02 0.00 1.34
100 0.03 0.01 1.34
∞ 0.07 0.02 1.36
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
54_C 31_L 1.59 0.92 0.46
38_D 35_R 1.46 0.86 0.35
129_F 14_K 1.43 0.84 0.33
47_N 29_Q 1.39 0.82 0.30
42_L 26_S 1.35 0.80 0.27
58_T 36_E 1.21 0.68 0.18
25_Q 35_R 1.17 0.64 0.16
55_A 34_I 1.16 0.63 0.15
28_E 25_F 1.14 0.61 0.14
43_N 26_S 1.13 0.60 0.14
41_L 26_S 1.10 0.57 0.13
107_V 14_K 1.01 0.47 0.09
50_L 31_L 1.00 0.47 0.09
37_V 41_K 0.97 0.44 0.08
40_L 35_R 0.97 0.43 0.08
50_L 3_A 0.96 0.43 0.08
120_E 27_V 0.96 0.42 0.07
45_P 22_I 0.95 0.42 0.07
96_S 12_K 0.94 0.41 0.07
132_S 36_E 0.93 0.40 0.07
94_T 19_I 0.93 0.39 0.07
41_L 24_L 0.92 0.39 0.07
118_T 11_I 0.92 0.38 0.06
29_Q 6_W 0.92 0.38 0.06
47_N 26_S 0.92 0.38 0.06
57_I 33_Y 0.92 0.38 0.06
128_R 37_V 0.91 0.38 0.06
127_T 41_K 0.91 0.37 0.06
55_A 31_L 0.91 0.37 0.06
125_L 34_I 0.90 0.37 0.06
50_L 4_Q 0.90 0.36 0.06
51_D 11_I 0.87 0.33 0.05
41_L 31_L 0.86 0.33 0.05
107_V 4_Q 0.85 0.32 0.05
114_K 35_R 0.85 0.32 0.05
132_S 18_T 0.85 0.31 0.05
79_G 25_F 0.84 0.31 0.05
55_A 11_I 0.84 0.31 0.05
132_S 34_I 0.83 0.30 0.04
104_K 5_F 0.83 0.30 0.04
100_E 9_A 0.82 0.29 0.04
52_L 22_I 0.82 0.29 0.04
76_A 42_E 0.80 0.28 0.04
113_G 2_S 0.80 0.27 0.04
108_S 26_S 0.79 0.27 0.04
122_A 6_W 0.79 0.27 0.04
125_L 5_F 0.79 0.26 0.04
94_T 41_K 0.78 0.25 0.04
78_P 14_K 0.78 0.25 0.04
30_Y 17_V 0.77 0.25 0.03
130_G 45_F 0.77 0.25 0.03
119_L 28_V 0.76 0.24 0.03
113_G 8_R 0.76 0.24 0.03
35_E 45_F 0.76 0.24 0.03
137_I 48_A 0.75 0.23 0.03
86_T 3_A 0.74 0.23 0.03
132_S 29_Q 0.74 0.23 0.03
23_G 22_I 0.73 0.22 0.03
37_V 33_Y 0.72 0.21 0.03
114_K 22_I 0.72 0.21 0.03
39_H 34_I 0.71 0.21 0.03
113_G 45_F 0.71 0.21 0.03
134_A 29_Q 0.71 0.20 0.03
100_E 30_R 0.71 0.20 0.03
57_I 7_N 0.71 0.20 0.03
24_I 27_V 0.70 0.20 0.03
78_P 21_Y 0.70 0.20 0.02
118_T 33_Y 0.69 0.19 0.02
62_E 33_Y 0.69 0.19 0.02
50_L 29_Q 0.69 0.19 0.02
116_K 6_W 0.69 0.19 0.02
34_L 33_Y 0.69 0.19 0.02
38_D 10_S 0.68 0.19 0.02
24_I 34_I 0.68 0.18 0.02
50_L 26_S 0.68 0.18 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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